diff --git a/docs/source/journal-article.bib b/docs/source/journal-article.bib index 0e5243e1..2cc5c2fc 100644 --- a/docs/source/journal-article.bib +++ b/docs/source/journal-article.bib @@ -1,3772 +1,4039 @@ @article{abdelhamidMicrophaseSeparationBinary2016, title = {Microphase {{Separation}} of {{Binary Liquids Confined}} in {{Cylindrical Pores}}}, - author = {Abdel Hamid, A. Razzak and Mhanna, Ramona and Lefort, Ronan and Ghoufi, Aziz and {Alba-Simionesco}, Christiane and Frick, Bernhard and Morineau, Denis}, - year = {2016}, - month = may, - journal = {The Journal of Physical Chemistry C}, + author = {Abdel Hamid, A. Razzak and Mhanna, Ramona and Lefort, Ronan and Ghoufi, Aziz and Alba-Simionesco, Christiane and Frick, Bernhard and Morineau, Denis}, + date = {2016-05-05}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {120}, number = {17}, pages = {9245--9252}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.6b01446}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.6b01446}, urldate = {2023-06-09}, - abstract = {We have investigated the structure of tert-butanol-toluene liquid mixtures when confined in the cylindrical channels of MCM-41 mesoporous silicate, and we can conclude on the existence of a microphase-separated tubular structure of these binary liquids although fully miscible in bulk conditions. Neutron diffraction experiments with selective isotopic compositions have been performed to vary systematically the scattering length density and thus to highlight different mixture components. The observed apparently anomalous variation of the intensity of the Bragg peaks of the MCM-41 after filling demonstrates without further analysis that the liquid mixture must be inhomogeneous at the nanoscale. Our experimental observations can be rationalized when comparing with the predictions of simple core-shell models. Within this core- shell model, we deduce that tert-butanol segregates as a pore surface layer of about one atomic size surrounding a toluene-rich core of two to three atomic layers.}, + abstract = {We have investigated the structure of tert-butanol−toluene liquid mixtures when confined in the cylindrical channels of MCM-41 mesoporous silicate, and we can conclude on the existence of a microphase-separated tubular structure of these binary liquids although fully miscible in bulk conditions. Neutron diffraction experiments with selective isotopic compositions have been performed to vary systematically the scattering length density and thus to highlight different mixture components. The observed apparently anomalous variation of the intensity of the Bragg peaks of the MCM-41 after filling demonstrates without further analysis that the liquid mixture must be inhomogeneous at the nanoscale. Our experimental observations can be rationalized when comparing with the predictions of simple core−shell models. Within this core− shell model, we deduce that tert-butanol segregates as a pore surface layer of about one atomic size surrounding a toluene-rich core of two to three atomic layers.}, langid = {english}, keywords = {mixture}, - file = {/home/simon/Zotero/storage/BYUTA6LB/Abdel Hamid et al. - 2016 - Microphase Separation of Binary Liquids Confined i.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BYUTA6LB/Abdel Hamid et al. - 2016 - Microphase Separation of Binary Liquids Confined i.pdf} } @article{abrahamGROMACSHighPerformance2015, title = {{{GROMACS}}: {{High}} Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers}, shorttitle = {{{GROMACS}}}, - author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik}, - year = {2015}, - month = sep, - journal = {SoftwareX}, + author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik}, + date = {2015-09}, + journaltitle = {SoftwareX}, + shortjournal = {SoftwareX}, volume = {1--2}, pages = {19--25}, issn = {23527110}, doi = {10.1016/j.softx.2015.06.001}, - abstract = {GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU{\textendash}GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2352711015000059}, + abstract = {GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.}, langid = {english}, keywords = {ff,MD}, - file = {/home/simon/Zotero/storage/4T9HQ4MY/Abraham et al. - 2015 - GROMACS High performance molecular simulations th.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4T9HQ4MY/Abraham et al. - 2015 - GROMACS High performance molecular simulations th.pdf} } -@misc{AdsorptionLinearAlcohols, +@online{AdsorptionLinearAlcohols, title = {Adsorption of {{Linear Alcohols}} in {{Amorphous Activated Carbons}}: {{Implications}} for {{Energy Storage Applications}}}, shorttitle = {Adsorption of {{Linear Alcohols}} in {{Amorphous Activated Carbons}}}, doi = {10.1021/acssuschemeng.1c06315}, + url = {https://pubs.acs.org/doi/epdf/10.1021/acssuschemeng.1c06315}, urldate = {2023-10-21}, - howpublished = {https://pubs.acs.org/doi/epdf/10.1021/acssuschemeng.1c06315}, langid = {english}, - file = {/home/simon/Zotero/storage/VHDL72T2/Adsorption of Linear Alcohols in Amorphous Activat.pdf;/home/simon/Zotero/storage/MDQQ2HLC/acssuschemeng.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VHDL72T2/Adsorption of Linear Alcohols in Amorphous Activat.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/MDQQ2HLC/acssuschemeng.html} } @article{agrawalViscousPeelingNanosheet2022, title = {Viscous Peeling of a Nanosheet}, author = {Agrawal, Adyant and Gravelle, Simon and Kamal, Catherine and Botto, Lorenzo}, - year = {2022}, - journal = {Soft Matter}, + date = {2022}, + journaltitle = {Soft Matter}, + shortjournal = {Soft Matter}, volume = {18}, number = {20}, pages = {3967--3980}, issn = {1744-683X, 1744-6848}, doi = {10.1039/D1SM01743H}, + url = {http://xlink.rsc.org/?DOI=D1SM01743H}, urldate = {2023-03-22}, abstract = {We carry out molecular dynamics of peeling of a graphene nanosheet from a flat substrate, for the case in which the system is completely immersed in water. Entrance effects are shown to dominate the dynamics of the peeling front. , Combining molecular dynamics (MD) and continuum simulations, we study the dynamics of propagation of a peeling front in a system composed of multilayered graphene nanosheets completely immersed in water. Peeling is induced by lifting one of the nanosheet edges with an assigned pulling velocity normal to the flat substrate. Using MD, we compute the pulling force as a function of the pulling velocity, and quantify the viscous resistance to the advancement of the peeling front. We compare the MD results to a 1D continuum model of a sheet loaded with modelled hydrodynamic loads. Our results show that the viscous dependence of the force on the velocity is negligible below a threshold velocity. Above this threshold, the hydrodynamics is mainly controlled by the viscous resistance associated to the flow near the crack opening, while lubrication forces are negligible owing to the large hydrodynamic slip at the liquid-solid boundary. Two dissipative mechanisms are identified: a drag resistance to the upward motion of the edge, and a resistance to the gap opening associated to the curvature of the flow streamlines near the entrance. Surprisingly, the shape of the sheet was found to be approximately independent of the pulling velocity even for the largest velocities considered.}, langid = {english}, keywords = {entrance,MD,self}, - file = {/home/simon/Zotero/storage/WJ6EYELG/Agrawal et al. - 2022 - Viscous peeling of a nanosheet.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WJ6EYELG/Agrawal et al. - 2022 - Viscous peeling of a nanosheet.pdf} } @article{aidasQuantumMechanicsMolecular2013, title = {A Quantum Mechanics/Molecular Dynamics Study of Electric Field Gradient Fluctuations in the Liquid Phase. {{The}} Case of {{Na}} {\textsuperscript{+}} in Aqueous Solution}, - author = {Aidas, K{\k{e}}stutis and {\AA}gren, Hans and Kongsted, Jacob and Laaksonen, Aatto and Mocci, Francesca}, - year = {2013}, - journal = {Phys. Chem. Chem. Phys.}, + author = {Aidas, Kęstutis and Ågren, Hans and Kongsted, Jacob and Laaksonen, Aatto and Mocci, Francesca}, + date = {2013}, + journaltitle = {Phys. Chem. Chem. Phys.}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {15}, number = {5}, pages = {1621--1631}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C2CP41993A}, + url = {http://xlink.rsc.org/?DOI=C2CP41993A}, urldate = {2023-05-25}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/WIEB8525/Aidas et al. - 2013 - A quantum mechanicsmolecular dynamics study of el.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WIEB8525/Aidas et al. - 2013 - A quantum mechanicsmolecular dynamics study of el.pdf} } @article{amayuelasMechanismWaterIntrusion2023, title = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}: {{Liquid Is Not Vapor}}}, shorttitle = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}}, - author = {Amayuelas, Eder and Tortora, Marco and Bartolom{\'e}, Luis and Littlefair, Josh David and Paulo, Gon{\c c}alo and Le Donne, Andrea and Trump, Benjamin and Yakovenko, Andrey Andreevich and Chor{\k{a}}{\.z}ewski, Miros{\l}aw and Giacomello, Alberto and Zajdel, Pawe{\l} and Meloni, Simone and Grosu, Yaroslav}, - year = {2023}, - month = jun, - journal = {Nano Letters}, + author = {Amayuelas, Eder and Tortora, Marco and Bartolomé, Luis and Littlefair, Josh David and Paulo, Gonçalo and Le Donne, Andrea and Trump, Benjamin and Yakovenko, Andrey Andreevich and Chorążewski, Mirosław and Giacomello, Alberto and Zajdel, Paweł and Meloni, Simone and Grosu, Yaroslav}, + date = {2023-06-28}, + journaltitle = {Nano Letters}, + shortjournal = {Nano Lett.}, volume = {23}, number = {12}, pages = {5430--5436}, issn = {1530-6984, 1530-6992}, doi = {10.1021/acs.nanolett.3c00235}, + url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.3c00235}, urldate = {2023-07-05}, abstract = {Zeolitic Imidazolate Frameworks (ZIF) find application in storage and dissipation of mechanical energy. Their distinctive properties linked to their (sub)nanometer size and hydrophobicity allow for water intrusion only under high hydrostatic pressure. Here we focus on the popular ZIF-8 material investigating the intrusion mechanism in its nanoscale cages, which is the key to its rational exploitation in target applications. In this work, we used a joint experimental/theoretical approach combining in operando synchrotron experiments during highpressure intrusion experiments, molecular dynamics simulations, and stochastic models to reveal that water intrusion into ZIF-8 occurs by a cascade filling of connected cages rather than a condensation process as previously assumed. The reported results allowed us to establish structure/function relations in this prototypical microporous material, representing an important step to devise design rules to synthesize porous media.}, langid = {english}, keywords = {MD,nanofluid,zif}, - file = {/home/simon/Zotero/storage/AXI4Q8SG/Amayuelas et al. - 2023 - Mechanism of Water Intrusion into Flexible ZIF-8 .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/AXI4Q8SG/Amayuelas et al. - 2023 - Mechanism of Water Intrusion into Flexible ZIF-8 .pdf} } @article{amroucheExperimentalComputationalStudy2011, - title = {Experimental and {{Computational Study}} of {{Functionality Impact}} on {{Sodalite}}{\textendash}{{Zeolitic Imidazolate Frameworks}} for {{CO2 Separation}}}, - author = {Amrouche, Hedi and Aguado, Sonia and {P{\'e}rez-Pellitero}, Javier and Chizallet, C{\'e}line and Siperstein, Flor and Farrusseng, David and Bats, Nicolas and {Nieto-Draghi}, Carlos}, - year = {2011}, - month = aug, - journal = {The Journal of Physical Chemistry C}, + title = {Experimental and {{Computational Study}} of {{Functionality Impact}} on {{Sodalite}}–{{Zeolitic Imidazolate Frameworks}} for {{CO2 Separation}}}, + author = {Amrouche, Hedi and Aguado, Sonia and Pérez-Pellitero, Javier and Chizallet, Céline and Siperstein, Flor and Farrusseng, David and Bats, Nicolas and Nieto-Draghi, Carlos}, + date = {2011-08-25}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {115}, number = {33}, pages = {16425--16432}, publisher = {{American Chemical Society}}, issn = {1932-7447}, doi = {10.1021/jp202804g}, + url = {https://doi.org/10.1021/jp202804g}, urldate = {2023-11-16}, - abstract = {This study deals with the enhancement of CO2 uptake by ligand functionalization of zeolitic imidazolate framework (ZIF) materials. The ligand dipole moment could be considered as one of the main criteria for CO2 adsorption enhancement. To verify this hypothesis, an experimental{\textendash}computational study was performed on an isoreticular ZIF series with sodalite (SOD) topology using published structures (ZIF-8, ZIF-90, and ZIF-Cl) as well as hypothetical structures (ZIF-COOH and ZIF-NO2) designated using DFT calculations. An analysis of structural and adsorptive properties was proposed for these materials used to separate CO2 from CH4, CO, or N2 gas. The accuracy of the calculated results was validated by comparison with our own experimental results. An exponential relationship between the ligand dipole moments and the isosteric heat of adsorption of CO2 was highlighted. Modifying the nature of the linker (dipole moment) allows a 5- to 7-fold improvement in CO2 selectivity for CO2/CH4, CO2/N2, and CO2/CO mixtures.}, - file = {/home/simon/Zotero/storage/GJPXA52N/Amrouche et al. - 2011 - Experimental and Computational Study of Functional.pdf} + abstract = {This study deals with the enhancement of CO2 uptake by ligand functionalization of zeolitic imidazolate framework (ZIF) materials. The ligand dipole moment could be considered as one of the main criteria for CO2 adsorption enhancement. To verify this hypothesis, an experimental–computational study was performed on an isoreticular ZIF series with sodalite (SOD) topology using published structures (ZIF-8, ZIF-90, and ZIF-Cl) as well as hypothetical structures (ZIF-COOH and ZIF-NO2) designated using DFT calculations. An analysis of structural and adsorptive properties was proposed for these materials used to separate CO2 from CH4, CO, or N2 gas. The accuracy of the calculated results was validated by comparison with our own experimental results. An exponential relationship between the ligand dipole moments and the isosteric heat of adsorption of CO2 was highlighted. Modifying the nature of the linker (dipole moment) allows a 5- to 7-fold improvement in CO2 selectivity for CO2/CH4, CO2/N2, and CO2/CO mixtures.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/GJPXA52N/Amrouche et al. - 2011 - Experimental and Computational Study of Functional.pdf} } @article{aratonoThermodynamicStudySurface1997, title = {Thermodynamic {{Study}} on the {{Surface Formation}} of the {{Mixture}} of {{Water}} and {{Ethanol}}}, author = {Aratono, Makoto and Toyomasu, Takayuki and Villeneuve, Masumi and Uchizono, Yorie and Takiue, Takanori and Motomura, Kinsi and Ikeda, Norihiro}, - year = {1997}, - month = jul, - journal = {Journal of Colloid and Interface Science}, + date = {1997-07}, + journaltitle = {Journal of Colloid and Interface Science}, + shortjournal = {Journal of Colloid and Interface Science}, volume = {191}, number = {1}, pages = {146--153}, issn = {00219797}, doi = {10.1006/jcis.1997.4929}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021979797949298}, urldate = {2023-07-18}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/8K3KQAJR/Aratono et al. - 1997 - Thermodynamic Study on the Surface Formation of th.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/8K3KQAJR/Aratono et al. - 1997 - Thermodynamic Study on the Surface Formation of th.pdf} } @article{ardeleanPrinciplesUnconventionalAspects, - title = {Principles and {{Unconventional Aspects}} of {{NMR Diffusometry}}}, + title = {Principles and {{Unconventional Aspects}} of {{NMR Diffusometry}}}, author = {Ardelean, Ioan and Kimmich, Rainer}, langid = {english}, - file = {/home/simon/Zotero/storage/WT5LSVDN/Ardelean and Kimmich - Principles and Unconventional Aspects of NMR Diffus.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WT5LSVDN/Ardelean and Kimmich - Principles and Unconventional Aspects of NMR Diffus.pdf} } @article{ashbaughAlkaneAdsorptionWater2003, - title = {Alkane {{Adsorption}} at the {{Water}}-{{Vapor Interface}}}, + title = {Alkane {{Adsorption}} at the {{Water}}−{{Vapor Interface}}}, author = {Ashbaugh, Henry S. and Pethica, Brian A.}, - year = {2003}, - month = sep, - journal = {Langmuir}, + date = {2003-09-01}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {19}, number = {18}, pages = {7638--7645}, issn = {0743-7463, 1520-5827}, doi = {10.1021/la034559z}, + url = {https://pubs.acs.org/doi/10.1021/la034559z}, urldate = {2023-06-20}, langid = {english}, keywords = {mixture}, - file = {/home/simon/Zotero/storage/GDID2PK4/Ashbaugh and Pethica - 2003 - Alkane Adsorption at the Water−Vapor Interface.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/GDID2PK4/Ashbaugh and Pethica - 2003 - Alkane Adsorption at the Water−Vapor Interface.pdf} } @article{ayantCalculDensitesSpectrales1975, - title = {{Calcul des densit{\'e}s spectrales r{\'e}sultant d'un mouvement al{\'e}atoire de translation en relaxation par interaction dipolaire magn{\'e}tique dans les liquides}}, + title = {Calcul des densités spectrales résultant d'un mouvement aléatoire de translation en relaxation par interaction dipolaire magnétique dans les liquides}, author = {Ayant, Y. and Belorizky, E. and Aluzon, J. and Gallice, J.}, - year = {1975}, - month = oct, - journal = {Journal de Physique}, + date = {1975-10-01}, + journaltitle = {Journal de Physique}, + shortjournal = {J. Phys. France}, volume = {36}, number = {10}, pages = {991--1004}, - publisher = {{Soci{\'e}t{\'e} Fran{\c c}aise de Physique}}, + publisher = {{Société Française de Physique}}, issn = {0302-0738, 2777-3396}, doi = {10.1051/jphys:019750036010099100}, + url = {http://dx.doi.org/10.1051/jphys:019750036010099100}, urldate = {2023-07-09}, - abstract = {Journal de Physique, Journal de Physique Archives repr{\'e}sente une mine d informations facile {\`a} consulter sur la mani{\`e}re dont la physique a {\'e}t{\'e} publi{\'e}e depuis 1872.}, + abstract = {Journal de Physique, Journal de Physique Archives représente une mine d informations facile à consulter sur la manière dont la physique a été publiée depuis 1872.}, langid = {french}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/FSRVZ3LC/Ayant et al. - 1975 - Calcul des densités spectrales résultant d'un mouv.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/FSRVZ3LC/Ayant et al. - 1975 - Calcul des densités spectrales résultant d'un mouv.pdf} } @article{ayralSolGelSynthesisFine2018, title = {Sol-{{Gel Synthesis}} and {{Fine Characterization}} of {{Hierarchically Porous}} and {{Multifunctional Silica-Based Membranes}}}, - author = {Ayral, Andr{\'e}}, - year = {2018}, - month = jul, - journal = {The Chemical Record}, + author = {Ayral, André}, + date = {2018-07}, + journaltitle = {The Chemical Record}, + shortjournal = {Chem. Rec.}, volume = {18}, number = {7-8}, pages = {878--890}, issn = {15278999}, doi = {10.1002/tcr.201700079}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/tcr.201700079}, urldate = {2023-03-29}, langid = {english}, keywords = {silica}, - file = {/home/simon/Zotero/storage/9W5EGYAA/Ayral - 2018 - Sol-Gel Synthesis and Fine Characterization of Hie.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/9W5EGYAA/Ayral - 2018 - Sol-Gel Synthesis and Fine Characterization of Hie.pdf} } @article{bakoWaterMethanolMixtures2008, - title = {Water{\textendash}Methanol Mixtures: Topology of Hydrogen Bonded Network}, - shorttitle = {Water{\textendash}Methanol Mixtures}, - author = {Bak{\'o}, Imre and Megyes, T{\"u}nde and B{\'a}lint, Szabolcs and Gr{\'o}sz, Tam{\'a}s and Chihaia, Viorel}, - year = {2008}, - journal = {Physical Chemistry Chemical Physics}, + title = {Water–Methanol Mixtures: Topology of Hydrogen Bonded Network}, + shorttitle = {Water–Methanol Mixtures}, + author = {Bakó, Imre and Megyes, Tünde and Bálint, Szabolcs and Grósz, Tamás and Chihaia, Viorel}, + date = {2008}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {10}, number = {32}, pages = {5004}, issn = {1463-9076, 1463-9084}, doi = {10.1039/b808326f}, + url = {http://xlink.rsc.org/?DOI=b808326f}, urldate = {2023-03-22}, langid = {english}, keywords = {MD,mixture}, - file = {/home/simon/Zotero/storage/USXGFJJU/Bakó et al. - 2008 - Water–methanol mixtures topology of hydrogen bond.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/USXGFJJU/Bakó et al. - 2008 - Water–methanol mixtures topology of hydrogen bond.pdf} } @article{ballalHydrophobicHydrophilicInteractions2013, title = {Hydrophobic and Hydrophilic Interactions in Aqueous Mixtures of Alcohols at a Hydrophobic Surface}, author = {Ballal, Deepti and Chapman, Walter G.}, - year = {2013}, - month = sep, - journal = {The Journal of Chemical Physics}, + date = {2013-09-21}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {139}, number = {11}, pages = {114706}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4821604}, + url = {http://aip.scitation.org/doi/10.1063/1.4821604}, urldate = {2023-03-28}, langid = {english}, keywords = {HB,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/VNU4ZZYK/Ballal and Chapman - 2013 - Hydrophobic and hydrophilic interactions in aqueou.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VNU4ZZYK/Ballal and Chapman - 2013 - Hydrophobic and hydrophilic interactions in aqueou.pdf} } @article{bampoulisStructureDynamicsConfined2016, - title = {Structure and {{Dynamics}} of {{Confined Alcohol}}{\textendash}{{Water Mixtures}}}, + title = {Structure and {{Dynamics}} of {{Confined Alcohol}}–{{Water Mixtures}}}, author = {Bampoulis, Pantelis and Witteveen, Jorn P. and Kooij, E. Stefan and Lohse, Detlef and Poelsema, Bene and Zandvliet, Harold J. W.}, - year = {2016}, - month = jul, - journal = {ACS Nano}, + date = {2016-07-26}, + journaltitle = {ACS Nano}, + shortjournal = {ACS Nano}, volume = {10}, number = {7}, pages = {6762--6768}, issn = {1936-0851, 1936-086X}, doi = {10.1021/acsnano.6b02333}, + url = {https://pubs.acs.org/doi/10.1021/acsnano.6b02333}, urldate = {2023-07-10}, - abstract = {The effect of confinement between mica and graphene on the structure and dynamics of alcohol-water mixtures has been studied in situ and in real time at the molecular level by atomic force microscopy (AFM) at room temperature. AFM images reveal that the adsorbed molecules are segregated into faceted alcohol-rich islands on top of an ice layer on mica, surrounded by a pre-existing multilayer water-rich film. These faceted islands are in direct contact with the graphene surface, revealing a preferred adsorption site. Moreover, alcohol adsorption at low relative humidity (RH) reveals a strong preference of the alcohol molecules for the ordered ice interface. The growth dynamics of the alcohol islands is governed by supersaturation, temperature, the free energy of attachment of molecules to the island edge and two-dimensional (2D) diffusion. The measured diffusion coefficients display a size dependence on the molecular size of the alcohols, and are about 6 orders of magnitude smaller than the bulk diffusion coefficients, demonstrating the effect of confinement on the behavior of the alcohols. These experimental results provide new insights into the behavior of multicomponent fluids in confined geometries, which is of paramount importance in nanofluidics and biology.}, + abstract = {The effect of confinement between mica and graphene on the structure and dynamics of alcohol−water mixtures has been studied in situ and in real time at the molecular level by atomic force microscopy (AFM) at room temperature. AFM images reveal that the adsorbed molecules are segregated into faceted alcohol-rich islands on top of an ice layer on mica, surrounded by a pre-existing multilayer water-rich film. These faceted islands are in direct contact with the graphene surface, revealing a preferred adsorption site. Moreover, alcohol adsorption at low relative humidity (RH) reveals a strong preference of the alcohol molecules for the ordered ice interface. The growth dynamics of the alcohol islands is governed by supersaturation, temperature, the free energy of attachment of molecules to the island edge and two-dimensional (2D) diffusion. The measured diffusion coefficients display a size dependence on the molecular size of the alcohols, and are about 6 orders of magnitude smaller than the bulk diffusion coefficients, demonstrating the effect of confinement on the behavior of the alcohols. These experimental results provide new insights into the behavior of multicomponent fluids in confined geometries, which is of paramount importance in nanofluidics and biology.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/5NQRB4QC/Bampoulis et al. - 2016 - Structure and Dynamics of Confined Alcohol–Water M.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5NQRB4QC/Bampoulis et al. - 2016 - Structure and Dynamics of Confined Alcohol–Water M.pdf} } @article{becherMolecularDynamicsSimulations2021, title = {Molecular Dynamics Simulations vs Field-Cycling {{NMR}} Relaxometry: {{Structural}} Relaxation Mechanisms in the Glass-Former Glycerol Revisited}, shorttitle = {Molecular Dynamics Simulations vs Field-Cycling {{NMR}} Relaxometry}, - author = {Becher, M. and Wohlfromm, T. and R{\"o}ssler, E. A. and Vogel, M.}, - year = {2021}, - month = mar, - journal = {The Journal of Chemical Physics}, + author = {Becher, M. and Wohlfromm, T. and Rössler, E. A. and Vogel, M.}, + date = {2021-03-28}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {J. Chem. Phys.}, volume = {154}, number = {12}, pages = {124503}, issn = {0021-9606, 1089-7690}, doi = {10.1063/5.0048131}, + url = {https://pubs.aip.org/aip/jcp/article/380743}, urldate = {2023-07-03}, - abstract = {We combine field-cycling (FC) relaxometry and molecular dynamics (MD) simulations to study the rotational and translational dynamics associated with the glassy slowdown of glycerol. The 1H NMR spin-lattice relaxation rates R1({$\omega$}) probed in the FC measurements for different isotope-labelled compounds are computed from the MD trajectories for broad frequency and temperature ranges. We find high correspondence between experiment and simulation. Concerning the rotational motion, we observe that the aliphatic and hydroxyl groups show similar correlation times but different stretching parameters, while the overall reorientation associated with the structural relaxation remains largely isotropic. Additional analysis of the simulation results reveals that transitions between different molecular configurations are slow on the time scale of the structural relaxation at least at sufficiently high temperatures, indicating that glycerol rotates at a rigid entity, but the reorientation is slower for elongated than for compact conformers. The translational contribution to R1({$\omega$}) is well described by the force-free hard sphere model. At sufficiently low frequencies, universal square-root laws provide access to the molecular diffusion coefficients. In both experiment and simulation, the time scales of the rotational and translational motions show an unusually large separation, which is at variance with the Stokes{\textendash}Einstein{\textendash}Debye relation. To further explore this effect, we investigate the structure and dynamics on various length scales in the simulations. We observe that a prepeak in the static structure factor S(q), which is related to a local segregation of aliphatic and hydroxyl groups, is accompanied by a peak in the correlation times {$\tau$}(q) from coherent scattering functions.}, + abstract = {We combine field-cycling (FC) relaxometry and molecular dynamics (MD) simulations to study the rotational and translational dynamics associated with the glassy slowdown of glycerol. The 1H NMR spin-lattice relaxation rates R1(ω) probed in the FC measurements for different isotope-labelled compounds are computed from the MD trajectories for broad frequency and temperature ranges. We find high correspondence between experiment and simulation. Concerning the rotational motion, we observe that the aliphatic and hydroxyl groups show similar correlation times but different stretching parameters, while the overall reorientation associated with the structural relaxation remains largely isotropic. Additional analysis of the simulation results reveals that transitions between different molecular configurations are slow on the time scale of the structural relaxation at least at sufficiently high temperatures, indicating that glycerol rotates at a rigid entity, but the reorientation is slower for elongated than for compact conformers. The translational contribution to R1(ω) is well described by the force-free hard sphere model. At sufficiently low frequencies, universal square-root laws provide access to the molecular diffusion coefficients. In both experiment and simulation, the time scales of the rotational and translational motions show an unusually large separation, which is at variance with the Stokes–Einstein–Debye relation. To further explore this effect, we investigate the structure and dynamics on various length scales in the simulations. We observe that a prepeak in the static structure factor S(q), which is related to a local segregation of aliphatic and hydroxyl groups, is accompanied by a peak in the correlation times τ(q) from coherent scattering functions.}, langid = {english}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/5C8W2VF5/Becher et al. - 2021 - Molecular dynamics simulations vs field-cycling NM.pdf;/home/simon/Zotero/storage/5WQEXAVI/SI.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5C8W2VF5/Becher et al. - 2021 - Molecular dynamics simulations vs field-cycling NM.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/5WQEXAVI/SI.pdf} } @article{belfortMembraneFiltrationLiquids2019, title = {Membrane {{Filtration}} with {{Liquids}}: {{A Global Approach}} with {{Prior Successes}}, {{New Developments}} and {{Unresolved Challenges}}}, shorttitle = {Membrane {{Filtration}} with {{Liquids}}}, author = {Belfort, Georges}, - year = {2019}, - journal = {Angewandte Chemie}, + date = {2019}, + journaltitle = {Angewandte Chemie}, volume = {131}, number = {7}, pages = {1908--1918}, issn = {1521-3757}, doi = {10.1002/ange.201809548}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ange.201809548}, urldate = {2023-08-28}, - abstract = {After 70 years, modern pressure-driven polymer membrane processes with liquids are mature and accepted in many industries due to their good performance, ease of scale-up, low energy consumption, modular compact construction, and low operating costs compared with thermal systems. Successful isothermal operation of synthetic membranes with liquids requires consideration of three critical aspects or ``legs'' in order of relevance: selectivity, capacity (i.e. permeation flow rate per unit area) and transport of mass and momentum comprising concentration polarization (CP) and fouling (F). Major challenges remain with respect to increasing selectivity and controlling mass transport in, to and away from membranes. Thus, prediction and control of membrane morphology and a deep understanding of the mechanism of dissolved and suspended solute transport near and in the membrane (i.e. diffusional and convective mass transport) is essential. Here, we focus on materials development to address the relatively poor selectivity of liquid membrane filtration with polymers and discuss the critical aspects of transport limitations. Machine learning could help optimize membrane structure design and transport conditions for improved membrane filtration performance.}, + abstract = {After 70 years, modern pressure-driven polymer membrane processes with liquids are mature and accepted in many industries due to their good performance, ease of scale-up, low energy consumption, modular compact construction, and low operating costs compared with thermal systems. Successful isothermal operation of synthetic membranes with liquids requires consideration of three critical aspects or “legs” in order of relevance: selectivity, capacity (i.e. permeation flow rate per unit area) and transport of mass and momentum comprising concentration polarization (CP) and fouling (F). Major challenges remain with respect to increasing selectivity and controlling mass transport in, to and away from membranes. Thus, prediction and control of membrane morphology and a deep understanding of the mechanism of dissolved and suspended solute transport near and in the membrane (i.e. diffusional and convective mass transport) is essential. Here, we focus on materials development to address the relatively poor selectivity of liquid membrane filtration with polymers and discuss the critical aspects of transport limitations. Machine learning could help optimize membrane structure design and transport conditions for improved membrane filtration performance.}, langid = {english}, - file = {/home/simon/Zotero/storage/KPQIHCX5/Belfort - 2019 - Membrane Filtration with Liquids A Global Approac.pdf;/home/simon/Zotero/storage/UUST7G3P/ange.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/KPQIHCX5/Belfort - 2019 - Membrane Filtration with Liquids A Global Approac.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/UUST7G3P/ange.html} +} + +@article{berendsenMissingTermEffective1987, + title = {The Missing Term in Effective Pair Potentials}, + author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.}, + date = {1987-11-01}, + journaltitle = {The Journal of Physical Chemistry}, + shortjournal = {J. Phys. Chem.}, + volume = {91}, + number = {24}, + pages = {6269--6271}, + publisher = {{American Chemical Society}}, + issn = {0022-3654}, + doi = {10.1021/j100308a038}, + url = {https://doi.org/10.1021/j100308a038}, + urldate = {2024-01-08}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/E22JML7Z/Berendsen et al. - 1987 - The missing term in effective pair potentials.pdf} } @article{bernalSeparationCO2N22004, title = {Separation of {{CO2}}/{{N2}} Mixtures Using {{MFI-type}} Zeolite Membranes}, - author = {Bernal, M. P. and Coronas, J. and Men{\'e}ndez, M. and Santamar{\'i}a, J.}, - year = {2004}, - journal = {AIChE Journal}, + author = {Bernal, M. P. and Coronas, J. and Menéndez, M. and Santamaría, J.}, + date = {2004}, + journaltitle = {AIChE Journal}, volume = {50}, number = {1}, pages = {127--135}, issn = {1547-5905}, doi = {10.1002/aic.10012}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aic.10012}, urldate = {2023-11-06}, - abstract = {MFI-type zeolite (ZSM5) membranes were prepared on alumina and stainless steel tubular supports and tested for the separation of CO2/N2 mixtures. The effect of several operating variables (temperature, feed and permeate pressures, feed composition, use of sweep gas, presence of water in the feed, membrane module configuration) was investigated. The separation between CO2 and N2 takes place because of the preferential adsorption of CO2, which hinders the permeation of N2 through the zeolite pore network. The best results in this work were obtained with a Na-ZSM5 membrane, and using a large pressure gradient. In this case, a permeation flux as large as 9.2 kg/(m2 {$\cdot$} h) [permeance of 2.6 {\texttimes} 10-6 mol/(m2 {$\cdot$} s {$\cdot$} Pa)] with a CO2/N2 separation factor of 13.7 was obtained. {\textcopyright} 2004 American Institute of Chemical Engineers AIChE J, 50: 127{\textendash}135, 2004}, + abstract = {MFI-type zeolite (ZSM5) membranes were prepared on alumina and stainless steel tubular supports and tested for the separation of CO2/N2 mixtures. The effect of several operating variables (temperature, feed and permeate pressures, feed composition, use of sweep gas, presence of water in the feed, membrane module configuration) was investigated. The separation between CO2 and N2 takes place because of the preferential adsorption of CO2, which hinders the permeation of N2 through the zeolite pore network. The best results in this work were obtained with a Na-ZSM5 membrane, and using a large pressure gradient. In this case, a permeation flux as large as 9.2 kg/(m2 · h) [permeance of 2.6 × 10−6 mol/(m2 · s · Pa)] with a CO2/N2 separation factor of 13.7 was obtained. © 2004 American Institute of Chemical Engineers AIChE J, 50: 127–135, 2004}, langid = {english}, keywords = {CO2 permeation,CO2/N2 separation,zeolite membrane,ZSM5}, - file = {/home/simon/Zotero/storage/VZLFCYC8/Bernal et al. - 2004 - Separation of CO2N2 mixtures using MFI-type zeoli.pdf;/home/simon/Zotero/storage/YFDWUC52/aic.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VZLFCYC8/Bernal et al. - 2004 - Separation of CO2N2 mixtures using MFI-type zeoli.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/YFDWUC52/aic.html} } @article{bloembergenRelaxationEffectsNuclear1948, title = {Relaxation {{Effects}} in {{Nuclear Magnetic Resonance Absorption}}}, author = {Bloembergen, N. and Purcell, E. M. and Pound, R. V.}, - year = {1948}, - month = apr, - journal = {Physical Review}, + date = {1948-04-01}, + journaltitle = {Physical Review}, + shortjournal = {Phys. Rev.}, volume = {73}, number = {7}, pages = {679--712}, issn = {0031-899X}, doi = {10.1103/PhysRev.73.679}, + url = {https://link.aps.org/doi/10.1103/PhysRev.73.679}, urldate = {2023-06-07}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/652XEHWU/bloembergen1948.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/652XEHWU/bloembergen1948.pdf} } @article{bonnaudMolecularSimulationWater2010, title = {Molecular Simulation of Water Confined in Nanoporous Silica}, author = {Bonnaud, P A and Coasne, B and Pellenq, R J-M}, - year = {2010}, - month = jul, - journal = {Journal of Physics: Condensed Matter}, + date = {2010-07-21}, + journaltitle = {Journal of Physics: Condensed Matter}, + shortjournal = {J. Phys.: Condens. Matter}, volume = {22}, number = {28}, pages = {284110}, issn = {0953-8984, 1361-648X}, doi = {10.1088/0953-8984/22/28/284110}, + url = {https://iopscience.iop.org/article/10.1088/0953-8984/22/28/284110}, urldate = {2023-07-12}, - abstract = {This paper reports on a molecular simulation study of the thermodynamics, structure and dynamics of water confined at ambient temperature in hydroxylated silica nanopores of a width H = 10 and 20 A{\r{}} . The adsorption isotherms for water in these nanopores resemble those observed for experimental samples; the adsorbed amount increases continuously in the multilayer adsorption regime until a jump occurs due to capillary condensation of the fluid within the pore. Strong layering of water in the vicinity of the silica surfaces is observed as marked density oscillations are observed up to 8 A{\r{}} from the surface in the density profiles for confined water. Our results indicate that water molecules within the first adsorbed layer tend to adopt a H-down orientation with respect to the silica substrate. For all pore sizes and adsorbed amounts, the self-diffusivity of confined water is lower than the bulk, due to the hydrophilic interaction between the water molecules and the hydroxylated silica surface. Our results also suggest that the self-diffusivity of confined water is sensitive to the adsorbed amount.}, + abstract = {This paper reports on a molecular simulation study of the thermodynamics, structure and dynamics of water confined at ambient temperature in hydroxylated silica nanopores of a width H = 10 and 20 A˚ . The adsorption isotherms for water in these nanopores resemble those observed for experimental samples; the adsorbed amount increases continuously in the multilayer adsorption regime until a jump occurs due to capillary condensation of the fluid within the pore. Strong layering of water in the vicinity of the silica surfaces is observed as marked density oscillations are observed up to 8 A˚ from the surface in the density profiles for confined water. Our results indicate that water molecules within the first adsorbed layer tend to adopt a H-down orientation with respect to the silica substrate. For all pore sizes and adsorbed amounts, the self-diffusivity of confined water is lower than the bulk, due to the hydrophilic interaction between the water molecules and the hydroxylated silica surface. Our results also suggest that the self-diffusivity of confined water is sensitive to the adsorbed amount.}, langid = {english}, keywords = {confinnement,heat,MD}, - file = {/home/simon/Zotero/storage/4BRC6NSR/Bonnaud et al. - 2010 - Molecular simulation of water confined in nanoporo.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4BRC6NSR/Bonnaud et al. - 2010 - Molecular simulation of water confined in nanoporo.pdf} } @article{borahDeuteriumNMRWater1982, title = {Deuterium {{NMR}} of Water in Immobilized Protein Systems}, author = {Borah, B. and Bryant, R.G.}, - year = {1982}, - month = apr, - journal = {Biophysical Journal}, + date = {1982-04}, + journaltitle = {Biophysical Journal}, + shortjournal = {Biophysical Journal}, volume = {38}, number = {1}, pages = {47--52}, issn = {00063495}, doi = {10.1016/S0006-3495(82)84529-3}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349582845293}, urldate = {2023-08-02}, abstract = {Deuterium NMR spectra are reported for lysozyme crystals, powders, and frozen solutions. At high water contents the spectrum is a superposition of a narrow central component and a quadrupole doublet. The quadrupole splitting and the relaxation rates of both components, monitored as a function of water content and temperature, are discussed in terms of models for the water-protein interaction. The anisotropy of the water molecule motion is clearly demonstrated by the deuterium quadrupole splitting observed in the protein single crystal, but such splittings were not found in protein powders and frozen protein solutions. We therefore suggest that the most useful view of such data is to consider the water-protein interactions at the surface to be mixed rapidly and that a distribution of interactions be invoked rather than an oversimplified view often taken of a two or n-site mixing where n is small.}, langid = {english}, keywords = {HEWL,NMR}, - file = {/home/simon/Zotero/storage/QY5KAQ4Z/Borah and Bryant - 1982 - Deuterium NMR of water in immobilized protein syst.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QY5KAQ4Z/Borah and Bryant - 1982 - Deuterium NMR of water in immobilized protein syst.pdf} } @article{botanBottomupModelAdsorption2015, title = {Bottom-up Model of Adsorption and Transport in Multiscale Porous Media}, - author = {Bo{\c t}an, Alexandru and Ulm, Franz-Josef and Pellenq, Roland J.-M. and Coasne, Benoit}, - year = {2015}, - month = mar, - journal = {Physical Review E}, + author = {Boţan, Alexandru and Ulm, Franz-Josef and Pellenq, Roland J.-M. and Coasne, Benoit}, + date = {2015-03-20}, + journaltitle = {Physical Review E}, + shortjournal = {Phys. Rev. E}, volume = {91}, number = {3}, pages = {032133}, publisher = {{American Physical Society}}, doi = {10.1103/PhysRevE.91.032133}, + url = {https://link.aps.org/doi/10.1103/PhysRevE.91.032133}, urldate = {2023-08-31}, - abstract = {We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential {$\mu$}(r) and density {$\rho$}(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorption-transport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.}, - file = {/home/simon/Zotero/storage/9EBRWVCZ/Boţan et al. - 2015 - Bottom-up model of adsorption and transport in mul.pdf;/home/simon/Zotero/storage/CHWVNLI8/PhysRevE.91.html} + abstract = {We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential μ(r) and density ρ(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorption-transport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/9EBRWVCZ/Boţan et al. - 2015 - Bottom-up model of adsorption and transport in mul.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/CHWVNLI8/PhysRevE.91.html} } @article{bousigeBridgingScalesDisordered2021, title = {Bridging Scales in Disordered Porous Media by Mapping Molecular Dynamics onto Intermittent {{Brownian}} Motion}, author = {Bousige, Colin and Levitz, Pierre and Coasne, Benoit}, - year = {2021}, - month = feb, - journal = {Nature Communications}, + date = {2021-02-15}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, volume = {12}, number = {1}, pages = {1043}, publisher = {{Nature Publishing Group}}, issn = {2041-1723}, doi = {10.1038/s41467-021-21252-x}, + url = {https://www.nature.com/articles/s41467-021-21252-x}, urldate = {2023-09-30}, - abstract = {Owing to their complex morphology and surface, disordered nanoporous media possess a rich diffusion landscape leading to specific transport phenomena. The unique diffusion mechanisms in such solids stem from restricted pore relocation and ill-defined surface boundaries. While diffusion fundamentals in simple geometries are well-established, fluids in complex materials challenge existing frameworks. Here, we invoke the intermittent surface/pore diffusion formalism to map molecular dynamics onto random walk in disordered media. Our hierarchical strategy allows bridging microscopic/mesoscopic dynamics with parameters obtained from simple laws. The residence and relocation times {\textendash} tA, tB {\textendash} are shown to derive from pore size d and temperature-rescaled surface interaction {$\epsilon$}/kBT. tA obeys a transition state theory with a barrier\,{\textasciitilde}{$\epsilon$}/kBT and a prefactor\,{\textasciitilde}10-12 s corrected for pore diameter d. tB scales with d which is rationalized through a cutoff in the relocation first passage distribution. This approach provides a formalism to predict any fluid diffusion in complex media using parameters available to simple experiments.}, - copyright = {2021 The Author(s)}, + abstract = {Owing to their complex morphology and surface, disordered nanoporous media possess a rich diffusion landscape leading to specific transport phenomena. The unique diffusion mechanisms in such solids stem from restricted pore relocation and ill-defined surface boundaries. While diffusion fundamentals in simple geometries are well-established, fluids in complex materials challenge existing frameworks. Here, we invoke the intermittent surface/pore diffusion formalism to map molecular dynamics onto random walk in disordered media. Our hierarchical strategy allows bridging microscopic/mesoscopic dynamics with parameters obtained from simple laws. The residence and relocation times – tA, tB – are shown to derive from pore size d and temperature-rescaled surface interaction ε/kBT. tA obeys a transition state theory with a barrier\,\textasciitilde ε/kBT and a prefactor\,\textasciitilde 10−12 s corrected for pore diameter d. tB scales with d which is rationalized through a cutoff in the relocation first passage distribution. This approach provides a formalism to predict any fluid diffusion in complex media using parameters available to simple experiments.}, + issue = {1}, langid = {english}, - file = {/home/simon/Zotero/storage/DRAH32NM/Bousige et al. - 2021 - Bridging scales in disordered porous media by mapp.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DRAH32NM/Bousige et al. - 2021 - Bridging scales in disordered porous media by mapp.pdf} } @article{buddHighlyPermeablePolymers2010, title = {Highly Permeable Polymers for Gas Separation Membranes}, author = {Budd, Peter M. and McKeown, Neil B.}, - year = {2010}, - month = feb, - journal = {Polymer Chemistry}, + date = {2010-02-09}, + journaltitle = {Polymer Chemistry}, + shortjournal = {Polym. Chem.}, volume = {1}, number = {1}, pages = {63--68}, publisher = {{The Royal Society of Chemistry}}, issn = {1759-9962}, doi = {10.1039/B9PY00319C}, + url = {https://pubs.rsc.org/en/content/articlelanding/2010/py/b9py00319c}, urldate = {2023-10-04}, abstract = {For gas separation membranes, materials are required that offer high permeability as well as good selectivity for a desired separation. For glassy polymers, the gas transport properties depend on the amount and distribution of free volume and on chain mobility. The most highly permeable polymers have rigid, twisted macromolecular backbones that give rise to microvoids. Examples include substituted polyacetylenes, perfluoropolymers, addition-type polynorbornene, polymers of intrinsic microporosity (PIMs) and some polyimides. High permeability membranes may also be produced by thermal rearrangement of precursor polymers.}, langid = {english}, - file = {/home/simon/Zotero/storage/WRYVVY2Z/Budd and McKeown - 2010 - Highly permeable polymers for gas separation membr.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WRYVVY2Z/Budd and McKeown - 2010 - Highly permeable polymers for gas separation membr.pdf} } @article{bychukAnomalousDiffusionLiquid1995, title = {Anomalous {{Diffusion}} at {{Liquid Surfaces}}}, author = {Bychuk, Oleg V. and O'Shaughnessy, Ben}, - year = {1995}, - month = mar, - journal = {Physical Review Letters}, + date = {1995-03-06}, + journaltitle = {Physical Review Letters}, + shortjournal = {Phys. Rev. Lett.}, volume = {74}, number = {10}, pages = {1795--1798}, issn = {0031-9007, 1079-7114}, doi = {10.1103/PhysRevLett.74.1795}, + url = {https://link.aps.org/doi/10.1103/PhysRevLett.74.1795}, urldate = {2023-09-18}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/BXH5ZS4L/Bychuk and O'Shaughnessy - 1995 - Anomalous Diffusion at Liquid Surfaces.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BXH5ZS4L/Bychuk and O'Shaughnessy - 1995 - Anomalous Diffusion at Liquid Surfaces.pdf} } @article{calero1HNuclearSpin2015, title = {{{1H Nuclear Spin Relaxation}} of {{Liquid Water}} from {{Molecular Dynamics Simulations}}}, - author = {Calero, C. and Mart{\'i}, J. and Gu{\`a}rdia, E.}, - year = {2015}, - month = feb, - journal = {The Journal of Physical Chemistry B}, + author = {Calero, C. and Martí, J. and Guàrdia, E.}, + date = {2015-02-05}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {119}, number = {5}, pages = {1966--1973}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp510013q}, + url = {https://pubs.acs.org/doi/10.1021/jp510013q}, urldate = {2023-07-03}, - abstract = {We have investigated the nuclear spin relaxation properties of 1H in liquid water with the help of molecular dynamics simulations. We have computed the 1H nuclear spin relaxation times T1 and T2 and determined the contribution of the different interactions to the relaxation at different temperatures and for different classical water models (SPC/E, TIP3P, TIP4P, and TIP4P/2005). Among the water models considered, the TIP4P/2005 model exhibits the best agreement with the experiment. The same analysis was performed with Car-Parrinello ab initio molecular dynamics simulations of bulk water at T = 330 K, which provided results close to the experimental values at room temperature. To complete the study, we have successfully accounted for the temperature-dependence of T1 and T2 in terms of a simplified model, which considers the reorientation in finite angle jumps and the diffusive translation of water molecules.}, + abstract = {We have investigated the nuclear spin relaxation properties of 1H in liquid water with the help of molecular dynamics simulations. We have computed the 1H nuclear spin relaxation times T1 and T2 and determined the contribution of the different interactions to the relaxation at different temperatures and for different classical water models (SPC/E, TIP3P, TIP4P, and TIP4P/2005). Among the water models considered, the TIP4P/2005 model exhibits the best agreement with the experiment. The same analysis was performed with Car−Parrinello ab initio molecular dynamics simulations of bulk water at T = 330 K, which provided results close to the experimental values at room temperature. To complete the study, we have successfully accounted for the temperature-dependence of T1 and T2 in terms of a simplified model, which considers the reorientation in finite angle jumps and the diffusive translation of water molecules.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/JID463BZ/Calero et al. - 2015 - 1 H Nuclear Spin Relaxation of Liquid W.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/JID463BZ/Calero et al. - 2015 - 1 H Nuclear Spin Relaxation of Liquid W.pdf} } @article{carlssonAbsoluteRelativeEntropies2005, title = {Absolute and {{Relative Entropies}} from {{Computer Simulation}} with {{Applications}} to {{Ligand Binding}}}, - author = {Carlsson, Jens and {\AA}qvist, Johan}, - year = {2005}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + author = {Carlsson, Jens and Åqvist, Johan}, + date = {2005-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {109}, number = {13}, pages = {6448--6456}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp046022f}, + url = {https://pubs.acs.org/doi/10.1021/jp046022f}, urldate = {2023-05-02}, langid = {english}, - file = {/home/simon/Zotero/storage/2AK8VAHB/Carlsson and Åqvist - 2005 - Absolute and Relative Entropies from Computer Simu.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2AK8VAHB/Carlsson and Åqvist - 2005 - Absolute and Relative Entropies from Computer Simu.pdf} } @article{caroAccurateSchemesCalculation2016, title = {Accurate Schemes for Calculation of Thermodynamic Properties of Liquid Mixtures from Molecular Dynamics Simulations}, - author = {Caro, Miguel A. and Laurila, Tomi and {Lopez-Acevedo}, Olga}, - year = {2016}, - month = dec, - journal = {The Journal of Chemical Physics}, + author = {Caro, Miguel A. and Laurila, Tomi and Lopez-Acevedo, Olga}, + date = {2016-12-28}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {J. Chem. Phys.}, volume = {145}, number = {24}, pages = {244504}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4973001}, + url = {https://pubs.aip.org/aip/jcp/article/931951}, urldate = {2023-04-26}, langid = {english}, keywords = {MD,mixture}, - file = {/home/simon/Zotero/storage/CHDKBAS6/Caro et al. - 2016 - Accurate schemes for calculation of thermodynamic .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CHDKBAS6/Caro et al. - 2016 - Accurate schemes for calculation of thermodynamic .pdf} } @article{carofAccurateQuadrupolarNMR2014, title = {Accurate {{Quadrupolar NMR Relaxation Rates}} of {{Aqueous Cations}} from {{Classical Molecular Dynamics}}}, author = {Carof, Antoine and Salanne, Mathieu and Charpentier, Thibault and Rotenberg, Benjamin}, - year = {2014}, - month = nov, - journal = {The Journal of Physical Chemistry B}, + date = {2014-11-20}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {118}, number = {46}, pages = {13252--13257}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp5105054}, + url = {https://pubs.acs.org/doi/10.1021/jp5105054}, urldate = {2023-05-24}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/2D3VHZFY/jp5105054.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2D3VHZFY/jp5105054.pdf} } @article{cartaNovelPolymersIntrinsic2009, title = {Novel Polymers of Intrinsic Microporosity ({{PIMs}}) Derived from 1,1-Spiro-Bis(1,2,3,4-Tetrahydronaphthalene)-Based Monomers}, author = {Carta, Mariolino and Msayib, Kadhum J. and McKeown, Neil B.}, - year = {2009}, - month = oct, - journal = {Tetrahedron Letters}, + date = {2009-10-28}, + journaltitle = {Tetrahedron Letters}, + shortjournal = {Tetrahedron Lett.}, volume = {50}, number = {43}, pages = {5954--5957}, issn = {0040-4039}, doi = {10.1016/j.tetlet.2009.08.032}, + url = {https://www.sciencedirect.com/science/article/pii/S0040403909015846}, urldate = {2023-10-04}, - abstract = {The synthesis of novel monomers based upon the rigid 1,1{${'}$}-spiro-bis(1,2,4,5-tetrahydro-6,7-dihydroxynaphthalene) framework is reported. These monomers can be used for the synthesis of polymers of intrinsic microporosity (PIMs) due to their reactive catechol units and nonlinear shape, which introduces the necessary sites of contortion into the resulting PIM.}, - file = {/home/simon/Zotero/storage/UUKS9AK8/Carta et al. - 2009 - Novel polymers of intrinsic microporosity (PIMs) d.pdf;/home/simon/Zotero/storage/TKZVZTMX/S0040403909015846.html} + abstract = {The synthesis of novel monomers based upon the rigid 1,1′-spiro-bis(1,2,4,5-tetrahydro-6,7-dihydroxynaphthalene) framework is reported. These monomers can be used for the synthesis of polymers of intrinsic microporosity (PIMs) due to their reactive catechol units and nonlinear shape, which introduces the necessary sites of contortion into the resulting PIM.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/UUKS9AK8/Carta et al. - 2009 - Novel polymers of intrinsic microporosity (PIMs) d.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/TKZVZTMX/S0040403909015846.html} } @article{chamorroHeavyWaterModels2021, title = {Heavy {{Water Models}} for {{Classical Molecular Dynamics}}: {{Effective Inclusion}} of {{Nuclear Quantum Effects}}}, shorttitle = {Heavy {{Water Models}} for {{Classical Molecular Dynamics}}}, author = {Chamorro, Victor Cruces and Tempra, Carmelo and Jungwirth, Pavel}, - year = {2021}, - month = may, - journal = {The Journal of Physical Chemistry B}, + date = {2021-05-06}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {125}, number = {17}, pages = {4514--4519}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.1c02235}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.1c02235}, urldate = {2023-11-07}, - abstract = {Small differences in physical and chemical properties of H2O and D2O, such as melting and boiling points or pKa, can be traced back to a slightly stronger hydrogen bonding in heavy versus normal water. In particular, deuteration reduces zeropoint vibrational energies as a demonstration of nuclear quantum effects. In principle, computationally demanding quantum molecular dynamics is required to model such effects. However, as already demonstrated by Feynmann and Hibbs, zero-point vibrations can be effectively accounted for by modifying the interaction potential within classical dynamics. In the spirit of the Feymann-Hibbs approach, we develop here two water models for classical molecular dynamics by fitting experimental differences between H2O and D2O. We show that a three-site SPCE-based model accurately reproduces differences between properties of the two water isotopes, with a four-site TIP4P-2005/based model in addition capturing also the absolute values of key properties of heavy water. The present models are computationally simple enough to allow for extensive simulations of biomolecules in heavy water relevant, for example, for experimental techniques such as NMR or neutron scattering.}, + abstract = {Small differences in physical and chemical properties of H2O and D2O, such as melting and boiling points or pKa, can be traced back to a slightly stronger hydrogen bonding in heavy versus normal water. In particular, deuteration reduces zeropoint vibrational energies as a demonstration of nuclear quantum effects. In principle, computationally demanding quantum molecular dynamics is required to model such effects. However, as already demonstrated by Feynmann and Hibbs, zero-point vibrations can be effectively accounted for by modifying the interaction potential within classical dynamics. In the spirit of the Feymann−Hibbs approach, we develop here two water models for classical molecular dynamics by fitting experimental differences between H2O and D2O. We show that a three-site SPCE-based model accurately reproduces differences between properties of the two water isotopes, with a four-site TIP4P-2005/based model in addition capturing also the absolute values of key properties of heavy water. The present models are computationally simple enough to allow for extensive simulations of biomolecules in heavy water relevant, for example, for experimental techniques such as NMR or neutron scattering.}, langid = {english}, - file = {/home/simon/Zotero/storage/RGWB6MIU/Chamorro et al. - 2021 - Heavy Water Models for Classical Molecular Dynamic.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/RGWB6MIU/Chamorro et al. - 2021 - Heavy Water Models for Classical Molecular Dynamic.pdf} } @article{chawlaMembranesCO2CH42020, title = {Membranes for {{CO2}} /{{CH4}} and {{CO2}}/{{N2 Gas Separation}}}, author = {Chawla, Muhammad and Saulat, Hammad and Masood Khan, Muhammad and Mahmood Khan, Muhammad and Rafiq, Sikander and Cheng, Linjuan and Iqbal, Tanveer and Rasheed, M. Imran and Farooq, Muhammad Zohaib and Saeed, Muhammad and Ahmad, Nasir M. and Khan Niazi, Muhammad Bilal and Saqib, Sidra and Jamil, Farrukh and Mukhtar, Ahmad and Muhammad, Nawshad}, - year = {2020}, - journal = {Chemical Engineering \& Technology}, + date = {2020}, + journaltitle = {Chemical Engineering \& Technology}, volume = {43}, number = {2}, pages = {184--199}, issn = {1521-4125}, doi = {10.1002/ceat.201900375}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ceat.201900375}, urldate = {2023-11-06}, abstract = {Membrane technology has emerged as a leading tool worldwide for effective CO2 separation because of its well-known advantages, including high surface area, compact design, ease of maintenance, environmentally friendly nature, and cost-effectiveness. Polymeric and inorganic membranes are generally utilized for the separation of gas mixtures. The mixed-matrix membrane (MMM) utilizes the advantages of both polymeric and inorganic membranes to surpass the trade-off limits. The high permeability and selectivity of MMMs by incorporating different types of fillers exhibit the best performance for CO2 separation from natural gas and other flue gases. The recent progress made in the field of MMMs having different types of fillers is emphasized. Specifically, CO2/CH4 and CO2/N2 separation from various types of MMMs are comprehensively reviewed that are closely relevant to natural gas purification and compositional flue gas treatment}, langid = {english}, keywords = {CO2 separation,Composite membranes,Gas membranes,Mixed-matrix membranes,Permeability}, - file = {/home/simon/Zotero/storage/DG76WYTR/Chawla et al. - 2020 - Membranes for CO2 CH4 and CO2N2 Gas Separation.pdf;/home/simon/Zotero/storage/XSKMJTFN/ceat.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DG76WYTR/Chawla et al. - 2020 - Membranes for CO2 CH4 and CO2N2 Gas Separation.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/XSKMJTFN/ceat.html} } @article{chemmiNoninvasiveExperimentalEvidence2016, title = {Noninvasive {{Experimental Evidence}} of the {{Linear Pore Size Dependence}} of {{Water Diffusion}} in {{Nanoconfinement}}}, author = {Chemmi, Houria and Petit, Dominique and Levitz, Pierre and Denoyel, Renaud and Galarneau, Anne and Korb, Jean-Pierre}, - year = {2016}, - month = feb, - journal = {The Journal of Physical Chemistry Letters}, + date = {2016-02-04}, + journaltitle = {The Journal of Physical Chemistry Letters}, + shortjournal = {J. Phys. Chem. Lett.}, volume = {7}, number = {3}, pages = {393--398}, issn = {1948-7185, 1948-7185}, doi = {10.1021/acs.jpclett.5b02718}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.5b02718}, urldate = {2023-09-18}, abstract = {We show that nuclear magnetic relaxation experiments at variable magnetic fields (NMRD) provide noninvasive means for probing the spatial dependence of liquid diffusion close to solid interfaces. These experiments performed on samples of cylindrical and spherical nanopore geometries demonstrate that the average diffusion coefficient parallel to the interface is proportional to the pore radii in different dynamics regimes. A master curve method allows extraction of gradients of diffusion coefficients in proximity of the pore surfaces, indicative of the efficiency of coupling between liquid layers. Due to their selectivity in frequency, NMRD experiments are able to differentiate the different water dynamical events induced by heterogeneous surfaces or composed dynamical processes. This analysis relevant in physical and biological confinements highlights the interplay between the molecular and continuous description of fluid dynamics near interfaces.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/NVBVFC66/Chemmi et al. - 2016 - Noninvasive Experimental Evidence of the Linear Po.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NVBVFC66/Chemmi et al. - 2016 - Noninvasive Experimental Evidence of the Linear Po.pdf} } @article{chengAdsorptionEthanolVapor2012, title = {Adsorption of {{Ethanol Vapor}} on {{Mica Surface}} under {{Different Relative Humidities}}: {{A Molecular Simulation Study}}}, shorttitle = {Adsorption of {{Ethanol Vapor}} on {{Mica Surface}} under {{Different Relative Humidities}}}, author = {Cheng, Tao and Sun, Huai}, - year = {2012}, - month = aug, - journal = {The Journal of Physical Chemistry C}, + date = {2012-08-09}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {116}, number = {31}, pages = {16436--16446}, issn = {1932-7447, 1932-7455}, doi = {10.1021/jp3020595}, + url = {https://pubs.acs.org/doi/10.1021/jp3020595}, urldate = {2023-08-09}, abstract = {The adsorption of ethanol vapor on a mica surface at 298 K and different relative humidities (RHs) are studied using grand canonical Monte Carlo and molecular dynamics simulations. The simulations show that the adsorbed ethanol molecules form a monolayer on the mica surface, sharply contrasting the behavior of water, which forms multiple adsorption layers on the mica surface. Simulations of an ethanol and water mixture reveal that the adsorbed molecules are segregated into a water-rich domain near the mica surface and an ethanol-rich domain on top of the water-rich domain. The water-rich domain exhibits multilayers unless the RH is extremely low ({$<$}1\%), whereas the ethanol-rich domain exhibits a monolayer. These findings are supported by calculations of the isosteric heats of adsorption and analyses of configurations, concentrations, and diffusivities of molecules in different layers.}, langid = {english}, keywords = {ethanol,MD}, - file = {/home/simon/Zotero/storage/EB6I6IRC/Cheng and Sun - 2012 - Adsorption of Ethanol Vapor on Mica Surface under .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/EB6I6IRC/Cheng and Sun - 2012 - Adsorption of Ethanol Vapor on Mica Surface under .pdf} } @article{chengAdsorptionEthanolVapor2012a, title = {Adsorption of {{Ethanol Vapor}} on {{Mica Surface}} under {{Different Relative Humidities}}: {{A Molecular Simulation Study}}}, shorttitle = {Adsorption of {{Ethanol Vapor}} on {{Mica Surface}} under {{Different Relative Humidities}}}, author = {Cheng, Tao and Sun, Huai}, - year = {2012}, - month = aug, - journal = {The Journal of Physical Chemistry C}, + date = {2012-08-09}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {116}, number = {31}, pages = {16436--16446}, issn = {1932-7447, 1932-7455}, doi = {10.1021/jp3020595}, + url = {https://pubs.acs.org/doi/10.1021/jp3020595}, urldate = {2023-07-12}, abstract = {The adsorption of ethanol vapor on a mica surface at 298 K and different relative humidities (RHs) are studied using grand canonical Monte Carlo and molecular dynamics simulations. The simulations show that the adsorbed ethanol molecules form a monolayer on the mica surface, sharply contrasting the behavior of water, which forms multiple adsorption layers on the mica surface. Simulations of an ethanol and water mixture reveal that the adsorbed molecules are segregated into a water-rich domain near the mica surface and an ethanol-rich domain on top of the water-rich domain. The water-rich domain exhibits multilayers unless the RH is extremely low ({$<$}1\%), whereas the ethanol-rich domain exhibits a monolayer. These findings are supported by calculations of the isosteric heats of adsorption and analyses of configurations, concentrations, and diffusivities of molecules in different layers.}, langid = {english}, keywords = {heat,MD,water-ethanol}, - file = {/home/simon/Zotero/storage/SVFSQXNV/Cheng and Sun - 2012 - Adsorption of Ethanol Vapor on Mica Surface under .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SVFSQXNV/Cheng and Sun - 2012 - Adsorption of Ethanol Vapor on Mica Surface under .pdf} } @article{chenMultiscaleModelingSimulations2019, title = {Multiscale Modeling and Simulations of Responsive Polymers}, author = {Chen, Zheng and Huo, Jinhao and Hao, Linxia and Zhou, Jian}, - year = {2019}, - month = mar, - journal = {Current Opinion in Chemical Engineering}, + date = {2019-03}, + journaltitle = {Current Opinion in Chemical Engineering}, + shortjournal = {Current Opinion in Chemical Engineering}, volume = {23}, pages = {21--33}, issn = {22113398}, doi = {10.1016/j.coche.2019.02.004}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2211339818300662}, urldate = {2023-10-04}, langid = {english}, - file = {/home/simon/Zotero/storage/P3L6BMN8/Chen et al. - 2019 - Multiscale modeling and simulations of responsive .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/P3L6BMN8/Chen et al. - 2019 - Multiscale modeling and simulations of responsive .pdf} } @article{chenRoleHydrogenBonding2018, title = {Role of Hydrogen Bonding in Hysteresis Observed in Sorption-Induced Swelling of Soft Nanoporous Polymers}, author = {Chen, Mingyang and Coasne, Benoit and Guyer, Robert and Derome, Dominique and Carmeliet, Jan}, - year = {2018}, - month = aug, - journal = {Nature Communications}, + date = {2018-08-29}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, volume = {9}, number = {1}, pages = {3507}, issn = {2041-1723}, doi = {10.1038/s41467-018-05897-9}, + url = {https://www.nature.com/articles/s41467-018-05897-9}, urldate = {2023-05-04}, - abstract = {Abstract Hysteresis is observed in sorption-induced swelling in various soft nanoporous polymers. The associated coupling mechanism responsible for the observed sorption-induced swelling and associated hysteresis needs to be unraveled. Here we report a microscopic scenario for the molecular mechanism responsible for hysteresis in sorption-induced swelling in natural polymers such as cellulose using atom-scale simulation; moisture content and swelling exhibit hysteresis upon ad- and desorption but not swelling versus moisture content. Different hydrogen bond networks are examined; cellulose swells to form water{\textendash}cellulose bonds upon adsorption but these bonds do not break upon desorption at the same chemical potential. These findings, which are supported by mechanical testing and cellulose textural assessment upon sorption, shed light on experimental observations for wood and other related materials.}, + abstract = {Abstract Hysteresis is observed in sorption-induced swelling in various soft nanoporous polymers. The associated coupling mechanism responsible for the observed sorption-induced swelling and associated hysteresis needs to be unraveled. Here we report a microscopic scenario for the molecular mechanism responsible for hysteresis in sorption-induced swelling in natural polymers such as cellulose using atom-scale simulation; moisture content and swelling exhibit hysteresis upon ad- and desorption but not swelling versus moisture content. Different hydrogen bond networks are examined; cellulose swells to form water–cellulose bonds upon adsorption but these bonds do not break upon desorption at the same chemical potential. These findings, which are supported by mechanical testing and cellulose textural assessment upon sorption, shed light on experimental observations for wood and other related materials.}, langid = {english}, keywords = {HB,MD}, - file = {/home/simon/Zotero/storage/EP3VGKT8/Chen et al. - 2018 - Role of hydrogen bonding in hysteresis observed in.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/EP3VGKT8/Chen et al. - 2018 - Role of hydrogen bonding in hysteresis observed in.pdf} } @article{choudhuryEnthalpyEntropyContributions2006, - title = {{{Enthalpy}}-{{Entropy Contributions}} to the {{Potential}} of {{Mean Force}} of {{Nanoscopic Hydrophobic Solutes}}}, + title = {{{Enthalpy}}−{{Entropy Contributions}} to the {{Potential}} of {{Mean Force}} of {{Nanoscopic Hydrophobic Solutes}}}, author = {Choudhury, Niharendu and Pettitt, B. Montgomery}, - year = {2006}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + date = {2006-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {110}, number = {16}, pages = {8459--8463}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp056909r}, + url = {https://pubs.acs.org/doi/10.1021/jp056909r}, urldate = {2023-07-07}, abstract = {Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water have been calculated using molecular dynamics simulations in isothermal-isobaric (NPT) ensemble and with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution in spite of a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.}, langid = {english}, keywords = {MD,PMF}, - file = {/home/simon/Zotero/storage/5PIX3MV2/Choudhury and Pettitt - 2006 - Enthalpy−Entropy Contributions to the Potential of.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5PIX3MV2/Choudhury and Pettitt - 2006 - Enthalpy−Entropy Contributions to the Potential of.pdf} } @article{chubakNMRRelaxationRates2021, title = {{{NMR Relaxation Rates}} of {{Quadrupolar Aqueous Ions}} from {{Classical Molecular Dynamics Using Force-Field Specific Sternheimer Factors}}}, author = {Chubak, Iurii and Scalfi, Laura and Carof, Antoine and Rotenberg, Benjamin}, - year = {2021}, - month = oct, - journal = {Journal of Chemical Theory and Computation}, + date = {2021-10-12}, + journaltitle = {Journal of Chemical Theory and Computation}, + shortjournal = {J. Chem. Theory Comput.}, volume = {17}, number = {10}, pages = {6006--6017}, issn = {1549-9618, 1549-9626}, doi = {10.1021/acs.jctc.1c00690}, + url = {https://pubs.acs.org/doi/10.1021/acs.jctc.1c00690}, urldate = {2023-05-25}, - abstract = {The nuclear magnetic resonance (NMR) relaxation of quadrupolar nuclei is governed by the electric field gradient (EFG) fluctuations at their position. In classical molecular dynamics (MD), the electron cloud contribution to the EFG can be included via the Sternheimer approximation, in which the full EFG at the nucleus that can be computed using quantum density functional theory (DFT) is considered to be proportional to that arising from the external, classical charge distribution. In this work, we systematically assess the quality of the Sternheimer approximation as well as the impact of the classical force field (FF) on the NMR relaxation rates of aqueous quadrupolar ions at infinite dilution. In particular, we compare the rates obtained using an ab initio parametrized polarizable FF, a recently developed empirical FF with scaled ionic charges and a simple empirical nonpolarizable FF with formal ionic charges. Surprisingly, all three FFs considered yield good values for the rates of smaller and less polarizable solutes (Li+, Na+, K+, Cl-), provided that a model-specific Sternheimer parametrization is employed. Yet, the polarizable and scaled charge FFs yield better estimates for divalent and more polarizable species (Mg2+, Ca2+, Cs+). We find that a linear relationship between the quantum and classical EFGs holds well in all of the cases considered; however, such an approximation often leads to quite large errors in the resulting EFG variance, which is directly proportional to the computed rate. We attempted to reduce the errors by including first order nonlinear corrections to the EFG, yet no clear improvement for the resulting variance has been found. The latter result indicates that more refined methods for determining the EFG at the ion position, in particular those that take into account the instantaneous atomic environment around an ion, might be necessary to systematically improve the NMR relaxation rate estimates in classical MD.}, + abstract = {The nuclear magnetic resonance (NMR) relaxation of quadrupolar nuclei is governed by the electric field gradient (EFG) fluctuations at their position. In classical molecular dynamics (MD), the electron cloud contribution to the EFG can be included via the Sternheimer approximation, in which the full EFG at the nucleus that can be computed using quantum density functional theory (DFT) is considered to be proportional to that arising from the external, classical charge distribution. In this work, we systematically assess the quality of the Sternheimer approximation as well as the impact of the classical force field (FF) on the NMR relaxation rates of aqueous quadrupolar ions at infinite dilution. In particular, we compare the rates obtained using an ab initio parametrized polarizable FF, a recently developed empirical FF with scaled ionic charges and a simple empirical nonpolarizable FF with formal ionic charges. Surprisingly, all three FFs considered yield good values for the rates of smaller and less polarizable solutes (Li+, Na+, K+, Cl−), provided that a model-specific Sternheimer parametrization is employed. Yet, the polarizable and scaled charge FFs yield better estimates for divalent and more polarizable species (Mg2+, Ca2+, Cs+). We find that a linear relationship between the quantum and classical EFGs holds well in all of the cases considered; however, such an approximation often leads to quite large errors in the resulting EFG variance, which is directly proportional to the computed rate. We attempted to reduce the errors by including first order nonlinear corrections to the EFG, yet no clear improvement for the resulting variance has been found. The latter result indicates that more refined methods for determining the EFG at the ion position, in particular those that take into account the instantaneous atomic environment around an ion, might be necessary to systematically improve the NMR relaxation rate estimates in classical MD.}, langid = {english}, - file = {/home/simon/Zotero/storage/ZIU97H7W/Chubak et al. - 2021 - NMR Relaxation Rates of Quadrupolar Aqueous Ions f.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ZIU97H7W/Chubak et al. - 2021 - NMR Relaxation Rates of Quadrupolar Aqueous Ions f.pdf} } @article{chubakQuadrupolar23NaNMR2023, title = {Quadrupolar {{23Na}}+ {{NMR}} Relaxation as a Probe of Subpicosecond Collective Dynamics in Aqueous Electrolyte Solutions}, author = {Chubak, Iurii and Alon, Leeor and Silletta, Emilia V. and Madelin, Guillaume and Jerschow, Alexej and Rotenberg, Benjamin}, - year = {2023}, - month = jan, - journal = {Nature Communications}, + date = {2023-01-05}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, volume = {14}, number = {1}, pages = {84}, issn = {2041-1723}, doi = {10.1038/s41467-022-35695-3}, + url = {https://www.nature.com/articles/s41467-022-35695-3}, urldate = {2023-05-24}, abstract = {Abstract Nuclear magnetic resonance relaxometry represents a powerful tool for extracting dynamic information. Yet, obtaining links to molecular motion is challenging for many ions that relax through the quadrupolar mechanism, which is mediated by electric field gradient fluctuations and lacks a detailed microscopic description. For sodium ions in aqueous electrolytes, we combine ab initio calculations to account for electron cloud effects with classical molecular dynamics to sample long-time fluctuations, and obtain relaxation rates in good agreement with experiments over broad concentration and temperature ranges. We demonstrate that quadrupolar nuclear relaxation is sensitive to subpicosecond dynamics not captured by previous models based on water reorientation or cluster rotation. While ions affect the overall water retardation, experimental trends are mainly explained by dynamics in the first two solvation shells of sodium, which contain mostly water. This work thus paves the way to the quantitative understanding of quadrupolar relaxation in electrolyte and bioelectrolyte systems.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/NRB37QJC/Chubak et al. - 2023 - Quadrupolar 23Na+ NMR relaxation as a probe of sub.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NRB37QJC/Chubak et al. - 2023 - Quadrupolar 23Na+ NMR relaxation as a probe of sub.pdf} } @article{coasneMultiscaleAdsorptionTransport2016, title = {Multiscale Adsorption and Transport in Hierarchical Porous Materials}, author = {Coasne, Benoit}, - year = {2016}, - journal = {New Journal of Chemistry}, + date = {2016}, + journaltitle = {New Journal of Chemistry}, + shortjournal = {New J. Chem.}, volume = {40}, number = {5}, pages = {4078--4094}, publisher = {{Royal Society of Chemistry}}, doi = {10.1039/C5NJ03194J}, + url = {https://pubs.rsc.org/en/content/articlelanding/2016/nj/c5nj03194j}, urldate = {2023-08-29}, langid = {english}, - file = {/home/simon/Zotero/storage/87CKEHC4/Coasne - 2016 - Multiscale adsorption and transport in hierarchica.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/87CKEHC4/Coasne - 2016 - Multiscale adsorption and transport in hierarchica.pdf} } @article{coudertMolecularMechanismSwing2017, - title = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}-8: {{Continuous Deformation}} upon {{Adsorption}}}, - shorttitle = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}-8}, - author = {Coudert, Fran{\c c}ois-Xavier}, - year = {2017}, - month = oct, - journal = {ChemPhysChem}, + title = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}‐8: {{Continuous Deformation}} upon {{Adsorption}}}, + shorttitle = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}‐8}, + author = {Coudert, François‐Xavier}, + date = {2017-10-06}, + journaltitle = {ChemPhysChem}, + shortjournal = {ChemPhysChem}, volume = {18}, number = {19}, pages = {2732--2738}, issn = {1439-4235, 1439-7641}, doi = {10.1002/cphc.201700463}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/cphc.201700463}, urldate = {2023-07-19}, langid = {english}, keywords = {MD,zif}, - file = {/home/simon/Zotero/storage/75JDXXWH/Coudert - 2017 - Molecular Mechanism of Swing Effect in Zeolitic Im.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/75JDXXWH/Coudert - 2017 - Molecular Mechanism of Swing Effect in Zeolitic Im.pdf} } @article{cousin-saint-remiApplyingWaveTheory2017, title = {Applying the Wave Theory to Fixed-Bed Dynamics of {{Metal-Organic Frameworks}} Exhibiting Stepped Adsorption Isotherms: {{Water}}/Ethanol Separation on {{ZIF-8}}}, shorttitle = {Applying the Wave Theory to Fixed-Bed Dynamics of {{Metal-Organic Frameworks}} Exhibiting Stepped Adsorption Isotherms}, - author = {{Cousin-Saint-Remi}, Julien and Denayer, Joeri F.M.}, - year = {2017}, - month = sep, - journal = {Chemical Engineering Journal}, + author = {Cousin-Saint-Remi, Julien and Denayer, Joeri F.M.}, + date = {2017-09}, + journaltitle = {Chemical Engineering Journal}, + shortjournal = {Chemical Engineering Journal}, volume = {324}, pages = {313--323}, issn = {13858947}, doi = {10.1016/j.cej.2017.04.126}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1385894717306691}, urldate = {2023-07-19}, - abstract = {Zeolitic Imidazolate Framework-8 (ZIF-8) is a promising material for the energy-efficient recovery of bioalcohols from aqueous mixtures. Its adsorption isotherms have inflection points and breakthrough curves obtained in dynamic column separation experiments exhibit stepped profiles. With the aim to optimize this adsorptive alcohol recovery process using ZIF-8, the correlation between the shape of the adsorption isotherms and the breakthrough curves was further explored in this work by means of liquid phase batch measurements and breakthrough experiments, with diluted ethanol/water mixtures. The shape of the concentration profiles, in adsorption mode as well in desorption mode, have been carefully analyzed making use of simple theoretical tools, including an axial dispersion model and a wave theory based approach. It was shown that, as a direct expression of the adsorption isotherm and the feed concentration, the concentration profiles were composed of different ``shock waves'' and ``dispersive waves'' propagating at different velocities along the column length. The description of the breakthrough and desorption curves in terms of propagation velocities enabled to gain insights into the fundamental role of the adsorption isotherm into the characteristics and the formation of the concentration profiles. The concept of ``fractional used bed capacity'' (FUBC) was introduced to illustrate the effect of the adsorption isotherm shape on the dynamic capacity at breakthrough point. According to the shape of the adsorption isotherm, efficient desorption could be achieved with the ZIF-8 material. This work provides, with limited computational effort, new perspectives for the further development and optimization of adsorptive separation processes with MOF materials, such as the recovery of bio-alcohols from aqueous mixtures with the ZIF-8 adsorbent.}, + abstract = {Zeolitic Imidazolate Framework-8 (ZIF-8) is a promising material for the energy-efficient recovery of bioalcohols from aqueous mixtures. Its adsorption isotherms have inflection points and breakthrough curves obtained in dynamic column separation experiments exhibit stepped profiles. With the aim to optimize this adsorptive alcohol recovery process using ZIF-8, the correlation between the shape of the adsorption isotherms and the breakthrough curves was further explored in this work by means of liquid phase batch measurements and breakthrough experiments, with diluted ethanol/water mixtures. The shape of the concentration profiles, in adsorption mode as well in desorption mode, have been carefully analyzed making use of simple theoretical tools, including an axial dispersion model and a wave theory based approach. It was shown that, as a direct expression of the adsorption isotherm and the feed concentration, the concentration profiles were composed of different ‘‘shock waves” and ‘‘dispersive waves” propagating at different velocities along the column length. The description of the breakthrough and desorption curves in terms of propagation velocities enabled to gain insights into the fundamental role of the adsorption isotherm into the characteristics and the formation of the concentration profiles. The concept of ‘‘fractional used bed capacity” (FUBC) was introduced to illustrate the effect of the adsorption isotherm shape on the dynamic capacity at breakthrough point. According to the shape of the adsorption isotherm, efficient desorption could be achieved with the ZIF-8 material. This work provides, with limited computational effort, new perspectives for the further development and optimization of adsorptive separation processes with MOF materials, such as the recovery of bio-alcohols from aqueous mixtures with the ZIF-8 adsorbent.}, langid = {english}, keywords = {water-ethanol,zif}, - file = {/home/simon/Zotero/storage/JTLL4QQY/Cousin-Saint-Remi and Denayer - 2017 - Applying the wave theory to fixed-bed dynamics of .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/JTLL4QQY/Cousin-Saint-Remi and Denayer - 2017 - Applying the wave theory to fixed-bed dynamics of .pdf} } @article{cousinsaintremiBiobutanolSeparationMetalOrganic2011, title = {Biobutanol {{Separation}} with the {{Metal-Organic Framework ZIF-8}}}, - author = {Cousin Saint Remi, Julien and R{\'e}my, Tom and Van Hunskerken, Vincent and {van de Perre}, Stijn and Duerinck, Tim and Maes, Michael and De Vos, Dirk and Gobechiya, Elena and Kirschhock, Christine E. A. and Baron, Gino V. and Denayer, Joeri F. M.}, - year = {2011}, - month = aug, - journal = {ChemSusChem}, + author = {Cousin Saint Remi, Julien and Rémy, Tom and Van Hunskerken, Vincent and family=Perre, given=Stijn, prefix=van de, useprefix=true and Duerinck, Tim and Maes, Michael and De Vos, Dirk and Gobechiya, Elena and Kirschhock, Christine E. A. and Baron, Gino V. and Denayer, Joeri F. M.}, + date = {2011-08-22}, + journaltitle = {ChemSusChem}, + shortjournal = {ChemSusChem}, volume = {4}, number = {8}, pages = {1074--1077}, issn = {18645631}, doi = {10.1002/cssc.201100261}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/cssc.201100261}, urldate = {2023-07-19}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/YS2F4QLG/Cousin Saint Remi et al. - 2011 - Biobutanol Separation with the Metal-Organic Frame.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YS2F4QLG/Cousin Saint Remi et al. - 2011 - Biobutanol Separation with the Metal-Organic Frame.pdf} } @article{daiPredictionHeatMixing2005, title = {Prediction of the Heat of Mixing for Binary Fluids Using Molecular Dynamics Simulation}, author = {Dai, Jianxing and Wu, Chuanjie and Bao, Xiaoguang and Sun, Huai}, - year = {2005}, - month = sep, - journal = {Fluid Phase Equilibria}, + date = {2005-09}, + journaltitle = {Fluid Phase Equilibria}, + shortjournal = {Fluid Phase Equilibria}, volume = {236}, number = {1-2}, pages = {78--85}, issn = {03783812}, doi = {10.1016/j.fluid.2005.05.007}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0378381205001585}, urldate = {2023-03-22}, - abstract = {Isothermal{\textendash}isobaric ensemble (NPT) molecular dynamics (MD) simulation was applied to calculate the heats of mixing for binary fluids based on an all-atom force field. The calculation protocol was tested on mixtures of 1-propanol/n-heptane, n-butylamine/n-heptane and n-butylamine/water at various temperatures and compositions. Based on a simple error analysis and comparisons of calculated and experimental data, we propose that a necessary but not sufficient condition in the predictions of the heats of mixing is to have a force field highly accurate in evaluating energetic properties for pure substances. More work is required in order to find out the sufficient conditions.}, + abstract = {Isothermal–isobaric ensemble (NPT) molecular dynamics (MD) simulation was applied to calculate the heats of mixing for binary fluids based on an all-atom force field. The calculation protocol was tested on mixtures of 1-propanol/n-heptane, n-butylamine/n-heptane and n-butylamine/water at various temperatures and compositions. Based on a simple error analysis and comparisons of calculated and experimental data, we propose that a necessary but not sufficient condition in the predictions of the heats of mixing is to have a force field highly accurate in evaluating energetic properties for pure substances. More work is required in order to find out the sufficient conditions.}, langid = {english}, keywords = {MD,mixture}, - file = {/home/simon/Zotero/storage/WX74E8TJ/Dai et al. - 2005 - Prediction of the heat of mixing for binary fluids.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WX74E8TJ/Dai et al. - 2005 - Prediction of the heat of mixing for binary fluids.pdf} } @article{darrigoSoundPropagationWater1988, - title = {Sound Propagation in Water{\textendash}Ethanol Mixtures at Low Temperatures. {{I}}. {{Ultrasonic}} Velocity}, - author = {D'Arrigo, G. and Paparelli, A.}, - year = {1988}, - month = jan, - journal = {The Journal of Chemical Physics}, + title = {Sound Propagation in Water–Ethanol Mixtures at Low Temperatures. {{I}}. {{Ultrasonic}} Velocity}, + author = {D’Arrigo, G. and Paparelli, A.}, + date = {1988-01}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {88}, number = {1}, pages = {405--415}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.454616}, + url = {https://pubs.aip.org/aip/jcp/article/88/1/405-415/91403}, urldate = {2023-05-20}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/P9YMFRTD/D’Arrigo and Paparelli - 1988 - Sound propagation in water–ethanol mixtures at low.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/P9YMFRTD/D’Arrigo and Paparelli - 1988 - Sound propagation in water–ethanol mixtures at low.pdf} } @article{demessenceAdsorptionPropertiesHigh2010, title = {Adsorption Properties in High Optical Quality {{nanoZIF-8}} Thin Films with Tunable Thickness}, - author = {Demessence, Aude and Boissi{\`e}re, C{\'e}dric and Grosso, David and Horcajada, Patricia and Serre, Christian and F{\'e}rey, G{\'e}rard and {Soler-Illia}, Galo J. A. A. and Sanchez, Cl{\'e}ment}, - year = {2010}, - journal = {Journal of Materials Chemistry}, + author = {Demessence, Aude and Boissière, Cédric and Grosso, David and Horcajada, Patricia and Serre, Christian and Férey, Gérard and Soler-Illia, Galo J. A. A. and Sanchez, Clément}, + date = {2010}, + journaltitle = {Journal of Materials Chemistry}, + shortjournal = {J. Mater. Chem.}, volume = {20}, number = {36}, pages = {7676}, issn = {0959-9428, 1364-5501}, doi = {10.1039/c0jm00500b}, + url = {http://xlink.rsc.org/?DOI=c0jm00500b}, urldate = {2023-07-19}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/FSGGD2B4/Demessence et al. - 2010 - Adsorption properties in high optical quality nano.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/FSGGD2B4/Demessence et al. - 2010 - Adsorption properties in high optical quality nano.pdf} } -@misc{DiffusionNanoporousMaterials, +@online{DiffusionNanoporousMaterials, title = {Diffusion in Nanoporous Materials: Fundamental Principles, Insights and Challenges - {{New Journal}} of {{Chemistry}} ({{RSC Publishing}}) {{DOI}}:10.1039/{{C5NJ02836A}}}, + url = {https://pubs.rsc.org/en/content/articlehtml/2016/nj/c5nj02836a}, urldate = {2023-09-30}, - howpublished = {https://pubs.rsc.org/en/content/articlehtml/2016/nj/c5nj02836a}, - file = {/home/simon/Zotero/storage/CB7683ER/c5nj02836a.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CB7683ER/c5nj02836a.html} } @article{dixitMolecularSegregationObserved2002, - title = {Molecular Segregation Observed in a Concentrated Alcohol{\textendash}Water Solution}, + title = {Molecular Segregation Observed in a Concentrated Alcohol–Water Solution}, author = {Dixit, S. and Crain, J. and Poon, W. C. K. and Finney, J. L. and Soper, A. K.}, - year = {2002}, - month = apr, - journal = {Nature}, + date = {2002-04}, + journaltitle = {Nature}, + shortjournal = {Nature}, volume = {416}, number = {6883}, pages = {829--832}, issn = {0028-0836, 1476-4687}, doi = {10.1038/416829a}, + url = {http://www.nature.com/articles/416829a}, urldate = {2023-04-26}, langid = {english}, keywords = {HB,mixture}, - file = {/home/simon/Zotero/storage/ECVIVFZT/Dixit et al. - 2002 - Molecular segregation observed in a concentrated a.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ECVIVFZT/Dixit et al. - 2002 - Molecular segregation observed in a concentrated a.pdf} } @article{duComparativeAnalysisCalculation2020, title = {Comparative Analysis of Calculation Method of Adsorption Isosteric Heat: {{Case}} Study of {{CO2}} Capture Using {{MOFs}}}, shorttitle = {Comparative Analysis of Calculation Method of Adsorption Isosteric Heat}, author = {Du, Zhenyu and Nie, Xianhua and Deng, Shuai and Zhao, Li and Li, Shuangjun and Zhang, Yue and Zhao, Jie}, - year = {2020}, - month = may, - journal = {Microporous and Mesoporous Materials}, + date = {2020-05}, + journaltitle = {Microporous and Mesoporous Materials}, + shortjournal = {Microporous and Mesoporous Materials}, volume = {298}, pages = {110053}, issn = {13871811}, doi = {10.1016/j.micromeso.2020.110053}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1387181120300561}, urldate = {2023-07-18}, abstract = {The isosteric heat of adsorption (qst) is a critical parameter to describe the CO2 adsorption separation system for the determination of energy consumption of regeneration. The qst could be easily determined using the ensemble fluctuation approach as well as indirect approaches, including the isosteric and analytic ones; however the obtained qst values could be affected by the method used to determine them. To date, only a few studies compared these approaches using the same criteria, leading to challenges in identifying the proper approach for calculating qst.}, langid = {english}, keywords = {heat}, - file = {/home/simon/Zotero/storage/N4CRF7DI/Du et al. - 2020 - Comparative analysis of calculation method of adso.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/N4CRF7DI/Du et al. - 2020 - Comparative analysis of calculation method of adso.pdf} } @article{edwardMolecularVolumesStokesEinstein1970, title = {Molecular Volumes and the {{Stokes-Einstein}} Equation}, author = {Edward, John T.}, - year = {1970}, - month = apr, - journal = {Journal of Chemical Education}, + date = {1970-04}, + journaltitle = {Journal of Chemical Education}, + shortjournal = {J. Chem. Educ.}, volume = {47}, number = {4}, pages = {261}, issn = {0021-9584, 1938-1328}, doi = {10.1021/ed047p261}, + url = {https://pubs.acs.org/doi/abs/10.1021/ed047p261}, urldate = {2023-06-01}, langid = {english}, keywords = {propane}, - file = {/home/simon/Zotero/storage/22EDXW9Z/Edward - 1970 - Molecular volumes and the Stokes-Einstein equation.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/22EDXW9Z/Edward - 1970 - Molecular volumes and the Stokes-Einstein equation.pdf} } @article{emamiForceFieldSurface2014, title = {Force {{Field}} and a {{Surface Model Database}} for {{Silica}} to {{Simulate Interfacial Properties}} in {{Atomic Resolution}}}, author = {Emami, Fateme S. and Puddu, Valeria and Berry, Rajiv J. and Varshney, Vikas and Patwardhan, Siddharth V. and Perry, Carole C. and Heinz, Hendrik}, - year = {2014}, - month = apr, - journal = {Chemistry of Materials}, + date = {2014-04-22}, + journaltitle = {Chemistry of Materials}, + shortjournal = {Chem. Mater.}, volume = {26}, number = {8}, pages = {2647--2658}, issn = {0897-4756, 1520-5002}, doi = {10.1021/cm500365c}, + url = {https://pubs.acs.org/doi/10.1021/cm500365c}, urldate = {2023-03-22}, - abstract = {Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100\% to less than 5\%. In addition, a silica surface model database is introduced for the full range of variable surface chemistry and pH (Q2, Q3, Q4 environments with adjustable degree of ionization) that have shown to determine selective molecular recognition. The force field enables accurate computational predictions of aqueous interfacial properties of all types of silica, which is substantiated by extensive comparisons to experimental measurements. The parameters are integrated into multiple force fields for broad applicability to biomolecules, polymers, and inorganic materials (AMBER, CHARMM, COMPASS, CVFF, PCFF, INTERFACE force fields). We also explain mechanistic details of molecular adsorption of water vapor, as well as significant variations in the amount and dissociation depth of superficial cations at silica-water interfaces that correlate with {$\zeta$}potential measurements and create a wide range of aqueous environments for adsorption and self-assembly of complex molecules. The systematic analysis of binding conformations and adsorption free energies of distinct peptides to silica surfaces will be reported separately in a companion paper. The models aid to understand and design silica nanomaterials in 3D atomic resolution and are extendable to chemical reactions.}, + abstract = {Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100\% to less than 5\%. In addition, a silica surface model database is introduced for the full range of variable surface chemistry and pH (Q2, Q3, Q4 environments with adjustable degree of ionization) that have shown to determine selective molecular recognition. The force field enables accurate computational predictions of aqueous interfacial properties of all types of silica, which is substantiated by extensive comparisons to experimental measurements. The parameters are integrated into multiple force fields for broad applicability to biomolecules, polymers, and inorganic materials (AMBER, CHARMM, COMPASS, CVFF, PCFF, INTERFACE force fields). We also explain mechanistic details of molecular adsorption of water vapor, as well as significant variations in the amount and dissociation depth of superficial cations at silica−water interfaces that correlate with ζpotential measurements and create a wide range of aqueous environments for adsorption and self-assembly of complex molecules. The systematic analysis of binding conformations and adsorption free energies of distinct peptides to silica surfaces will be reported separately in a companion paper. The models aid to understand and design silica nanomaterials in 3D atomic resolution and are extendable to chemical reactions.}, langid = {english}, keywords = {ff,MD,silica}, - file = {/home/simon/Zotero/storage/UQ7QC7B4/Emami et al. - 2014 - Force Field and a Surface Model Database for Silic.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/UQ7QC7B4/Emami et al. - 2014 - Force Field and a Surface Model Database for Silic.pdf} } @article{fanInvestigationInteractionPolar2016, title = {Investigation of the {{Interaction}} of {{Polar Molecules}} on {{Graphite Surface}}: {{Prediction}} of {{Isosteric Heat}} of {{Adsorption}} at {{Zero Surface Coverage}}}, shorttitle = {Investigation of the {{Interaction}} of {{Polar Molecules}} on {{Graphite Surface}}}, author = {Fan, Wu and Chakraborty, Anutosh}, - year = {2016}, - month = oct, - journal = {The Journal of Physical Chemistry C}, + date = {2016-10-20}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {120}, number = {41}, pages = {23490--23499}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.6b06119}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.6b06119}, urldate = {2023-07-19}, - abstract = {The interactions of polar molecules with various orientations on graphite surface are calculated employing molecular simulation under static conditions in which the multiple-sites Lennard-Jones (LJ), electrostatic, and dipole induction potentials are considered. The Henry's constant and the potential energy as a function of polar molecule-graphite separation distance (z) are used to calculate the isosteric heat of adsorption at zero surface coverage (qsot), and the results are compared to experimentally measure qsot data of various polar molecules such as water, ammonia, methanol, and ethanol + graphite systems. The maximum qsot values are observed for the z values ranging from 2.5 to 4 {\AA} with respect to various polar molecule orientations. The LJ potential contributes more than 90\% and the induction potential adds less than 10\% of total potentials at the maximum potential well depth, whereas the electrostatic contributions are found to be less than 1\% of total potential energy. It is also found that the induction potential increases exponentially for the separation distance decreasing from 3 to 0 {\AA} for all polar molecules presented in this Article.}, + abstract = {The interactions of polar molecules with various orientations on graphite surface are calculated employing molecular simulation under static conditions in which the multiple-sites Lennard-Jones (LJ), electrostatic, and dipole induction potentials are considered. The Henry’s constant and the potential energy as a function of polar molecule−graphite separation distance (z) are used to calculate the isosteric heat of adsorption at zero surface coverage (qsot), and the results are compared to experimentally measure qsot data of various polar molecules such as water, ammonia, methanol, and ethanol + graphite systems. The maximum qsot values are observed for the z values ranging from 2.5 to 4 Å with respect to various polar molecule orientations. The LJ potential contributes more than 90\% and the induction potential adds less than 10\% of total potentials at the maximum potential well depth, whereas the electrostatic contributions are found to be less than 1\% of total potential energy. It is also found that the induction potential increases exponentially for the separation distance decreasing from 3 to 0 Å for all polar molecules presented in this Article.}, langid = {english}, keywords = {heat,water-ethanol}, - file = {/home/simon/Zotero/storage/JYZMVRXT/Fan and Chakraborty - 2016 - Investigation of the Interaction of Polar Molecule.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/JYZMVRXT/Fan and Chakraborty - 2016 - Investigation of the Interaction of Polar Molecule.pdf} } @article{fauxNuclearMagneticResonance2013, title = {Nuclear Magnetic Resonance Relaxometry of Water in Two and Quasi-Two Dimensions}, author = {Faux, D. A. and McDonald, P. J. and Howlett, N. C. and Bhatt, J. S. and Churakov, S. V.}, - year = {2013}, - month = jun, - journal = {Physical Review E}, + date = {2013-06-17}, + journaltitle = {Physical Review E}, + shortjournal = {Phys. Rev. E}, volume = {87}, number = {6}, pages = {062309}, issn = {1539-3755, 1550-2376}, doi = {10.1103/PhysRevE.87.062309}, + url = {https://link.aps.org/doi/10.1103/PhysRevE.87.062309}, urldate = {2023-12-12}, langid = {english}, - file = {/home/simon/Zotero/storage/3I2PU5X9/Faux et al. - 2013 - Nuclear magnetic resonance relaxometry of water in.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3I2PU5X9/Faux et al. - 2013 - Nuclear magnetic resonance relaxometry of water in.pdf} } @article{filetiRelativeStrengthHydrogen2004, - title = {Relative Strength of Hydrogen Bond Interaction in Alcohol{\textendash}Water Complexes}, + title = {Relative Strength of Hydrogen Bond Interaction in Alcohol–Water Complexes}, author = {Fileti, Eudes E. and Chaudhuri, Puspitapallab and Canuto, Sylvio}, - year = {2004}, - month = dec, - journal = {Chemical Physics Letters}, + date = {2004-12}, + journaltitle = {Chemical Physics Letters}, + shortjournal = {Chemical Physics Letters}, volume = {400}, number = {4-6}, pages = {494--499}, issn = {00092614}, doi = {10.1016/j.cplett.2004.10.149}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0009261404017142}, urldate = {2023-04-27}, - abstract = {Hydrogen binding energies are calculated for the different isomers of 1:1 complexes of methanol, ethanol and water using ab initio methods from MP2 to CCSD(T). Zero-point energy vibration and counterpoise corrections are considered and electron correlation effects are analyzed. In methanol{\textendash}water and ethanol{\textendash}water the most stable heterodimer is the one where the water plays the role of proton donor. In methanol{\textendash}ethanol the two isomers have essentially the same energy and no favorite heterodimer could be discerned. The interplay between the relative binding energy is briefly discussed in conjunction with the incomplete mixing of alcohol{\textendash}water systems.}, + abstract = {Hydrogen binding energies are calculated for the different isomers of 1:1 complexes of methanol, ethanol and water using ab initio methods from MP2 to CCSD(T). Zero-point energy vibration and counterpoise corrections are considered and electron correlation effects are analyzed. In methanol–water and ethanol–water the most stable heterodimer is the one where the water plays the role of proton donor. In methanol–ethanol the two isomers have essentially the same energy and no favorite heterodimer could be discerned. The interplay between the relative binding energy is briefly discussed in conjunction with the incomplete mixing of alcohol–water systems.}, langid = {english}, keywords = {HB,mixture}, - file = {/home/simon/Zotero/storage/Q3PE5JEV/Fileti et al. - 2004 - Relative strength of hydrogen bond interaction in .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Q3PE5JEV/Fileti et al. - 2004 - Relative strength of hydrogen bond interaction in .pdf} } @article{finneranHydrogenBondingEthanol2015, - title = {Hydrogen Bonding in the Ethanol{\textendash}Water Dimer}, + title = {Hydrogen Bonding in the Ethanol–Water Dimer}, author = {Finneran, Ian A. and Carroll, P. Brandon and Allodi, Marco A. and Blake, Geoffrey A.}, - year = {2015}, - journal = {Physical Chemistry Chemical Physics}, + date = {2015}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {17}, number = {37}, pages = {24210--24214}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C5CP03589A}, + url = {http://xlink.rsc.org/?DOI=C5CP03589A}, urldate = {2023-03-24}, - abstract = {We report the first rotational spectrum of the ground state of the isolated ethanol{\textendash}water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8{\textendash}18 GHz. , We report the first rotational spectrum of the ground state of the isolated ethanol{\textendash}water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8{\textendash}18 GHz. With the aid of isotopic substitutions, and ab initio calculations, we identify the measured conformer as a water-donor/ethanol-acceptor structure. Ethanol is found to be in the gauche conformation, while the monomer distances and orientations likely reflect a cooperation between the strong (O{\textendash}H{$\cdots$}O) and weak (C{\textendash}H{$\cdots$}O) hydrogen bonds that stabilizes the measured conformer. No other conformers were assigned in an argon expansion, confirming that this is the ground-state structure. This result is consistent with previous vibrationally-resolved Raman and infrared work, but sheds additional light on the structure, due to the specificity of rotational spectroscopy.}, + abstract = {We report the first rotational spectrum of the ground state of the isolated ethanol–water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8–18 GHz. , We report the first rotational spectrum of the ground state of the isolated ethanol–water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8–18 GHz. With the aid of isotopic substitutions, and ab initio calculations, we identify the measured conformer as a water-donor/ethanol-acceptor structure. Ethanol is found to be in the gauche conformation, while the monomer distances and orientations likely reflect a cooperation between the strong (O–H⋯O) and weak (C–H⋯O) hydrogen bonds that stabilizes the measured conformer. No other conformers were assigned in an argon expansion, confirming that this is the ground-state structure. This result is consistent with previous vibrationally-resolved Raman and infrared work, but sheds additional light on the structure, due to the specificity of rotational spectroscopy.}, langid = {english}, - file = {/home/simon/Zotero/storage/Y62FLCJF/Finneran et al. - 2015 - Hydrogen bonding in the ethanol–water dimer.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Y62FLCJF/Finneran et al. - 2015 - Hydrogen bonding in the ethanol–water dimer.pdf} } @article{foroutanReviewStructureDynamics2017, title = {A Review of the Structure and Dynamics of Nanoconfined Water and Ionic Liquids via Molecular Dynamics Simulation}, author = {Foroutan, Masumeh and Fatemi, S. Mahmood and Esmaeilian, Farshad}, - year = {2017}, - month = feb, - journal = {The European Physical Journal E}, + date = {2017-02}, + journaltitle = {The European Physical Journal E}, + shortjournal = {Eur. Phys. J. E}, volume = {40}, number = {2}, pages = {19}, issn = {1292-8941, 1292-895X}, doi = {10.1140/epje/i2017-11507-7}, + url = {http://link.springer.com/10.1140/epje/i2017-11507-7}, urldate = {2023-10-12}, abstract = {During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.}, langid = {english}, - file = {/home/simon/Zotero/storage/3PEY2RSP/Foroutan et al. - 2017 - A review of the structure and dynamics of nanoconf.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3PEY2RSP/Foroutan et al. - 2017 - A review of the structure and dynamics of nanoconf.pdf} } @article{frankFreeVolumeEntropy1945, title = {Free {{Volume}} and {{Entropy}} in {{Condensed Systems III}}. {{Entropy}} in {{Binary Liquid Mixtures}}; {{Partial Molal Entropy}} in {{Dilute Solutions}}; {{Structure}} and {{Thermodynamics}} in {{Aqueous Electrolytes}}}, author = {Frank, Henry S. and Evans, Marjorie W.}, - year = {1945}, - month = nov, - journal = {The Journal of Chemical Physics}, + date = {1945-11}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {13}, number = {11}, pages = {507--532}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.1723985}, + url = {https://pubs.aip.org/aip/jcp/article/13/11/507-532/186083}, urldate = {2023-06-21}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/HKWJ7LQB/Frank and Evans - 1945 - Free Volume and Entropy in Condensed Systems III. .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/HKWJ7LQB/Frank and Evans - 1945 - Free Volume and Entropy in Condensed Systems III. .pdf} } @article{frauxStructureDynamicsThermodynamics2019, title = {Structure, {{Dynamics}}, and {{Thermodynamics}} of {{Intruded Electrolytes}} in {{ZIF-8}}}, - author = {Fraux, Guillaume and Boutin, Anne and Fuchs, Alain H. and Coudert, Fran{\c c}ois-Xavier}, - year = {2019}, - month = jun, - journal = {The Journal of Physical Chemistry C}, + author = {Fraux, Guillaume and Boutin, Anne and Fuchs, Alain H. and Coudert, François-Xavier}, + date = {2019-06-27}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {123}, number = {25}, pages = {15589--15598}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.9b02718}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.9b02718}, urldate = {2023-07-29}, - abstract = {We report here the properties of LiCl aqueous solutions at various concentrations confined inside the pores of the ZIF-8 metal-organic framework, on the basis of classical molecular dynamics simulations. This system has been proposed for applications in the storage or dissipation of mechanical energy, using the liquid-phase intrusion of concentrated electrolytes in the hydrophobic framework. We describe the structure of the liquids and the influence of confinement, their dynamics, the mechanical properties of ZIF-8, and the impact of liquid intrusion on them. We show that the presence of the electrolyte has a moderate impact on the ZIF-8 framework whereas the presence of the ZIF-8 matrix strongly influences the behavior of the confined aqueous solution, affecting the overall properties of the system. We also computed the free energy profile for the entry of water molecules and ions into the nanopores, showing a difference between anions and cations.}, + abstract = {We report here the properties of LiCl aqueous solutions at various concentrations confined inside the pores of the ZIF-8 metal−organic framework, on the basis of classical molecular dynamics simulations. This system has been proposed for applications in the storage or dissipation of mechanical energy, using the liquid-phase intrusion of concentrated electrolytes in the hydrophobic framework. We describe the structure of the liquids and the influence of confinement, their dynamics, the mechanical properties of ZIF-8, and the impact of liquid intrusion on them. We show that the presence of the electrolyte has a moderate impact on the ZIF-8 framework whereas the presence of the ZIF-8 matrix strongly influences the behavior of the confined aqueous solution, affecting the overall properties of the system. We also computed the free energy profile for the entry of water molecules and ions into the nanopores, showing a difference between anions and cations.}, langid = {english}, keywords = {ff,MD,zif}, - file = {/home/simon/Zotero/storage/SKTCJED5/Fraux et al. - 2019 - Structure, Dynamics, and Thermodynamics of Intrude.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SKTCJED5/Fraux et al. - 2019 - Structure, Dynamics, and Thermodynamics of Intrude.pdf} } @article{friesMonteCarloCalculation1983, title = {Monte {{Carlo}} Calculation of the Intermolecular Dipolar Spin Relaxation in a Liquid Solution}, author = {Fries, P. H. and Belorizky, E.}, - year = {1983}, - month = aug, - journal = {The Journal of Chemical Physics}, + date = {1983-08-01}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {79}, number = {3}, pages = {1166--1169}, issn = {0021-9606}, doi = {10.1063/1.445919}, + url = {https://doi.org/10.1063/1.445919}, urldate = {2023-07-09}, abstract = {The time correlation function characteristic of the intermolecular dipolar spin relaxation in a liquid solution is calculated by a Monte Carlo diffusive simulation. The validity of the Monte Carlo method for modeling molecular dynamics is examined referring to the careful analysis by Hilhorst and Deutch of the Monte Carlo work on polymer kinetics of Verdier et al. The Monte Carlo estimates of the time correlation function are compared with those obtained by analytical solutions of translational diffusion equations. The normalized solutions of the Smoluchowski diffusion equation, including the effects of the nonuniform radial molecular distribution, are appropriate for describing the relative random walks of two given molecules in the liquid.}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/D96JAF5C/Fries and Belorizky - 1983 - Monte Carlo calculation of the intermolecular dipo.pdf;/home/simon/Zotero/storage/BEH6WMXT/Monte-Carlo-calculation-of-the-intermolecular.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/D96JAF5C/Fries and Belorizky - 1983 - Monte Carlo calculation of the intermolecular dipo.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/BEH6WMXT/Monte-Carlo-calculation-of-the-intermolecular.html} } @article{fuentes-azcatlNonPolarizableForceField2014, - title = {Non-{{Polarizable Force Field}} of {{Water Based}} on the {{Dielectric Constant}}: {{TIP4P}}/{$\epsilon$}}, + title = {Non-{{Polarizable Force Field}} of {{Water Based}} on the {{Dielectric Constant}}: {{TIP4P}}/ε}, shorttitle = {Non-{{Polarizable Force Field}} of {{Water Based}} on the {{Dielectric Constant}}}, - author = {{Fuentes-Azcatl}, Ra{\'u}l and Alejandre, Jos{\'e}}, - year = {2014}, - month = feb, - journal = {The Journal of Physical Chemistry B}, + author = {Fuentes-Azcatl, Raúl and Alejandre, José}, + date = {2014-02-06}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {118}, number = {5}, pages = {1263--1272}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp410865y}, + url = {https://pubs.acs.org/doi/10.1021/jp410865y}, urldate = {2023-06-21}, - abstract = {The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/{$\epsilon$} force field of water. The TIP4P parameters are used as a starting point. The key step, to determine simultaneously both properties, is to perform simulations at 240 K where a molecular dipole moment of minimum density is found. The minimum is shifted to larger values of {$\mu$} as the distance between the oxygen atom and site M, lOM, decreases. First, the parameters that define the dipole moment are adjusted to reproduce the experimental dielectric constant and then the Lennard-Jones parameters are varied to match the temperature of maximum density. The minimum on density at 240 K allows understanding why reported TIP4P models fail to reproduce the temperature of maximum density, the dielectric constant, or both properties. The new model reproduces some of the thermodynamic and transport anomalies of water. Additionally, the dielectric constant, thermodynamics, and dynamical and structural properties at different temperatures and pressures are in excellent agreement with experimental data. The computational cost of the new model is the same as that of the TIP4P.}, + abstract = {The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/ε force field of water. The TIP4P parameters are used as a starting point. The key step, to determine simultaneously both properties, is to perform simulations at 240 K where a molecular dipole moment of minimum density is found. The minimum is shifted to larger values of μ as the distance between the oxygen atom and site M, lOM, decreases. First, the parameters that define the dipole moment are adjusted to reproduce the experimental dielectric constant and then the Lennard-Jones parameters are varied to match the temperature of maximum density. The minimum on density at 240 K allows understanding why reported TIP4P models fail to reproduce the temperature of maximum density, the dielectric constant, or both properties. The new model reproduces some of the thermodynamic and transport anomalies of water. Additionally, the dielectric constant, thermodynamics, and dynamical and structural properties at different temperatures and pressures are in excellent agreement with experimental data. The computational cost of the new model is the same as that of the TIP4P.}, langid = {english}, keywords = {ff,MD}, - file = {/home/simon/Zotero/storage/KH3MNTLL/Fuentes-Azcatl and Alejandre - 2014 - Non-Polarizable Force Field of Water Based on the .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/KH3MNTLL/Fuentes-Azcatl and Alejandre - 2014 - Non-Polarizable Force Field of Water Based on the .pdf} } @article{gaoEffectAdsorbedAlcohol2017, title = {Effect of {{Adsorbed Alcohol Layers}} on the {{Behavior}} of {{Water Molecules Confined}} in a {{Graphene Nanoslit}}: {{A Molecular Dynamics Study}}}, shorttitle = {Effect of {{Adsorbed Alcohol Layers}} on the {{Behavior}} of {{Water Molecules Confined}} in a {{Graphene Nanoslit}}}, author = {Gao, Qingwei and Zhu, Yudan and Ruan, Yang and Zhang, Yumeng and Zhu, Wei and Lu, Xiaohua and Lu, Linghong}, - year = {2017}, - month = oct, - journal = {Langmuir}, + date = {2017-10-24}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {33}, number = {42}, pages = {11467--11474}, issn = {0743-7463, 1520-5827}, doi = {10.1021/acs.langmuir.7b02038}, + url = {https://pubs.acs.org/doi/10.1021/acs.langmuir.7b02038}, urldate = {2023-07-10}, - abstract = {With the rapid development of a two-dimensional (2D) nanomaterial, the confined liquid binary mixture has attracted increasing attention, which has significant potential in membrane separation. Alcohol/water is one of the most common systems in liquid-liquid separation. As one of the most focused systems, recent studies have found that ethanol molecules were preferentially adsorbed on the inner surface of the pore wall and formed an adsorbed ethanol layer under 2D nanoconfinement. To evaluate the effect of the alcohol adsorption layer on the mobility of water molecules, molecular simulations were performed to investigate four types of alcohol/water binary mixtures confined under a 20 {\AA} graphene slit. Residence times of the water molecules covering the alcohol layer were in the order of methanol/water {$<$} ethanol/water {$<$} 1-propanol/water {$<$} 1-butanol/water. Detailed microstructural analysis of the hydrogen bonding (H-bond) network elucidated the underlying mechanism on the molecular scale in which a small average number of H-bonds between the preferentially adsorbed alcohol molecules and the surrounding water molecules could induce a small degree of damage to the H-bond network of the water molecules covering the alcohol layer, resulting in the long residence time of the water molecules.}, + abstract = {With the rapid development of a two-dimensional (2D) nanomaterial, the confined liquid binary mixture has attracted increasing attention, which has significant potential in membrane separation. Alcohol/water is one of the most common systems in liquid−liquid separation. As one of the most focused systems, recent studies have found that ethanol molecules were preferentially adsorbed on the inner surface of the pore wall and formed an adsorbed ethanol layer under 2D nanoconfinement. To evaluate the effect of the alcohol adsorption layer on the mobility of water molecules, molecular simulations were performed to investigate four types of alcohol/water binary mixtures confined under a 20 Å graphene slit. Residence times of the water molecules covering the alcohol layer were in the order of methanol/water {$<$} ethanol/water {$<$} 1-propanol/water {$<$} 1-butanol/water. Detailed microstructural analysis of the hydrogen bonding (H-bond) network elucidated the underlying mechanism on the molecular scale in which a small average number of H-bonds between the preferentially adsorbed alcohol molecules and the surrounding water molecules could induce a small degree of damage to the H-bond network of the water molecules covering the alcohol layer, resulting in the long residence time of the water molecules.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/UFMAWUMG/Gao et al. - 2017 - Effect of Adsorbed Alcohol Layers on the Behavior .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/UFMAWUMG/Gao et al. - 2017 - Effect of Adsorbed Alcohol Layers on the Behavior .pdf} } @article{garrettMolecularSimulationsTransport2006, title = {Molecular {{Simulations}} of the {{Transport}} of {{Molecules}} across the {{Liquid}}/{{Vapor Interface}} of {{Water}}}, author = {Garrett, Bruce C. and Schenter, Gregory K. and Morita, Akihiro}, - year = {2006}, - month = apr, - journal = {Chemical Reviews}, + date = {2006-04-01}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, volume = {106}, number = {4}, pages = {1355--1374}, issn = {0009-2665, 1520-6890}, doi = {10.1021/cr040370w}, + url = {https://pubs.acs.org/doi/10.1021/cr040370w}, urldate = {2023-08-08}, langid = {english}, keywords = {MD,mixture}, - file = {/home/simon/Zotero/storage/97DSQZUX/Garrett et al. - 2006 - Molecular Simulations of the Transport of Molecule.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/97DSQZUX/Garrett et al. - 2006 - Molecular Simulations of the Transport of Molecule.pdf} } @article{gerebenInvestigationStructureEthanol2015, - title = {Investigation of the {{Structure}} of {{Ethanol}}{\textendash}{{Water Mixtures}} by {{Molecular Dynamics Simulation I}}: {{Analyses Concerning}} the {{Hydrogen-Bonded Pairs}}}, - shorttitle = {Investigation of the {{Structure}} of {{Ethanol}}{\textendash}{{Water Mixtures}} by {{Molecular Dynamics Simulation I}}}, - author = {Gereben, Orsolya and Pusztai, L{\'a}szl{\'o}}, - year = {2015}, - month = feb, - journal = {The Journal of Physical Chemistry B}, + title = {Investigation of the {{Structure}} of {{Ethanol}}–{{Water Mixtures}} by {{Molecular Dynamics Simulation I}}: {{Analyses Concerning}} the {{Hydrogen-Bonded Pairs}}}, + shorttitle = {Investigation of the {{Structure}} of {{Ethanol}}–{{Water Mixtures}} by {{Molecular Dynamics Simulation I}}}, + author = {Gereben, Orsolya and Pusztai, László}, + date = {2015-02-19}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {119}, number = {7}, pages = {3070--3084}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp510490y}, + url = {https://pubs.acs.org/doi/10.1021/jp510490y}, urldate = {2023-05-04}, - abstract = {Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol \% ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80\% the SWM-DP, for 60 mol \% the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol \% mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.}, + abstract = {Series of molecular dynamics simulations for ethanol−water mixtures with 20−80 mol \% ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol−water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80\% the SWM-DP, for 60 mol \% the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol \% mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen−oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol−ethanol first coordination sphere expands with increasing water concentration while the size of the first water−water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen−bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.}, langid = {english}, keywords = {HB,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/DNNQ3ASD/Gereben and Pusztai - 2015 - Investigation of the Structure of Ethanol–Water Mi.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DNNQ3ASD/Gereben and Pusztai - 2015 - Investigation of the Structure of Ethanol–Water Mi.pdf} } @article{geskeMolecularDynamicsSimulations2018, title = {Molecular {{Dynamics Simulations}} of {{Water}}, {{Silica}}, and {{Aqueous Mixtures}} in {{Bulk}} and {{Confinement}}}, - author = {Geske, Julian and Harrach, Michael and Heckmann, Lotta and Horstmann, Robin and Klameth, Felix and M{\"u}ller, Niels and Pafong, Elvira and Wohlfromm, Timothy and Drossel, Barbara and Vogel, Michael}, - year = {2018}, - month = jul, - journal = {Zeitschrift f{\"u}r Physikalische Chemie}, + author = {Geske, Julian and Harrach, Michael and Heckmann, Lotta and Horstmann, Robin and Klameth, Felix and Müller, Niels and Pafong, Elvira and Wohlfromm, Timothy and Drossel, Barbara and Vogel, Michael}, + date = {2018-07-26}, + journaltitle = {Zeitschrift für Physikalische Chemie}, volume = {232}, number = {7-8}, pages = {1187--1225}, issn = {2196-7156, 0942-9352}, doi = {10.1515/zpch-2017-1042}, + url = {https://www.degruyter.com/document/doi/10.1515/zpch-2017-1042/html}, urldate = {2023-06-09}, abstract = {Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.}, langid = {english}, keywords = {MD,mixture}, - file = {/home/simon/Zotero/storage/IVFM5CBM/Geske et al. - 2018 - Molecular Dynamics Simulations of Water, Silica, a.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/IVFM5CBM/Geske et al. - 2018 - Molecular Dynamics Simulations of Water, Silica, a.pdf} } @article{ghoshEnhancedDensityFluctuations, title = {Enhanced Density Fluctuations in Water-Ethanol Mixtures at Low Ethanol Concentrations: {{Temperature}} Dependent Studies}, author = {Ghosh, Rikhia and Bagchi, Biman}, - abstract = {Since the structural transformations observed in water-ethanol binary mixtures are apparently driven by relatively weak intermolecular forces (like hydrophobicity and hydrogen bonding) that often cooperate to form self-assembled structures, one expects the aggregation properties to show strong temperature dependence. We study the effect of temperature on the formation of transient ethanol clusters as well as on the dynamic density heterogeneity induced in the system due to such clustering. The dynamic heterogeneity is expected to occur on small length scales with short lifetime {\textendash} both are expected to be temperature dependent. Indeed, a major finding of the work is strong temperature dependence of the extent of structural heterogeneity. Distinct signature of static and dynamic heterogeneity of ethanol molecules is also found to appear with lowering of temperature. This is attributed to the formation of transient ethanol clusters that are known to exhibit considerably small lifetime (order of a few picosecond). The transient dynamical features of dynamic heterogeneity are expected to affect those relaxation processes occurring at subpicosecond time scales. On the other hand, strong temperature dependence of micro-structure formation can be anticipated to be due to enhanced structural order stimulated in the system with lowering of temperature. Present analyses reveal a number of interesting features which were not explored beforehand in this widely studied binary mixture.}, + abstract = {Since the structural transformations observed in water-ethanol binary mixtures are apparently driven by relatively weak intermolecular forces (like hydrophobicity and hydrogen bonding) that often cooperate to form self-assembled structures, one expects the aggregation properties to show strong temperature dependence. We study the effect of temperature on the formation of transient ethanol clusters as well as on the dynamic density heterogeneity induced in the system due to such clustering. The dynamic heterogeneity is expected to occur on small length scales with short lifetime – both are expected to be temperature dependent. Indeed, a major finding of the work is strong temperature dependence of the extent of structural heterogeneity. Distinct signature of static and dynamic heterogeneity of ethanol molecules is also found to appear with lowering of temperature. This is attributed to the formation of transient ethanol clusters that are known to exhibit considerably small lifetime (order of a few picosecond). The transient dynamical features of dynamic heterogeneity are expected to affect those relaxation processes occurring at subpicosecond time scales. On the other hand, strong temperature dependence of micro-structure formation can be anticipated to be due to enhanced structural order stimulated in the system with lowering of temperature. Present analyses reveal a number of interesting features which were not explored beforehand in this widely studied binary mixture.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/YRG64T4H/Ghosh and Bagchi - Enhanced density fluctuations in water-ethanol mix.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YRG64T4H/Ghosh and Bagchi - Enhanced density fluctuations in water-ethanol mix.pdf} } @article{ghoufiPhysicalPropertiesHydrogenBonding2016, - title = {Physical {{Properties}} and {{Hydrogen-Bonding Network}} of {{Water}}{\textendash}{{Ethanol Mixtures}} from {{Molecular Dynamics Simulations}}}, + title = {Physical {{Properties}} and {{Hydrogen-Bonding Network}} of {{Water}}–{{Ethanol Mixtures}} from {{Molecular Dynamics Simulations}}}, author = {Ghoufi, A. and Artzner, F. and Malfreyt, P.}, - year = {2016}, - month = feb, - journal = {The Journal of Physical Chemistry B}, + date = {2016-02-04}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {120}, number = {4}, pages = {793--802}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.5b11776}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.5b11776}, urldate = {2023-03-20}, - abstract = {While many numerical and experimental works were focused on water-ethanol mixtures at low ethanol concentration, this work reports predictions of a few physical properties (thermodynamical, interfacial, dynamical, and dielectrical properties) of water-ethanol mixture at high alcohol concentrations by means of molecular dynamics simulations. By using a standard force field a good agreement was found between experiment and molecular simulation. This was allowed us to explore the dynamics, structure, and interplay between both hydrogen-bonding networks of water and ethanol.}, + abstract = {While many numerical and experimental works were focused on water−ethanol mixtures at low ethanol concentration, this work reports predictions of a few physical properties (thermodynamical, interfacial, dynamical, and dielectrical properties) of water−ethanol mixture at high alcohol concentrations by means of molecular dynamics simulations. By using a standard force field a good agreement was found between experiment and molecular simulation. This was allowed us to explore the dynamics, structure, and interplay between both hydrogen-bonding networks of water and ethanol.}, langid = {english}, keywords = {HB,MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/3CJ4K699/Ghoufi et al. - 2016 - Physical Properties and Hydrogen-Bonding Network o.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3CJ4K699/Ghoufi et al. - 2016 - Physical Properties and Hydrogen-Bonding Network o.pdf} } @article{gonzalez-salgadoExcessPropertiesAqueous2006, title = {Excess Properties of Aqueous Mixtures of Methanol: {{Simulation}} versus Experiment}, shorttitle = {Excess Properties of Aqueous Mixtures of Methanol}, - author = {{Gonz{\'a}lez-Salgado}, Diego and Nezbeda, Ivo}, - year = {2006}, - month = feb, - journal = {Fluid Phase Equilibria}, + author = {González-Salgado, Diego and Nezbeda, Ivo}, + date = {2006-02}, + journaltitle = {Fluid Phase Equilibria}, + shortjournal = {Fluid Phase Equilibria}, volume = {240}, number = {2}, pages = {161--166}, issn = {03783812}, doi = {10.1016/j.fluid.2005.12.007}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0378381205004966}, urldate = {2023-04-26}, - abstract = {We report molecular simulation results for both the excess mixing and partial molar properties of water{\textendash}methanol mixtures over the entire concentration range with the particular emphasis on the low concentration ends. It is shown that the mixing properties are very sensitive to potential models and that the used realistic potentials (TIP4P for water and OPLS for methanol) give a reasonably good agreement with experiment only for volumetric properties although the qualitative trend of the partial molar volume at low concentrations is not reproduced. As regards excess enthalpy, the results are rather bad and only its sign is predicted correctly.}, + abstract = {We report molecular simulation results for both the excess mixing and partial molar properties of water–methanol mixtures over the entire concentration range with the particular emphasis on the low concentration ends. It is shown that the mixing properties are very sensitive to potential models and that the used realistic potentials (TIP4P for water and OPLS for methanol) give a reasonably good agreement with experiment only for volumetric properties although the qualitative trend of the partial molar volume at low concentrations is not reproduced. As regards excess enthalpy, the results are rather bad and only its sign is predicted correctly.}, langid = {english}, keywords = {HB,mixture}, - file = {/home/simon/Zotero/storage/BFRKUNPJ/González-Salgado and Nezbeda - 2006 - Excess properties of aqueous mixtures of methanol.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BFRKUNPJ/González-Salgado and Nezbeda - 2006 - Excess properties of aqueous mixtures of methanol.pdf} } @article{goreNMRRelaxationWater1989, title = {{{NMR}} Relaxation of Water in Hydrogel Polymers: {{A}} Model for Tissue}, shorttitle = {{{NMR}} Relaxation of Water in Hydrogel Polymers}, author = {Gore, John C. and Brown, Mark S. and Zhong, Jianhui and Mueller, K. Fritz and Good, William}, - year = {1989}, - month = mar, - journal = {Magnetic Resonance in Medicine}, + date = {1989-03}, + journaltitle = {Magnetic Resonance in Medicine}, + shortjournal = {Magn. Reson. Med.}, volume = {9}, number = {3}, pages = {325--332}, issn = {07403194, 15222594}, doi = {10.1002/mrm.1910090304}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/mrm.1910090304}, urldate = {2023-07-07}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/2NWNULTF/Gore et al. - 1989 - NMR relaxation of water in hydrogel polymers A mo.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2NWNULTF/Gore et al. - 1989 - NMR relaxation of water in hydrogel polymers A mo.pdf} } @article{gravelleAdsorptionKineticsOpen2019, title = {Adsorption {{Kinetics}} in {{Open Nanopores}} as a {{Source}} of {{Low-Frequency Noise}}}, - author = {Gravelle, Simon and Netz, Roland R. and Bocquet, Lyd{\'e}ric}, - year = {2019}, - month = oct, - journal = {Nano Letters}, + author = {Gravelle, Simon and Netz, Roland R. and Bocquet, Lydéric}, + date = {2019-10-09}, + journaltitle = {Nano Letters}, + shortjournal = {Nano Lett.}, volume = {19}, number = {10}, pages = {7265--7272}, issn = {1530-6984, 1530-6992}, doi = {10.1021/acs.nanolett.9b02858}, + url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.9b02858}, urldate = {2023-03-22}, - abstract = {Ionic current measurements through solid-state nanopores consistently show a power spectral density that scales as 1/f {$\alpha$} at low frequency f, with an exponent {$\alpha$} {$\sim$} 0.5-1.5, but strikingly, the physical origin of this behavior remains elusive. Here, we perform simulations of particles reversibly adsorbing at the surface of a nanopore and show that the fluctuations in the number of adsorbed particles exhibit low-frequency pink noise. We furthermore propose theoretical modeling for the timedependent adsorption of particles on the nanopore surface for various geometries, which predicts a frequency spectrum in very good agreement with the simulation results. Altogether, our results highlight that the low-frequency noise takes its origin in the reversible adsorption of ions at the pore surface combined with the long-lasting excursions of the ions in the reservoirs. The scaling regime of the power spectrum extends down to a cutoff frequency which is far smaller than simple diffusion estimates. Using realistic values for the pore dimensions and the adsorption-desorption kinetics, this predicts the observation of pink noise for frequencies down to the hertz for a typical solid-state nanopore, in good agreement with experiments.}, + abstract = {Ionic current measurements through solid-state nanopores consistently show a power spectral density that scales as 1/f α at low frequency f, with an exponent α ∼ 0.5−1.5, but strikingly, the physical origin of this behavior remains elusive. Here, we perform simulations of particles reversibly adsorbing at the surface of a nanopore and show that the fluctuations in the number of adsorbed particles exhibit low-frequency pink noise. We furthermore propose theoretical modeling for the timedependent adsorption of particles on the nanopore surface for various geometries, which predicts a frequency spectrum in very good agreement with the simulation results. Altogether, our results highlight that the low-frequency noise takes its origin in the reversible adsorption of ions at the pore surface combined with the long-lasting excursions of the ions in the reservoirs. The scaling regime of the power spectrum extends down to a cutoff frequency which is far smaller than simple diffusion estimates. Using realistic values for the pore dimensions and the adsorption−desorption kinetics, this predicts the observation of pink noise for frequencies down to the hertz for a typical solid-state nanopore, in good agreement with experiments.}, langid = {english}, keywords = {noise,self}, - file = {/home/simon/Zotero/storage/BSN3DLUC/Gravelle et al. - Supplementary Information Adsorption Kinetics in .pdf;/home/simon/Zotero/storage/V6SSRVHT/Gravelle et al. - 2019 - Adsorption Kinetics in Open Nanopores as a Source .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BSN3DLUC/Gravelle et al. - Supplementary Information Adsorption Kinetics in .pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/V6SSRVHT/Gravelle et al. - 2019 - Adsorption Kinetics in Open Nanopores as a Source .pdf} } @article{gravelleAssessingValidityNMR2023, - title = {Assessing the {{Validity}} of {{NMR Relaxation Rates Obtained}} from {{Coarse-Grained Simulations}} of {{PEG}}{\textendash}{{Water Mixtures}}}, + title = {Assessing the {{Validity}} of {{NMR Relaxation Rates Obtained}} from {{Coarse-Grained Simulations}} of {{PEG}}–{{Water Mixtures}}}, author = {Gravelle, Simon and Beyer, David and Brito, Mariano and Schlaich, Alexander and Holm, Christian}, - year = {2023}, - month = jun, - journal = {The Journal of Physical Chemistry B}, + date = {2023-06-29}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {127}, number = {25}, pages = {5601--5608}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.3c01646}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.3c01646}, urldate = {2023-07-09}, - abstract = {NMR relaxometry is a powerful and wellestablished experimental approach for characterizing dynamic processes in soft matter systems. All-atom (AA) resolved simulations are typically employed to gain further microscopic insights while reproducing the relaxation rates R1. However, such approaches are limited to time and length scales that prevent to model systems such as long polymer chains or hydrogels. Coarse graining (CG) can overcome this barrier at the cost of losing atomistic details that impede the calculation of NMR relaxation rates. Here, we address this issue by performing a systematic characterization of dipolar relaxation rates R1 on a PEG-H2O mixture at two different levels of details: AA and CG. Remarkably, we show that NMR relaxation rates R1 obtained at the CG level obey the same trends when compared to AA calculations but with a systematic offset. This offset is due to, on the one hand, the lack of an intramonomer component and, on the other hand, the inexact positioning of the spin carriers. We show that the offset can be corrected for quantitatively by reconstructing a posteriori the atomistic details for the CG trajectories.}, + abstract = {NMR relaxometry is a powerful and wellestablished experimental approach for characterizing dynamic processes in soft matter systems. All-atom (AA) resolved simulations are typically employed to gain further microscopic insights while reproducing the relaxation rates R1. However, such approaches are limited to time and length scales that prevent to model systems such as long polymer chains or hydrogels. Coarse graining (CG) can overcome this barrier at the cost of losing atomistic details that impede the calculation of NMR relaxation rates. Here, we address this issue by performing a systematic characterization of dipolar relaxation rates R1 on a PEG−H2O mixture at two different levels of details: AA and CG. Remarkably, we show that NMR relaxation rates R1 obtained at the CG level obey the same trends when compared to AA calculations but with a systematic offset. This offset is due to, on the one hand, the lack of an intramonomer component and, on the other hand, the inexact positioning of the spin carriers. We show that the offset can be corrected for quantitatively by reconstructing a posteriori the atomistic details for the CG trajectories.}, langid = {english}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/2H2WZ3KN/Gravelle et al. - 2023 - Assessing the Validity of NMR Relaxation Rates Obt.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2H2WZ3KN/Gravelle et al. - 2023 - Assessing the Validity of NMR Relaxation Rates Obt.pdf} } @article{gravelleCarbonMembranesEfficient2016, title = {Carbon Membranes for Efficient Water-Ethanol Separation}, - author = {Gravelle, Simon and Yoshida, Hiroaki and Joly, Laurent and Ybert, Christophe and Bocquet, Lyd{\'e}ric}, - year = {2016}, - month = sep, - journal = {The Journal of Chemical Physics}, + author = {Gravelle, Simon and Yoshida, Hiroaki and Joly, Laurent and Ybert, Christophe and Bocquet, Lydéric}, + date = {2016-09-28}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {J. Chem. Phys.}, volume = {145}, number = {12}, pages = {124708}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4963098}, + url = {http://aip.scitation.org/doi/10.1063/1.4963098}, urldate = {2023-03-20}, langid = {english}, keywords = {confinnement,entrance,MD,mixture,self,water-ethanol}, - file = {/home/simon/Zotero/storage/J39NH687/Gravelle et al. - 2016 - Carbon membranes for efficient water-ethanol separ.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/J39NH687/Gravelle et al. - 2016 - Carbon membranes for efficient water-ethanol separ.pdf} } -@article{gravelleMultiscaleModelFluid2020a, +@article{gravelleMultiscaleModelFluid2020, title = {A Multi-Scale Model for Fluid Transport through a Bio-Inspired Passive Valve}, author = {Gravelle, Simon and Dumais, Jacques}, - year = {2020}, - month = jan, - journal = {The Journal of Chemical Physics}, + date = {2020-01-03}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {152}, number = {1}, pages = {014502}, issn = {0021-9606}, doi = {10.1063/1.5126481}, + url = {https://doi.org/10.1063/1.5126481}, urldate = {2023-10-12}, - abstract = {Tillandsia landbeckii is a rootless plant thriving in the hyper-arid Atacama Desert of Chile. These plants use unique cellulose-based microscopic structures called trichomes to collect fresh water from coastal fog. The trichomes rely on a passive mechanism to maintain an asymmetrical transport of water: they allow for the fast absorption of liquid water deposited by sporadic fog events while preventing evaporation during extended drought periods. Inspired by the trichome's design, we study fluid transport through a micrometric valve. Combining Grand Canonical Monte Carlo with Non-Equilibrium Molecular Dynamics simulations, we first analyze the adsorption and transport of a fluid through a single nanopore at different chemical potentials. We then scale up the atomic results using a lattice approach, and simulate the transport at the micrometric scale. Results obtained for a model Lennard-Jones fluid and TIP4P/2005 water were compared, allowing us to identify the key physical parameters for achieving a passive hydraulic valve. Our results show that the difference in transport properties of water vapor and liquid water within the cellulose layer is the basis for the ability of the Tillandsia trichome to function as a water valve. Finally, we predict a critical pore dimension above which the cellulose layer can form an efficient valve.}, - file = {/home/simon/Zotero/storage/BNT6RCM4/Gravelle and Dumais - 2020 - A multi-scale model for fluid transport through a .pdf;/home/simon/Zotero/storage/EVSZ5SSE/A-multi-scale-model-for-fluid-transport-through-a.html} + abstract = {Tillandsia landbeckii is a rootless plant thriving in the hyper-arid Atacama Desert of Chile. These plants use unique cellulose-based microscopic structures called trichomes to collect fresh water from coastal fog. The trichomes rely on a passive mechanism to maintain an asymmetrical transport of water: they allow for the fast absorption of liquid water deposited by sporadic fog events while preventing evaporation during extended drought periods. Inspired by the trichome’s design, we study fluid transport through a micrometric valve. Combining Grand Canonical Monte Carlo with Non-Equilibrium Molecular Dynamics simulations, we first analyze the adsorption and transport of a fluid through a single nanopore at different chemical potentials. We then scale up the atomic results using a lattice approach, and simulate the transport at the micrometric scale. Results obtained for a model Lennard-Jones fluid and TIP4P/2005 water were compared, allowing us to identify the key physical parameters for achieving a passive hydraulic valve. Our results show that the difference in transport properties of water vapor and liquid water within the cellulose layer is the basis for the ability of the Tillandsia trichome to function as a water valve. Finally, we predict a critical pore dimension above which the cellulose layer can form an efficient valve.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BNT6RCM4/Gravelle and Dumais - 2020 - A multi-scale model for fluid transport through a .pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/EVSZ5SSE/A-multi-scale-model-for-fluid-transport-through-a.html} } @article{gravelleNMRInvestigationWater2023, title = {{{NMR Investigation}} of {{Water}} in {{Salt Crusts}}: {{Insights}} from {{Experiments}} and {{Molecular Simulations}}}, shorttitle = {{{NMR Investigation}} of {{Water}} in {{Salt Crusts}}}, - author = {Gravelle, Simon and {Haber-Pohlmeier}, Sabina and Mattea, Carlos and Stapf, Siegfried and Holm, Christian and Schlaich, Alexander}, - year = {2023}, - month = jun, - journal = {Langmuir}, + author = {Gravelle, Simon and Haber-Pohlmeier, Sabina and Mattea, Carlos and Stapf, Siegfried and Holm, Christian and Schlaich, Alexander}, + date = {2023-06-06}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {39}, number = {22}, pages = {7548--7556}, publisher = {{American Chemical Society}}, issn = {0743-7463}, doi = {10.1021/acs.langmuir.3c00036}, + url = {https://doi.org/10.1021/acs.langmuir.3c00036}, urldate = {2023-07-09}, - abstract = {The evaporation of water from bare soil is often accompanied by the formation of a layer of crystallized salt, a process that must be understood in order to address the issue of soil salinization. Here, we use nuclear magnetic relaxation dispersion measurements to better understand the dynamic properties of water within two types of salt crusts: sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our experimental results display a stronger dispersion of the relaxation time T1 with frequency for the case of sodium sulfate as compared to sodium chloride salt crusts. To gain insight into these results, we perform molecular dynamics simulations of salt solutions confined within slit nanopores made of either NaCl or Na2SO4. We find a strong dependence of the value of the relaxation time T1 on pore size and salt concentration. Our simulations reveal the complex interplay between the adsorption of ions at the solid surface, the structure of water near the interface, and the dispersion of T1 at low frequency, which we attribute to adsorption{\textendash}desorption events.}, + abstract = {The evaporation of water from bare soil is often accompanied by the formation of a layer of crystallized salt, a process that must be understood in order to address the issue of soil salinization. Here, we use nuclear magnetic relaxation dispersion measurements to better understand the dynamic properties of water within two types of salt crusts: sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our experimental results display a stronger dispersion of the relaxation time T1 with frequency for the case of sodium sulfate as compared to sodium chloride salt crusts. To gain insight into these results, we perform molecular dynamics simulations of salt solutions confined within slit nanopores made of either NaCl or Na2SO4. We find a strong dependence of the value of the relaxation time T1 on pore size and salt concentration. Our simulations reveal the complex interplay between the adsorption of ions at the solid surface, the structure of water near the interface, and the dispersion of T1 at low frequency, which we attribute to adsorption–desorption events.}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/42B7N3CW/Gravelle et al. - 2023 - NMR Investigation of Water in Salt Crusts Insight.pdf;/home/simon/Zotero/storage/BZMZVNR8/acs.langmuir.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/42B7N3CW/Gravelle et al. - 2023 - NMR Investigation of Water in Salt Crusts Insight.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/BZMZVNR8/acs.langmuir.html} } @article{gravelleNMRInvestigationWater2023a, title = {{{NMR Investigation}} of {{Water}} in {{Salt Crusts}}: {{Insights}} from {{Experiments}} and {{Molecular Simulations}}}, shorttitle = {{{NMR Investigation}} of {{Water}} in {{Salt Crusts}}}, - author = {Gravelle, Simon and {Haber-Pohlmeier}, Sabina and Mattea, Carlos and Stapf, Siegfried and Holm, Christian and Schlaich, Alexander}, - year = {2023}, - month = jun, - journal = {Langmuir}, + author = {Gravelle, Simon and Haber-Pohlmeier, Sabina and Mattea, Carlos and Stapf, Siegfried and Holm, Christian and Schlaich, Alexander}, + date = {2023-06-06}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {39}, number = {22}, pages = {7548--7556}, issn = {0743-7463, 1520-5827}, doi = {10.1021/acs.langmuir.3c00036}, + url = {https://pubs.acs.org/doi/10.1021/acs.langmuir.3c00036}, urldate = {2024-01-04}, - abstract = {The evaporation of water from bare soil is often accompanied by the formation of a layer of crystallized salt, a process that must be understood in order to address the issue of soil salinization. Here, we use nuclear magnetic relaxation dispersion measurements to better understand the dynamic properties of water within two types of salt crusts: sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our experimental results display a stronger dispersion of the relaxation time T1 with frequency for the case of sodium sulfate as compared to sodium chloride salt crusts. To gain insight into these results, we perform molecular dynamics simulations of salt solutions confined within slit nanopores made of either NaCl or Na2SO4. We find a strong dependence of the value of the relaxation time T1 on pore size and salt concentration. Our simulations reveal the complex interplay between the adsorption of ions at the solid surface, the structure of water near the interface, and the dispersion of T1 at low frequency, which we attribute to adsorption- desorption events.}, + abstract = {The evaporation of water from bare soil is often accompanied by the formation of a layer of crystallized salt, a process that must be understood in order to address the issue of soil salinization. Here, we use nuclear magnetic relaxation dispersion measurements to better understand the dynamic properties of water within two types of salt crusts: sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our experimental results display a stronger dispersion of the relaxation time T1 with frequency for the case of sodium sulfate as compared to sodium chloride salt crusts. To gain insight into these results, we perform molecular dynamics simulations of salt solutions confined within slit nanopores made of either NaCl or Na2SO4. We find a strong dependence of the value of the relaxation time T1 on pore size and salt concentration. Our simulations reveal the complex interplay between the adsorption of ions at the solid surface, the structure of water near the interface, and the dispersion of T1 at low frequency, which we attribute to adsorption− desorption events.}, langid = {english}, - file = {/home/simon/Zotero/storage/Z9UWTBY3/Gravelle et al. - 2023 - NMR Investigation of Water in Salt Crusts Insight.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Z9UWTBY3/Gravelle et al. - 2023 - NMR Investigation of Water in Salt Crusts Insight.pdf} } @article{gravelleOptimizingWaterPermeability2013, title = {Optimizing Water Permeability through the Hourglass Shape of Aquaporins}, - author = {Gravelle, Simon and Joly, Laurent and Detcheverry, Fran{\c c}ois and Ybert, Christophe and {Cottin-Bizonne}, C{\'e}cile and Bocquet, Lyd{\'e}ric}, - year = {2013}, - month = oct, - journal = {Proceedings of the National Academy of Sciences}, + author = {Gravelle, Simon and Joly, Laurent and Detcheverry, François and Ybert, Christophe and Cottin-Bizonne, Cécile and Bocquet, Lydéric}, + date = {2013-10-08}, + journaltitle = {Proceedings of the National Academy of Sciences}, + shortjournal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {110}, number = {41}, pages = {16367--16372}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1306447110}, + url = {https://pnas.org/doi/full/10.1073/pnas.1306447110}, urldate = {2023-03-22}, abstract = {Significance Aquaporin channels are able to selectively conduct water across cell membranes, with remarkable efficiency. Although molecular details are crucial to the pore performance, permeability is also strongly limited by viscous dissipation at the entrances. Could the hourglass shape of aquaporins optimize such entrance effects? We show that conical entrances with suitable opening angle can indeed provide a large increase of the channel permeability. Strikingly, the optimal opening angles compare well with the angles measured in a large variety of aquaporins, suggesting that their hourglass shape could be the result of a natural selection process toward optimal permeability. This work also provides guidelines to optimize the performances of artificial nanopores, with applications in desalination, ultrafiltration, or energy conversion. , The ubiquitous aquaporin channels are able to conduct water across cell membranes, combining the seemingly antagonist functions of a very high selectivity with a remarkable permeability. Whereas molecular details are obvious keys to perform these tasks, the overall efficiency of transport in such nanopores is also strongly limited by viscous dissipation arising at the connection between the nanoconstriction and the nearby bulk reservoirs. In this contribution, we focus on these so-called entrance effects and specifically examine whether the characteristic hourglass shape of aquaporins may arise from a geometrical optimum for such hydrodynamic dissipation. Using a combination of finite-element calculations and analytical modeling, we show that conical entrances with suitable opening angle can indeed provide a large increase of the overall channel permeability. Moreover, the optimal opening angles that maximize the permeability are found to compare well with the angles measured in a large variety of aquaporins. This suggests that the hourglass shape of aquaporins could be the result of a natural selection process toward optimal hydrodynamic transport. Finally, in a biomimetic perspective, these results provide guidelines to design artificial nanopores with optimal performances.}, langid = {english}, keywords = {entrance,self}, - file = {/home/simon/Zotero/storage/YDVJQKKZ/Gravelle et al. - 2013 - Optimizing water permeability through the hourglas.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YDVJQKKZ/Gravelle et al. - 2013 - Optimizing water permeability through the hourglas.pdf} } @article{gravelleTransportThinWater2022, title = {Transport of Thin Water Films: {{From}} Thermally Activated Random Walks to Hydrodynamics}, shorttitle = {Transport of Thin Water Films}, author = {Gravelle, Simon and Holm, Christian and Schlaich, Alexander}, - year = {2022}, - month = sep, - journal = {The Journal of Chemical Physics}, + date = {2022-09-13}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {157}, number = {10}, pages = {104702}, issn = {0021-9606}, doi = {10.1063/5.0099646}, + url = {https://doi.org/10.1063/5.0099646}, urldate = {2023-07-12}, abstract = {Under ambient atmospheric conditions, a thin film of water wets many solid surfaces, including insulators, ice, and salt. The film thickness as well as its transport behavior sensitively depend on the surrounding humidity. Understanding this intricate interplay is of the highest relevance for water transport through porous media, particularly in the context of soil salinization induced by evaporation. Here, we use molecular simulations to evaluate the transport properties of thin water films on prototypical salt and soil interfaces, namely NaCl and silica solid surfaces. Our results show two distinct regimes for water transport: at low water coverage, the film permeance scales linearly with the adsorbed amount, in agreement with the activated random walk model. For thicker water films, the permeance scales as the adsorbed amount to the power of 3, in line with the Stokes equation. By comparing results obtained for silica and NaCl surfaces, we find that, at low water coverage, water permeance at the silica surface is considerably lower than at the NaCl surface, which we attribute to difference in hydrogen bonding. We also investigate the effect of atomic surface defects on the transport properties. Finally, in the context of water transport through the porous material, we determine the humidity-dependent crossover between a vapor-dominated and a thin film-dominated transport regimes depending on the pore size.}, keywords = {heat,MD}, - file = {/home/simon/Zotero/storage/ICVCW5H2/Gravelle et al. - 2022 - Transport of thin water films From thermally acti.pdf;/home/simon/Zotero/storage/5RLD45XY/Transport-of-thin-water-films-From-thermally.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ICVCW5H2/Gravelle et al. - 2022 - Transport of thin water films From thermally acti.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/5RLD45XY/Transport-of-thin-water-films-From-thermally.html} } @article{greiner-schmidSelfDiffusionCompressed1991, - title = {Self-diffusion in the Compressed Fluid Lower Alkanes: {{Methane}}, Ethane, and Propane}, - shorttitle = {Self-diffusion in the Compressed Fluid Lower Alkanes}, - author = {Greiner-Schmid, A. and Wappmann, S. and Has, M. and L{\"u}demann, H.-D.}, - year = {1991}, - month = apr, - journal = {The Journal of Chemical Physics}, + title = {Self‐diffusion in the Compressed Fluid Lower Alkanes: {{Methane}}, Ethane, and Propane}, + shorttitle = {Self‐diffusion in the Compressed Fluid Lower Alkanes}, + author = {Greiner‐Schmid, A. and Wappmann, S. and Has, M. and Lüdemann, H.‐D.}, + date = {1991-04-15}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {94}, number = {8}, pages = {5643--5649}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.460474}, + url = {https://pubs.aip.org/aip/jcp/article/94/8/5643-5649/441946}, urldate = {2023-05-30}, langid = {english}, keywords = {NMR,propane}, - file = {/home/simon/Zotero/storage/CC7SSQEN/Greiner‐Schmid et al. - 1991 - Self‐diffusion in the compressed fluid lower alkan.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CC7SSQEN/Greiner‐Schmid et al. - 1991 - Self‐diffusion in the compressed fluid lower alkan.pdf} } @article{grivetNMRRelaxationParameters2005, title = {{{NMR}} Relaxation Parameters of a {{Lennard-Jones}} Fluid from Molecular-Dynamics Simulations}, author = {Grivet, Jean-Philippe}, - year = {2005}, - month = jul, - journal = {The Journal of Chemical Physics}, + date = {2005-07-15}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {123}, number = {3}, pages = {034503}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.1955447}, + url = {https://pubs.aip.org/aip/jcp/article/918916}, urldate = {2023-06-06}, langid = {english}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/6SQ6RUSL/Grivet - 2005 - NMR relaxation parameters of a Lennard-Jones fluid.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6SQ6RUSL/Grivet - 2005 - NMR relaxation parameters of a Lennard-Jones fluid.pdf} } @article{guevara-carrionPredictionTransportProperties2008, title = {Prediction of {{Transport Properties}} by {{Molecular Simulation}}: {{Methanol}} and {{Ethanol}} and {{Their Mixture}}}, shorttitle = {Prediction of {{Transport Properties}} by {{Molecular Simulation}}}, - author = {{Guevara-Carrion}, Gabriela and {Nieto-Draghi}, Carlos and Vrabec, Jadran and Hasse, Hans}, - year = {2008}, - month = dec, - journal = {The Journal of Physical Chemistry B}, + author = {Guevara-Carrion, Gabriela and Nieto-Draghi, Carlos and Vrabec, Jadran and Hasse, Hans}, + date = {2008-12-25}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {112}, number = {51}, pages = {16664--16674}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp805584d}, + url = {https://pubs.acs.org/doi/10.1021/jp805584d}, urldate = {2023-07-26}, langid = {english}, keywords = {ethanol}, - file = {/home/simon/Zotero/storage/8CZ9K37B/Guevara-Carrion et al. - 2008 - Prediction of Transport Properties by Molecular Si.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/8CZ9K37B/Guevara-Carrion et al. - 2008 - Prediction of Transport Properties by Molecular Si.pdf} } @article{guoApplicationConductivePolymer2022, title = {Application of Conductive Polymer Hydrogels in Flexible Electronics}, - author = {Guo, Xin and Li, Jiean and Wang, Fanyu and Zhang, Jia-Han and Zhang, Jing and Shi, Yi and Pan, Lijia}, - year = {2022}, - month = sep, - journal = {Journal of Polymer Science}, + author = {Guo, Xin and Li, Jiean and Wang, Fanyu and Zhang, Jia‐Han and Zhang, Jing and Shi, Yi and Pan, Lijia}, + date = {2022-09-15}, + journaltitle = {Journal of Polymer Science}, + shortjournal = {J. Polym. Sci.}, volume = {60}, number = {18}, pages = {2635--2662}, issn = {2642-4150, 2642-4169}, doi = {10.1002/pol.20210933}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/pol.20210933}, urldate = {2023-10-17}, abstract = {Flexible electronic devices to obtain accurate and efficient information interactions between humans and machines have gained increasing attention in recent years. A series of soft materials for flexible electronics have been developed to improve device performance in terms of electrical and mechanical properties. Among them, conductive polymer-based hydrogels (CPHs), which combine the tunable electronic properties of conductive polymers and the soft mechanical properties of hydrogels, are promising candidates for nextgeneration wearable electronic devices. This review summarized the material design and preparation of CPHs, and presented the properties of CPHs, including tunable conductivity, outstanding mechanical performance, biocompatibility, self-healing capability, resistance to freezing, and solution processability. In particular, their emerging applications in flexible electronics devices including flexible supercapacitors, flexible sensors, and biomedical electronics are highlighted. Furthermore, perspectives on existing challenges and opportunities in this field are discussed.}, langid = {english}, - file = {/home/simon/Zotero/storage/J4USMGKW/Guo et al. - 2022 - Application of conductive polymer hydrogels in fle.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/J4USMGKW/Guo et al. - 2022 - Application of conductive polymer hydrogels in fle.pdf} } @article{guoLocalMicrophaseSeparation2014, title = {Local {{Microphase Separation}} of a {{Binary Liquid}} under {{Nanoscale Confinement}}}, author = {Guo, Xiang-Yang and Watermann, Tobias and Sebastiani, Daniel}, - year = {2014}, - month = aug, - journal = {The Journal of Physical Chemistry B}, + date = {2014-08-28}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {118}, number = {34}, pages = {10207--10213}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp505203t}, + url = {https://pubs.acs.org/doi/10.1021/jp505203t}, urldate = {2023-06-09}, - abstract = {The structural and diffusive properties of an ethanol-water mixture under hydrophilic nanoscale confinement are investigated by means of molecular dynamics simulations based on the CHARMM force field. The resulting density profiles illustrate that demixing of solvents occurs at the pore wall region, which is composed of silanol molecules in our case. Ethanol molecules are more likely to attach to the wall via hydrogen bonds than water molecules. A noticeable O-H bond orientation is observed for the ethanol molecules in this region, which can be explained by the formation of two specific hydrogen bonds between ethanol and silanol. Water, in contrast, resides mostly outside the interfacial region and is in favor of forming small hydrogen bonded strings and clusters with other water molecules. This phenomenon is corroborated by both the orientation of ethanol hydroxyl groups and the radial distribution functions of the solvent oxygen atom to the silanol hydrogen atom. Ethanol selectively attaches to the wall and forms a layer close to the wall. The hydrophobic headgroups of these ethanol molecules lead to an internal hydrophobic interface layer, which in turn yields cluster structures in the adjacent water. The self-diffusion of water in the confined ethanol-water mixture at the center of the pore is faster than that of water in the bulk ethanol-water mixture; ethanol, on the other hand, diffuses slower when it is confined.}, + abstract = {The structural and diffusive properties of an ethanol−water mixture under hydrophilic nanoscale confinement are investigated by means of molecular dynamics simulations based on the CHARMM force field. The resulting density profiles illustrate that demixing of solvents occurs at the pore wall region, which is composed of silanol molecules in our case. Ethanol molecules are more likely to attach to the wall via hydrogen bonds than water molecules. A noticeable O−H bond orientation is observed for the ethanol molecules in this region, which can be explained by the formation of two specific hydrogen bonds between ethanol and silanol. Water, in contrast, resides mostly outside the interfacial region and is in favor of forming small hydrogen bonded strings and clusters with other water molecules. This phenomenon is corroborated by both the orientation of ethanol hydroxyl groups and the radial distribution functions of the solvent oxygen atom to the silanol hydrogen atom. Ethanol selectively attaches to the wall and forms a layer close to the wall. The hydrophobic headgroups of these ethanol molecules lead to an internal hydrophobic interface layer, which in turn yields cluster structures in the adjacent water. The self-diffusion of water in the confined ethanol−water mixture at the center of the pore is faster than that of water in the bulk ethanol−water mixture; ethanol, on the other hand, diffuses slower when it is confined.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/2ABM7J5U/Guo et al. - 2014 - Local Microphase Separation of a Binary Liquid und.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2ABM7J5U/Guo et al. - 2014 - Local Microphase Separation of a Binary Liquid und.pdf} } @article{halderUnravellingCompositionDependentAnomalies2018, - title = {Unravelling the {{Composition-Dependent Anomalies}} of {{Pair Hydrophobicity}} in {{Water}}{\textendash}{{Ethanol Binary Mixtures}}}, + title = {Unravelling the {{Composition-Dependent Anomalies}} of {{Pair Hydrophobicity}} in {{Water}}–{{Ethanol Binary Mixtures}}}, author = {Halder, Ritaban and Jana, Biman}, - year = {2018}, - month = jul, - journal = {The Journal of Physical Chemistry B}, + date = {2018-07-05}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {122}, number = {26}, pages = {6801--6809}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.8b02528}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.8b02528}, urldate = {2023-05-02}, - abstract = {Aqueous binary mixtures have received immense attention in recent years because of their extensive application in several biological and industrial processes. The water-ethanol binary mixture serves as a unique system because it exhibits composition-dependent alteration of dynamic and thermodynamic properties. Our present work demonstrates how different compositions of water-ethanol binary mixtures affect the pair hydrophobicity of different hydrophobes. Pair hydrophobicity is measured by the depth of the first minimum (contact minima) of potential of mean force (PMF) profile between two hydrophobes. The pair hydrophobicity is found to be increased with addition of ethanol to water up to a mole fraction of xEtOH = 0.10 and decreased with further addition of ethanol. This observation is shown to be true for three (methane-methane, isobutane-isobutane, and toluene-toluene) different pairs of hydrophobes. Decomposition of PMF into enthalpic and entropic contribution indicates a switch from entropic to enthalpic stabilization of the contact minimum upon addition of ethanol to water. The gain in mixing enthalpy of the binary solvent system upon association of two hydrophobes is found to be the determining factor for the stabilization of contact minimum. Several static/ dynamics quantities (average composition fluctuations, diffusion coefficients, fluctuations in total dipole moment, propensity of ethyl-ethyl association, etc) of the ethanol-water binary mixture also show irregularities around xEtOH = 0.10-0.15. We have also discovered that the hydrogen bonding pattern of ethanol rather than water reveals a change in trend near the similar composition range. As the anomalous behavior of the physical/dynamical properties along with the pair hydrophobicity in an aqueous binary mixture of amphiphilic solutes is a common phenomenon, our results may provide a general viewpoint on these aspects.}, + abstract = {Aqueous binary mixtures have received immense attention in recent years because of their extensive application in several biological and industrial processes. The water−ethanol binary mixture serves as a unique system because it exhibits composition-dependent alteration of dynamic and thermodynamic properties. Our present work demonstrates how different compositions of water−ethanol binary mixtures affect the pair hydrophobicity of different hydrophobes. Pair hydrophobicity is measured by the depth of the first minimum (contact minima) of potential of mean force (PMF) profile between two hydrophobes. The pair hydrophobicity is found to be increased with addition of ethanol to water up to a mole fraction of xEtOH = 0.10 and decreased with further addition of ethanol. This observation is shown to be true for three (methane−methane, isobutane−isobutane, and toluene−toluene) different pairs of hydrophobes. Decomposition of PMF into enthalpic and entropic contribution indicates a switch from entropic to enthalpic stabilization of the contact minimum upon addition of ethanol to water. The gain in mixing enthalpy of the binary solvent system upon association of two hydrophobes is found to be the determining factor for the stabilization of contact minimum. Several static/ dynamics quantities (average composition fluctuations, diffusion coefficients, fluctuations in total dipole moment, propensity of ethyl−ethyl association, etc) of the ethanol−water binary mixture also show irregularities around xEtOH = 0.10−0.15. We have also discovered that the hydrogen bonding pattern of ethanol rather than water reveals a change in trend near the similar composition range. As the anomalous behavior of the physical/dynamical properties along with the pair hydrophobicity in an aqueous binary mixture of amphiphilic solutes is a common phenomenon, our results may provide a general viewpoint on these aspects.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/CBQJ9Z83/Halder and Jana - 2018 - Unravelling the Composition-Dependent Anomalies of.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CBQJ9Z83/Halder and Jana - 2018 - Unravelling the Composition-Dependent Anomalies of.pdf} } @article{halleInterpretationMagneticResonance1981, title = {Interpretation of Magnetic Resonance Data from Water Nuclei in Heterogeneous Systems}, - author = {Halle, Bertil and Wennerstr{\"o}m, H{\aa}kan}, - year = {1981}, - month = aug, - journal = {The Journal of Chemical Physics}, + author = {Halle, Bertil and Wennerström, Håkan}, + date = {1981-08-15}, + journaltitle = {The Journal of Chemical Physics}, volume = {75}, number = {4}, pages = {1928--1943}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.442218}, + url = {https://pubs.aip.org/jcp/article/75/4/1928/438499/Interpretation-of-magnetic-resonance-data-from}, urldate = {2023-09-30}, - abstract = {Nuclear magnetic resonance (NMR) data from water nuclei (1H, 2H, and 17O) can provide much information about the state of water in heterogeneous systems. In the present work, we present a theoretical framework for the interpretation of such data and discuss the implications of the theory. Due to the local anisotropy in heterogeneous systems, it is necessary to consider two components of water motion: a fast anisotropic reorientation superposed on a more extensive slow motion. On the basis of the experimentally verified assumption that these motions occur on different time scales, we develop a ''two-step'' model of relaxation, showing that both motions may give important contributions to the relaxation. We derive a simple expression for the relevant correlation function, valid for isotropic systems. Anisotropic systems are also treated, making use of a new symmetry theorem for time correlation functions. The proof of this theorem is given in an Appendix. The magnitudes of the water 2H and 17O quadrupole coupling constants are estimated to 0.222 and 6.67 MHz, respectively. Results of ab\hphantom{,}initio quantum chemical calculations are presented, demonstrating the insensitivity of the water 17O field gradient to nearby ionic species. The possibilities and limitations of the NMR technique in answering the fundamental questions about water structure and dynamics in heterogeneous systems are discussed. We suggest a novel interpretation of the well-known invariance of the ratio of 1H and 2H splittings. Furthermore, we argue that the available NMR data are consistent with a short-ranged ({$\lessequivlnt$}2 molecular layers) perturbation of the water tumbling rate and anisotropy.}, + abstract = {Nuclear magnetic resonance (NMR) data from water nuclei (1H, 2H, and 17O) can provide much information about the state of water in heterogeneous systems. In the present work, we present a theoretical framework for the interpretation of such data and discuss the implications of the theory. Due to the local anisotropy in heterogeneous systems, it is necessary to consider two components of water motion: a fast anisotropic reorientation superposed on a more extensive slow motion. On the basis of the experimentally verified assumption that these motions occur on different time scales, we develop a ’’two-step’’ model of relaxation, showing that both motions may give important contributions to the relaxation. We derive a simple expression for the relevant correlation function, valid for isotropic systems. Anisotropic systems are also treated, making use of a new symmetry theorem for time correlation functions. The proof of this theorem is given in an Appendix. The magnitudes of the water 2H and 17O quadrupole coupling constants are estimated to 0.222 and 6.67 MHz, respectively. Results of ab\hphantom{,}initio quantum chemical calculations are presented, demonstrating the insensitivity of the water 17O field gradient to nearby ionic species. The possibilities and limitations of the NMR technique in answering the fundamental questions about water structure and dynamics in heterogeneous systems are discussed. We suggest a novel interpretation of the well-known invariance of the ratio of 1H and 2H splittings. Furthermore, we argue that the available NMR data are consistent with a short-ranged (≲2 molecular layers) perturbation of the water tumbling rate and anisotropy.}, langid = {english}, - file = {/home/simon/Zotero/storage/K7QXT8AZ/Halle and Wennerström - 1981 - Interpretation of magnetic resonance data from wat.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/K7QXT8AZ/Halle and Wennerström - 1981 - Interpretation of magnetic resonance data from wat.pdf} } @article{heEnhancedCompatibilitySelectivity2023, title = {Enhanced Compatibility and Selectivity in Mixed Matrix Membranes for Propylene/Propane Separation}, author = {He, Rongrong and Cong, Shenzhen and Peng, Donglai and Zhang, Yatao and Shan, Meixia and Zhu, Junyong and Wang, Jing and Gascon, Jorge}, - year = {2023}, - month = mar, - journal = {AIChE Journal}, + date = {2023-03}, + journaltitle = {AIChE Journal}, + shortjournal = {AIChE Journal}, volume = {69}, number = {3}, issn = {0001-1541, 1547-5905}, doi = {10.1002/aic.17948}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/aic.17948}, urldate = {2023-05-26}, - abstract = {Mixed matrix membranes (MMMs) based on metal{\textendash}organic framework (MOF) have great promising application in separation of gas mixtures. However, achieving a good interfacial compatibility between polymer and MOF is not straightforward. In this work, focusing on one of the most challenging olefin/paraffin separations: propylene/ propane (C3H6/C3H8), we demonstrate that modification of the MOF filler via dopamine polymerization using a double solvent approach strongly improves interfacial compatibility. The resulting membranes show an outstanding separation performance and long-term stability with propylene permeability nearly 90 Barrer and propylene/ propane selectivity close to 75. We anticipate that similar MOF modification strategies may help solve the problem of interface defects in the manufacture of MMMs and be extended to other porous fillers.}, + abstract = {Mixed matrix membranes (MMMs) based on metal–organic framework (MOF) have great promising application in separation of gas mixtures. However, achieving a good interfacial compatibility between polymer and MOF is not straightforward. In this work, focusing on one of the most challenging olefin/paraffin separations: propylene/ propane (C3H6/C3H8), we demonstrate that modification of the MOF filler via dopamine polymerization using a double solvent approach strongly improves interfacial compatibility. The resulting membranes show an outstanding separation performance and long-term stability with propylene permeability nearly 90 Barrer and propylene/ propane selectivity close to 75. We anticipate that similar MOF modification strategies may help solve the problem of interface defects in the manufacture of MMMs and be extended to other porous fillers.}, langid = {english}, keywords = {ff,propane}, - file = {/home/simon/Zotero/storage/CRRS37PL/He et al. - 2023 - Enhanced compatibility and selectivity in mixed ma.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CRRS37PL/He et al. - 2023 - Enhanced compatibility and selectivity in mixed ma.pdf} } @article{henryInfluenceVibrationalMotion1985, title = {Influence of Vibrational Motion on Solid State Line Shapes and {{NMR}} Relaxation}, author = {Henry, Eric R. and Szabo, Attila}, - year = {1985}, - month = jun, - journal = {The Journal of Chemical Physics}, + date = {1985-06}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {82}, number = {11}, pages = {4753--4761}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.448692}, + url = {https://pubs.aip.org/aip/jcp/article/82/11/4753-4761/609243}, urldate = {2023-05-26}, langid = {english}, keywords = {NMR,propane}, - file = {/home/simon/Zotero/storage/L2P2BNAH/Henry and Szabo - 1985 - Influence of vibrational motion on solid state lin.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/L2P2BNAH/Henry and Szabo - 1985 - Influence of vibrational motion on solid state lin.pdf} } @article{hiltonProtonNuclearMagnetic1977, title = {Proton Nuclear Magnetic Resonance Relaxation of Water on Lysozyme Powders}, author = {Hilton, B. D. and Hsi, E. and Bryant, R. G.}, - year = {1977}, - month = dec, - journal = {Journal of the American Chemical Society}, + date = {1977-12}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, volume = {99}, number = {26}, pages = {8483--8490}, issn = {0002-7863, 1520-5126}, doi = {10.1021/ja00468a017}, + url = {https://pubs.acs.org/doi/abs/10.1021/ja00468a017}, urldate = {2023-08-02}, abstract = {Nuclear magnetic resonance transverse and longitudinal relaxation rates are reported at 30 MHz for water protons adsorbed on lysozyme powders from the gas phase as a function of temperature and water content. The free induction decay amplitude accounts for all of the water protons in the sample over the range of water concentrations studies. Two types of model are considered to interpret the transverse NMR relaxation data. It is shown that a multisite fast exchange model which assumes water concentration independent protein binding sites is inconsistent with the data. A crude model that includes the possibility that water molecule motion at all sites may be influenced by subsequent addition of water does account for the observations. A chemical exchange model and a cross-relaxation model are considered as sources of the nonexponential decay observed in the longitudinal relaxation data throughout the temperature and concentration range studied. It is shown that when cross-relaxation between protein protons and water protons is included, long water molecule residence times at protein sites are not required and that the usual approaches to the analysis of water relaxation at surfaces must be altered. The data demonstrate that the rate of water molecule motion decreases with decreasing water content, even though some distribution of motional correlation times may be appropriate. The water in the immediate vicinity of the protein surface appears to be best characterized as a viscous liquid but not as a solid.}, langid = {english}, keywords = {HEWL,NMR}, - file = {/home/simon/Zotero/storage/HWKC75E6/Hilton et al. - 1977 - Proton nuclear magnetic resonance relaxation of wa.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/HWKC75E6/Hilton et al. - 1977 - Proton nuclear magnetic resonance relaxation of wa.pdf} } @article{hindmanRelaxationProcessesWater2003, - title = {Relaxation Processes in Water. {{A}} Study of the Proton Spin-lattice Relaxation Time}, + title = {Relaxation Processes in Water. {{A}} Study of the Proton Spin‐lattice Relaxation Time}, author = {Hindman, J. C. and Svirmickas, A. and Wood, M.}, - year = {2003}, - month = sep, - journal = {The Journal of Chemical Physics}, + date = {2003-09-04}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {59}, number = {3}, pages = {1517--1522}, issn = {0021-9606}, doi = {10.1063/1.1680209}, + url = {https://doi.org/10.1063/1.1680209}, urldate = {2024-01-05}, - abstract = {An experimental study of the proton spin-lattice relaxation time T1 has been made for H2O over the temperature interval from -16 to 145{\textdegree}C. It is found that after correction for spin-rotational interaction, the experimental T1 behavior can be represented by the double exponential form of the rate expression used to treat the relaxation for the quadrupolar nuclei 2H and 17O in water. The oxygen-17 data are used to calculate the intramolecular contribution to the proton T1. The activation energies E1=9.4{$\pm$} 0.8\,kcal/mole and E2=3.6{$\pm$} 0.1\,kcal/mole for the two contributions to the intermolecular relaxation are in sufficiently good agreement with those for the intramolecular relaxation to indicate that the relaxation mechanism is the same in both cases. This mechanism involves two processes. The data indicate the process dominant at high temperature can be described as a rotational diffusion where the amplitude of angular motion increases with increasing temperature.}, - file = {/home/simon/Zotero/storage/4BC8KSSG/Hindman et al. - 2003 - Relaxation processes in water. A study of the prot.pdf;/home/simon/Zotero/storage/IRZFL38N/Relaxation-processes-in-water-A-study-of-the.html} + abstract = {An experimental study of the proton spin‐lattice relaxation time T1 has been made for H2O over the temperature interval from −16 to 145°C. It is found that after correction for spin‐rotational interaction, the experimental T1 behavior can be represented by the double exponential form of the rate expression used to treat the relaxation for the quadrupolar nuclei 2H and 17O in water. The oxygen‐17 data are used to calculate the intramolecular contribution to the proton T1. The activation energies E1=9.4± 0.8\,kcal/mole and E2=3.6± 0.1\,kcal/mole for the two contributions to the intermolecular relaxation are in sufficiently good agreement with those for the intramolecular relaxation to indicate that the relaxation mechanism is the same in both cases. This mechanism involves two processes. The data indicate the process dominant at high temperature can be described as a rotational diffusion where the amplitude of angular motion increases with increasing temperature.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4BC8KSSG/Hindman et al. - 2003 - Relaxation processes in water. A study of the prot.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/IRZFL38N/Relaxation-processes-in-water-A-study-of-the.html} } @article{hirasakiFluidRockCharacterization, - title = {Fluid {\textendash}{{Rock Characterization}} and {{Interactions}} In}, + title = {Fluid –{{Rock Characterization}} and {{Interactions}} In}, author = {Hirasaki, George J}, langid = {english}, - file = {/home/simon/Zotero/storage/G9557PM9/Hirasaki - Fluid –Rock Characterization and Interactions in.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/G9557PM9/Hirasaki - Fluid –Rock Characterization and Interactions in.pdf} } @article{horowitzCarbonOxygenHydrogenBonding2012, title = {Carbon-{{Oxygen Hydrogen Bonding}} in {{Biological Structure}} and {{Function}}}, author = {Horowitz, Scott and Trievel, Raymond C.}, - year = {2012}, - month = dec, - journal = {Journal of Biological Chemistry}, + date = {2012-12}, + journaltitle = {Journal of Biological Chemistry}, + shortjournal = {Journal of Biological Chemistry}, volume = {287}, number = {50}, pages = {41576--41582}, issn = {00219258}, doi = {10.1074/jbc.R112.418574}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820438086}, urldate = {2023-04-19}, langid = {english}, keywords = {bio,HB}, - file = {/home/simon/Zotero/storage/IQRJW5XL/Horowitz and Trievel - 2012 - Carbon-Oxygen Hydrogen Bonding in Biological Struc.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/IQRJW5XL/Horowitz and Trievel - 2012 - Carbon-Oxygen Hydrogen Bonding in Biological Struc.pdf} } @article{hospital-benitoDirectAirCapture2023, title = {Direct Air Capture Based on Ionic Liquids: {{From}} Molecular Design to Process Assessment}, shorttitle = {Direct Air Capture Based on Ionic Liquids}, - author = {{Hospital-Benito}, D. and Moya, C. and Gazzani, M. and Palomar, J.}, - year = {2023}, - month = jul, - journal = {Chemical Engineering Journal}, + author = {Hospital-Benito, D. and Moya, C. and Gazzani, M. and Palomar, J.}, + date = {2023-07}, + journaltitle = {Chemical Engineering Journal}, + shortjournal = {Chemical Engineering Journal}, volume = {468}, pages = {143630}, issn = {13858947}, doi = {10.1016/j.cej.2023.143630}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1385894723023616}, urldate = {2023-11-06}, - abstract = {Direct air capture is a key carbon dioxide removal technology to mitigate climate change and keep the global average temperature rise below 1.5{\textendash}2 {$\smwhtcircle$}C. This work addresses for the first time the use of ionic liquids for direct air capture connecting their material design by molecular simulation to process modelling. First, 26 different ionic liquids were designed through quantum chemical calculations and their isotherms were computed to identify those with a positive cyclic working capacity at conditions relevant for direct air capture. Then, the most promising ionic liquids were assessed via process simulations in Aspen Plus. A wide range of operating config\- urations were screened by modifying the key process variables: air velocity (1 {\textendash} 3 m/s), solvent mass flow (5 {\textendash} 50 t/h) and temperature (293 {\textendash} 323 K), and regeneration pressure (0.1 {\textendash} 1 bar) and temperature (373 {\textendash} 393 K). Exergy, energy and productivity were computed to detect optimal operating conditions; moreover, a simplified economic analysis was carried out to highlight the major cost components. The direct air capture system based on [P66614][Im] exhibited the most exergy (5.44 {\textendash} 16.73 MJ/kg) and energy (15.15 {\textendash} 35.42 MJ/kg) efficiency for similar productivity (0.5 {\textendash} 1.3 kg/(m3{$\cdot$}h)) thanks to its enhanced cyclic capacity (0.6 {\textendash} 0.3 mol/kg). The mini\- mum exergy required by [P66614][Im]-based DAC process is slightly better than alkali scrubbing (6.21 MJ/kg) and in line with amine (5.59 MJ/kg) scrubbing. In addition, the assessed DAC process has a theoretical potential to operate in the range of 200 \$/tCO2 under reasonable energy and plant expenses. We conclude this work providing guidelines to address future development of direct air capture technologies based on ionic liquids.}, + abstract = {Direct air capture is a key carbon dioxide removal technology to mitigate climate change and keep the global average temperature rise below 1.5–2 ◦C. This work addresses for the first time the use of ionic liquids for direct air capture connecting their material design by molecular simulation to process modelling. First, 26 different ionic liquids were designed through quantum chemical calculations and their isotherms were computed to identify those with a positive cyclic working capacity at conditions relevant for direct air capture. Then, the most promising ionic liquids were assessed via process simulations in Aspen Plus. A wide range of operating config­ urations were screened by modifying the key process variables: air velocity (1 – 3 m/s), solvent mass flow (5 – 50 t/h) and temperature (293 – 323 K), and regeneration pressure (0.1 – 1 bar) and temperature (373 – 393 K). Exergy, energy and productivity were computed to detect optimal operating conditions; moreover, a simplified economic analysis was carried out to highlight the major cost components. The direct air capture system based on [P66614][Im] exhibited the most exergy (5.44 – 16.73 MJ/kg) and energy (15.15 – 35.42 MJ/kg) efficiency for similar productivity (0.5 – 1.3 kg/(m3⋅h)) thanks to its enhanced cyclic capacity (0.6 – 0.3 mol/kg). The mini­ mum exergy required by [P66614][Im]-based DAC process is slightly better than alkali scrubbing (6.21 MJ/kg) and in line with amine (5.59 MJ/kg) scrubbing. In addition, the assessed DAC process has a theoretical potential to operate in the range of 200 \$/tCO2 under reasonable energy and plant expenses. We conclude this work providing guidelines to address future development of direct air capture technologies based on ionic liquids.}, langid = {english}, - file = {/home/simon/Zotero/storage/Y4CYFURU/Hospital-Benito et al. - 2023 - Direct air capture based on ionic liquids From mo.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Y4CYFURU/Hospital-Benito et al. - 2023 - Direct air capture based on ionic liquids From mo.pdf} } @article{hubbardpauls.TheoryElectronnucleusOverhauser1966, title = {Theory of Electron-Nucleus {{Overhauser}} Effects in Liquids Containing Free Radicals}, author = {Hubbard, Paul S., Paul S.}, - year = {1966}, - month = apr, - journal = {Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences}, + date = {1966-04-26}, + journaltitle = {Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences}, + shortjournal = {Proc. R. Soc. Lond. A}, volume = {291}, number = {1427}, pages = {537--555}, issn = {0080-4630, 2053-9169}, doi = {10.1098/rspa.1966.0113}, + url = {https://royalsocietypublishing.org/doi/10.1098/rspa.1966.0113}, urldate = {2023-09-29}, - abstract = {The nuclear magnetic relaxation and the electron-nucleus Overhauser effect on spin {$\frac{1}{2}$} nuclei in solutions containing free radicals are calculated on the assumption that the nuclei and electrons interact by means of magnetic dipole{\textendash}dipole interactions and scalar spin{\textendash}spin interactions. The time dependence of the dipole{\textendash}dipole interactions is assumed to be due to the translational diffusion of the free radicals and the molecules containing the nuclei. Two models are employed for the scalar interactions. In the first of these, there is a scalar interaction only while a molecule is stuck to a free radical, and the time for which they are stuck is a random variable. In the second model, the hypothesis is made that the scalar interaction is a very short range interaction with magnitude {$\Elzxh$}A ( d/R ) exp [{\textendash} {$\lambda$} ( R{\textendash}d )], where {$\lambda$} d {$\gg$} 1, A and {$\lambda$} are constants, R is the distance between a nucleus and an electron, and d is a distance of closest approach, inside of which the interaction is zero. In the second model, the time dependence of the scalar interaction, as in the case of the dipole{\textendash}dipole interactions, is due to the relative diffusion of the molecules and free radicals in the solution. For the second model, it is found that the frequency dependence of the spectral density of a scalar interaction is very similar to the frequency dependence of the spectral density of a dipole{\textendash}dipole interaction, no matter how short range the scalar interaction is made by making {$\lambda$}d very large. For both models of the scalar interaction it is found that the sign of the steady-state Overhauser effect may change from positive to negative as the magnetic field is increased, but that this is more likely to happen for the first model of the scalar interactions than for the second. The interpretation of experiments in terms of the results derived here is discussed, with particular attention given to experiments performed at two different magnetic fields. It is found that in some cases it may be possible to determine which model of the scalar interactions gives better agreement with experiment, and to determine values for the contributions of the scalar and the dipolar interactions, the distance of closest approach, and the relative diffusion coefficient.}, + abstract = {The nuclear magnetic relaxation and the electron-nucleus Overhauser effect on spin ½ nuclei in solutions containing free radicals are calculated on the assumption that the nuclei and electrons interact by means of magnetic dipole–dipole interactions and scalar spin–spin interactions. The time dependence of the dipole–dipole interactions is assumed to be due to the translational diffusion of the free radicals and the molecules containing the nuclei. Two models are employed for the scalar interactions. In the first of these, there is a scalar interaction only while a molecule is stuck to a free radical, and the time for which they are stuck is a random variable. In the second model, the hypothesis is made that the scalar interaction is a very short range interaction with magnitude ħA ( d/R ) exp [– λ ( R–d )], where λ d ≫ 1, A and λ are constants, R is the distance between a nucleus and an electron, and d is a distance of closest approach, inside of which the interaction is zero. In the second model, the time dependence of the scalar interaction, as in the case of the dipole–dipole interactions, is due to the relative diffusion of the molecules and free radicals in the solution. For the second model, it is found that the frequency dependence of the spectral density of a scalar interaction is very similar to the frequency dependence of the spectral density of a dipole–dipole interaction, no matter how short range the scalar interaction is made by making λd very large. For both models of the scalar interaction it is found that the sign of the steady-state Overhauser effect may change from positive to negative as the magnetic field is increased, but that this is more likely to happen for the first model of the scalar interactions than for the second. The interpretation of experiments in terms of the results derived here is discussed, with particular attention given to experiments performed at two different magnetic fields. It is found that in some cases it may be possible to determine which model of the scalar interactions gives better agreement with experiment, and to determine values for the contributions of the scalar and the dipolar interactions, the distance of closest approach, and the relative diffusion coefficient.}, langid = {english}, - file = {/home/simon/Zotero/storage/F7MVKPF8/1966 - Theory of electron-nucleus Overhauser effects in l.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/F7MVKPF8/1966 - Theory of electron-nucleus Overhauser effects in l.pdf} } @article{hubbardTheoryNuclearMagnetic1963, title = {Theory of {{Nuclear Magnetic Relaxation}} by {{Spin-Rotational Interactions}} in {{Liquids}}}, author = {Hubbard, Paul S.}, - year = {1963}, - month = aug, - journal = {Physical Review}, + date = {1963-08-01}, + journaltitle = {Physical Review}, + shortjournal = {Phys. Rev.}, volume = {131}, number = {3}, pages = {1155--1165}, issn = {0031-899X}, doi = {10.1103/PhysRev.131.1155}, + url = {https://link.aps.org/doi/10.1103/PhysRev.131.1155}, urldate = {2023-07-01}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/TTDND5V4/Hubbard - 1963 - Theory of Nuclear Magnetic Relaxation by Spin-Rota.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/TTDND5V4/Hubbard - 1963 - Theory of Nuclear Magnetic Relaxation by Spin-Rota.pdf} } @article{hubOrganicMoleculesSurface2012, - title = {Organic Molecules on the Surface of Water Droplets {\textendash} an Energetic Perspective}, + title = {Organic Molecules on the Surface of Water Droplets – an Energetic Perspective}, author = {Hub, Jochen S. and Caleman, Carl and Van Der Spoel, David}, - year = {2012}, - journal = {Physical Chemistry Chemical Physics}, + date = {2012}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {14}, number = {27}, pages = {9537}, issn = {1463-9076, 1463-9084}, doi = {10.1039/c2cp40483d}, + url = {http://xlink.rsc.org/?DOI=c2cp40483d}, urldate = {2023-07-07}, langid = {english}, keywords = {MD,PMF}, - file = {/home/simon/Zotero/storage/H48Z2IT3/Hub et al. - 2012 - Organic molecules on the surface of water droplets.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/H48Z2IT3/Hub et al. - 2012 - Organic molecules on the surface of water droplets.pdf} } @article{huitemaCanMonteCarlo1999, title = {Can {{Monte Carlo}} Simulation Describe Dynamics? {{A}} Test on {{Lennard-Jones}} Systems}, shorttitle = {Can {{Monte Carlo}} Simulation Describe Dynamics?}, author = {Huitema, H. E. A. and Van Der Eerden, J. P.}, - year = {1999}, - month = feb, - journal = {The Journal of Chemical Physics}, + date = {1999-02-15}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {110}, number = {7}, pages = {3267--3274}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.478192}, + url = {https://pubs.aip.org/aip/jcp/article/110/7/3267-3274/475514}, urldate = {2023-07-09}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/I7B7MDX5/Huitema and Van Der Eerden - 1999 - Can Monte Carlo simulation describe dynamics A te.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/I7B7MDX5/Huitema and Van Der Eerden - 1999 - Can Monte Carlo simulation describe dynamics A te.pdf} } @article{hwangDynamicEffectsPair1975, title = {Dynamic Effects of Pair Correlation Functions on Spin Relaxation by Translational Diffusion in Liquids}, author = {Hwang, Lian-Pin and Freed, Jack H.}, - year = {1975}, - month = nov, - journal = {The Journal of Chemical Physics}, + date = {1975-11-01}, + journaltitle = {The Journal of Chemical Physics}, volume = {63}, number = {9}, pages = {4017--4025}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.431841}, + url = {https://pubs.aip.org/jcp/article/63/9/4017/215553/Dynamic-effects-of-pair-correlation-functions-on}, urldate = {2023-09-29}, - abstract = {It is shown how the equilibrium pair correlation function between spin-bearing molecules in liquids may be incorporated as an effective force in the relative diffusion expressions, and how one may solve for the resulting time correlation functions and spectral densities needed for studies of spin relaxation by translational diffusion. The use of finite difference methods permits the solution no matter how complex the form of the pair correlation function (pcf) utilized. In particular, a Percus{\textendash}Yevick pcf as well as one corrected from computer dynamics, both for hard spheres, are utilized. Good agreement with the experiments of Harmon and Muller on dipolar relaxation in liquid ethane is obtained from this analysis. Effects of ionic interactions in electrolyte solutions upon dipolar relaxation are also obtained in terms of Debye{\textendash}H{\"u}ckel theory for the pcf. Analytic solutions are given which are appropriate for the proper boundary-value problem for the relative diffusion of molecules (i.e., a distance of minimum approach) that has usually been neglected in the spin relaxation theories. Other molecular dynamics aspects of spin relaxation by translational diffusion in liquids are briefly discussed.}, + abstract = {It is shown how the equilibrium pair correlation function between spin-bearing molecules in liquids may be incorporated as an effective force in the relative diffusion expressions, and how one may solve for the resulting time correlation functions and spectral densities needed for studies of spin relaxation by translational diffusion. The use of finite difference methods permits the solution no matter how complex the form of the pair correlation function (pcf) utilized. In particular, a Percus–Yevick pcf as well as one corrected from computer dynamics, both for hard spheres, are utilized. Good agreement with the experiments of Harmon and Muller on dipolar relaxation in liquid ethane is obtained from this analysis. Effects of ionic interactions in electrolyte solutions upon dipolar relaxation are also obtained in terms of Debye–Hückel theory for the pcf. Analytic solutions are given which are appropriate for the proper boundary-value problem for the relative diffusion of molecules (i.e., a distance of minimum approach) that has usually been neglected in the spin relaxation theories. Other molecular dynamics aspects of spin relaxation by translational diffusion in liquids are briefly discussed.}, langid = {english}, - file = {/home/simon/Zotero/storage/HYAW38ND/Hwang and Freed - 1975 - Dynamic effects of pair correlation functions on s.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/HYAW38ND/Hwang and Freed - 1975 - Dynamic effects of pair correlation functions on s.pdf} } @article{hwangDynamicEffectsPair2008, title = {Dynamic Effects of Pair Correlation Functions on Spin Relaxation by Translational Diffusion in Liquids}, - author = {Hwang, Lian-Pin and Freed, Jack H.}, - year = {2008}, - month = sep, - journal = {The Journal of Chemical Physics}, + author = {Hwang, Lian‐Pin and Freed, Jack H.}, + date = {2008-09-03}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {63}, number = {9}, pages = {4017--4025}, issn = {0021-9606}, doi = {10.1063/1.431841}, + url = {https://doi.org/10.1063/1.431841}, urldate = {2023-07-09}, - abstract = {It is shown how the equilibrium pair correlation function between spin-bearing molecules in liquids may be incorporated as an effective force in the relative diffusion expressions, and how one may solve for the resulting time correlation functions and spectral densities needed for studies of spin relaxation by translational diffusion. The use of finite difference methods permits the solution no matter how complex the form of the pair correlation function (pcf) utilized. In particular, a Percus{\textendash}Yevick pcf as well as one corrected from computer dynamics, both for hard spheres, are utilized. Good agreement with the experiments of Harmon and Muller on dipolar relaxation in liquid ethane is obtained from this analysis. Effects of ionic interactions in electrolyte solutions upon dipolar relaxation are also obtained in terms of Debye{\textendash}H{\"u}ckel theory for the pcf. Analytic solutions are given which are appropriate for the proper boundary-value problem for the relative diffusion of molecules (i.e., a distance of minimum approach) that has usually been neglected in the spin relaxation theories. Other molecular dynamics aspects of spin relaxation by translational diffusion in liquids are briefly discussed.}, + abstract = {It is shown how the equilibrium pair correlation function between spin‐bearing molecules in liquids may be incorporated as an effective force in the relative diffusion expressions, and how one may solve for the resulting time correlation functions and spectral densities needed for studies of spin relaxation by translational diffusion. The use of finite difference methods permits the solution no matter how complex the form of the pair correlation function (pcf) utilized. In particular, a Percus–Yevick pcf as well as one corrected from computer dynamics, both for hard spheres, are utilized. Good agreement with the experiments of Harmon and Muller on dipolar relaxation in liquid ethane is obtained from this analysis. Effects of ionic interactions in electrolyte solutions upon dipolar relaxation are also obtained in terms of Debye–Hückel theory for the pcf. Analytic solutions are given which are appropriate for the proper boundary‐value problem for the relative diffusion of molecules (i.e., a distance of minimum approach) that has usually been neglected in the spin relaxation theories. Other molecular dynamics aspects of spin relaxation by translational diffusion in liquids are briefly discussed.}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/K52U5843/Hwang and Freed - 2008 - Dynamic effects of pair correlation functions on s.pdf;/home/simon/Zotero/storage/E8CX729J/Dynamic-effects-of-pair-correlation-functions-on.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/K52U5843/Hwang and Freed - 2008 - Dynamic effects of pair correlation functions on s.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/E8CX729J/Dynamic-effects-of-pair-correlation-functions-on.html} } -@article{hydeSurfacePropertiesEthanol2019a, +@article{hydeSurfacePropertiesEthanol2019, title = {Surface Properties of the Ethanol/Water Mixture: {{Thickness}} and Composition}, shorttitle = {Surface Properties of the Ethanol/Water Mixture}, author = {Hyde, Anita E. and Ohshio, Maho and Nguyen, Cuong V. and Yusa, Shin-ichi and Yamada, Norifumi L. and Phan, Chi M.}, - year = {2019}, - month = sep, - journal = {Journal of Molecular Liquids}, + date = {2019-09}, + journaltitle = {Journal of Molecular Liquids}, + shortjournal = {Journal of Molecular Liquids}, volume = {290}, pages = {111005}, issn = {01677322}, doi = {10.1016/j.molliq.2019.111005}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0167732218364869}, urldate = {2023-06-08}, - abstract = {Ethanol is a common amphiphilic solvent often used in conjunction with water. However, despite its widespread use, key questions regarding the thickness and composition of molecules at the ethanol/water/air surface remain unclear. Recent thermodynamic analyses, Bagheri and co-authors (2016) and Santos and Reis (2018), indicated that the interfacial thickness is not constant. However, the interfacial thickness from these two analyses follows opposite trends. This study aims to provide a detailed description of the thickness and composition of the interfacial layer by combining neutron reflectivity (NR) experiments with rigorous molecular simulation. The interfacial composition was determined from molecular simulations and, in conjunction with the Gibbs excess concentration, used to calculate the interfacial thickness. It was found that the thickness decreased exponentially and reached a plateau of {\textasciitilde} 8.2 {\AA}. The results confirm the trends obtained thermodynamically from surface tension. The study also provides a new theoretical framework to describe the interfacial layer of water/alcohol mixtures.}, + abstract = {Ethanol is a common amphiphilic solvent often used in conjunction with water. However, despite its widespread use, key questions regarding the thickness and composition of molecules at the ethanol/water/air surface remain unclear. Recent thermodynamic analyses, Bagheri and co-authors (2016) and Santos and Reis (2018), indicated that the interfacial thickness is not constant. However, the interfacial thickness from these two analyses follows opposite trends. This study aims to provide a detailed description of the thickness and composition of the interfacial layer by combining neutron reflectivity (NR) experiments with rigorous molecular simulation. The interfacial composition was determined from molecular simulations and, in conjunction with the Gibbs excess concentration, used to calculate the interfacial thickness. It was found that the thickness decreased exponentially and reached a plateau of \textasciitilde{} 8.2 Å. The results confirm the trends obtained thermodynamically from surface tension. The study also provides a new theoretical framework to describe the interfacial layer of water/alcohol mixtures.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/BKXSZBZW/Hyde et al. - 2019 - Surface properties of the ethanolwater mixture T.pdf;/home/simon/Zotero/storage/GEMCN6UH/1-s2.0-S016773221935442X-main.pdf;/home/simon/Zotero/storage/Y5LXPJM8/S0167732218364869.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BKXSZBZW/Hyde et al. - 2019 - Surface properties of the ethanolwater mixture T.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/GEMCN6UH/1-s2.0-S016773221935442X-main.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/Y5LXPJM8/S0167732218364869.html} } @article{jacobsonProtonMagneticResonance1954, title = {A {{Proton Magnetic Resonance Study}} of the {{Hydration}} of {{Deoxyribonucleic Acid}}}, author = {Jacobson, Bertil and Anderson, Weston A. and Arnold, James T.}, - year = {1954}, - month = apr, - journal = {Nature}, + date = {1954-04}, + journaltitle = {Nature}, volume = {173}, number = {4408}, pages = {772--773}, publisher = {{Nature Publishing Group}}, issn = {1476-4687}, doi = {10.1038/173772a0}, + url = {https://www.nature.com/articles/173772a0}, urldate = {2023-07-09}, abstract = {DILUTE solutions of deoxyribonucleic acid have high viscosity, very large increment of dielectric constant and high osmotic pressure. It has been suggested that these properties result from the formation of large hydration shells with a higher degree of lattice order than that prevailing in pure water1. In order to investigate these phenomena further, we have studied proton magnetic resonances of some deoxyribonucleic acid solutions and gels.}, - copyright = {1954 Springer Nature Limited}, + issue = {4408}, langid = {english}, keywords = {bio,NMR}, - file = {/home/simon/Zotero/storage/B74ULAHH/Jacobson et al. - 1954 - A Proton Magnetic Resonance Study of the Hydration.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/B74ULAHH/Jacobson et al. - 1954 - A Proton Magnetic Resonance Study of the Hydration.pdf} } @article{jaffelProbingMicrostructureEvolution2006, title = {Probing {{Microstructure Evolution}} during the {{Hardening}} of {{Gypsum}} by {{Proton NMR Relaxometry}}}, - author = {Jaffel, Hamouda and Korb, Jean-Pierre and {Ndobo-Epoy}, Jean-Philippe and Morin, Vincent and Guicquero, Jean-Pierre}, - year = {2006}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + author = {Jaffel, Hamouda and Korb, Jean-Pierre and Ndobo-Epoy, Jean-Philippe and Morin, Vincent and Guicquero, Jean-Pierre}, + date = {2006-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {110}, number = {14}, pages = {7385--7391}, publisher = {{American Chemical Society}}, issn = {1520-6106}, doi = {10.1021/jp058276m}, + url = {https://doi.org/10.1021/jp058276m}, urldate = {2023-09-30}, - abstract = {We report a comprehensive proton NMR relaxation study of the water confined in the evolving porous structure of hardened gypsum prepared with different water-to-plaster ratios (w/p) and increasing additions of crushed gypsum. This study gives some new information on the microstructure, the water distribution, and the hydration kinetics without any drying or perturbing preparation. The bi-exponential transverse magnetization decay reveals the existence of two water populations in slow exchange. However, the different behaviors of these populations during saturation and desaturation experiments show evidence of a fast exchange of each population with the surface. Two modes of organization of the microstructure of this material are identified through an original model of exchange as a function of the water-to-plaster ratio (0.4 {$\leq$} w/p {$\leq$} 0.6 and 0.7 {$\leq$} w/p {$\leq$} 1). A clear gap is shown in the exchange rate value above w/p = 0.6 that could be representative of a percolation threshold. Both the method and the theory presented can be applied more widely to other porous media with reactive surface areas.}, - file = {/home/simon/Zotero/storage/3XKHSW6C/Jaffel et al. - 2006 - Probing Microstructure Evolution during the Harden.pdf;/home/simon/Zotero/storage/AJDYU6CX/jp058276m.html} + abstract = {We report a comprehensive proton NMR relaxation study of the water confined in the evolving porous structure of hardened gypsum prepared with different water-to-plaster ratios (w/p) and increasing additions of crushed gypsum. This study gives some new information on the microstructure, the water distribution, and the hydration kinetics without any drying or perturbing preparation. The bi-exponential transverse magnetization decay reveals the existence of two water populations in slow exchange. However, the different behaviors of these populations during saturation and desaturation experiments show evidence of a fast exchange of each population with the surface. Two modes of organization of the microstructure of this material are identified through an original model of exchange as a function of the water-to-plaster ratio (0.4 ≤ w/p ≤ 0.6 and 0.7 ≤ w/p ≤ 1). A clear gap is shown in the exchange rate value above w/p = 0.6 that could be representative of a percolation threshold. Both the method and the theory presented can be applied more widely to other porous media with reactive surface areas.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3XKHSW6C/Jaffel et al. - 2006 - Probing Microstructure Evolution during the Harden.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/AJDYU6CX/jp058276m.html} +} + +@article{jorgensenComparisonSimplePotential1983, + title = {Comparison of Simple Potential Functions for Simulating Liquid Water}, + author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.}, + date = {1983-07-15}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, + volume = {79}, + number = {2}, + pages = {926--935}, + issn = {0021-9606}, + doi = {10.1063/1.445869}, + url = {https://doi.org/10.1063/1.445869}, + urldate = {2024-01-08}, + abstract = {Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25\,°C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18\% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6PKDUEUI/Jorgensen et al. - 1983 - Comparison of simple potential functions for simul.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/Q4I69697/Comparison-of-simple-potential-functions-for.html} } @article{jorgensenDevelopmentTestingOPLS1996, title = {Development and {{Testing}} of the {{OPLS All-Atom Force Field}} on {{Conformational Energetics}} and {{Properties}} of {{Organic Liquids}}}, - author = {Jorgensen, William L. and Maxwell, David S. and {Tirado-Rives}, Julian}, - year = {1996}, - month = nov, - journal = {Journal of the American Chemical Society}, + author = {Jorgensen, William L. and Maxwell, David S. and Tirado-Rives, Julian}, + date = {1996-11-13}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, volume = {118}, number = {45}, pages = {11225--11236}, issn = {0002-7863, 1520-5126}, doi = {10.1021/ja9621760}, + url = {https://pubs.acs.org/doi/10.1021/ja9621760}, urldate = {2023-06-21}, abstract = {The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Average errors in comparison with experimental data are 2\% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermolecular degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liquids.}, langid = {english}, keywords = {ff}, - file = {/home/simon/Zotero/storage/2MXJ2RVY/Jorgensen et al. - 1996 - Development and Testing of the OPLS All-Atom Force.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2MXJ2RVY/Jorgensen et al. - 1996 - Development and Testing of the OPLS All-Atom Force.pdf} } @article{kamalAlignmentFlexiblePlatelike2021, title = {Alignment of a Flexible Platelike Particle in Shear Flow: {{Effect}} of Surface Slip and Edges}, shorttitle = {Alignment of a Flexible Platelike Particle in Shear Flow}, author = {Kamal, Catherine and Gravelle, Simon and Botto, Lorenzo}, - year = {2021}, - month = aug, - journal = {Physical Review Fluids}, + date = {2021-08-18}, + journaltitle = {Physical Review Fluids}, + shortjournal = {Phys. Rev. Fluids}, volume = {6}, number = {8}, pages = {084102}, issn = {2469-990X}, doi = {10.1103/PhysRevFluids.6.084102}, + url = {https://link.aps.org/doi/10.1103/PhysRevFluids.6.084102}, urldate = {2023-05-22}, langid = {english}, - file = {/home/simon/Zotero/storage/XKRDSQM7/Kamal et al. - 2021 - Alignment of a flexible platelike particle in shea.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/XKRDSQM7/Kamal et al. - 2021 - Alignment of a flexible platelike particle in shea.pdf} } @article{kargerDiffusionNanoporousMaterials2016, title = {Diffusion in Nanoporous Materials: Fundamental Principles, Insights and Challenges}, shorttitle = {Diffusion in Nanoporous Materials}, - author = {K{\"a}rger, J{\"o}rg and M.~Ruthven, Douglas}, - year = {2016}, - journal = {New Journal of Chemistry}, + author = {Kärger, Jörg and M.~Ruthven, Douglas}, + date = {2016}, + journaltitle = {New Journal of Chemistry}, volume = {40}, number = {5}, pages = {4027--4048}, publisher = {{Royal Society of Chemistry}}, doi = {10.1039/C5NJ02836A}, + url = {https://pubs.rsc.org/en/content/articlelanding/2016/nj/c5nj02836a}, urldate = {2023-09-30}, langid = {english}, - file = {/home/simon/Zotero/storage/FJ2G2IUJ/Kärger and M. Ruthven - 2016 - Diffusion in nanoporous materials fundamental pri.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/FJ2G2IUJ/Kärger and M. Ruthven - 2016 - Diffusion in nanoporous materials fundamental pri.pdf} } @article{karlickyInterplayEthanolAdsorption2015, title = {Interplay between {{Ethanol Adsorption}} to {{High-Energy Sites}} and {{Clustering}} on {{Graphene}} and {{Graphite Alters}} the {{Measured Isosteric Adsorption Enthalpies}}}, - author = {Karlick{\'y}, Franti{\v s}ek and Otyepkov{\'a}, Eva and Ban{\'a}{\v s}, Pavel and Lazar, Petr and Kocman, Mikul{\'a}{\v s} and Otyepka, Michal}, - year = {2015}, - month = sep, - journal = {The Journal of Physical Chemistry C}, + author = {Karlický, František and Otyepková, Eva and Banáš, Pavel and Lazar, Petr and Kocman, Mikuláš and Otyepka, Michal}, + date = {2015-09-03}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {119}, number = {35}, pages = {20535--20543}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.5b06755}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.5b06755}, urldate = {2023-07-19}, - abstract = {We present a combined experimental and theoretical study aimed at understanding the behavior of polar probe ethanol on graphene and graphite hydrophobic surfaces. We measured isosteric adsorption enthalpies and entropies by inverse gas chromatography for coverages ranging from 0.1 to 20\%. The adsorption enthalpies were found to vary with surface coverage and differed considerably between the materials at low coverage. However, they approached the same adsorption enthalpy value of -12.0 {$\pm$} 0.4 kcal/mol for T centered at 303-393 K and coverages above 5\%. We explained the observed behavior using molecular dynamics simulations by employing empirical force-field and density functional theory calculations on two graphene models: circumcoronene and infinite graphene. The simulations showed that various hydrogen-bonded ethanol clusters formed spontaneously from isolated ethanol molecules on graphene and provided a distribution of cluster sizes. Nonlocal density functional theory was used to calculate adsorption enthalpies for various sizes of ethanol clusters. A theoretical adsorption enthalpy of -11.6 kcal/mol at 340 K was obtained from the weighted average of the cluster size distribution, while the adsorption enthalpy of single ethanol molecule to graphene was -6.3 kcal/mol at 323 K.}, + abstract = {We present a combined experimental and theoretical study aimed at understanding the behavior of polar probe ethanol on graphene and graphite hydrophobic surfaces. We measured isosteric adsorption enthalpies and entropies by inverse gas chromatography for coverages ranging from 0.1 to 20\%. The adsorption enthalpies were found to vary with surface coverage and differed considerably between the materials at low coverage. However, they approached the same adsorption enthalpy value of −12.0 ± 0.4 kcal/mol for T centered at 303−393 K and coverages above 5\%. We explained the observed behavior using molecular dynamics simulations by employing empirical force-field and density functional theory calculations on two graphene models: circumcoronene and infinite graphene. The simulations showed that various hydrogen-bonded ethanol clusters formed spontaneously from isolated ethanol molecules on graphene and provided a distribution of cluster sizes. Nonlocal density functional theory was used to calculate adsorption enthalpies for various sizes of ethanol clusters. A theoretical adsorption enthalpy of −11.6 kcal/mol at 340 K was obtained from the weighted average of the cluster size distribution, while the adsorption enthalpy of single ethanol molecule to graphene was −6.3 kcal/mol at 323 K.}, langid = {english}, keywords = {heat}, - file = {/home/simon/Zotero/storage/QMHGYP7U/Karlický et al. - 2015 - Interplay between Ethanol Adsorption to High-Energ.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QMHGYP7U/Karlický et al. - 2015 - Interplay between Ethanol Adsorption to High-Energ.pdf} } @article{karnesUnusualStructureDynamics2016, - title = {Unusual {{Structure}} and {{Dynamics}} at {{Silica}}/{{Methanol}} and {{Silica}}/{{Ethanol Interfaces}}{\textemdash}{{A Molecular Dynamics}} and {{Nonlinear Optical Study}}}, + title = {Unusual {{Structure}} and {{Dynamics}} at {{Silica}}/{{Methanol}} and {{Silica}}/{{Ethanol Interfaces}}—{{A Molecular Dynamics}} and {{Nonlinear Optical Study}}}, author = {Karnes, John J. and Gobrogge, Eric A. and Walker, Robert A. and Benjamin, Ilan}, - year = {2016}, - month = mar, - journal = {The Journal of Physical Chemistry B}, + date = {2016-03-03}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {120}, number = {8}, pages = {1569--1578}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.5b07777}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.5b07777}, urldate = {2023-07-18}, - abstract = {Vibrational sum frequency (VSF) spectroscopy and molecular dynamics simulations are used to investigate ethanol-silica and methanol-silica interfaces. We describe the subtle differences in molecular organization that result in the observed differences in the VSF spectra for methanol and ethanol at the alcohol-silica interface. Alcohol molecules hydrogen-bonded to the silica surface induce orientational opposition in an adjacent low-population region, which implies VSF signal reduction. This low population region is essentially of zero density in the ethanol system, implying less signal cancelation. Simulated silica defect sites increase the population of this region in both systems. Interestingly, the induced orientation in this region influences subsequent molecular orientation only in the ethanol-silica system, preserving the interfacial anisotropy. These effects suggest a stronger VSF response from the ethanol-silica system versus the methanol-silica system, where more methanol molecules reside in the low-population region, and this region does not induce order in subsequent solvent layers.}, + abstract = {Vibrational sum frequency (VSF) spectroscopy and molecular dynamics simulations are used to investigate ethanol−silica and methanol−silica interfaces. We describe the subtle differences in molecular organization that result in the observed differences in the VSF spectra for methanol and ethanol at the alcohol−silica interface. Alcohol molecules hydrogen-bonded to the silica surface induce orientational opposition in an adjacent low-population region, which implies VSF signal reduction. This low population region is essentially of zero density in the ethanol system, implying less signal cancelation. Simulated silica defect sites increase the population of this region in both systems. Interestingly, the induced orientation in this region influences subsequent molecular orientation only in the ethanol−silica system, preserving the interfacial anisotropy. These effects suggest a stronger VSF response from the ethanol−silica system versus the methanol−silica system, where more methanol molecules reside in the low-population region, and this region does not induce order in subsequent solvent layers.}, langid = {english}, keywords = {MD,spectro}, - file = {/home/simon/Zotero/storage/VBMFMYKU/Karnes et al. - 2016 - Unusual Structure and Dynamics at SilicaMethanol .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VBMFMYKU/Karnes et al. - 2016 - Unusual Structure and Dynamics at SilicaMethanol .pdf} } @article{kashefolghetaEvaluationNineCondensedphase2021, title = {Evaluation of Nine Condensed-Phase Force Fields of the {{GROMOS}}, {{CHARMM}}, {{OPLS}}, {{AMBER}}, and {{OpenFF}} Families against Experimental Cross-Solvation Free Energies}, - author = {Kashefolgheta, Sadra and Wang, Shuzhe and Acree, William E. and H{\"u}nenberger, Philippe H.}, - year = {2021}, - journal = {Physical Chemistry Chemical Physics}, + author = {Kashefolgheta, Sadra and Wang, Shuzhe and Acree, William E. and Hünenberger, Philippe H.}, + date = {2021}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {23}, number = {23}, pages = {13055--13074}, issn = {1463-9076, 1463-9084}, doi = {10.1039/D1CP00215E}, + url = {http://xlink.rsc.org/?DOI=D1CP00215E}, urldate = {2023-05-26}, - abstract = {Nine force fields are compared in their abilities to reproduce the experimental cross-solvation matrix of 25 molecules. , Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al. , J. Chem. Theory. Comput ., 2020, 16 , 7556{\textendash}7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N {\texttimes} N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 {\texttimes} 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol -1 , and average errors (AVEEs) from -1.5 to +1.0 kJ mol -1 . In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol -1 ), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol -1 ), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol -1 ). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.}, + abstract = {Nine force fields are compared in their abilities to reproduce the experimental cross-solvation matrix of 25 molecules. , Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al. , J. Chem. Theory. Comput ., 2020, 16 , 7556–7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N × N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 × 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol −1 , and average errors (AVEEs) from −1.5 to +1.0 kJ mol −1 . In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol −1 ), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol −1 ), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol −1 ). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.}, langid = {english}, keywords = {ff,MD}, - file = {/home/simon/Zotero/storage/P464WJPW/Kashefolgheta et al. - 2021 - Evaluation of nine condensed-phase force fields of.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/P464WJPW/Kashefolgheta et al. - 2021 - Evaluation of nine condensed-phase force fields of.pdf} } @article{kholmurodovMolecularDynamicsSimulation2011, title = {Molecular Dynamics Simulation of the Interaction of Ethanol-Water Mixture with a {{Pt}} Surface}, author = {Kholmurodov, Kholmirzo and Dushanov, Ermuhammad and Yasuoka, Kenji and Khalil, Hagar and Galal, Ahmed and Ahmed, Sameh and Sweilam, Nasser and Moharram, Hatem}, - year = {2011}, - journal = {Natural Science}, + date = {2011}, + journaltitle = {Natural Science}, + shortjournal = {Nat. sci.}, volume = {03}, number = {12}, pages = {1011--1021}, issn = {2150-4091, 2150-4105}, doi = {10.4236/ns.2011.312126}, + url = {http://www.scirp.org/journal/doi.aspx?DOI=10.4236/ns.2011.312126}, urldate = {2023-07-18}, - abstract = {An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL\_POLY\_2.19 code. The structure and diffusion properties of an ethanol{\textendash}water system have been studied at various temperatures from 250 to 600 K. We have measured the self-diffusion coefficients of the 50:50\% ethanol-water solution; in the absence of a Pt surface our results show an excellent agreement{\textemdash}within an error of 7.4\%{\textemdash}with the experimental data. An increase in the self-diffusion coefficients with the inclusion of a Pt surface has been observed. The estimation of the diffusion coefficients of both water and ethanol in the presence of a Pt surface shows that they obey the Arrhenius equation; the calculated activation energies of diffusion of ethanol and water are 2.47 and 2.98 Kcal/mole, respectively. The radial distribution function graphs and density profiles have been built; their correlations with the self-diffusion coefficients of both ethanol and water molecules are also illustrated.}, + abstract = {An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL\_POLY\_2.19 code. The structure and diffusion properties of an ethanol–water system have been studied at various temperatures from 250 to 600 K. We have measured the self-diffusion coefficients of the 50:50\% ethanol-water solution; in the absence of a Pt surface our results show an excellent agreement—within an error of 7.4\%—with the experimental data. An increase in the self-diffusion coefficients with the inclusion of a Pt surface has been observed. The estimation of the diffusion coefficients of both water and ethanol in the presence of a Pt surface shows that they obey the Arrhenius equation; the calculated activation energies of diffusion of ethanol and water are 2.47 and 2.98 Kcal/mole, respectively. The radial distribution function graphs and density profiles have been built; their correlations with the self-diffusion coefficients of both ethanol and water molecules are also illustrated.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/6BHMLE5C/Kholmurodov et al. - 2011 - Molecular dynamics simulation of the interaction o.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6BHMLE5C/Kholmurodov et al. - 2011 - Molecular dynamics simulation of the interaction o.pdf} } @article{khudozhitkovDynamicsPropenePropane2020, title = {Dynamics of Propene and Propane in {{ZIF-8}} Probed by Solid-State {\textsuperscript{2}} {{H NMR}}}, author = {Khudozhitkov, Alexander E. and Arzumanov, Sergei S. and Kolokolov, Daniil I. and Freude, Dieter and Stepanov, Alexander G.}, - year = {2020}, - journal = {Physical Chemistry Chemical Physics}, + date = {2020}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {22}, number = {10}, pages = {5976--5984}, issn = {1463-9076, 1463-9084}, doi = {10.1039/D0CP00270D}, + url = {http://xlink.rsc.org/?DOI=D0CP00270D}, urldate = {2023-05-26}, - abstract = {On the basis of 2 H NMR spin relaxation analysis, the motional mechanism for propene and propane within a ZIF-8 framework is elucidated and microscopic translational diffusion characteristics for these hydrocarbons have been estimated. , We present a detailed 2 H NMR characterization of molecular mobility of propene and propane propagating though the microporous ZIF-8, a zeolitic imidazolate framework renowned for its outstandingly high separation selectivity for industrially relevant propene/propane mixtures. Experimental characterization of both propene and propane diffusivity in ZIF-8 has been provided. Using 2 H NMR spin relaxation analysis, the motional mechanisms for propene and propane guests trapped within the ZIF-8 framework have been elucidated. Kinetic parameters for each type of motion were derived. The characteristic times for microscopic translational diffusion and activation barriers ( E C3H8 = 38 kJ mol -1 , E C3H6 = 13.5 kJ mol -1 ) for propane and propene diffusivities have been estimated. A notable difference in the observed activation barriers emphasizes that the ZIF-8 window crossing is associated with the ``gate-opening'' and represents an extremely shape selective process. Finally, we show that the 2 H NMR technique is capable of providing reliable information on microscopic diffusivity in the ZIF-8 MOF even for molecules with slow diffusivity ({$<$}10 -14 m 2 s -1 ).}, + abstract = {On the basis of 2 H NMR spin relaxation analysis, the motional mechanism for propene and propane within a ZIF-8 framework is elucidated and microscopic translational diffusion characteristics for these hydrocarbons have been estimated. , We present a detailed 2 H NMR characterization of molecular mobility of propene and propane propagating though the microporous ZIF-8, a zeolitic imidazolate framework renowned for its outstandingly high separation selectivity for industrially relevant propene/propane mixtures. Experimental characterization of both propene and propane diffusivity in ZIF-8 has been provided. Using 2 H NMR spin relaxation analysis, the motional mechanisms for propene and propane guests trapped within the ZIF-8 framework have been elucidated. Kinetic parameters for each type of motion were derived. The characteristic times for microscopic translational diffusion and activation barriers ( E C3H8 = 38 kJ mol −1 , E C3H6 = 13.5 kJ mol −1 ) for propane and propene diffusivities have been estimated. A notable difference in the observed activation barriers emphasizes that the ZIF-8 window crossing is associated with the “gate-opening” and represents an extremely shape selective process. Finally, we show that the 2 H NMR technique is capable of providing reliable information on microscopic diffusivity in the ZIF-8 MOF even for molecules with slow diffusivity ({$<$}10 −14 m 2 s −1 ).}, langid = {english}, keywords = {ff,NMR,propane}, - file = {/home/simon/Zotero/storage/B867BR32/Khudozhitkov et al. - 2020 - Dynamics of propene and propane in ZIF-8 probed by.pdf;/home/simon/Zotero/storage/MB68ZAPC/d0cp00270d.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/B867BR32/Khudozhitkov et al. - 2020 - Dynamics of propene and propane in ZIF-8 probed by.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/MB68ZAPC/d0cp00270d.pdf} } @article{klaudaCHARMMForceField2008, title = {{{CHARMM Force Field Parameters}} for {{Nitroalkanes}} and {{Nitroarenes}}}, author = {Klauda, Jeffery B. and Brooks, Bernard R.}, - year = {2008}, - month = jan, - journal = {Journal of Chemical Theory and Computation}, + date = {2008-01-01}, + journaltitle = {Journal of Chemical Theory and Computation}, + shortjournal = {J. Chem. Theory Comput.}, volume = {4}, number = {1}, pages = {107--115}, issn = {1549-9618, 1549-9626}, doi = {10.1021/ct700191v}, + url = {https://pubs.acs.org/doi/10.1021/ct700191v}, urldate = {2023-05-30}, abstract = {New CHARMM force field (FF) parameters are developed for nitro compounds, referred to here as C27rn, for subsequent use in molecular dynamics (MD) simulations. The nonbonded terms are adjusted to best fit densities and hydration energies of nitropropane and nitrobenzene. High-level quantum mechanical calculations are used to obtain accurate conformational energies of nitroalkanes and nitrobenzene and to adjust the torsional potential of the CHARMM FF. For nitroalkanes, the calculated gauche (g) conformer of the C-C-C-N torsion is more stable than trans (t). Consequently, nitropropane MD simulations with C27rn result in 74\% population of this g conformer. The C27rn FF is in excellent agreement with experiment for various bulk (density, isothermal compressibility, and heat of vaporization) and interfacial (surface tension) properties of nitropropane, nitrobutane, and nitrobenzene. MD simulations with the OPLS-AA FF for nitropropane and nitrobenzene result in similar property predictions as C27rn, except a reduced stability of the C-C-C-N g conformer.}, langid = {english}, keywords = {ff,propane}, - file = {/home/simon/Zotero/storage/KXW9HRZA/Klauda and Brooks - 2008 - CHARMM Force Field Parameters for Nitroalkanes and.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/KXW9HRZA/Klauda and Brooks - 2008 - CHARMM Force Field Parameters for Nitroalkanes and.pdf} } @article{klippensteinIntroducingMemoryCoarseGrained2021, title = {Introducing {{Memory}} in {{Coarse-Grained Molecular Simulations}}}, - author = {Klippenstein, Viktor and Tripathy, Madhusmita and Jung, Gerhard and Schmid, Friederike and {van der Vegt}, Nico F. A.}, - year = {2021}, - month = may, - journal = {The Journal of Physical Chemistry B}, + author = {Klippenstein, Viktor and Tripathy, Madhusmita and Jung, Gerhard and Schmid, Friederike and family=Vegt, given=Nico F. A., prefix=van der, useprefix=true}, + date = {2021-05-20}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {125}, number = {19}, pages = {4931--4954}, publisher = {{American Chemical Society}}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.1c01120}, + url = {https://doi.org/10.1021/acs.jpcb.1c01120}, urldate = {2024-01-05}, - abstract = {Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori{\textendash}Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In this Review, we describe some of the recent studies in this regard. We focus on the construction and simulation of dynamically consistent systematic CG models based on the GLE, both in the simple Markovian limit and the non-Markovian case. Some recent studies of physical effects of memory are also discussed. The Review is aimed at summarizing recent developments in the field while highlighting the major challenges and possible future directions.}, - file = {/home/simon/Zotero/storage/P5Z93LLU/Klippenstein et al. - 2021 - Introducing Memory in Coarse-Grained Molecular Sim.pdf} + abstract = {Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori–Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In this Review, we describe some of the recent studies in this regard. We focus on the construction and simulation of dynamically consistent systematic CG models based on the GLE, both in the simple Markovian limit and the non-Markovian case. Some recent studies of physical effects of memory are also discussed. The Review is aimed at summarizing recent developments in the field while highlighting the major challenges and possible future directions.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/P5Z93LLU/Klippenstein et al. - 2021 - Introducing Memory in Coarse-Grained Molecular Sim.pdf} } @article{kommuSeparationEthanolWater2017, title = {Separation of {{Ethanol}} and {{Water Using Graphene}} and {{Hexagonal Boron Nitride Slit Pores}}: {{A Molecular Dynamics Study}}}, shorttitle = {Separation of {{Ethanol}} and {{Water Using Graphene}} and {{Hexagonal Boron Nitride Slit Pores}}}, author = {Kommu, Anitha and Singh, Jayant K.}, - year = {2017}, - month = apr, - journal = {The Journal of Physical Chemistry C}, + date = {2017-04-13}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {121}, number = {14}, pages = {7867--7880}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.7b00172}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.7b00172}, urldate = {2023-06-09}, - abstract = {The industries discharge a variety of pollutants, such as heavy metals, organic toxins, and oils, in water resources. Exposure of these contaminants in water causes adverse health effects on various forms of life. Novel materials are needed for the effective removal of pollutants from industrial wastewater. Graphene and hexagonal boron nitride (hBN) sheets are promising materials for removal of organic pollutants. In this work, the suitability of the sheets for the separation of the ethanol-water mixture is investigated by studying the adsorption and structural behavior of ethanol-water mixtures in slit pores with variable width (7-13 {\AA}) using molecular dynamics simulations. The selectivity of ethanol is found to depend on the pore-width and nature of the pore walls. The selectivity of ethanol is highest for 9 {\AA} pores and lowest for 7 {\AA} pores, irrespective of the nature of the pore walls. However, selectivity of ethanol is relatively higher for hBN pores compared to the graphene pores, for all the considered pore widths. At a lower pore width, molecular sieving plays an important role for selective adsorption of ethanol molecules. On the other hand, at a higher pore width, selective adsorption of ethanol molecules is affected by the nature of the pore walls. The diffusion coefficients of water and ethanol molecules substantially decrease with a decrease in pore width for both graphene and hBN surfaces. The resident time of water and ethanol molecules decreases with increase in the slit-width. Furthermore, water and ethanol molecules confined in hBN pores show higher residence time and lower diffusion coefficient values compared to graphene pores. The adsorption behavior of water and ethanol molecules in the slit pores are analyzed using the potential mean forces, for water and ethanol molecules on the graphene and hBN surfaces, which are determined by umbrella sampling technique.}, + abstract = {The industries discharge a variety of pollutants, such as heavy metals, organic toxins, and oils, in water resources. Exposure of these contaminants in water causes adverse health effects on various forms of life. Novel materials are needed for the effective removal of pollutants from industrial wastewater. Graphene and hexagonal boron nitride (hBN) sheets are promising materials for removal of organic pollutants. In this work, the suitability of the sheets for the separation of the ethanol−water mixture is investigated by studying the adsorption and structural behavior of ethanol−water mixtures in slit pores with variable width (7−13 Å) using molecular dynamics simulations. The selectivity of ethanol is found to depend on the pore-width and nature of the pore walls. The selectivity of ethanol is highest for 9 Å pores and lowest for 7 Å pores, irrespective of the nature of the pore walls. However, selectivity of ethanol is relatively higher for hBN pores compared to the graphene pores, for all the considered pore widths. At a lower pore width, molecular sieving plays an important role for selective adsorption of ethanol molecules. On the other hand, at a higher pore width, selective adsorption of ethanol molecules is affected by the nature of the pore walls. The diffusion coefficients of water and ethanol molecules substantially decrease with a decrease in pore width for both graphene and hBN surfaces. The resident time of water and ethanol molecules decreases with increase in the slit-width. Furthermore, water and ethanol molecules confined in hBN pores show higher residence time and lower diffusion coefficient values compared to graphene pores. The adsorption behavior of water and ethanol molecules in the slit pores are analyzed using the potential mean forces, for water and ethanol molecules on the graphene and hBN surfaces, which are determined by umbrella sampling technique.}, langid = {english}, keywords = {confinnement,MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/9HQVJLGL/Kommu and Singh - 2017 - Separation of Ethanol and Water Using Graphene and.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/9HQVJLGL/Kommu and Singh - 2017 - Separation of Ethanol and Water Using Graphene and.pdf} } @article{korbNuclearMagneticRelaxation2011, title = {Nuclear Magnetic Relaxation of Liquids in Porous Media}, author = {Korb, J-P}, - year = {2011}, - month = mar, - journal = {New Journal of Physics}, + date = {2011-03-22}, + journaltitle = {New Journal of Physics}, + shortjournal = {New J. Phys.}, volume = {13}, number = {3}, pages = {035016}, issn = {1367-2630}, doi = {10.1088/1367-2630/13/3/035016}, + url = {https://iopscience.iop.org/article/10.1088/1367-2630/13/3/035016}, urldate = {2023-07-14}, - abstract = {Nuclear magnetic relaxation is useful for probing physical and chemical properties of liquids in porous media. Examples are given on high surface area porous materials including calibrated porous silica glasses, granular packings, plaster pastes, cement-based materials and natural porous materials, such as sandstone and carbonate rocks. Here, we outline our recent NMR relaxation work for these very different porous materials. For instance, low field NMR relaxation of water in calibrated granular packings leads to striking different pore-size dependencies of the relaxation times T1 and T2 when changing the amount of surface paramagnetic impurities. This allows separation of the diffusion and surface limited regimes of relaxation in these macroporous media. The magnetic field dependence of the nuclear spin{\textendash}lattice relaxation rate 1/T1({$\omega$}0) is also a rich source of dynamical information for characterizing the molecular dynamics of liquids in porous media. This allows a continuous characterization of the evolving microstructure of various cementitious materials. Our recent applications of two-dimensional (2D) T1{\textendash}T2 and T2-z-store-T2 correlation experiments have evidenced the water exchange in connected micropores of cement pastes. The direct probing of water adsorption time on a solid surface gives access to an original characterization of the surface nano-wettability of porous plaster pastes. We show that such a parameter depends directly on the physical chemistry of the pore surfaces. Lastly, we outline our recent measurements of wettability in oil/brine/reservoir carbonate rocks.}, + abstract = {Nuclear magnetic relaxation is useful for probing physical and chemical properties of liquids in porous media. Examples are given on high surface area porous materials including calibrated porous silica glasses, granular packings, plaster pastes, cement-based materials and natural porous materials, such as sandstone and carbonate rocks. Here, we outline our recent NMR relaxation work for these very different porous materials. For instance, low field NMR relaxation of water in calibrated granular packings leads to striking different pore-size dependencies of the relaxation times T1 and T2 when changing the amount of surface paramagnetic impurities. This allows separation of the diffusion and surface limited regimes of relaxation in these macroporous media. The magnetic field dependence of the nuclear spin–lattice relaxation rate 1/T1(ω0) is also a rich source of dynamical information for characterizing the molecular dynamics of liquids in porous media. This allows a continuous characterization of the evolving microstructure of various cementitious materials. Our recent applications of two-dimensional (2D) T1–T2 and T2-z-store-T2 correlation experiments have evidenced the water exchange in connected micropores of cement pastes. The direct probing of water adsorption time on a solid surface gives access to an original characterization of the surface nano-wettability of porous plaster pastes. We show that such a parameter depends directly on the physical chemistry of the pore surfaces. Lastly, we outline our recent measurements of wettability in oil/brine/reservoir carbonate rocks.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/P6M2IBUW/Korb - 2011 - Nuclear magnetic relaxation of liquids in porous m.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/P6M2IBUW/Korb - 2011 - Nuclear magnetic relaxation of liquids in porous m.pdf} } @book{kowalewskiNuclearSpinRelaxation2006, title = {Nuclear Spin Relaxation in Liquids: Theory, Experiments, and Applications}, shorttitle = {Nuclear Spin Relaxation in Liquids}, - author = {Kowalewski, J{\'o}zef and M{\"a}ler, Lena}, - year = {2006}, + author = {Kowalewski, Józef and Mäler, Lena}, + date = {2006}, series = {Series in Chemical Physics}, number = {2}, publisher = {{Taylor \& Francis}}, - address = {{New York}}, + location = {{New York}}, isbn = {978-0-7503-0964-6}, langid = {english}, - lccn = {QC173.4.R44 K69 2006}, + pagetotal = {426}, keywords = {NMR}, annotation = {OCLC: ocm61694919}, - file = {/home/simon/Zotero/storage/SP9A8CLC/Kowalewski and Mäler - 2006 - Nuclear spin relaxation in liquids theory, experi.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SP9A8CLC/Kowalewski and Mäler - 2006 - Nuclear spin relaxation in liquids theory, experi.pdf} } @article{krebsProtonSpinPolarization2004, title = {Proton {{Spin Polarization}} of {{Water Adsorbed}} on {{Sucrose Chars}}}, author = {Krebs, James J.}, - year = {2004}, - month = aug, - journal = {The Journal of Chemical Physics}, + date = {2004-08-06}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {34}, number = {1}, pages = {326--329}, issn = {0021-9606}, doi = {10.1063/1.1731588}, + url = {https://doi.org/10.1063/1.1731588}, urldate = {2023-07-09}, - abstract = {By saturating forbidden electron-nuclear double transitions in paramagnetic materials, it is possible to considerably enhance the nuclear polarization in a positive or negative sense. This effect has been investigated experimentally using the protons of water adsorbed on paramagnetic charred sucrose. The dependence of the enhancement on the saturating microwave power is derived for the case of overlapping allowed and forbidden transitions, and predicts a linear change in polarization at low power levels. The general features of the enhancement found are in agreement with those predicted by perturbation theory using a simple dipole-dipole electron-nuclear interaction. However, the plot of log (polarization change) vs log (power) has a slope of 0.82{$\pm$}0.04 instead of 1.0. In addition, the field separation between the points of maximum positive and maximum negative enhancement is too small in those chars for which inhomogeneous broadening is suspected.}, + abstract = {By saturating forbidden electron‐nuclear double transitions in paramagnetic materials, it is possible to considerably enhance the nuclear polarization in a positive or negative sense. This effect has been investigated experimentally using the protons of water adsorbed on paramagnetic charred sucrose. The dependence of the enhancement on the saturating microwave power is derived for the case of overlapping allowed and forbidden transitions, and predicts a linear change in polarization at low power levels. The general features of the enhancement found are in agreement with those predicted by perturbation theory using a simple dipole‐dipole electron‐nuclear interaction. However, the plot of log (polarization change) vs log (power) has a slope of 0.82±0.04 instead of 1.0. In addition, the field separation between the points of maximum positive and maximum negative enhancement is too small in those chars for which inhomogeneous broadening is suspected.}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/WDK4NNZ9/Krebs - 2004 - Proton Spin Polarization of Water Adsorbed on Sucr.pdf;/home/simon/Zotero/storage/S8A7FEKR/Proton-Spin-Polarization-of-Water-Adsorbed-on.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WDK4NNZ9/Krebs - 2004 - Proton Spin Polarization of Water Adsorbed on Sucr.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/S8A7FEKR/Proton-Spin-Polarization-of-Water-Adsorbed-on.html} } @article{krynickiProtonSpinlatticeRelaxation1966, - title = {Proton Spin-Lattice Relaxation in Pure Water between 0{\textdegree}{{C}} and 100{\textdegree}{{C}}}, + title = {Proton Spin-Lattice Relaxation in Pure Water between 0°{{C}} and 100°{{C}}}, author = {Krynicki, K.}, - year = {1966}, - month = jan, - journal = {Physica}, + date = {1966-01-01}, + journaltitle = {Physica}, + shortjournal = {Physica}, volume = {32}, number = {1}, pages = {167--178}, issn = {0031-8914}, doi = {10.1016/0031-8914(66)90113-3}, + url = {https://www.sciencedirect.com/science/article/pii/0031891466901133}, urldate = {2024-01-05}, - abstract = {Proton spin-lattice relaxation times, T1, at 28 MHz by a recovery from saturation, are reported for very pure water between 0 and 100{\textdegree}C. Our experimental T1 values for water are the longest values which have been observed. In this temperature region the most effective spin-lattice relaxation mechanism in water is by proton dipole-dipole intra- and intermolecular interactions modulated by thermal molecular motion. Measurements for water of dielectric relaxation, X ray diffraction, self diffusion, viscosity and slow neutron inelastic scattering are used in the interpretation of the proton T1 results. The intermolecular contribution to T-11 has been determined with the aid of X ray radial distribution curves and Hubbard's correction for the off-centre proton effect. There is excellent agreement between the temperature dependence of the experimental proton spin-lattice relaxation times and the reciprocals of the dielectric relaxation times. The ratio of the dielectric relaxation time to the molecular reorientation NMR correlation time is found independent of temperature and equal to 3.7 instead of the expected value, three. This result provides an evidence for a small value of the single jump angle in the Brownian reorientation of water molecules and may be accounted for by an internal field correction factor of 0.81. This compares with the value 0.69 obtained for water from the Powles formula.}, - file = {/home/simon/Zotero/storage/L4WKSIUB/Krynicki - PROTON SPIN-LATTICE RELAXATION IN PURE WATER BETWE.pdf;/home/simon/Zotero/storage/7RGA5G9U/0031891466901133.html} + abstract = {Proton spin-lattice relaxation times, T1, at 28 MHz by a recovery from saturation, are reported for very pure water between 0 and 100°C. Our experimental T1 values for water are the longest values which have been observed. In this temperature region the most effective spin-lattice relaxation mechanism in water is by proton dipole-dipole intra- and intermolecular interactions modulated by thermal molecular motion. Measurements for water of dielectric relaxation, X ray diffraction, self diffusion, viscosity and slow neutron inelastic scattering are used in the interpretation of the proton T1 results. The intermolecular contribution to T-11 has been determined with the aid of X ray radial distribution curves and Hubbard's correction for the off-centre proton effect. There is excellent agreement between the temperature dependence of the experimental proton spin-lattice relaxation times and the reciprocals of the dielectric relaxation times. The ratio of the dielectric relaxation time to the molecular reorientation NMR correlation time is found independent of temperature and equal to 3.7 instead of the expected value, three. This result provides an evidence for a small value of the single jump angle in the Brownian reorientation of water molecules and may be accounted for by an internal field correction factor of 0.81. This compares with the value 0.69 obtained for water from the Powles formula.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/L4WKSIUB/Krynicki - PROTON SPIN-LATTICE RELAXATION IN PURE WATER BETWE.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/7RGA5G9U/0031891466901133.html} } @article{kumariMixturesAlcoholsWater2018, title = {Mixtures of {{Alcohols}} and {{Water}} Confined in {{Mesoporous Silica}}: {{A Combined Solid-State NMR}} and {{Molecular Dynamics Simulation Study}}}, shorttitle = {Mixtures of {{Alcohols}} and {{Water}} Confined in {{Mesoporous Silica}}}, - author = {Kumari, Bharti and Brodrecht, Martin and Breitzke, Hergen and Werner, Mayke and Gr{\"u}nberg, Bob and Limbach, Hans-Heinrich and Forg, Sandra and Sanjon, Elvira P. and Drossel, Barbara and Gutmann, Torsten and Buntkowsky, Gerd}, - year = {2018}, - month = aug, - journal = {The Journal of Physical Chemistry C}, + author = {Kumari, Bharti and Brodrecht, Martin and Breitzke, Hergen and Werner, Mayke and Grünberg, Bob and Limbach, Hans-Heinrich and Forg, Sandra and Sanjon, Elvira P. and Drossel, Barbara and Gutmann, Torsten and Buntkowsky, Gerd}, + date = {2018-08-30}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {122}, number = {34}, pages = {19540--19550}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.8b04745}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.8b04745}, urldate = {2023-06-09}, - abstract = {The behavior of mixtures of 1-octanol with water with different molar ratios confined inside the mesoporous silica SBA-15 was investigated by a combination of solid-state NMR spectroscopy and molecular dynamics (MD) simulations. Two-dimensional 1H-29Si FSLG-HETCOR NMR spectra revealed the orientation of 1-octanol relative to the pore walls. These arrangements are in good agreement with the preferred structures found by MD. In addition, MD simulations also shed light on molecular orientations and interactions in the pore center region, which are not resolvable by solid-state NMR.}, + abstract = {The behavior of mixtures of 1-octanol with water with different molar ratios confined inside the mesoporous silica SBA-15 was investigated by a combination of solid-state NMR spectroscopy and molecular dynamics (MD) simulations. Two-dimensional 1H−29Si FSLG-HETCOR NMR spectra revealed the orientation of 1-octanol relative to the pore walls. These arrangements are in good agreement with the preferred structures found by MD. In addition, MD simulations also shed light on molecular orientations and interactions in the pore center region, which are not resolvable by solid-state NMR.}, langid = {english}, keywords = {MD,mixture,NMR}, - file = {/home/simon/Zotero/storage/D9P32KVG/Kumari et al. - 2018 - Mixtures of Alcohols and Water confined in Mesopor.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/D9P32KVG/Kumari et al. - 2018 - Mixtures of Alcohols and Water confined in Mesopor.pdf} } @article{levitzMolecularIntermittentDynamics2013, title = {Molecular Intermittent Dynamics of Interfacial Water: Probing Adsorption and Bulk Confinement}, shorttitle = {Molecular Intermittent Dynamics of Interfacial Water}, author = {Levitz, P. and Bonnaud, P. A. and Cazade, P.-A. and Pellenq, R. J.-M. and Coasne, B.}, - year = {2013}, - journal = {Soft Matter}, + date = {2013}, + journaltitle = {Soft Matter}, + shortjournal = {Soft Matter}, volume = {9}, number = {36}, pages = {8654}, issn = {1744-683X, 1744-6848}, doi = {10.1039/c3sm51940f}, + url = {http://xlink.rsc.org/?DOI=c3sm51940f}, urldate = {2023-07-14}, langid = {english}, keywords = {confinnement,MD,NMR}, - file = {/home/simon/Zotero/storage/AMRFJ63G/Levitz et al. - 2013 - Molecular intermittent dynamics of interfacial wat.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/AMRFJ63G/Levitz et al. - 2013 - Molecular intermittent dynamics of interfacial wat.pdf} } @article{levitzProbingInterfacialDynamics2019, title = {Probing Interfacial Dynamics of Water in Confined Nanoporous Systems by {{NMRD}}}, author = {Levitz, Pierre}, - year = {2019}, - month = apr, - journal = {Molecular Physics}, + date = {2019-04-18}, + journaltitle = {Molecular Physics}, volume = {117}, number = {7-8}, pages = {952--959}, publisher = {{Taylor \& Francis}}, issn = {0026-8976}, doi = {10.1080/00268976.2018.1527960}, + url = {https://doi.org/10.1080/00268976.2018.1527960}, urldate = {2023-09-30}, - abstract = {The confined dynamics of water molecules inside a pore involves an intermittence between adsorption steps near the interface and surface diffusion and excursions in the pore network. Depending on the strength of the interaction in the layer(s) close to the surface and the dynamical confinement of the distal bulk liquid, exchange dynamics can vary significantly. The average time spent in the surface proximal region (also called the adsorption layer) between a first entry and a consecutive exit allows estimating the level of `nanowettablity' of water. As shown in several seminal works, NMRD is an efficient experimental method to follow such intermittent dynamics close to an interface. In this paper, the intermittent dynamics of a confined fluid inside nanoporous materials is discussed. Special attention is devoted to the interplay between bulk diffusion, adsorption and surface diffusion on curved pore interfaces. Considering the nano or meso length scale confinement of the pore network, an analytical model for calculating the inter-dipolar spin{\textendash}lattice relaxation dispersion curves is proposed. In the low-frequency regime (50 KHz{\textendash}100 MHz), this model is successfully compared with numerical simulations performed using a 3D-off lattice reconstruction of Vycor glass. Comparison with experimental data available in the literature is finally discussed.}, - file = {/home/simon/Zotero/storage/6H4NDLUV/Levitz - 2019 - Probing interfacial dynamics of water in confined .pdf} + abstract = {The confined dynamics of water molecules inside a pore involves an intermittence between adsorption steps near the interface and surface diffusion and excursions in the pore network. Depending on the strength of the interaction in the layer(s) close to the surface and the dynamical confinement of the distal bulk liquid, exchange dynamics can vary significantly. The average time spent in the surface proximal region (also called the adsorption layer) between a first entry and a consecutive exit allows estimating the level of ‘nanowettablity’ of water. As shown in several seminal works, NMRD is an efficient experimental method to follow such intermittent dynamics close to an interface. In this paper, the intermittent dynamics of a confined fluid inside nanoporous materials is discussed. Special attention is devoted to the interplay between bulk diffusion, adsorption and surface diffusion on curved pore interfaces. Considering the nano or meso length scale confinement of the pore network, an analytical model for calculating the inter-dipolar spin–lattice relaxation dispersion curves is proposed. In the low-frequency regime (50 KHz–100 MHz), this model is successfully compared with numerical simulations performed using a 3D-off lattice reconstruction of Vycor glass. Comparison with experimental data available in the literature is finally discussed.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6H4NDLUV/Levitz - 2019 - Probing interfacial dynamics of water in confined .pdf} } @article{levitzRandomFlightsConfining2005, title = {Random Flights in Confining Interfacial Systems}, author = {Levitz, Pierre}, - year = {2005}, - month = dec, - journal = {Journal of Physics: Condensed Matter}, + date = {2005-12-14}, + journaltitle = {Journal of Physics: Condensed Matter}, + shortjournal = {J. Phys.: Condens. Matter}, volume = {17}, number = {49}, pages = {S4059-S4074}, issn = {0953-8984, 1361-648X}, doi = {10.1088/0953-8984/17/49/004}, + url = {https://iopscience.iop.org/article/10.1088/0953-8984/17/49/004}, urldate = {2023-09-18}, - abstract = {Porous materials, concentrated colloidal suspensions are examples of confining systems developing large specific surface and presenting a rich variety of shapes. Such an interfacial confinement strongly influences the molecular dynamics of embedded fluids and the diffusive motion of entrapped Brownian particles. An individual trajectory near the interface can be described as an alternate succession of adsorption steps and random flights in the bulk. Statistical properties of these random flights in various interfacial confining systems are needed as prerequisites in order to understand the full transport process. Related to first passage processes, these properties play a central role in numerous problems such as the mean first exit time in a bounded domain, heterogeneous catalytic reactivity and nuclear magnetic relaxation in complex and biological fluids. In the present work, we first consider the various possibilities of connecting two points of a smooth interface by a random flight in the bulk. Second, we analyse from the theoretical and experimental points of view a way to probe Brownian flight statistics. From the experimental point of view, we investigate the slow fluid dynamics near some colloidal interfaces by field-cycling NMR relaxometry. This is a way to follow slow dynamical correlations from 1 ns to 10 {\textmu}s. This spectroscopy appears to be a good choice, considering that the algebraic nature of the probability of the first return to a surface builds a long-time memory. The experimental part confirms that the embedded fluid dynamics is sensitive to possible morphologic crossover and provides information about interface geometry. We also believe that such an approach can be used to probe interfacial dynamics by itself, for example in the case of a colloidal system undergoing a phase transition (dynamical arrest, rotational blockage, . . .).}, + abstract = {Porous materials, concentrated colloidal suspensions are examples of confining systems developing large specific surface and presenting a rich variety of shapes. Such an interfacial confinement strongly influences the molecular dynamics of embedded fluids and the diffusive motion of entrapped Brownian particles. An individual trajectory near the interface can be described as an alternate succession of adsorption steps and random flights in the bulk. Statistical properties of these random flights in various interfacial confining systems are needed as prerequisites in order to understand the full transport process. Related to first passage processes, these properties play a central role in numerous problems such as the mean first exit time in a bounded domain, heterogeneous catalytic reactivity and nuclear magnetic relaxation in complex and biological fluids. In the present work, we first consider the various possibilities of connecting two points of a smooth interface by a random flight in the bulk. Second, we analyse from the theoretical and experimental points of view a way to probe Brownian flight statistics. From the experimental point of view, we investigate the slow fluid dynamics near some colloidal interfaces by field-cycling NMR relaxometry. This is a way to follow slow dynamical correlations from 1 ns to 10 µs. This spectroscopy appears to be a good choice, considering that the algebraic nature of the probability of the first return to a surface builds a long-time memory. The experimental part confirms that the embedded fluid dynamics is sensitive to possible morphologic crossover and provides information about interface geometry. We also believe that such an approach can be used to probe interfacial dynamics by itself, for example in the case of a colloidal system undergoing a phase transition (dynamical arrest, rotational blockage, . . .).}, langid = {english}, - file = {/home/simon/Zotero/storage/7FVUM6UE/Levitz - 2005 - Random flights in confining interfacial systems.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7FVUM6UE/Levitz - 2005 - Random flights in confining interfacial systems.pdf} } @article{levitzSlowDynamicsEmbedded2003, title = {Slow Dynamics of Embedded Fluid in Mesoscopic Confining Systems as Probed by {{NMR}} Relaxometry}, author = {Levitz, P. and Korb, J. P. and Petit, D.}, - year = {2003}, - month = sep, - journal = {The European Physical Journal E}, + date = {2003-09}, + journaltitle = {The European Physical Journal E}, + shortjournal = {Eur. Phys. J. E}, volume = {12}, number = {1}, pages = {29--33}, issn = {1292-8941, 1292-895X}, doi = {10.1140/epje/i2003-10046-2}, + url = {http://link.springer.com/10.1140/epje/i2003-10046-2}, urldate = {2023-09-18}, abstract = {Mesoscopic media such as porous materials or colloidal dispersions strongly influence the dynamics of the embedded fluid. In the strong-adsorption regime, it was recently proposed that the effective surface diffusion on flat surface is anomalous and exhibits long-time pathology, enlarging the time domain of the embedded-fluid dynamics towards the low-frequency regime. An interesting way to probe such a slow interfacial process is to use the field-cycling NMR relaxometry. This technique is used here to probe the fluid dynamics in two types of interfacial systems: i) a colloidal glass made of thin and flat particles; ii) a fully saturated porous media, the Vycor glass. Experimental results are critically compared to either a simple theoretical model of NMR dispersion involving elementary steps of the fluid dynamics near an interface (loops, trains, tails) or Brownian-dynamics simulations performed inside 3D reconstructions of these confined systems.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/GSPN64QM/Levitz et al. - 2003 - Slow dynamics of embedded fluid in mesoscopic conf.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/GSPN64QM/Levitz et al. - 2003 - Slow dynamics of embedded fluid in mesoscopic conf.pdf} +} + +@article{liBackmappingCoarsegrainedMacromolecules2020, + title = {Backmapping Coarse-Grained Macromolecules: {{An}} Efficient and Versatile Machine Learning Approach}, + shorttitle = {Backmapping Coarse-Grained Macromolecules}, + author = {Li, Wei and Burkhart, Craig and Polińska, Patrycja and Harmandaris, Vagelis and Doxastakis, Manolis}, + date = {2020-07-27}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, + volume = {153}, + number = {4}, + pages = {041101}, + issn = {0021-9606}, + doi = {10.1063/5.0012320}, + url = {https://doi.org/10.1063/5.0012320}, + urldate = {2024-01-06}, + abstract = {Multiscale modeling of polymers exchanges information between coarse and fine representations of molecules to capture material properties over a wide range of spatial and temporal scales. Restoring details at a finer scale requires us to generate information following embedded physics and statistics of the models at two different levels of description. Techniques designed to address this persistent challenge balance among accuracy, efficiency, and general applicability. In this work, we present an image-based approach for structural backmapping from coarse-grained to atomistic models with cis-1,4 polyisoprene melts as an illustrative example. Through machine learning, we train conditional generative adversarial networks on the correspondence between configurations at the levels considered. The trained model is subsequently applied to provide predictions of atomistic structures from the input coarse-grained configurations. The effect of different data representation schemes on training and prediction quality is examined. Our proposed backmapping approach shows remarkable efficiency and transferability over different molecular weights in the melt based on training sets constructed from oligomeric compounds. We anticipate that this versatile backmapping approach can be readily extended to other complex systems to provide high-fidelity initial configurations with minimal human intervention.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/LC8QMIRN/Li et al. - 2020 - Backmapping coarse-grained macromolecules An effi.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/V67PRVIY/SI_backmapping_r.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/9HBQZ4XD/Backmapping-coarse-grained-macromolecules-An.html} } @article{lieseHydrationEffectsTurn2017, title = {Hydration {{Effects Turn}} a {{Highly Stretched Polymer}} from an {{Entropic}} into an {{Energetic Spring}}}, - author = {Liese, Susanne and Gensler, Manuel and Krysiak, Stefanie and Schwarzl, Richard and Achazi, Andreas and Paulus, Beate and Hugel, Thorsten and Rabe, J{\"u}rgen P. and Netz, Roland R.}, - year = {2017}, - month = jan, - journal = {ACS Nano}, + author = {Liese, Susanne and Gensler, Manuel and Krysiak, Stefanie and Schwarzl, Richard and Achazi, Andreas and Paulus, Beate and Hugel, Thorsten and Rabe, Jürgen P. and Netz, Roland R.}, + date = {2017-01-24}, + journaltitle = {ACS Nano}, + shortjournal = {ACS Nano}, volume = {11}, number = {1}, pages = {702--712}, issn = {1936-0851, 1936-086X}, doi = {10.1021/acsnano.6b07071}, + url = {https://pubs.acs.org/doi/10.1021/acsnano.6b07071}, urldate = {2023-04-27}, - abstract = {Polyethylene glycol (PEG) is a structurally simple and nontoxic water-soluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG's elastic response against conformational deformations is key to its function. According to text-book knowledge, a polymer reacts to the stretching of its end-to-end separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of single-molecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretching-induced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom.}, + abstract = {Polyethylene glycol (PEG) is a structurally simple and nontoxic water-soluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG’s elastic response against conformational deformations is key to its function. According to text-book knowledge, a polymer reacts to the stretching of its end-to-end separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of single-molecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretching-induced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom.}, langid = {english}, keywords = {bio,HB,MD}, - file = {/home/simon/Zotero/storage/FZWC452Q/Liese et al. - 2017 - Hydration Effects Turn a Highly Stretched Polymer .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/FZWC452Q/Liese et al. - 2017 - Hydration Effects Turn a Highly Stretched Polymer .pdf} } @article{liHydrophobicInteractionHydrogenbond2007, title = {Hydrophobic Interaction and Hydrogen-Bond Network for a Methane Pair in Liquid Water}, author = {Li, Je-Luen and Car, Roberto and Tang, Chao and Wingreen, Ned S.}, - year = {2007}, - month = feb, - journal = {Proceedings of the National Academy of Sciences}, + date = {2007-02-20}, + journaltitle = {Proceedings of the National Academy of Sciences}, + shortjournal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {104}, number = {8}, pages = {2626--2630}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0610945104}, + url = {https://pnas.org/doi/full/10.1073/pnas.0610945104}, urldate = {2023-03-22}, - abstract = {We employ fully quantum-mechanical molecular dynamics simulations to evaluate the force between two methanes dissolved in water, as a model for hydrophobic association. A stable configuration is found near the methane{\textendash}methane contact separation, while a shallow second potential minimum occurs for the solvent-separated configuration. The strength and shape of the potential of mean force are in conflict with earlier classical force-field simulations but agree well with a simple hydrophobic burial model which is based on solubility experiments. Examination of solvent dynamics reveals stable water cages at several specific methane{\textendash}methane separations.}, + abstract = {We employ fully quantum-mechanical molecular dynamics simulations to evaluate the force between two methanes dissolved in water, as a model for hydrophobic association. A stable configuration is found near the methane–methane contact separation, while a shallow second potential minimum occurs for the solvent-separated configuration. The strength and shape of the potential of mean force are in conflict with earlier classical force-field simulations but agree well with a simple hydrophobic burial model which is based on solubility experiments. Examination of solvent dynamics reveals stable water cages at several specific methane–methane separations.}, langid = {english}, keywords = {HB,MD,mixture}, - file = {/home/simon/Zotero/storage/DCUE6IMQ/Li et al. - 2007 - Hydrophobic interaction and hydrogen-bond network .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DCUE6IMQ/Li et al. - 2007 - Hydrophobic interaction and hydrogen-bond network .pdf} } @article{liInterfacialFreeEnergy2010, title = {Interfacial {{Free Energy Governs Single Polystyrene Chain Collapse}} in {{Water}} and {{Aqueous Solutions}}}, author = {Li, Isaac T. S. and Walker, Gilbert C.}, - year = {2010}, - month = may, - journal = {Journal of the American Chemical Society}, + date = {2010-05-12}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, volume = {132}, number = {18}, pages = {6530--6540}, issn = {0002-7863, 1520-5126}, doi = {10.1021/ja101155h}, + url = {https://pubs.acs.org/doi/10.1021/ja101155h}, urldate = {2023-08-09}, abstract = {The hydrophobic interaction is significantly responsible for driving protein folding and selfassembly. To understand it, the thermodynamics, the role of water structure, the dewetting process surrounding hydrophobes, and related aspects have undergone extensive investigations. Here, we examine the hypothesis that polymer-solvent interfacial free energy is adequate to describe the energetics of the collapse of a hydrophobic homopolymer chain at fixed temperature, which serves as a much simplified model for studying the hydrophobic collapse of a protein. This implies that changes in polymer-solvent interfacial free energy should be directly proportional to the force to extend a collapsed polymer into a bad solvent. To test this hypothesis, we undertook single-molecule force spectroscopy on a collapsed, single, polystyrene chain in water-ethanol and water-salt mixtures where we measured the monomer solvation free energy from an ensemble average conformations. Different proportions within the binary mixture were used to create solvents with different interfacial free energies with polystyrene. In these mixed solvents, we observed a linear correlation between the interfacial free energy and the force required to extend the chain into solution, which is a direct measure of the solvation free energy per monomer on a single chain at room temperature. A simple analytical model compares favorably with the experimental results. This knowledge supports a common assumption that explicit water solvent may not be necessary for cases whose primary concerns are hydrophobic interactions and hydrophobic hydration.}, langid = {english}, - file = {/home/simon/Zotero/storage/6WBPEPWX/Li and Walker - 2010 - Interfacial Free Energy Governs Single Polystyrene.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6WBPEPWX/Li and Walker - 2010 - Interfacial Free Energy Governs Single Polystyrene.pdf} } @article{linHighZIF8Loading2021, title = {A High {{ZIF-8}} Loading {{PVA}} Mixed Matrix Membrane on Alumina Hollow Fiber with Enhanced Ethanol Dehydration}, author = {Lin, Geng-Sheng and Chen, Yi-Rui and Chang, Ta-Hsuan and Huang, Tse-Chiang and Zhuang, Guo-Liang and Huang, Wei-Zhi and Liu, Yu-Cheng and Matsuyama, Hideto and Wu, Kevin C.-W and Tung, Kuo-Lun}, - year = {2021}, - month = mar, - journal = {Journal of Membrane Science}, + date = {2021-03}, + journaltitle = {Journal of Membrane Science}, + shortjournal = {Journal of Membrane Science}, volume = {621}, pages = {118935}, issn = {03767388}, doi = {10.1016/j.memsci.2020.118935}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S037673882031509X}, urldate = {2023-07-21}, - abstract = {In this work, a zeolitic imidazolate framework-8 (ZIF-8)/polyvinyl alcohol (PVA) mixed matrix membrane (MMM) was coated onto {$\alpha$}-aluminum oxide ({$\alpha$}-Al2O3) hollow fibers for ethanol dehydration by utilizing the pervaporation technique. ZIF-8/PVA solution was prepared via a drying-free, water-based method to obtain a uniform distribution MMM. Before coating the MMM onto the hollow fiber, a pristine PVA solution was first dipcoated onto hollow fiber as a gutter layer to prevent phase separation. Different weight ratios of ZIF-8-loaded MMMs were prepared. The results showed that at high ZIF-8 loading (39 wt \%), a high permeate flux (685 g/ m2 h) and high separation factor (4821) can be observed. Furthermore, compared with free-standing ZIF-8/PVA MMMs, hollow fiber supported ZIF-8/PVA MMMs exhibit a thinner coating thickness but higher pervaporation separation index (approximately 1.5{\textendash}2 times). The main contribution of this study is not only fabricated the high loading ZIF-8/PVA composite membrane with enhanced performance, but also coated onto the hollow fiber membrane which opens a gate for scale-up production.}, + abstract = {In this work, a zeolitic imidazolate framework-8 (ZIF-8)/polyvinyl alcohol (PVA) mixed matrix membrane (MMM) was coated onto α-aluminum oxide (α-Al2O3) hollow fibers for ethanol dehydration by utilizing the pervaporation technique. ZIF-8/PVA solution was prepared via a drying-free, water-based method to obtain a uniform distribution MMM. Before coating the MMM onto the hollow fiber, a pristine PVA solution was first dipcoated onto hollow fiber as a gutter layer to prevent phase separation. Different weight ratios of ZIF-8-loaded MMMs were prepared. The results showed that at high ZIF-8 loading (39 wt \%), a high permeate flux (685 g/ m2 h) and high separation factor (4821) can be observed. Furthermore, compared with free-standing ZIF-8/PVA MMMs, hollow fiber supported ZIF-8/PVA MMMs exhibit a thinner coating thickness but higher pervaporation separation index (approximately 1.5–2 times). The main contribution of this study is not only fabricated the high loading ZIF-8/PVA composite membrane with enhanced performance, but also coated onto the hollow fiber membrane which opens a gate for scale-up production.}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/66UNGMLT/Lin et al. - 2021 - A high ZIF-8 loading PVA mixed matrix membrane on .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/66UNGMLT/Lin et al. - 2021 - A high ZIF-8 loading PVA mixed matrix membrane on .pdf} } @article{lippensRelaxationTimeWater1993, title = {T 1 Relaxation Time of Water from a Molecular Dynamics Simulation}, author = {Lippens, G. and Van Belle, D. and Wodak, S.J. and Jeener, J.}, - year = {1993}, - month = dec, - journal = {Molecular Physics}, + date = {1993-12-20}, + journaltitle = {Molecular Physics}, volume = {80}, number = {6}, pages = {1469--1484}, publisher = {{Taylor \& Francis}}, issn = {0026-8976}, doi = {10.1080/00268979300103151}, + url = {https://doi.org/10.1080/00268979300103151}, urldate = {2023-07-09}, abstract = {The T 1 relaxation time of the proton Zeeman magnetization is calculated in a molecular dynamics simulation of two different water models, the single point charge (SPC) model and the polarizable SPC model. First, the possibility to treat such a system as an assembly of independent protons neglecting spin correlations of the two proton spins on the same water molecule is theoretically justified. The relaxation times are then calculated for both water models. This provides a parameter that can directly be compared with the experimental value, and its decomposition in intra- and intermolecular parts gives an indication to where those water models can be improved.}, - file = {/home/simon/Zotero/storage/AVTNWTPA/Lippens et al. - 1993 - T 1 relaxation time of water from a molecular dyna.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/AVTNWTPA/Lippens et al. - 1993 - T 1 relaxation time of water from a molecular dyna.pdf} } @article{liuGraphenebasedMembranes2015, title = {Graphene-Based Membranes}, author = {Liu, Gongping and Jin, Wanqin and Xu, Nanping}, - year = {2015}, - journal = {Chemical Society Reviews}, + date = {2015}, + journaltitle = {Chemical Society Reviews}, volume = {44}, number = {15}, pages = {5016--5030}, publisher = {{Royal Society of Chemistry}}, doi = {10.1039/C4CS00423J}, + url = {https://pubs.rsc.org/en/content/articlelanding/2015/cs/c4cs00423j}, urldate = {2023-10-20}, langid = {english}, - file = {/home/simon/Zotero/storage/DJERLM2U/Liu et al. - 2015 - Graphene-based membranes.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DJERLM2U/Liu et al. - 2015 - Graphene-based membranes.pdf} } @article{liuInterfacialLayerStructure2005, title = {Interfacial Layer Structure at Alcohol/Silica Interfaces Probed by Sum-Frequency Vibrational Spectroscopy}, author = {Liu, Weitao and Zhang, Luning and Shen, Y.R.}, - year = {2005}, - month = aug, - journal = {Chemical Physics Letters}, + date = {2005-08}, + journaltitle = {Chemical Physics Letters}, + shortjournal = {Chemical Physics Letters}, volume = {412}, number = {1-3}, pages = {206--209}, issn = {00092614}, doi = {10.1016/j.cplett.2005.06.113}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S000926140500936X}, urldate = {2023-07-18}, - abstract = {Sum-frequency vibrational spectroscopy was used to probe the adsorption of C1{\textendash}C4 1-alcohol molecules at both vapor/silica and liquid/silica interfaces. The observed CH stretching spectra show that alcohol molecules adsorbed on silica with methyl groups pointing away from the interface. Reduction of the symmetric modes and enhancement of the antisymmetric modes of alcohol at liquid/silica interfaces are understood from a model of oppositely oriented molecules forming a bilayer at the interfaces.}, + abstract = {Sum-frequency vibrational spectroscopy was used to probe the adsorption of C1–C4 1-alcohol molecules at both vapor/silica and liquid/silica interfaces. The observed CH stretching spectra show that alcohol molecules adsorbed on silica with methyl groups pointing away from the interface. Reduction of the symmetric modes and enhancement of the antisymmetric modes of alcohol at liquid/silica interfaces are understood from a model of oppositely oriented molecules forming a bilayer at the interfaces.}, langid = {english}, keywords = {mixture,spectro}, - file = {/home/simon/Zotero/storage/ALCGLYGE/Liu et al. - 2005 - Interfacial layer structure at alcoholsilica inte.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ALCGLYGE/Liu et al. - 2005 - Interfacial layer structure at alcoholsilica inte.pdf} } @article{mackerellAllAtomEmpiricalPotential1998, title = {All-{{Atom Empirical Potential}} for {{Molecular Modeling}} and {{Dynamics Studies}} of {{Proteins}}}, - author = {MacKerell, A. D. and Bashford, D. and Bellott, M. and Dunbrack, R. L. and Evanseck, J. D. and Field, M. J. and Fischer, S. and Gao, J. and Guo, H. and Ha, S. and {Joseph-McCarthy}, D. and Kuchnir, L. and Kuczera, K. and Lau, F. T. K. and Mattos, C. and Michnick, S. and Ngo, T. and Nguyen, D. T. and Prodhom, B. and Reiher, W. E. and Roux, B. and Schlenkrich, M. and Smith, J. C. and Stote, R. and Straub, J. and Watanabe, M. and {Wi{\'o}rkiewicz-Kuczera}, J. and Yin, D. and Karplus, M.}, - year = {1998}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + author = {MacKerell, A. D. and Bashford, D. and Bellott, M. and Dunbrack, R. L. and Evanseck, J. D. and Field, M. J. and Fischer, S. and Gao, J. and Guo, H. and Ha, S. and Joseph-McCarthy, D. and Kuchnir, L. and Kuczera, K. and Lau, F. T. K. and Mattos, C. and Michnick, S. and Ngo, T. and Nguyen, D. T. and Prodhom, B. and Reiher, W. E. and Roux, B. and Schlenkrich, M. and Smith, J. C. and Stote, R. and Straub, J. and Watanabe, M. and Wiórkiewicz-Kuczera, J. and Yin, D. and Karplus, M.}, + date = {1998-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {102}, number = {18}, pages = {3586--3616}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp973084f}, + url = {https://pubs.acs.org/doi/10.1021/jp973084f}, urldate = {2023-05-30}, langid = {english}, keywords = {ff,propane}, - file = {/home/simon/Zotero/storage/RJF8HNPV/MacKerell et al. - 1998 - All-Atom Empirical Potential for Molecular Modelin.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/RJF8HNPV/MacKerell et al. - 1998 - All-Atom Empirical Potential for Molecular Modelin.pdf} } @article{malaebReverseOsmosisTechnology2011, title = {Reverse Osmosis Technology for Water Treatment: {{State}} of the Art Review}, shorttitle = {Reverse Osmosis Technology for Water Treatment}, author = {Malaeb, Lilian and Ayoub, George M.}, - year = {2011}, - month = feb, - journal = {Desalination}, + date = {2011-02}, + journaltitle = {Desalination}, + shortjournal = {Desalination}, volume = {267}, number = {1}, pages = {1--8}, issn = {00119164}, doi = {10.1016/j.desal.2010.09.001}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0011916410006351}, urldate = {2023-10-23}, langid = {english}, - file = {/home/simon/Zotero/storage/GW8G95FY/Malaeb and Ayoub - 2011 - Reverse osmosis technology for water treatment St.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/GW8G95FY/Malaeb and Ayoub - 2011 - Reverse osmosis technology for water treatment St.pdf} } @article{markthalerLessonsLearnedCalculation2019, title = {Lessons {{Learned}} from the {{Calculation}} of {{One-Dimensional Potentials}} of {{Mean Force}} [{{Article}} v1.0]}, author = {Markthaler, Daniel and Jakobtorweihen, Sven and Hansen, Niels}, - year = {2019}, - journal = {Living Journal of Computational Molecular Science}, + date = {2019}, + journaltitle = {Living Journal of Computational Molecular Science}, + shortjournal = {LiveCoMS}, volume = {1}, number = {1}, issn = {25756524}, doi = {10.33011/livecoms.1.2.11073}, + url = {https://www.livecomsjournal.org/article/11073-lessons-learned-from-the-calculation-of-one-dimensional-potentials-of-mean-force-article-v1-0}, urldate = {2023-07-07}, - abstract = {The origins of different computational artifacts that may occur in the calculation of one-dimensional potentials of mean force (PMF) via umbrella sampling molecular dynamics simulations and manifest as free energy offset between bulk solvent regions are investigated. By systematic studies, three distinct causes are elucidated: (i) an unfortunate choice of reference points for the umbrella distance restraint; (ii) a misfit in probability distributions between bound and unbound umbrella windows in case of multiple binding modes; (iii) artifacts introduced by the free energy estimator. Starting with a fully symmetric model system consisting of methane binding to a cylindrical host, complexity is increased through the introduction of dipolar interactions between the host and the solvent, the host and the guest molecule or between all involved species, respectively. The manifestation of artifacts is illustrated and their origin and prevention is discussed. Finally, the consequences for the calculation of standard binding free enthalpies is illustrated using the complexation of primary alcohols with {$\alpha$}-cyclodextrin as an example.}, + abstract = {The origins of different computational artifacts that may occur in the calculation of one-dimensional potentials of mean force (PMF) via umbrella sampling molecular dynamics simulations and manifest as free energy offset between bulk solvent regions are investigated. By systematic studies, three distinct causes are elucidated: (i) an unfortunate choice of reference points for the umbrella distance restraint; (ii) a misfit in probability distributions between bound and unbound umbrella windows in case of multiple binding modes; (iii) artifacts introduced by the free energy estimator. Starting with a fully symmetric model system consisting of methane binding to a cylindrical host, complexity is increased through the introduction of dipolar interactions between the host and the solvent, the host and the guest molecule or between all involved species, respectively. The manifestation of artifacts is illustrated and their origin and prevention is discussed. Finally, the consequences for the calculation of standard binding free enthalpies is illustrated using the complexation of primary alcohols with α-cyclodextrin as an example.}, langid = {english}, keywords = {PMF}, - file = {/home/simon/Zotero/storage/WNG3L77C/Markthaler et al. - 2019 - Lessons Learned from the Calculation of One-Dimens.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WNG3L77C/Markthaler et al. - 2019 - Lessons Learned from the Calculation of One-Dimens.pdf} } @article{masunovBondShorteningHydrogenBond2001, - title = {{{C}}-{{H Bond-Shortening}} upon {{Hydrogen Bond Formation}}: {{Influence}} of an {{Electric Field}}}, - shorttitle = {{{C}}-{{H Bond-Shortening}} upon {{Hydrogen Bond Formation}}}, - author = {Masunov, Art{\"e}m and Dannenberg, J. J. and Contreras, Rub{\'e}n H.}, - year = {2001}, - month = may, - journal = {The Journal of Physical Chemistry A}, + title = {{{C}}−{{H Bond-Shortening}} upon {{Hydrogen Bond Formation}}: {{Influence}} of an {{Electric Field}}}, + shorttitle = {{{C}}−{{H Bond-Shortening}} upon {{Hydrogen Bond Formation}}}, + author = {Masunov, Artëm and Dannenberg, J. J. and Contreras, Rubén H.}, + date = {2001-05-01}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, volume = {105}, number = {19}, pages = {4737--4740}, issn = {1089-5639, 1520-5215}, doi = {10.1021/jp0043470}, + url = {https://pubs.acs.org/doi/10.1021/jp0043470}, urldate = {2023-03-24}, langid = {english}, keywords = {HB,mixture}, - file = {/home/simon/Zotero/storage/TV2HT7YF/Masunov et al. - 2001 - C−H Bond-Shortening upon Hydrogen Bond Formation .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/TV2HT7YF/Masunov et al. - 2001 - C−H Bond-Shortening upon Hydrogen Bond Formation .pdf} } @article{mhannaDynamicHeterogeneitiesLiquid2020, title = {Dynamic {{Heterogeneities}} in {{Liquid Mixtures Confined}} in {{Nanopores}}}, author = {Mhanna, Ramona and Catrou, Pierre and Dutta, Sujeet and Lefort, Ronan and Essafri, Ilham and Ghoufi, Aziz and Muthmann, Matthias and Zamponi, Michaela and Frick, Bernhard and Morineau, Denis}, - year = {2020}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + date = {2020-04-16}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {124}, number = {15}, pages = {3152--3162}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.0c01035}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.0c01035}, urldate = {2023-06-09}, - abstract = {Binary liquid mixtures can exhibit nanosegregation, albeit being fully miscible and homogeneous at the macroscopic scale. This tendency can be amplified by geometrical nanoconfinement, leading to remarkable properties. This work investigates the molecular dynamics of tert-butanol (TBA)-toluene (TOL) mixtures confined in silica nanochannels by quasielastic neutron scattering and molecular dynamics simulation. It reveals a decoupling of the molecular motion of each constituent of the binary liquid, which can be followed independently by selective isotopic H/D labeling. We argue that this behavior is the signature of spatially segregated dynamic heterogeneities, which are due to the recently established core-shell nanophase separation induced by mesoporous confinement.}, + abstract = {Binary liquid mixtures can exhibit nanosegregation, albeit being fully miscible and homogeneous at the macroscopic scale. This tendency can be amplified by geometrical nanoconfinement, leading to remarkable properties. This work investigates the molecular dynamics of tert-butanol (TBA)−toluene (TOL) mixtures confined in silica nanochannels by quasielastic neutron scattering and molecular dynamics simulation. It reveals a decoupling of the molecular motion of each constituent of the binary liquid, which can be followed independently by selective isotopic H/D labeling. We argue that this behavior is the signature of spatially segregated dynamic heterogeneities, which are due to the recently established core−shell nanophase separation induced by mesoporous confinement.}, langid = {english}, keywords = {mixture}, - file = {/home/simon/Zotero/storage/5YIAIPFB/Mhanna et al. - 2020 - Dynamic Heterogeneities in Liquid Mixtures Confine.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5YIAIPFB/Mhanna et al. - 2020 - Dynamic Heterogeneities in Liquid Mixtures Confine.pdf} } @article{mijakovicEthanolwaterMixturesUltrasonics2011, title = {Ethanol-Water Mixtures: Ultrasonics, {{Brillouin}} Scattering and Molecular Dynamics}, shorttitle = {Ethanol-Water Mixtures}, - author = {Mijakovi{\'c}, M. and Ke{\v z}i{\'c}, B. and Zorani{\'c}, L. and Sokoli{\'c}, F. and Asenbaum, A. and Pruner, C. and Wilhelm, Emmerich and Perera, A.}, - year = {2011}, - month = nov, - journal = {Journal of Molecular Liquids}, + author = {Mijaković, M. and Kežić, B. and Zoranić, L. and Sokolić, F. and Asenbaum, A. and Pruner, C. and Wilhelm, Emmerich and Perera, A.}, + date = {2011-11}, + journaltitle = {Journal of Molecular Liquids}, + shortjournal = {Journal of Molecular Liquids}, volume = {164}, number = {1-2}, pages = {66--73}, issn = {01677322}, doi = {10.1016/j.molliq.2011.06.009}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0167732211002145}, urldate = {2023-05-15}, abstract = {New ultrasonic and hypersonic measurements of the speed of sound in aqueous ethanol mixtures are presented, particularly in the temperature and ethanol-concentration domains of the maximum of sound. Molecular Dynamics studies indicate that these mixtures show aggregation of ethanol molecules in the low ethanol mole fraction x b 0.2, bicontinuous-like phase around x = 0.5, and weak water clustering above x = 0.8. The resulting micro-heterogeneity is seen to affect the long range part of all the correlation functions of the aggregating species. Nevertheless, simulation results help understanding the general trends seen in the experimental results: it is the structural change between ethanol's clustering and water-ethanol microsegregation that corresponds to the maximum observed in the speed of sound around x = 0.15.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/PQU9PTYB/Mijaković et al. - 2011 - Ethanol-water mixtures ultrasonics, Brillouin sca.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/PQU9PTYB/Mijaković et al. - 2011 - Ethanol-water mixtures ultrasonics, Brillouin sca.pdf} } @article{mondalEthanolExchangeTwo2022, title = {Ethanol Exchange between Two Graphene Surfaces in Nanoconfined Aqueous Solution: {{Rate}} and Mechanism}, shorttitle = {Ethanol Exchange between Two Graphene Surfaces in Nanoconfined Aqueous Solution}, author = {Mondal, Sangita and Acharya, Subhajit and Mondal, Sayantan and Bagchi, Biman}, - year = {2022}, - month = nov, - journal = {The Journal of Chemical Physics}, + date = {2022-11-21}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {J. Chem. Phys.}, volume = {157}, number = {19}, pages = {194703}, issn = {0021-9606, 1089-7690}, doi = {10.1063/5.0099621}, + url = {https://pubs.aip.org/aip/jcp/article/2842114}, urldate = {2023-06-09}, - abstract = {We observe, by computer simulations, a remarkable long-distance, rare, but repetitive, exchange of ethanol molecules between two parallel graphene surfaces in nanoconfined, aqueous, ethanol solutions. We compute the rate of exchange as a function of the separation (d) between the two surfaces. We discover that the initiating (or, the launching) step in this exchange is the attainment of an instantaneous orientation of the carbon{\textendash}oxygen bond vector relative to the graphene surface. This observation led us to construct a two-dimensional free energy surface for this exchange, with respect to two order parameters, namely, (i) the perpendicular distance of ethanol molecule from the graphene surfaces, z, and (ii) the orientation of the O{\textendash}C bond vector, {\texttheta}, of the tagged ethanol molecule. For d = 3~nm, the rate of exchange is found to be 0.44~ns -1 for the force field used. We also vary the force field and determine the sensitivity of the rate. From the free energy landscape, one could determine the minimum energy pathway. We use both, the transition state theory and Kramers' theory, to calculate the rate. The calculated rate agrees well with the simulated value as mentioned above. We find that the rate of exchange phenomenon is sensitive to the interaction strength of graphene and the hydrophobic group of ethanol. The free energy landscape exchange shows dependence on the distance separation of the two hydrophobic surfaces and reveals interesting features.}, + abstract = {We observe, by computer simulations, a remarkable long-distance, rare, but repetitive, exchange of ethanol molecules between two parallel graphene surfaces in nanoconfined, aqueous, ethanol solutions. We compute the rate of exchange as a function of the separation (d) between the two surfaces. We discover that the initiating (or, the launching) step in this exchange is the attainment of an instantaneous orientation of the carbon–oxygen bond vector relative to the graphene surface. This observation led us to construct a two-dimensional free energy surface for this exchange, with respect to two order parameters, namely, (i) the perpendicular distance of ethanol molecule from the graphene surfaces, z, and (ii) the orientation of the O–C bond vector, θ, of the tagged ethanol molecule. For d = 3~nm, the rate of exchange is found to be 0.44~ns −1 for the force field used. We also vary the force field and determine the sensitivity of the rate. From the free energy landscape, one could determine the minimum energy pathway. We use both, the transition state theory and Kramers’ theory, to calculate the rate. The calculated rate agrees well with the simulated value as mentioned above. We find that the rate of exchange phenomenon is sensitive to the interaction strength of graphene and the hydrophobic group of ethanol. The free energy landscape exchange shows dependence on the distance separation of the two hydrophobic surfaces and reveals interesting features.}, langid = {english}, keywords = {confinnement,MD}, - file = {/home/simon/Zotero/storage/XUBZBGEG/Mondal et al. - 2022 - Ethanol exchange between two graphene surfaces in .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/XUBZBGEG/Mondal et al. - 2022 - Ethanol exchange between two graphene surfaces in .pdf} } @article{moradiThermodynamicsInterfaces, title = {Thermodynamics of {{Interfaces}}}, author = {Moradi, Omid}, - journal = {Interaction Studies}, + journaltitle = {Interaction Studies}, langid = {english}, - file = {/home/simon/Zotero/storage/JPK9345T/Moradi - Thermodynamics of Interfaces.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/JPK9345T/Moradi - Thermodynamics of Interfaces.pdf} } @article{muthulakshmiEvidenceConfinementInduced2017, - title = {Evidence for Confinement Induced Phase Separation in Ethanol{\textendash}Water Mixture: A Positron Annihilation Study}, - shorttitle = {Evidence for Confinement Induced Phase Separation in Ethanol{\textendash}Water Mixture}, + title = {Evidence for Confinement Induced Phase Separation in Ethanol–Water Mixture: A Positron Annihilation Study}, + shorttitle = {Evidence for Confinement Induced Phase Separation in Ethanol–Water Mixture}, author = {Muthulakshmi, T. and Dutta, D. and Maheshwari, Priya and Pujari, P. K.}, - year = {2017}, - month = dec, - journal = {Journal of Physics: Condensed Matter}, + date = {2017-12}, + journaltitle = {Journal of Physics: Condensed Matter}, + shortjournal = {J. Phys.: Condens. Matter}, volume = {30}, number = {2}, pages = {025001}, publisher = {{IOP Publishing}}, issn = {0953-8984}, doi = {10.1088/1361-648X/aa9c12}, + url = {https://dx.doi.org/10.1088/1361-648X/aa9c12}, urldate = {2023-07-11}, - abstract = {We report an experimental evidence for the phase separation of ethanol{\textendash}water mixture confined in mesoporous silica with different pore size using positron annihilation lifetime spectroscopy (PALS). A bulk-like liquid in the core of the pore and a distinct interfacial region near the pore surface have been identified based on ortho-positronium lifetime components. The lifetime corresponding to the core liquid shows similar behavior to the bulk liquid mixture while the interfacial lifetime shows an abrupt rise within a particular range of ethanol concentration depending on the pore size. This abrupt increase is attributed to the appearance of excess free-volume near the interfacial region. The excess free-volume is originated due to microphase separation of confined ethanol{\textendash}water primarily at the vicinity of the pore wall. We envisage that probing free-volume changes at the interface using PALS is a sensitive way to investigate microphase separation under nanoconfinement.}, + abstract = {We report an experimental evidence for the phase separation of ethanol–water mixture confined in mesoporous silica with different pore size using positron annihilation lifetime spectroscopy (PALS). A bulk-like liquid in the core of the pore and a distinct interfacial region near the pore surface have been identified based on ortho-positronium lifetime components. The lifetime corresponding to the core liquid shows similar behavior to the bulk liquid mixture while the interfacial lifetime shows an abrupt rise within a particular range of ethanol concentration depending on the pore size. This abrupt increase is attributed to the appearance of excess free-volume near the interfacial region. The excess free-volume is originated due to microphase separation of confined ethanol–water primarily at the vicinity of the pore wall. We envisage that probing free-volume changes at the interface using PALS is a sensitive way to investigate microphase separation under nanoconfinement.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/VNHIJHJY/Muthulakshmi et al. - 2017 - Evidence for confinement induced phase separation .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VNHIJHJY/Muthulakshmi et al. - 2017 - Evidence for confinement induced phase separation .pdf} } @article{natal-santiagoMicrocalorimetricFTIRDFT1998, title = {Microcalorimetric, {{FTIR}}, and {{DFT Studies}} of the {{Adsorption}} of {{Methanol}}, {{Ethanol}}, and 2,2,2-{{Trifluoroethanol}} on {{Silica}}}, - author = {{Natal-Santiago}, M.A. and Dumesic, J.A.}, - year = {1998}, - month = apr, - journal = {Journal of Catalysis}, + author = {Natal-Santiago, M.A. and Dumesic, J.A.}, + date = {1998-04}, + journaltitle = {Journal of Catalysis}, + shortjournal = {Journal of Catalysis}, volume = {175}, number = {2}, pages = {252--268}, issn = {00219517}, doi = {10.1006/jcat.1998.2003}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021951798920036}, urldate = {2023-07-12}, langid = {english}, keywords = {heat,water-ethanol}, - file = {/home/simon/Zotero/storage/7AHARSLF/Natal-Santiago and Dumesic - 1998 - Microcalorimetric, FTIR, and DFT Studies of the Ad.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7AHARSLF/Natal-Santiago and Dumesic - 1998 - Microcalorimetric, FTIR, and DFT Studies of the Ad.pdf} } @article{newMolecularDynamicsCalculation1995, title = {Molecular {{Dynamics Calculation}} of the {{Effect}} of {{Solvent Polarizability}} on the {{Hydrophobic Interaction}}}, author = {New, Michael H. and Berne, B. J.}, - year = {1995}, - month = jul, - journal = {Journal of the American Chemical Society}, + date = {1995-07}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, volume = {117}, number = {27}, pages = {7172--7179}, issn = {0002-7863, 1520-5126}, doi = {10.1021/ja00132a017}, + url = {https://pubs.acs.org/doi/abs/10.1021/ja00132a017}, urldate = {2023-07-04}, - abstract = {The potential of mean force (PMF) between two methane molecules in water is calculated using molecular dynamics with Ewald boundary conditions for two water models, the WK model (a nonpolarizable model) and the PSRWK model (a polarizable model), for the purpose of understanding what role many-body polarization plays in the hydrophobic interaction. These models of neat water have the same static dielectric constants and similar structural and thermodynamic properties. The methane{\textemdash}water interaction is taken to be exactly the same in both fluids. Nevertheless, the simulated potential of mean force between two dissolved methane molecules is very different for these two models. In the polarizable model, solvent-separated pairing is dominant over contact-pairing, while in the nonpolarizable model the reverse is true.}, + abstract = {The potential of mean force (PMF) between two methane molecules in water is calculated using molecular dynamics with Ewald boundary conditions for two water models, the WK model (a nonpolarizable model) and the PSRWK model (a polarizable model), for the purpose of understanding what role many-body polarization plays in the hydrophobic interaction. These models of neat water have the same static dielectric constants and similar structural and thermodynamic properties. The methane—water interaction is taken to be exactly the same in both fluids. Nevertheless, the simulated potential of mean force between two dissolved methane molecules is very different for these two models. In the polarizable model, solvent-separated pairing is dominant over contact-pairing, while in the nonpolarizable model the reverse is true.}, langid = {english}, keywords = {HB}, - file = {/home/simon/Zotero/storage/QXRRYQS2/New and Berne - 1995 - Molecular Dynamics Calculation of the Effect of So.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QXRRYQS2/New and Berne - 1995 - Molecular Dynamics Calculation of the Effect of So.pdf} } @article{noskovMolecularDynamicsStudy2005, - title = {Molecular {{Dynamics Study}} of {{Hydration}} in {{Ethanol}}-{{Water Mixtures Using}} a {{Polarizable Force Field}}}, - author = {Noskov, Sergei Yu. and Lamoureux, Guillaume and Roux, Beno{\^i}t}, - year = {2005}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + title = {Molecular {{Dynamics Study}} of {{Hydration}} in {{Ethanol}}−{{Water Mixtures Using}} a {{Polarizable Force Field}}}, + author = {Noskov, Sergei Yu. and Lamoureux, Guillaume and Roux, Benoît}, + date = {2005-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {109}, number = {14}, pages = {6705--6713}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp045438q}, + url = {https://pubs.acs.org/doi/10.1021/jp045438q}, urldate = {2023-05-02}, langid = {english}, keywords = {HB,MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/39SBAE7Y/Noskov et al. - 2005 - Molecular Dynamics Study of Hydration in Ethanol−W.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/39SBAE7Y/Noskov et al. - 2005 - Molecular Dynamics Study of Hydration in Ethanol−W.pdf} } @article{nuhnenPracticalGuideCalculate2020, - title = {A Practical Guide to Calculate the Isosteric Heat/Enthalpy of Adsorption {\emph{via}} Adsorption Isotherms in Metal{\textendash}Organic Frameworks, {{MOFs}}}, + title = {A Practical Guide to Calculate the Isosteric Heat/Enthalpy of Adsorption {\emph{via}} Adsorption Isotherms in Metal–Organic Frameworks, {{MOFs}}}, author = {Nuhnen, Alexander and Janiak, Christoph}, - year = {2020}, - journal = {Dalton Transactions}, + date = {2020}, + journaltitle = {Dalton Transactions}, + shortjournal = {Dalton Trans.}, volume = {49}, number = {30}, pages = {10295--10307}, issn = {1477-9226, 1477-9234}, doi = {10.1039/D0DT01784A}, + url = {http://xlink.rsc.org/?DOI=D0DT01784A}, urldate = {2023-07-18}, - abstract = {This Perspective presents the procedure of the common Freundlich{\textendash}Langmuir fit/Clausius{\textendash}Clapeyron approach and the virial fit of adsorption isotherms with usable Excel sheets and Origin files for the subsequent derivation of {$\Delta$} H ads . , Porous materials such as MOFs are interesting candidates for gas separation and storage. An important parameter to gain deeper insights to the adsorption process of an adsorptive on an adsorbent is the isosteric enthalpy of adsorption, {$\Delta$} H ads which is defined as the heat to be released/required when an adsorptive binds to/detaches from the solid surface of an adsorbent. Two or three adsorption isotherms at different but close temperatures with {$\Delta$} T {$\leq$} 20 K for two and {$\Delta$} T {$\approx$} 10 K for three isotherms are the basis to derive the isosteric enthalpy of adsorption through the Clausius{\textendash}Clapeyron approach or the virial analysis. This Perspective presents the procedure of the common (dual-site) Freundlich{\textendash}Langmuir fit/Clausius{\textendash}Clapeyron approach and the virial fit of the isotherms with usable Excel sheets and Origin files for the subsequent derivation of {$\Delta$} H ads . Exemplary adsorption isotherms of CO 2 , SO 2 and H 2 at two temperatures on MOFs are analyzed. The detailed computational description and comparison of the Clausius{\textendash}Clapeyron approach and the virial analysis to determine {$\Delta$} H ads outlines the limitations of the two methods with respect to the available experimental data, especially at low pressure/low uptake values. It is emphasized that no extrapolation beyond the experimental data range should be done. The quality of the important and underlying isotherm fits must be checked and ensured with logarithmic-scale n / p isotherm plots for the (dual-site) Freundlich{\textendash}Langmuir fit in the low-pressure region and through low standard deviations for the coefficients in the virial analysis.}, + abstract = {This Perspective presents the procedure of the common Freundlich–Langmuir fit/Clausius–Clapeyron approach and the virial fit of adsorption isotherms with usable Excel sheets and Origin files for the subsequent derivation of Δ H ads . , Porous materials such as MOFs are interesting candidates for gas separation and storage. An important parameter to gain deeper insights to the adsorption process of an adsorptive on an adsorbent is the isosteric enthalpy of adsorption, Δ H ads which is defined as the heat to be released/required when an adsorptive binds to/detaches from the solid surface of an adsorbent. Two or three adsorption isotherms at different but close temperatures with Δ T ≤ 20 K for two and Δ T ≈ 10 K for three isotherms are the basis to derive the isosteric enthalpy of adsorption through the Clausius–Clapeyron approach or the virial analysis. This Perspective presents the procedure of the common (dual-site) Freundlich–Langmuir fit/Clausius–Clapeyron approach and the virial fit of the isotherms with usable Excel sheets and Origin files for the subsequent derivation of Δ H ads . Exemplary adsorption isotherms of CO 2 , SO 2 and H 2 at two temperatures on MOFs are analyzed. The detailed computational description and comparison of the Clausius–Clapeyron approach and the virial analysis to determine Δ H ads outlines the limitations of the two methods with respect to the available experimental data, especially at low pressure/low uptake values. It is emphasized that no extrapolation beyond the experimental data range should be done. The quality of the important and underlying isotherm fits must be checked and ensured with logarithmic-scale n / p isotherm plots for the (dual-site) Freundlich–Langmuir fit in the low-pressure region and through low standard deviations for the coefficients in the virial analysis.}, langid = {english}, keywords = {heat}, - file = {/home/simon/Zotero/storage/8J7FMJHD/Nuhnen and Janiak - 2020 - A practical guide to calculate the isosteric heat.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/8J7FMJHD/Nuhnen and Janiak - 2020 - A practical guide to calculate the isosteric heat.pdf} } @article{ochediCarbonDioxideCapture2021, title = {Carbon Dioxide Capture Using Liquid Absorption Methods: A Review}, shorttitle = {Carbon Dioxide Capture Using Liquid Absorption Methods}, author = {Ochedi, Friday O. and Yu, Jianglong and Yu, Hai and Liu, Yangxian and Hussain, Arshad}, - year = {2021}, - month = feb, - journal = {Environmental Chemistry Letters}, + date = {2021-02-01}, + journaltitle = {Environmental Chemistry Letters}, + shortjournal = {Environ Chem Lett}, volume = {19}, number = {1}, pages = {77--109}, issn = {1610-3661}, doi = {10.1007/s10311-020-01093-8}, + url = {https://doi.org/10.1007/s10311-020-01093-8}, urldate = {2023-11-06}, - abstract = {Anthropogenic emissions of greenhouse gases into the atmosphere is inducing global warming, ocean acidification, polar ice melting, rise in sea level, droughts and hurricanes, thus threatening human health and the global economy. Therefore, there is a need to develop cost-effective technologies for CO2 capture. For instance, solution absorption is promising due to a large processing capacity, high flexibility and reliability, and rich experience in engineering applications. Nonetheless, actual commercial solutions, solvents and processes for CO2 capture suffer from slow reaction kinetics, low absorption capacity, high-energy consumption, susceptibility to corrosion, toxicity, low stability and high costs. Therefore, current research focuses on developing more economical, effective, green and sustainable technologies. Here we review 2015{\textendash}2020 findings on CO2 capture using liquid absorption methods. Methods are based on various solutions, solvents and processes such as carbonate solution, ammonia solution, amine-based solution, ionic liquid, amino acid salt, phase changing absorbent, microcapsulated and membrane absorption, nanofluids and phenoxide salt solution. We discuss absorption performance, absorption mechanism, enhancement pathways and challenges. Amine- and NH3-based absorbents are widely used, yet they are limited by high regeneration energy, corrosiveness and degradation, reagent loss and secondary pollution caused by NH3 escape. Phase changing absorbents are getting more attention due to their lower cost and lower energy penalty. The incorporation of membrane and microencapsulation technologies to absorbing solvents could enhance CO2 absorption performance by reducing corrosion and increasing selectivity. Adding nanoparticles to solvents could improve CO2 absorption performance and reduce energy requirement. Besides, solvent blends and promoter-improved solvents performed better than single and non-promoted solvents because they combine the benefits of individual solvents and promoters.}, + abstract = {Anthropogenic emissions of greenhouse gases into the atmosphere is inducing global warming, ocean acidification, polar ice melting, rise in sea level, droughts and hurricanes, thus threatening human health and the global economy. Therefore, there is a need to develop cost-effective technologies for CO2 capture. For instance, solution absorption is promising due to a large processing capacity, high flexibility and reliability, and rich experience in engineering applications. Nonetheless, actual commercial solutions, solvents and processes for CO2 capture suffer from slow reaction kinetics, low absorption capacity, high-energy consumption, susceptibility to corrosion, toxicity, low stability and high costs. Therefore, current research focuses on developing more economical, effective, green and sustainable technologies. Here we review 2015–2020 findings on CO2 capture using liquid absorption methods. Methods are based on various solutions, solvents and processes such as carbonate solution, ammonia solution, amine-based solution, ionic liquid, amino acid salt, phase changing absorbent, microcapsulated and membrane absorption, nanofluids and phenoxide salt solution. We discuss absorption performance, absorption mechanism, enhancement pathways and challenges. Amine- and NH3-based absorbents are widely used, yet they are limited by high regeneration energy, corrosiveness and degradation, reagent loss and secondary pollution caused by NH3 escape. Phase changing absorbents are getting more attention due to their lower cost and lower energy penalty. The incorporation of membrane and microencapsulation technologies to absorbing solvents could enhance CO2 absorption performance by reducing corrosion and increasing selectivity. Adding nanoparticles to solvents could improve CO2 absorption performance and reduce energy requirement. Besides, solvent blends and promoter-improved solvents performed better than single and non-promoted solvents because they combine the benefits of individual solvents and promoters.}, langid = {english}, keywords = {Absorbent,Carbon capture,Greenhouse gases,Post-combustion capture,Solution absorption}, - file = {/home/simon/Zotero/storage/XNYNF46B/Ochedi et al. - 2021 - Carbon dioxide capture using liquid absorption met.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/XNYNF46B/Ochedi et al. - 2021 - Carbon dioxide capture using liquid absorption met.pdf} } @article{odeliusIntermolecularDipoleDipoleRelaxation1993, title = {Intermolecular {{Dipole-Dipole Relaxation}}. {{A Molecular Dynamics Simulation}}}, author = {Odelius, M. and Laaksonen, A. and Levitt, M.H. and Kowalewski, J.}, - year = {1993}, - month = dec, - journal = {Journal of Magnetic Resonance, Series A}, + date = {1993-12}, + journaltitle = {Journal of Magnetic Resonance, Series A}, + shortjournal = {Journal of Magnetic Resonance, Series A}, volume = {105}, number = {3}, pages = {289--294}, issn = {10641858}, doi = {10.1006/jmra.1993.1283}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1064185883712830}, urldate = {2023-07-03}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/SLCAYCCF/1-s2.0-S1064185883712830-main.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SLCAYCCF/1-s2.0-S1064185883712830-main.pdf} } @article{ortizInvestigatingPressureInducedAmorphization2013, title = {Investigating the {{Pressure-Induced Amorphization}} of {{Zeolitic Imidazolate Framework ZIF-8}}: {{Mechanical Instability Due}} to {{Shear Mode Softening}}}, shorttitle = {Investigating the {{Pressure-Induced Amorphization}} of {{Zeolitic Imidazolate Framework ZIF-8}}}, - author = {Ortiz, Aur{\'e}lie U. and Boutin, Anne and Fuchs, Alain H. and Coudert, Fran{\c c}ois-Xavier}, - year = {2013}, - month = jun, - journal = {The Journal of Physical Chemistry Letters}, + author = {Ortiz, Aurélie U. and Boutin, Anne and Fuchs, Alain H. and Coudert, François-Xavier}, + date = {2013-06-06}, + journaltitle = {The Journal of Physical Chemistry Letters}, + shortjournal = {J. Phys. Chem. Lett.}, volume = {4}, number = {11}, pages = {1861--1865}, issn = {1948-7185, 1948-7185}, doi = {10.1021/jz400880p}, + url = {https://pubs.acs.org/doi/10.1021/jz400880p}, urldate = {2023-07-19}, abstract = {We provide the first molecular dynamics study of the mechanical instability that is the cause of pressure-induced amorphization of zeolitic imidazolate framework ZIF8. By measuring the elastic constants of ZIF-8 up to the amorphization pressure, we show that the crystal-to-amorphous transition is triggered by the mechanical instability of ZIF-8 under compression, due to shear mode softening of the material. No similar softening was observed under temperature increase, explaining the absence of temperature-induced amorphization in ZIF-8. We also demonstrate the large impact of the presence of adsorbate in the pores on the mechanical stability and compressibility of the framework, increasing its shear stability. This first molecular dynamics study of ZIF mechanical properties under variations of pressure, temperature, and pore filling opens the way to a more comprehensive understanding of their mechanical stability, structural transitions, and amorphization.}, langid = {english}, keywords = {MD,zif}, - file = {/home/simon/Zotero/storage/DUMF99U5/Ortiz et al. - 2013 - Investigating the Pressure-Induced Amorphization o.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/DUMF99U5/Ortiz et al. - 2013 - Investigating the Pressure-Induced Amorphization o.pdf} } @article{ozkanCurrentStatusPillars2022, title = {Current Status and Pillars of Direct Air Capture Technologies}, author = {Ozkan, Mihrimah and Nayak, Saswat Priyadarshi and Ruiz, Anthony D. and Jiang, Wenmei}, - year = {2022}, - month = apr, - journal = {iScience}, + date = {2022-04}, + journaltitle = {iScience}, + shortjournal = {iScience}, volume = {25}, number = {4}, pages = {103990}, issn = {25890042}, doi = {10.1016/j.isci.2022.103990}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004222002607}, urldate = {2023-10-23}, - abstract = {Climate change calls for adaptation of negative emission technologies such as direct air capture (DAC) of carbon dioxide (CO2) to lower the global warming impacts of greenhouse gases. Recently, elevated global interests to the DAC technologies prompted implementation of new tax credits and new policies worldwide that motivated the existing DAC companies and prompted the startup boom. There are presently 19 DAC plants operating worldwide, capturing more than 0.01 Mt CO2/year. DAC active plants capturing in average 10,000 tons of CO2 annually are still in their infancy and are expensive. DAC technologies still need to improve in three areas: 1) Contactor, 2) Sorbent, and 3) Regeneration to drive down the costs. Technology-based economic development in all three areas are required to achieve {$<\$$}100/ton of CO2 which makes DAC economically viable. Current DAC cost is about 2{\textendash}6 times higher than the desired cost and depends highly on the source of energy used. In this review, we present the current status of commercial DAC technologies and elucidate the five pillars of technology including capture technologies, their energy demand, final costs, environmental impacts, and political support. We explain processing steps for liquid and solid carbon capture technologies and indicate their specific energy requirements. DAC capital and operational cost based on plant power energy sources, land and water needs of DAC are discussed in detail. At 0.01 Mt CO2/year capture capacity, DAC alone faces a challenge to meet the rates of carbon capture described in the goals of the Paris Agreement with 1.5{\textendash}2 C of global warming. However, DAC may partially help to offset difficult to avoid annual emissions from concrete (\$8\%), transportation (\$24\%), iron-steel industry (\$11\%), and wildfires (\$0.8\%).}, + abstract = {Climate change calls for adaptation of negative emission technologies such as direct air capture (DAC) of carbon dioxide (CO2) to lower the global warming impacts of greenhouse gases. Recently, elevated global interests to the DAC technologies prompted implementation of new tax credits and new policies worldwide that motivated the existing DAC companies and prompted the startup boom. There are presently 19 DAC plants operating worldwide, capturing more than 0.01 Mt CO2/year. DAC active plants capturing in average 10,000 tons of CO2 annually are still in their infancy and are expensive. DAC technologies still need to improve in three areas: 1) Contactor, 2) Sorbent, and 3) Regeneration to drive down the costs. Technology-based economic development in all three areas are required to achieve {$<\$$}100/ton of CO2 which makes DAC economically viable. Current DAC cost is about 2–6 times higher than the desired cost and depends highly on the source of energy used. In this review, we present the current status of commercial DAC technologies and elucidate the five pillars of technology including capture technologies, their energy demand, final costs, environmental impacts, and political support. We explain processing steps for liquid and solid carbon capture technologies and indicate their specific energy requirements. DAC capital and operational cost based on plant power energy sources, land and water needs of DAC are discussed in detail. At 0.01 Mt CO2/year capture capacity, DAC alone faces a challenge to meet the rates of carbon capture described in the goals of the Paris Agreement with 1.5–2 C of global warming. However, DAC may partially help to offset difficult to avoid annual emissions from concrete (\$8\%), transportation (\$24\%), iron-steel industry (\$11\%), and wildfires (\$0.8\%).}, langid = {english}, - file = {/home/simon/Zotero/storage/YJ7NDSY9/Ozkan et al. - 2022 - Current status and pillars of direct air capture t.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YJ7NDSY9/Ozkan et al. - 2022 - Current status and pillars of direct air capture t.pdf} } @article{parkMaximizingRightStuff2017, title = {Maximizing the Right Stuff: {{The}} Trade-off between Membrane Permeability and Selectivity}, shorttitle = {Maximizing the Right Stuff}, author = {Park, Ho Bum and Kamcev, Jovan and Robeson, Lloyd M. and Elimelech, Menachem and Freeman, Benny D.}, - year = {2017}, - month = jun, - journal = {Science}, + date = {2017-06-16}, + journaltitle = {Science}, + shortjournal = {Science}, volume = {356}, number = {6343}, pages = {eaab0530}, issn = {0036-8075, 1095-9203}, doi = {10.1126/science.aab0530}, + url = {https://www.science.org/doi/10.1126/science.aab0530}, urldate = {2023-09-28}, - abstract = {Filtering through to what's important Membranes are widely used for gas and liquid separations. Historical analysis of a range of gas pair separations indicated that there was an upper bound on the trade-off between membrane permeability, which limits flow rates, and the selectivity, which limits the quality of the separation process. Park et al. review the advances that have been made in attempts to break past this upper bound. Some inspiration has come from biological membranes. The authors also highlight cases where the challenges lie in areas other than improved separation performance. Science , this issue p. eaab0530 , BACKGROUND Synthetic membranes are used for desalination, dialysis, sterile filtration, food processing, dehydration of air and other industrial, medical, and environmental applications due to low energy requirements, compact design, and mechanical simplicity. New applications are emerging from the water-energy nexus, shale gas extraction, and environmental needs such as carbon capture. All membranes exhibit a trade-off between permeability{\textemdash}i.e., how fast molecules pass through a membrane material{\textemdash}and selectivity{\textemdash}i.e., to what extent the desired molecules are separated from the rest. However, biological membranes such as aquaporins and ion channels are both highly permeable and highly selective. Separation based on size difference is common, but there are other ways to either block one component or enhance transport of another through a membrane. Based on increasing molecular understanding of both biological and synthetic membranes, key design criteria for new membranes have emerged: (i) properly sized free-volume elements (or pores), (ii) narrow free-volume element (or pore size) distribution, (iii) a thin active layer, and (iv) highly tuned interactions between permeants of interest and the membrane. Here, we discuss the permeability/selectivity trade-off, highlight similarities and differences between synthetic and biological membranes, describe challenges for existing membranes, and identify fruitful areas of future research. ADVANCES Many organic, inorganic, and hybrid materials have emerged as potential membranes. In addition to polymers, used for most membranes today, materials such as carbon molecular sieves, ceramics, zeolites, various nanomaterials (e.g., graphene, graphene oxide, and metal organic frameworks), and their mixtures with polymers have been explored. Simultaneously, global challenges such as climate change and rapid population growth stimulate the search for efficient water purification and energy-generation technologies, many of which are membrane-based. Additional driving forces include wastewater reuse from shale gas extraction and improvement of chemical and petrochemical separation processes by increasing the use of light hydrocarbons for chemicals manufacturing. OUTLOOK Opportunities for advancing membranes include (i) more mechanically, chemically, and thermally robust materials; (ii) judiciously higher permeability and selectivity for applications where such improvements matter; and (iii) more emphasis on fundamental structure/property/processing relations. There is a pressing need for membranes with improved selectivity, rather than membranes with improved permeability, especially for water purification. Modeling at all length scales is needed to develop a coherent molecular understanding of membrane properties, provide insight for future materials design, and clarify the fundamental basis for trade-off behavior. Basic molecular-level understanding of thermodynamic and diffusion properties of water and ions in charged membranes for desalination and energy applications such as fuel cells is largely incomplete. Fundamental understanding of membrane structure optimization to control transport of minor species (e.g., trace-organic contaminants in desalination membranes, neutral compounds in charged membranes, and heavy hydrocarbons in membranes for natural gas separation) is needed. Laboratory evaluation of membranes is often conducted with highly idealized mixtures, so separation performance in real applications with complex mixtures is poorly understood. Lack of systematic understanding of methodologies to scale promising membranes from the few square centimeters needed for laboratory studies to the thousands of square meters needed for large applications stymies membrane deployment. Nevertheless, opportunities for membranes in both existing and emerging applications, together with an expanding set of membrane materials, hold great promise for membranes to effectively address separations needs. From intrinsic permeability/selectivity trade-off to practical performance in membranes. Polymer membranes for liquid and gas separation applications obey a permeability/selectivity trade-off{\textemdash}highly permeable membranes have low selectivity and vice versa{\textemdash}largely due to broad distributions of free-volume elements (or pores in porous membranes) and nonspecific interactions between small solutes and polymers. We highlight materials approaches to overcome this trade-off, including the development of inorganic, isoporous, mixed matrix, and aquaporin membranes. Further, materials must be processed into thin, typically supported membranes, fashioned into high surface/volume ratio modules, and used in optimized processes. Thus, factors that govern the practical feasibility of membranes such as mechanical strength, module design, and operating conditions are also discussed. , Increasing demands for energy-efficient separations in applications ranging from water purification to petroleum refining, chemicals production, and carbon capture have stimulated a vigorous search for novel, high-performance separation membranes. Synthetic membranes suffer a ubiquitous, pernicious trade-off: highly permeable membranes lack selectivity and vice versa. However, materials with both high permeability and high selectivity are beginning to emerge. For example, design features from biological membranes have been applied to break the permeability-selectivity trade-off. We review the basis for the permeability-selectivity trade-off, state-of-the-art approaches to membrane materials design to overcome the trade-off, and factors other than permeability and selectivity that govern membrane performance and, in turn, influence membrane design.}, + abstract = {Filtering through to what's important Membranes are widely used for gas and liquid separations. Historical analysis of a range of gas pair separations indicated that there was an upper bound on the trade-off between membrane permeability, which limits flow rates, and the selectivity, which limits the quality of the separation process. Park et al. review the advances that have been made in attempts to break past this upper bound. Some inspiration has come from biological membranes. The authors also highlight cases where the challenges lie in areas other than improved separation performance. Science , this issue p. eaab0530 , BACKGROUND Synthetic membranes are used for desalination, dialysis, sterile filtration, food processing, dehydration of air and other industrial, medical, and environmental applications due to low energy requirements, compact design, and mechanical simplicity. New applications are emerging from the water-energy nexus, shale gas extraction, and environmental needs such as carbon capture. All membranes exhibit a trade-off between permeability—i.e., how fast molecules pass through a membrane material—and selectivity—i.e., to what extent the desired molecules are separated from the rest. However, biological membranes such as aquaporins and ion channels are both highly permeable and highly selective. Separation based on size difference is common, but there are other ways to either block one component or enhance transport of another through a membrane. Based on increasing molecular understanding of both biological and synthetic membranes, key design criteria for new membranes have emerged: (i) properly sized free-volume elements (or pores), (ii) narrow free-volume element (or pore size) distribution, (iii) a thin active layer, and (iv) highly tuned interactions between permeants of interest and the membrane. Here, we discuss the permeability/selectivity trade-off, highlight similarities and differences between synthetic and biological membranes, describe challenges for existing membranes, and identify fruitful areas of future research. ADVANCES Many organic, inorganic, and hybrid materials have emerged as potential membranes. In addition to polymers, used for most membranes today, materials such as carbon molecular sieves, ceramics, zeolites, various nanomaterials (e.g., graphene, graphene oxide, and metal organic frameworks), and their mixtures with polymers have been explored. Simultaneously, global challenges such as climate change and rapid population growth stimulate the search for efficient water purification and energy-generation technologies, many of which are membrane-based. Additional driving forces include wastewater reuse from shale gas extraction and improvement of chemical and petrochemical separation processes by increasing the use of light hydrocarbons for chemicals manufacturing. OUTLOOK Opportunities for advancing membranes include (i) more mechanically, chemically, and thermally robust materials; (ii) judiciously higher permeability and selectivity for applications where such improvements matter; and (iii) more emphasis on fundamental structure/property/processing relations. There is a pressing need for membranes with improved selectivity, rather than membranes with improved permeability, especially for water purification. Modeling at all length scales is needed to develop a coherent molecular understanding of membrane properties, provide insight for future materials design, and clarify the fundamental basis for trade-off behavior. Basic molecular-level understanding of thermodynamic and diffusion properties of water and ions in charged membranes for desalination and energy applications such as fuel cells is largely incomplete. Fundamental understanding of membrane structure optimization to control transport of minor species (e.g., trace-organic contaminants in desalination membranes, neutral compounds in charged membranes, and heavy hydrocarbons in membranes for natural gas separation) is needed. Laboratory evaluation of membranes is often conducted with highly idealized mixtures, so separation performance in real applications with complex mixtures is poorly understood. Lack of systematic understanding of methodologies to scale promising membranes from the few square centimeters needed for laboratory studies to the thousands of square meters needed for large applications stymies membrane deployment. Nevertheless, opportunities for membranes in both existing and emerging applications, together with an expanding set of membrane materials, hold great promise for membranes to effectively address separations needs. From intrinsic permeability/selectivity trade-off to practical performance in membranes. Polymer membranes for liquid and gas separation applications obey a permeability/selectivity trade-off—highly permeable membranes have low selectivity and vice versa—largely due to broad distributions of free-volume elements (or pores in porous membranes) and nonspecific interactions between small solutes and polymers. We highlight materials approaches to overcome this trade-off, including the development of inorganic, isoporous, mixed matrix, and aquaporin membranes. Further, materials must be processed into thin, typically supported membranes, fashioned into high surface/volume ratio modules, and used in optimized processes. Thus, factors that govern the practical feasibility of membranes such as mechanical strength, module design, and operating conditions are also discussed. , Increasing demands for energy-efficient separations in applications ranging from water purification to petroleum refining, chemicals production, and carbon capture have stimulated a vigorous search for novel, high-performance separation membranes. Synthetic membranes suffer a ubiquitous, pernicious trade-off: highly permeable membranes lack selectivity and vice versa. However, materials with both high permeability and high selectivity are beginning to emerge. For example, design features from biological membranes have been applied to break the permeability-selectivity trade-off. We review the basis for the permeability-selectivity trade-off, state-of-the-art approaches to membrane materials design to overcome the trade-off, and factors other than permeability and selectivity that govern membrane performance and, in turn, influence membrane design.}, langid = {english}, - file = {/home/simon/Zotero/storage/QM62BF5F/Park et al. - 2017 - Maximizing the right stuff The trade-off between .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QM62BF5F/Park et al. - 2017 - Maximizing the right stuff The trade-off between .pdf} } @article{partayNewMethodDetermining2008, - title = {A New Method for Determining the Interfacial Molecules and Characterizing the Surface Roughness in Computer Simulations. {{Application}} to the Liquid{\textendash}Vapor Interface of Water}, - author = {P{\'a}rtay, L{\'i}via B. and Hantal, Gy{\"o}rgy and Jedlovszky, P{\'a}l and Vincze, {\'A}rp{\'a}d and Horvai, George}, - year = {2008}, - month = apr, - journal = {Journal of Computational Chemistry}, + title = {A New Method for Determining the Interfacial Molecules and Characterizing the Surface Roughness in Computer Simulations. {{Application}} to the Liquid–Vapor Interface of Water}, + author = {Pártay, Lívia B. and Hantal, György and Jedlovszky, Pál and Vincze, Árpád and Horvai, George}, + date = {2008-04-30}, + journaltitle = {Journal of Computational Chemistry}, + shortjournal = {J. Comput. Chem.}, volume = {29}, number = {6}, pages = {945--956}, issn = {01928651, 1096987X}, doi = {10.1002/jcc.20852}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.20852}, urldate = {2023-06-21}, - abstract = {A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen at molecular resolution, a situation that regularly occurs in computer simulations. In the new method, the surface is scanned by moving a probe sphere of a given radius along a large set of test lines that are perpendicular to the plane of the interface. The molecules that are hit by the probe spheres are regarded as interfacial ones, and the position of the test spheres when they are in contact with the interfacial molecules give an estimate of the surface. The dependence of the method on various parameters, in particular, on the size of the probe sphere is discussed in detail. Based on the list of molecules identified as truly interfacial ones, two measures of the molecular scale roughness of the surface are proposed. The bivariate distribution of the lateral and normal distances of two points of the interface provides a full description of the molecular scale morphology of the surface in a statistical sense. For practical purposes two parameters related to the dependence of the average normal distance of two surface points on their lateral distance can be used. These two parameters correspond to the frequency and amplitude of the surface roughness, respectively. The new method is applied for the analysis of the molecular level structure of the liquid{\textendash}vapor interface of water. As an immediate result of the application of the new method it is shown that the orientational preferences of the interfacial water molecules depend only on the local curvature of the interface, and hence the molecules located at wells of concave curvature of the rippled surface prefer the same orientations as waters located at the surface of small apolar solutes. The vast majority of the truly interfacial molecules are found to form a strongly percolating two-dimensional hydrogen bonded network at the surface, whereas no percolation is observed within the second molecular layer beyond the surface.}, + abstract = {A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen at molecular resolution, a situation that regularly occurs in computer simulations. In the new method, the surface is scanned by moving a probe sphere of a given radius along a large set of test lines that are perpendicular to the plane of the interface. The molecules that are hit by the probe spheres are regarded as interfacial ones, and the position of the test spheres when they are in contact with the interfacial molecules give an estimate of the surface. The dependence of the method on various parameters, in particular, on the size of the probe sphere is discussed in detail. Based on the list of molecules identified as truly interfacial ones, two measures of the molecular scale roughness of the surface are proposed. The bivariate distribution of the lateral and normal distances of two points of the interface provides a full description of the molecular scale morphology of the surface in a statistical sense. For practical purposes two parameters related to the dependence of the average normal distance of two surface points on their lateral distance can be used. These two parameters correspond to the frequency and amplitude of the surface roughness, respectively. The new method is applied for the analysis of the molecular level structure of the liquid–vapor interface of water. As an immediate result of the application of the new method it is shown that the orientational preferences of the interfacial water molecules depend only on the local curvature of the interface, and hence the molecules located at wells of concave curvature of the rippled surface prefer the same orientations as waters located at the surface of small apolar solutes. The vast majority of the truly interfacial molecules are found to form a strongly percolating two-dimensional hydrogen bonded network at the surface, whereas no percolation is observed within the second molecular layer beyond the surface.}, langid = {english}, - file = {/home/simon/Zotero/storage/IEEPMJQ6/Pártay et al. - 2008 - A new method for determining the interfacial molec.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/IEEPMJQ6/Pártay et al. - 2008 - A new method for determining the interfacial molec.pdf} } @article{pascalThermodynamicsLiquidsStandard2011, title = {Thermodynamics of Liquids: Standard Molar Entropies and Heat Capacities of Common Solvents from {{2PT}} Molecular Dynamics}, shorttitle = {Thermodynamics of Liquids}, author = {Pascal, Tod A. and Lin, Shiang-Tai and Goddard Iii, William A.}, - year = {2011}, - journal = {Phys. Chem. Chem. Phys.}, + date = {2011}, + journaltitle = {Phys. Chem. Chem. Phys.}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {13}, number = {1}, pages = {169--181}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C0CP01549K}, + url = {http://xlink.rsc.org/?DOI=C0CP01549K}, urldate = {2023-05-16}, langid = {english}, - file = {/home/simon/Zotero/storage/D3M72JAM/Pascal et al. - 2011 - Thermodynamics of liquids standard molar entropie.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/D3M72JAM/Pascal et al. - 2011 - Thermodynamics of liquids standard molar entropie.pdf} } @article{peemoellerWaterMoleculeDynamics1986, title = {Water Molecule Dynamics in Hydrated Lysozyme. {{A}} Deuteron Magnetic Resonance Study}, author = {Peemoeller, H. and Yeomans, F.G. and Kydon, D.W. and Sharp, A.R.}, - year = {1986}, - month = apr, - journal = {Biophysical Journal}, + date = {1986-04}, + journaltitle = {Biophysical Journal}, + shortjournal = {Biophysical Journal}, volume = {49}, number = {4}, pages = {943--948}, issn = {00063495}, doi = {10.1016/S0006-3495(86)83722-5}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349586837225}, urldate = {2023-07-31}, abstract = {Proton nuclear magnetic resonance relaxation investigations of water dynamics in hydrated protein powders have the serious drawback that protein-water intermolecular dipolar interactions make the unambiguous interpretation of the results difficult. To circumvent this difficulty, deuteron spin-lattice and spin-spin relaxation times in lysozyme powder hydrated with deuterium oxide were measured as a function of temperature and at two frequencies. Although the deuteron relaxation results are compatible with a water molecule dynamics model based on either a bimodal distribution of correlation times or anisotropic motion, a comparison of the present results with proton data suggests than an anisotropic motion model is more likely to provide a reasonable description of the water molecule motion. An analysis based on an anisotropic motion model that uses two correlation times to characterize the motion shows that most of the water molecules rotate about their twofold axis of symmetry at a rate that is only -100 times smaller than the rate of isotropic diffusion in the bulk liquid. The reorientation of the twofold axis of symmetry itself is characterized by a correlation time of 10-7 S.}, langid = {english}, keywords = {HEWL,NMR}, - file = {/home/simon/Zotero/storage/NHZYMAL6/Peemoeller et al. - 1986 - Water molecule dynamics in hydrated lysozyme. A de.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NHZYMAL6/Peemoeller et al. - 1986 - Water molecule dynamics in hydrated lysozyme. A de.pdf} } @article{pendhariApplicationPolymerComposites2008, title = {Application of Polymer Composites in Civil Construction: {{A}} General Review}, shorttitle = {Application of Polymer Composites in Civil Construction}, author = {Pendhari, Sandeep S. and Kant, Tarun and Desai, Yogesh M.}, - year = {2008}, - month = jul, - journal = {Composite Structures}, + date = {2008-07}, + journaltitle = {Composite Structures}, + shortjournal = {Compos. Struct.}, volume = {84}, number = {2}, pages = {114--124}, issn = {02638223}, doi = {10.1016/j.compstruct.2007.06.007}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S026382230700181X}, urldate = {2023-10-17}, abstract = {Different applications of fiber reinforced polymer composites (FRPCs) for external strengthening in civil construction are reviewed in this paper. Experimental as well as analytical and numerical research contributions have been focussed in the review. The main structural components such as beams, columns and beam-column joints, have been reviewed and structural behavior of each component is discussed briefly. Finally, general concluding remarks are made along with possible future directions of research.}, langid = {english}, - file = {/home/simon/Zotero/storage/X4WNJCFQ/Pendhari et al. - 2008 - Application of polymer composites in civil constru.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/X4WNJCFQ/Pendhari et al. - 2008 - Application of polymer composites in civil constru.pdf} } @article{pengMembranesBioethanolProduction2021, title = {Membranes for Bioethanol Production by Pervaporation}, author = {Peng, Ping and Lan, Yongqiang and Liang, Lun and Jia, Kemeng}, - year = {2021}, - month = jan, - journal = {Biotechnology for Biofuels}, + date = {2021-01-07}, + journaltitle = {Biotechnology for Biofuels}, + shortjournal = {Biotechnology for Biofuels}, volume = {14}, number = {1}, pages = {10}, issn = {1754-6834}, doi = {10.1186/s13068-020-01857-y}, + url = {https://doi.org/10.1186/s13068-020-01857-y}, urldate = {2023-10-23}, abstract = {Bioethanol as a renewable energy resource plays an important role in alleviating energy crisis and environmental protection. Pervaporation has achieved increasing attention because of its potential to be a useful way to separate ethanol from the biomass fermentation process.}, keywords = {Ethanol,Membrane,Pervaporation,Polymer}, - file = {/home/simon/Zotero/storage/WJ6SXH9X/Peng et al. - 2021 - Membranes for bioethanol production by pervaporati.pdf;/home/simon/Zotero/storage/896B9TF8/s13068-020-01857-y.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WJ6SXH9X/Peng et al. - 2021 - Membranes for bioethanol production by pervaporati.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/896B9TF8/s13068-020-01857-y.html} } @article{peregoMolecularDynamicsSimulations2015, title = {Molecular Dynamics Simulations of Solutions at Constant Chemical Potential}, author = {Perego, C. and Salvalaglio, M. and Parrinello, M.}, - year = {2015}, - month = apr, - journal = {The Journal of Chemical Physics}, + date = {2015-04-14}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {142}, number = {14}, pages = {144113}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4917200}, + url = {https://pubs.aip.org/aip/jcp/article/898424}, urldate = {2023-07-09}, langid = {english}, - file = {/home/simon/Zotero/storage/BRB6KV9E/1501.07825.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BRB6KV9E/1501.07825.pdf} } @article{pereraKirkwoodBuffIntegralsAqueous2006, title = {Kirkwood-{{Buff}} Integrals of Aqueous Alcohol Binary Mixtures}, - author = {Perera, A. and Sokoli{\'c}, F. and Alm{\'a}sy, L. and Koga, Y.}, - year = {2006}, - month = mar, - journal = {The Journal of Chemical Physics}, + author = {Perera, A. and Sokolić, F. and Almásy, L. and Koga, Y.}, + date = {2006-03-28}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {124}, number = {12}, pages = {124515}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.2178787}, + url = {https://pubs.aip.org/aip/jcp/article/929147}, urldate = {2023-06-21}, langid = {english}, keywords = {mixture}, - file = {/home/simon/Zotero/storage/SWIQHNL2/Perera et al. - 2006 - Kirkwood-Buff integrals of aqueous alcohol binary .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SWIQHNL2/Perera et al. - 2006 - Kirkwood-Buff integrals of aqueous alcohol binary .pdf} } @article{perrinWaterDynamicsIonomer2006, title = {Water {{Dynamics}} in {{Ionomer Membranes}} by {{Field-Cycling NMR Relaxometry}}}, author = {Perrin, Jean-Christophe and Lyonnard, Sandrine and Guillermo, Armel and Levitz, Pierre}, - year = {2006}, - month = mar, - journal = {The Journal of Physical Chemistry B}, + date = {2006-03-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {110}, number = {11}, pages = {5439--5444}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp057433e}, + url = {https://pubs.acs.org/doi/10.1021/jp057433e}, urldate = {2023-07-14}, langid = {english}, keywords = {NMR,polymer}, - file = {/home/simon/Zotero/storage/3GHW2AFH/Perrin et al. - 2006 - Water Dynamics in Ionomer Membranes by Field-Cycli.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3GHW2AFH/Perrin et al. - 2006 - Water Dynamics in Ionomer Membranes by Field-Cycli.pdf} } @article{peterCalculationNMRrelaxationParameters2001, title = {Calculation of {{NMR-relaxation}} Parameters for Flexible Molecules from Molecular Dynamics Simulations}, - author = {Peter, Christine and Daura, Xavier and {van Gunsteren}, Wilfred F}, - year = {2001}, - abstract = {Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages ( r-6 -1/6 or r-3 1/3) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of {$\beta$}-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.}, + author = {Peter, Christine and Daura, Xavier and family=Gunsteren, given=Wilfred F, prefix=van, useprefix=true}, + date = {2001}, + abstract = {Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages ( r−6 −1/6 or r−3 1/3) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of β-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.}, langid = {english}, - file = {/home/simon/Zotero/storage/7JR8CE2S/Peter et al. - Calculation of NMR-relaxation parameters for flexi.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7JR8CE2S/Peter et al. - Calculation of NMR-relaxation parameters for flexi.pdf} } @article{petitMultiscaleDynamics1H2010, title = {Multiscale Dynamics of {{1H}} and {{19F}} in Confined Ionogels for Lithium Batteries}, author = {Petit, Dominique and Korb, Jean-Pierre and Levitz, Pierre and LeBideau, Jean and Brevet, David}, - year = {2010}, - month = apr, - journal = {Comptes Rendus Chimie}, + date = {2010-04}, + journaltitle = {Comptes Rendus Chimie}, + shortjournal = {Comptes Rendus Chimie}, volume = {13}, number = {4}, pages = {409--411}, issn = {16310748}, doi = {10.1016/j.crci.2009.08.002}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1631074809001489}, urldate = {2023-09-18}, - abstract = {We present the first results of the nuclear magnetic relaxation dispersion (NMRD) of the confined proton-bearing cation (BMI) and fluorine-bearing anion (TFSI) pair of ionic liquids (Li+-ionogels) confined within a silica-like mesoporous matrices designed for lithium batteries. These results are in favour of a very-correlated dynamical motion of the anion{\textendash}cation pair within the solid and disordered silica matrix.}, + abstract = {We present the first results of the nuclear magnetic relaxation dispersion (NMRD) of the confined proton-bearing cation (BMI) and fluorine-bearing anion (TFSI) pair of ionic liquids (Li+-ionogels) confined within a silica-like mesoporous matrices designed for lithium batteries. These results are in favour of a very-correlated dynamical motion of the anion–cation pair within the solid and disordered silica matrix.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/TVBBDSZJ/Petit et al. - 2010 - Multiscale dynamics of 1H and 19F in confined iono.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/TVBBDSZJ/Petit et al. - 2010 - Multiscale dynamics of 1H and 19F in confined iono.pdf} } @article{petongWaterEthanolMixtures2000, - title = {{{Water}}-{{Ethanol Mixtures}} at {{Different Compositions}} and {{Temperatures}}. {{A Dieletric Relaxation Study}}}, + title = {{{Water}}−{{Ethanol Mixtures}} at {{Different Compositions}} and {{Temperatures}}. {{A Dieletric Relaxation Study}}}, author = {Petong, P. and Pottel, R. and Kaatze, U.}, - year = {2000}, - month = aug, - journal = {The Journal of Physical Chemistry A}, + date = {2000-08-01}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, volume = {104}, number = {32}, pages = {7420--7428}, issn = {1089-5639, 1520-5215}, doi = {10.1021/jp001393r}, + url = {https://pubs.acs.org/doi/10.1021/jp001393r}, urldate = {2023-04-26}, langid = {english}, keywords = {HB,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/V463FT4C/Petong et al. - 2000 - Water−Ethanol Mixtures at Different Compositions a.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/V463FT4C/Petong et al. - 2000 - Water−Ethanol Mixtures at Different Compositions a.pdf} } @article{phanFluidTransportHeterogeneous2020, title = {Fluid Transport through Heterogeneous Pore Matrices: {{Multiscale}} Simulation Approaches}, shorttitle = {Fluid Transport through Heterogeneous Pore Matrices}, author = {Phan, Anh and Fan, Dian (范典) and Striolo, Alberto}, - year = {2020}, - month = oct, - journal = {Physics of Fluids}, + date = {2020-10-09}, + journaltitle = {Physics of Fluids}, + shortjournal = {Phys. Fluids}, volume = {32}, number = {10}, pages = {101301}, issn = {1070-6631}, doi = {10.1063/5.0022481}, + url = {https://doi.org/10.1063/5.0022481}, urldate = {2023-10-04}, - abstract = {Fluids confined in nanopores exhibit several unique structural and dynamical characteristics that affect a number of applications in industry as well as natural phenomena. Understanding and predicting the complex fluid behavior under nano-confinement is therefore of key importance, and both experimental and computational approaches have been employed toward this goal. It is now feasible to employ both simulations and theoretical methods, the results of which can be validated by cutting-edge experimental quantification. Nevertheless, predicting fluid transport through heterogeneous pore networks at a scale large enough to be relevant for practical applications remains elusive because one should account for a variety of fluid{\textendash}rock interactions, a wide range of confined fluid states, as well as pore-edge effects and the existence of preferential pathways, which, together with many other phenomena, affect the results. The aim of this Review is to overview the significance of molecular phenomena on fluid transport in nanoporous media, the capability and shortcomings of both molecular and continuum fluid modeling approaches, and recent progress in multiscale modeling of fluid transport. In our interpretation, a multiscale approach couples a molecular picture for fluid interactions with solid surfaces at the single nanopore level with hierarchical transport analysis through realistic heterogeneous pore networks to balance physical accuracy with computational expense. When possible, comparison against experiments is provided as a guiding roadmap for selecting the appropriate computational methods. The appropriateness of an approach is certainly related to the final application of interest, as different sectors will require different levels of precision in the predictions.}, - file = {/home/simon/Zotero/storage/EKIKH58G/Phan et al. - 2020 - Fluid transport through heterogeneous pore matrice.pdf;/home/simon/Zotero/storage/2CH64P6G/1059198.html} + abstract = {Fluids confined in nanopores exhibit several unique structural and dynamical characteristics that affect a number of applications in industry as well as natural phenomena. Understanding and predicting the complex fluid behavior under nano-confinement is therefore of key importance, and both experimental and computational approaches have been employed toward this goal. It is now feasible to employ both simulations and theoretical methods, the results of which can be validated by cutting-edge experimental quantification. Nevertheless, predicting fluid transport through heterogeneous pore networks at a scale large enough to be relevant for practical applications remains elusive because one should account for a variety of fluid–rock interactions, a wide range of confined fluid states, as well as pore-edge effects and the existence of preferential pathways, which, together with many other phenomena, affect the results. The aim of this Review is to overview the significance of molecular phenomena on fluid transport in nanoporous media, the capability and shortcomings of both molecular and continuum fluid modeling approaches, and recent progress in multiscale modeling of fluid transport. In our interpretation, a multiscale approach couples a molecular picture for fluid interactions with solid surfaces at the single nanopore level with hierarchical transport analysis through realistic heterogeneous pore networks to balance physical accuracy with computational expense. When possible, comparison against experiments is provided as a guiding roadmap for selecting the appropriate computational methods. The appropriateness of an approach is certainly related to the final application of interest, as different sectors will require different levels of precision in the predictions.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/EKIKH58G/Phan et al. - 2020 - Fluid transport through heterogeneous pore matrice.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/2CH64P6G/1059198.html} } @article{phanPreferentialAdsorptionLiquid2014, - title = {Preferential {{Adsorption}} from {{Liquid Water}}{\textendash}{{Ethanol Mixtures}} in {{Alumina Pores}}}, + title = {Preferential {{Adsorption}} from {{Liquid Water}}–{{Ethanol Mixtures}} in {{Alumina Pores}}}, author = {Phan, Anh and Cole, David R. and Striolo, Alberto}, - year = {2014}, - month = jul, - journal = {Langmuir}, + date = {2014-07-15}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {30}, number = {27}, pages = {8066--8077}, publisher = {{American Chemical Society}}, issn = {0743-7463}, doi = {10.1021/la501177t}, + url = {https://doi.org/10.1021/la501177t}, urldate = {2023-07-11}, - abstract = {The sorptivity, structure, and dynamics of liquid water{\textendash}ethanol mixtures confined in alumina pores were studied by molecular dynamics simulations. Due to an effective stronger attraction between water and the alumina surface, our simulations show that water is preferentially adsorbed in alumina nanopores from bulk solutions of varying composition. These results are in good qualitative agreement with experimental data reported by Rao and Sircar (Adsorpt. Sci. Technol. 1993, 10, 93). Analysis of the simulated trajectories allows us to predict that water diffuses through the narrow pores more easily than ethanol, in part because of its smaller size. Our results suggest that ethanol has an antiplasticization effect on water within the narrow pores considered here, whereas it has a plasticization effect on water in the bulk. Rao and Sircar suggested that alumina could be used in concentration swing and/or concentration-thermal swing adsorption processes to separate water from ethanol. In addition, our results suggest the possibility of using alumina for manufacturing permselective membranes to produce anhydrous ethanol from liquid water{\textendash}ethanol solutions.}, - file = {/home/simon/Zotero/storage/66JC2E5T/Phan et al. - 2014 - Preferential Adsorption from Liquid Water–Ethanol .pdf;/home/simon/Zotero/storage/67TDJM9U/la501177t_si_001.pdf;/home/simon/Zotero/storage/D25JQT93/Phan et al. - 2014 - Preferential Adsorption from Liquid Water–Ethanol .pdf;/home/simon/Zotero/storage/V5FMNJWU/la501177t.html} + abstract = {The sorptivity, structure, and dynamics of liquid water–ethanol mixtures confined in alumina pores were studied by molecular dynamics simulations. Due to an effective stronger attraction between water and the alumina surface, our simulations show that water is preferentially adsorbed in alumina nanopores from bulk solutions of varying composition. These results are in good qualitative agreement with experimental data reported by Rao and Sircar (Adsorpt. Sci. Technol. 1993, 10, 93). Analysis of the simulated trajectories allows us to predict that water diffuses through the narrow pores more easily than ethanol, in part because of its smaller size. Our results suggest that ethanol has an antiplasticization effect on water within the narrow pores considered here, whereas it has a plasticization effect on water in the bulk. Rao and Sircar suggested that alumina could be used in concentration swing and/or concentration-thermal swing adsorption processes to separate water from ethanol. In addition, our results suggest the possibility of using alumina for manufacturing permselective membranes to produce anhydrous ethanol from liquid water–ethanol solutions.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/66JC2E5T/Phan et al. - 2014 - Preferential Adsorption from Liquid Water–Ethanol .pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/67TDJM9U/la501177t_si_001.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/D25JQT93/Phan et al. - 2014 - Preferential Adsorption from Liquid Water–Ethanol .pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/V5FMNJWU/la501177t.html} } @article{phanSurfaceTensionInterfacial, title = {The Surface Tension and Interfacial Composition of Water/Ethanol Mixture}, author = {Phan, Chi M}, - abstract = {This study develops a model to fit the surface tension of the water/ethanol mixture for the complete composition range from 0 to 1. The theoretical framework complements Van Der Waals's theory on the density gradient. The modelling results overcome the limitation of Gibbs adsorption isotherm, which completely ignores the composition of the interfacial layer. Furthermore, the model presents a new method to correctly calculate the composition of the interfacial layer for binary liquid mixture and surfactant solutions.}, + abstract = {This study develops a model to fit the surface tension of the water/ethanol mixture for the complete composition range from 0 to 1. The theoretical framework complements Van Der Waals’s theory on the density gradient. The modelling results overcome the limitation of Gibbs adsorption isotherm, which completely ignores the composition of the interfacial layer. Furthermore, the model presents a new method to correctly calculate the composition of the interfacial layer for binary liquid mixture and surfactant solutions.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/M24NNTX9/Phan - The surface tension and interfacial composition of.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/M24NNTX9/Phan - The surface tension and interfacial composition of.pdf} } @article{philipsProtonNMRRelaxation2019, title = {Proton {{NMR}} Relaxation from Molecular Dynamics: Intramolecular and Intermolecular Contributions in Water and Acetonitrile}, shorttitle = {Proton {{NMR}} Relaxation from Molecular Dynamics}, author = {Philips, Adam and Autschbach, Jochen}, - year = {2019}, - journal = {Physical Chemistry Chemical Physics}, + date = {2019}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {21}, number = {48}, pages = {26621--26629}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C9CP04976B}, + url = {http://xlink.rsc.org/?DOI=C9CP04976B}, urldate = {2023-05-24}, abstract = {NMR relaxation rates for protons in liquid water and neat acetonitrile were computed based on ab initio molecular dynamics (aiMD) with forces from Kohn-Sham (KS) theory as well as force-field (FF) based classical dynamics. Intra- and intermolecular dipole-dipole contributions were separated, and nearly quantitative agreement with experiment was obtained for water. Spinrotation (SR) contributions to the intramolecular relaxation rate in acetonitrile were computed using nuclear SR coupling tensors obtained from KS theory, and improved the total computed intramolecular rate to within a factor of two of experiment. Insufficient sampling of rare short-time collision events between neighboring acetonitrile molecules in the simulations is hypothesized as a major source of error in the intermolecular contributions.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/Q85Z2CE6/Philips and Autschbach - 2019 - Proton NMR relaxation from molecular dynamics int.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Q85Z2CE6/Philips and Autschbach - 2019 - Proton NMR relaxation from molecular dynamics int.pdf} } @article{philipsQuadrupolarNMRRelaxation2020, - title = {Quadrupolar {{NMR Relaxation}} of {{Aqueous}} {\textsuperscript{127}} {{I}} {\textsuperscript{{\textendash}}} , {\textsuperscript{131}} {{Xe}}, and {\textsuperscript{133}} {{Cs}} {\textsuperscript{+}} : {{A First-Principles Approach}} from {{Dynamics}} to {{Properties}}}, - shorttitle = {Quadrupolar {{NMR Relaxation}} of {{Aqueous}} {\textsuperscript{127}} {{I}} {\textsuperscript{{\textendash}}} , {\textsuperscript{131}} {{Xe}}, and {\textsuperscript{133}} {{Cs}} {\textsuperscript{+}}}, + title = {Quadrupolar {{NMR Relaxation}} of {{Aqueous}} {\textsuperscript{127}} {{I}} {\textsuperscript{–}} , {\textsuperscript{131}} {{Xe}}, and {\textsuperscript{133}} {{Cs}} {\textsuperscript{+}} : {{A First-Principles Approach}} from {{Dynamics}} to {{Properties}}}, + shorttitle = {Quadrupolar {{NMR Relaxation}} of {{Aqueous}} {\textsuperscript{127}} {{I}} {\textsuperscript{–}} , {\textsuperscript{131}} {{Xe}}, and {\textsuperscript{133}} {{Cs}} {\textsuperscript{+}}}, author = {Philips, Adam and Autschbach, Jochen}, - year = {2020}, - month = sep, - journal = {Journal of Chemical Theory and Computation}, + date = {2020-09-08}, + journaltitle = {Journal of Chemical Theory and Computation}, + shortjournal = {J. Chem. Theory Comput.}, volume = {16}, number = {9}, pages = {5835--5844}, issn = {1549-9618, 1549-9626}, doi = {10.1021/acs.jctc.0c00581}, + url = {https://pubs.acs.org/doi/10.1021/acs.jctc.0c00581}, urldate = {2023-05-24}, - abstract = {Quadrupolar NMR relaxation rates were computed for aqueous 133Cs+, 131Xe, and 127I- via Kohn-Sham (KS) density functional theory-based ab initio molecular dynamics and KS calculations of the electric field gradient (EFG) tensors along the trajectories. The resulting rates are within a factor of 1-3 of the experimental values and can be compared to available results from classical dynamics and EFGs from electrostatic models with corrections via Sternheimer antishielding factors. Relativistic effects are shown to have an enhancing effect on the magnitude of the EFGs. An analysis of the EFGs was carried out in terms of localized molecular orbitals to elucidate contributions from the solvent versus solute polarization and assess the validity of the Sternheimer approximation for these systems.}, + abstract = {Quadrupolar NMR relaxation rates were computed for aqueous 133Cs+, 131Xe, and 127I− via Kohn−Sham (KS) density functional theory-based ab initio molecular dynamics and KS calculations of the electric field gradient (EFG) tensors along the trajectories. The resulting rates are within a factor of 1−3 of the experimental values and can be compared to available results from classical dynamics and EFGs from electrostatic models with corrections via Sternheimer antishielding factors. Relativistic effects are shown to have an enhancing effect on the magnitude of the EFGs. An analysis of the EFGs was carried out in terms of localized molecular orbitals to elucidate contributions from the solvent versus solute polarization and assess the validity of the Sternheimer approximation for these systems.}, langid = {english}, keywords = {NMR}, - file = {/home/simon/Zotero/storage/E6SIT5NA/Philips and Autschbach - 2020 - Quadrupolar NMR Relaxation of Aqueous 127su.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/E6SIT5NA/Philips and Autschbach - 2020 - Quadrupolar NMR Relaxation of Aqueous 127su.pdf} } @article{pozarMicroheterogeneityClusteringBinary2016, title = {Micro-Heterogeneity versus Clustering in Binary Mixtures of Ethanol with Water or Alkanes}, - author = {Po{\v z}ar, Martina and Lovrin{\v c}evi{\'c}, Bernarda and Zorani{\'c}, Larisa and Primora{\'c}, Tomislav and Sokoli{\'c}, Franjo and Perera, Aur{\'e}lien}, - year = {2016}, - journal = {Physical Chemistry Chemical Physics}, + author = {Požar, Martina and Lovrinčević, Bernarda and Zoranić, Larisa and Primorać, Tomislav and Sokolić, Franjo and Perera, Aurélien}, + date = {2016}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {18}, number = {34}, pages = {23971--23979}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C6CP04676B}, + url = {http://xlink.rsc.org/?DOI=C6CP04676B}, urldate = {2023-06-21}, - abstract = {Snapshots of the difference in complex disorder, with analogy with direct (ethanol{\textendash}water) and inverse (ethanol{\textendash}alkanes) emulsions. , Ethanol is a hydrogen bonding liquid. When mixed in small concentrations with water or alkanes, it forms aggregate structures reminiscent of, respectively, the direct and inverse micellar aggregates found in emulsions, albeit at much smaller sizes. At higher concentrations, micro-heterogeneous mixing with segregated domains is found. We examine how different statistical methods, namely correlation function analysis, structure factor analysis and cluster distribution analysis, can describe efficiently these morphological changes in these mixtures. In particular, we explain how the neat alcohol pre-peak of the structure factor evolves into the domain pre-peak under mixing conditions, and how this evolution differs whether the co-solvent is water or alkane. This study clearly establishes the heuristic superiority of the correlation function/structure factor analysis to study the micro-heterogeneity, since cluster distribution analysis is insensitive to domain segregation. Correlation functions detect the domains, with a clear structure factor pre-peak signature, while the cluster techniques detect the cluster hierarchy within domains. The main conclusion is that, in micro-segregated mixtures, the domain structure is a more fundamental statistical entity than the underlying cluster structures. These findings could help better understand comparatively the radiation scattering experiments, which are sensitive to domains, versus the spectroscopy-NMR experiments, which are sensitive to clusters.}, + abstract = {Snapshots of the difference in complex disorder, with analogy with direct (ethanol–water) and inverse (ethanol–alkanes) emulsions. , Ethanol is a hydrogen bonding liquid. When mixed in small concentrations with water or alkanes, it forms aggregate structures reminiscent of, respectively, the direct and inverse micellar aggregates found in emulsions, albeit at much smaller sizes. At higher concentrations, micro-heterogeneous mixing with segregated domains is found. We examine how different statistical methods, namely correlation function analysis, structure factor analysis and cluster distribution analysis, can describe efficiently these morphological changes in these mixtures. In particular, we explain how the neat alcohol pre-peak of the structure factor evolves into the domain pre-peak under mixing conditions, and how this evolution differs whether the co-solvent is water or alkane. This study clearly establishes the heuristic superiority of the correlation function/structure factor analysis to study the micro-heterogeneity, since cluster distribution analysis is insensitive to domain segregation. Correlation functions detect the domains, with a clear structure factor pre-peak signature, while the cluster techniques detect the cluster hierarchy within domains. The main conclusion is that, in micro-segregated mixtures, the domain structure is a more fundamental statistical entity than the underlying cluster structures. These findings could help better understand comparatively the radiation scattering experiments, which are sensitive to domains, versus the spectroscopy-NMR experiments, which are sensitive to clusters.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/IZGDC28B/Požar et al. - 2016 - Micro-heterogeneity versus clustering in binary mi.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/IZGDC28B/Požar et al. - 2016 - Micro-heterogeneity versus clustering in binary mi.pdf} } -@misc{PreferentialAdsorptionLiquid, - title = {Preferential {{Adsorption}} from {{Liquid Water}}{\textendash}{{Ethanol Mixtures}} in {{Alumina Pores}} | {{Langmuir}}}, +@online{PreferentialAdsorptionLiquid, + title = {Preferential {{Adsorption}} from {{Liquid Water}}–{{Ethanol Mixtures}} in {{Alumina Pores}} | {{Langmuir}}}, + url = {https://pubs-acs-org.sidnomade-1.grenet.fr/doi/full/10.1021/la501177t}, urldate = {2023-07-11}, - howpublished = {https://pubs-acs-org.sidnomade-1.grenet.fr/doi/full/10.1021/la501177t}, - file = {/home/simon/Zotero/storage/2UJEKIE2/la501177t.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2UJEKIE2/la501177t.html} } @article{prsljaAdsorptionWaterMethanol2019, title = {Adsorption of Water, Methanol, and Their Mixtures in Slit Graphite Pores}, - author = {Pr{\v s}lja, Paulina and Lomba, Enrique and {G{\'o}mez-{\'A}lvarez}, Paula and Urbi{\v c}, Tomaz and Noya, Eva G.}, - year = {2019}, - month = jan, - journal = {The Journal of Chemical Physics}, + author = {Pršlja, Paulina and Lomba, Enrique and Gómez-Álvarez, Paula and Urbič, Tomaz and Noya, Eva G.}, + date = {2019-01-14}, + journaltitle = {The Journal of Chemical Physics}, volume = {150}, number = {2}, pages = {024705}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.5078603}, + url = {https://pubs.aip.org/jcp/article/150/2/024705/197290/Adsorption-of-water-methanol-and-their-mixtures-in}, urldate = {2023-07-24}, abstract = {The behavior of water, methanol, and water-methanol mixtures confined in narrow slit graphite pores as a function of pore size was investigated by Monte Carlo, hybrid Monte Carlo, and Molecular Dynamics simulations. Interactions were described using TIP4P/2005 for water, OPLS/2016 for methanol, and cross interactions fitted to excess water/methanol properties over the whole range of concentrations, which provide a rather accurate description of water-methanol mixtures. As expected for hydrophobic pores, whereas pure methanol is adsorbed already from the gas phase, pure water only enters the pore at pressures well beyond bulk saturation for all pore sizes considered. When adsorbed from a mixture, however, water adsorbs at much lower pressures due to the formation of hydrogen bonds with previously adsorbed methanol molecules. For all studied compositions and pore sizes, methanol adsorbs preferentially over water at liquid-vapor equilibrium conditions. In pure components, both water and methanol are microscopically structured in layers, the number of layers increasing with pore size. This is also the case in adsorbed mixtures, in which methanol has a higher affinity for the walls. This becomes more evident as the pore widens. Diffusion of pure water is higher than that of pure methanol for all pore sizes due to the larger size of the methyl group. In mixtures, both components present similar diffusivities at all pore sizes, which is explained in terms of the coupling of molecular movements due to strong hydrogen bonding between methanol and water molecules. This is particularly evident in very narrow pores, in which pure methanol diffusion is completely impeded on the time scale of our simulations, but the presence of a small amount of water molecules facilitates alcohol diffusion following a single-file mechanism. Additionally, our results indicate that pure water diffusivities display a non-monotonous dependence of pore size, due to effects of confinement (proximity to a fluid-solid-fluid transition induced by confinement as reported in previous work) and the dynamic anomalies of water.}, langid = {english}, - file = {/home/simon/Zotero/storage/RQX9456F/Pršlja et al. - 2019 - Adsorption of water, methanol, and their mixtures .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/RQX9456F/Pršlja et al. - 2019 - Adsorption of water, methanol, and their mixtures .pdf} } @article{rahbariChemicalPotentialsWater2018, title = {Chemical Potentials of Water, Methanol, Carbon Dioxide and Hydrogen Sulphide at Low Temperatures Using Continuous Fractional Component {{Gibbs}} Ensemble {{Monte Carlo}}}, - author = {Rahbari, Ahmadreza and Poursaeidesfahani, Ali and {Torres-Knoop}, Ariana and Dubbeldam, David and Vlugt, Thijs J. H.}, - year = {2018}, - month = mar, - journal = {Molecular Simulation}, + author = {Rahbari, Ahmadreza and Poursaeidesfahani, Ali and Torres-Knoop, Ariana and Dubbeldam, David and Vlugt, Thijs J. H.}, + date = {2018-03-24}, + journaltitle = {Molecular Simulation}, + shortjournal = {Molecular Simulation}, volume = {44}, number = {5}, pages = {405--414}, issn = {0892-7022, 1029-0435}, doi = {10.1080/08927022.2017.1391385}, + url = {https://www.tandfonline.com/doi/full/10.1080/08927022.2017.1391385}, urldate = {2023-11-24}, - abstract = {Chemical potentials of coexisting gas and liquid phases for water, methanol, hydrogen sulphide and carbon dioxide for the temperature range T = 220 K to T = 375 K are computed using two different methodologies: (1) Widom's test particle insertion (WTPI) method in the conventional Gibbs Ensemble (GE), and (2) the Continuous Fractional Component Gibbs Ensemble Monte Carlo (CFCGE MC) method. It is shown that the WTPI method fails to accurately compute the chemical potentials of water and methanol in the liquid phase at low temperatures, while accurate chemical potentials in the liquid phase are computed using CFCGE MC method. For the CFCGE MC method, the statistical uncertainty for computed chemical potentials of water and methanol in the liquid phase are considerably smaller compared to the WTPI method. For the water models considered in this study (SPC, TIP3P-EW, TIP4P-EW, TIP5P-EW), computed excess chemical potentials based on three-site models are in better agreement with the chemical potentials computed from an empirical equation of state from the NIST database. For water, orientational biasing is applied during test particle insertion to check whether certain orientations of test particle are energetically unfavourable. A two-dimensional Overlapping Distribution Method (ODM) in the NVT ensemble is derived for this purpose. It is shown that failure of the WTPI method for systems with a strong hydrogen bonding network does not depend on orientation of the test molecule in that system. For all systems in this study, the WTPI method breaks down when the void fraction of the system drops below approximately 0.50.}, + abstract = {Chemical potentials of coexisting gas and liquid phases for water, methanol, hydrogen sulphide and carbon dioxide for the temperature range T = 220 K to T = 375 K are computed using two different methodologies: (1) Widom’s test particle insertion (WTPI) method in the conventional Gibbs Ensemble (GE), and (2) the Continuous Fractional Component Gibbs Ensemble Monte Carlo (CFCGE MC) method. It is shown that the WTPI method fails to accurately compute the chemical potentials of water and methanol in the liquid phase at low temperatures, while accurate chemical potentials in the liquid phase are computed using CFCGE MC method. For the CFCGE MC method, the statistical uncertainty for computed chemical potentials of water and methanol in the liquid phase are considerably smaller compared to the WTPI method. For the water models considered in this study (SPC, TIP3P-EW, TIP4P-EW, TIP5P-EW), computed excess chemical potentials based on three-site models are in better agreement with the chemical potentials computed from an empirical equation of state from the NIST database. For water, orientational biasing is applied during test particle insertion to check whether certain orientations of test particle are energetically unfavourable. A two-dimensional Overlapping Distribution Method (ODM) in the NVT ensemble is derived for this purpose. It is shown that failure of the WTPI method for systems with a strong hydrogen bonding network does not depend on orientation of the test molecule in that system. For all systems in this study, the WTPI method breaks down when the void fraction of the system drops below approximately 0.50.}, langid = {english}, - file = {/home/simon/Zotero/storage/NGND5DSV/Rahbari et al. - 2018 - Chemical potentials of water, methanol, carbon dio.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NGND5DSV/Rahbari et al. - 2018 - Chemical potentials of water, methanol, carbon dio.pdf} } @article{raoLiquidphaseAdsorptionBulk1993, - title = {Liquid-Phase {{Adsorption}} of {{Bulk Ethanol}}{\textendash}{{Water Mixtures}} by {{Alumina}}}, + title = {Liquid-Phase {{Adsorption}} of {{Bulk Ethanol}}–{{Water Mixtures}} by {{Alumina}}}, author = {Rao, M.B. and Sircar, S.}, - year = {1993}, - month = mar, - journal = {Adsorption Science \& Technology}, + date = {1993-03-01}, + journaltitle = {Adsorption Science \& Technology}, volume = {10}, number = {1-4}, pages = {93--104}, publisher = {{SAGE Publications Ltd STM}}, issn = {0263-6174}, doi = {10.1177/0263617499010001-409}, - urldate = {2023-07-11}, - abstract = {Separation of ethanol{\textendash}water liquid mixtures can be carried out by selective adsorption of water on activated alumina. The moderate selectivity and heat of adsorption of water on the alumina permits easier and less energy intensive desorption of the adsorbed water. Experimental binary surface excess isotherms, liquid-phase adsorption kinetics and column dynamics for the adsorption of bulk water{\textendash}ethanol mixtures on Alcoa H152 alumina are reported. Model analyses of the data are carried out to quantify the selectivity of adsorption, adsorptive mass-transfer coefficients and the properties of the mass-transfer zones in adsorption columns.}, - langid = {english}, - keywords = {water-ethanol} + url = {https://doi.org/10.1177/0263617499010001-409}, + urldate = {2023-09-18}, + abstract = {Separation of ethanol–water liquid mixtures can be carried out by selective adsorption of water on activated alumina. The moderate selectivity and heat of adsorption of water on the alumina permits easier and less energy intensive desorption of the adsorbed water. Experimental binary surface excess isotherms, liquid-phase adsorption kinetics and column dynamics for the adsorption of bulk water–ethanol mixtures on Alcoa H152 alumina are reported. Model analyses of the data are carried out to quantify the selectivity of adsorption, adsorptive mass-transfer coefficients and the properties of the mass-transfer zones in adsorption columns.}, + langid = {english} } @article{raoLiquidphaseAdsorptionBulk1993a, - title = {Liquid-Phase {{Adsorption}} of {{Bulk Ethanol}}{\textendash}{{Water Mixtures}} by {{Alumina}}}, + title = {Liquid-Phase {{Adsorption}} of {{Bulk Ethanol}}–{{Water Mixtures}} by {{Alumina}}}, author = {Rao, M.B. and Sircar, S.}, - year = {1993}, - month = mar, - journal = {Adsorption Science \& Technology}, + date = {1993-03-01}, + journaltitle = {Adsorption Science \& Technology}, volume = {10}, number = {1-4}, pages = {93--104}, publisher = {{SAGE Publications Ltd STM}}, issn = {0263-6174}, doi = {10.1177/0263617499010001-409}, - urldate = {2023-09-18}, - abstract = {Separation of ethanol{\textendash}water liquid mixtures can be carried out by selective adsorption of water on activated alumina. The moderate selectivity and heat of adsorption of water on the alumina permits easier and less energy intensive desorption of the adsorbed water. Experimental binary surface excess isotherms, liquid-phase adsorption kinetics and column dynamics for the adsorption of bulk water{\textendash}ethanol mixtures on Alcoa H152 alumina are reported. Model analyses of the data are carried out to quantify the selectivity of adsorption, adsorptive mass-transfer coefficients and the properties of the mass-transfer zones in adsorption columns.}, - langid = {english} + url = {https://doi.org/10.1177/0263617499010001-409}, + urldate = {2023-07-11}, + abstract = {Separation of ethanol–water liquid mixtures can be carried out by selective adsorption of water on activated alumina. The moderate selectivity and heat of adsorption of water on the alumina permits easier and less energy intensive desorption of the adsorbed water. Experimental binary surface excess isotherms, liquid-phase adsorption kinetics and column dynamics for the adsorption of bulk water–ethanol mixtures on Alcoa H152 alumina are reported. Model analyses of the data are carried out to quantify the selectivity of adsorption, adsorptive mass-transfer coefficients and the properties of the mass-transfer zones in adsorption columns.}, + langid = {english}, + keywords = {water-ethanol} } @article{rauxDesignUnidirectionalWater2020, title = {Design of a Unidirectional Water Valve in {{Tillandsia}}}, author = {Raux, Pascal S. and Gravelle, Simon and Dumais, Jacques}, - year = {2020}, - month = jan, - journal = {Nature Communications}, + date = {2020-01-20}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, volume = {11}, number = {1}, pages = {396}, publisher = {{Nature Publishing Group}}, issn = {2041-1723}, doi = {10.1038/s41467-019-14236-5}, + url = {https://www.nature.com/articles/s41467-019-14236-5}, urldate = {2023-09-28}, - abstract = {The bromeliad Tillandsia landbeckii thrives in the Atacama desert of Chile using the fog captured by specialized leaf trichomes to satisfy its water needs. However, it is still unclear how the trichome of T. landbeckii and other Tillandsia species is able to absorb fine water droplets during intermittent fog events while also preventing evaporation when the plant is exposed to the desert's hyperarid conditions. Here, we explain how a 5800-fold asymmetry in water conductance arises from a clever juxtaposition of a thick hygroscopic wall and a semipermeable membrane. While absorption is achieved by osmosis of liquid water, evaporation under dry external conditions shifts the liquid-gas interface forcing water to diffuse through the thick trichome wall in the vapor phase. We confirm this mechanism by fabricating artificial composite membranes mimicking the trichome structure. The reliance on intrinsic material properties instead of moving parts makes the trichome a promising basis for the development of microfluidics valves.}, - copyright = {2020 The Author(s)}, + abstract = {The bromeliad Tillandsia landbeckii thrives in the Atacama desert of Chile using the fog captured by specialized leaf trichomes to satisfy its water needs. However, it is still unclear how the trichome of T. landbeckii and other Tillandsia species is able to absorb fine water droplets during intermittent fog events while also preventing evaporation when the plant is exposed to the desert’s hyperarid conditions. Here, we explain how a 5800-fold asymmetry in water conductance arises from a clever juxtaposition of a thick hygroscopic wall and a semipermeable membrane. While absorption is achieved by osmosis of liquid water, evaporation under dry external conditions shifts the liquid-gas interface forcing water to diffuse through the thick trichome wall in the vapor phase. We confirm this mechanism by fabricating artificial composite membranes mimicking the trichome structure. The reliance on intrinsic material properties instead of moving parts makes the trichome a promising basis for the development of microfluidics valves.}, + issue = {1}, langid = {english}, - file = {/home/simon/Zotero/storage/SM8VCVEP/Raux et al. - 2020 - Design of a unidirectional water valve in Tillands.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SM8VCVEP/Raux et al. - 2020 - Design of a unidirectional water valve in Tillands.pdf} } @article{reifNewInteractionParameters2012, title = {New {{Interaction Parameters}} for {{Charged Amino Acid Side Chains}} in the {{GROMOS Force Field}}}, - author = {Reif, Maria M. and H{\"u}nenberger, Philippe H. and Oostenbrink, Chris}, - year = {2012}, - month = oct, - journal = {Journal of Chemical Theory and Computation}, + author = {Reif, Maria M. and Hünenberger, Philippe H. and Oostenbrink, Chris}, + date = {2012-10-09}, + journaltitle = {Journal of Chemical Theory and Computation}, + shortjournal = {J. Chem. Theory Comput.}, volume = {8}, number = {10}, pages = {3705--3723}, issn = {1549-9618, 1549-9626}, doi = {10.1021/ct300156h}, + url = {https://pubs.acs.org/doi/10.1021/ct300156h}, urldate = {2023-06-21}, - abstract = {A GROMOS force-field parameter set 54A8 is developed, which is based on the latest 54A7 set [Schmid et al. Eur. Biophys. J. 2011, 40, 843-856] and involves a recalibration of the nonbonded interaction parameters for the charged amino acid side chains, based on ionic side chain analogs. After a thorough analysis of the available experimental data, conventional hydration free energies for the ammonium; mono-, di-, tri-, and tetramethyl-ammonium; formate; acetate; propanoate; imidazolium; and guanidinium ions are combined with a standard absolute intrinsic proton hydration free energy {$\Delta$}Gh{$\ominus$}yd[Hg+] = -1100 kJ{$\cdot$}mol-1 to yield absolute intrinsic single-ion hydration free energies serving as experimental target data. The raw hydration free energies calculated from atomistic simulations are affected by electrostatic and finite-size artifacts, and corrections are applied to reach methodological independence prior to comparison with these experimental values. Except for monomethyl-ammonium, ions with parameters derived directly from the 54A7 force field considerably underestimate (ammonium, formate, acetate, propanoate, guanidinium) or overestimate (di-, tri-, and tetramethyl-ammonium; imidazolium) the magnitude of the intrinsic hydration free energy, the largest deviation affecting the acetate ion (40.0 kJ{$\cdot$}mol-1). After reparameterization into 54A8, the mean and maximal absolute deviations between simulated and experimental data over the set of 10 ions are reduced from 23.1 and 40.0 kJ{$\cdot$}mol-1, respectively, to 1.8 and 6.3 kJ{$\cdot$}mol-1, respectively. Although the 54A7 and 54A8 parameter sets differ significantly in terms of the hydration free energies of the ions considered, other properties such as ion-water radial distribution functions and ion-ion potentials of mean force appear to be only moderately sensitive to this change. These properties are similar for the two sets and, in the case of the ion-water radial distribution functions, in good agreement with available experimental data.}, + abstract = {A GROMOS force-field parameter set 54A8 is developed, which is based on the latest 54A7 set [Schmid et al. Eur. Biophys. J. 2011, 40, 843−856] and involves a recalibration of the nonbonded interaction parameters for the charged amino acid side chains, based on ionic side chain analogs. After a thorough analysis of the available experimental data, conventional hydration free energies for the ammonium; mono-, di-, tri-, and tetramethyl-ammonium; formate; acetate; propanoate; imidazolium; and guanidinium ions are combined with a standard absolute intrinsic proton hydration free energy ΔGh⊖yd[Hg+] = −1100 kJ·mol−1 to yield absolute intrinsic single-ion hydration free energies serving as experimental target data. The raw hydration free energies calculated from atomistic simulations are affected by electrostatic and finite-size artifacts, and corrections are applied to reach methodological independence prior to comparison with these experimental values. Except for monomethyl-ammonium, ions with parameters derived directly from the 54A7 force field considerably underestimate (ammonium, formate, acetate, propanoate, guanidinium) or overestimate (di-, tri-, and tetramethyl-ammonium; imidazolium) the magnitude of the intrinsic hydration free energy, the largest deviation affecting the acetate ion (40.0 kJ·mol−1). After reparameterization into 54A8, the mean and maximal absolute deviations between simulated and experimental data over the set of 10 ions are reduced from 23.1 and 40.0 kJ·mol−1, respectively, to 1.8 and 6.3 kJ·mol−1, respectively. Although the 54A7 and 54A8 parameter sets differ significantly in terms of the hydration free energies of the ions considered, other properties such as ion−water radial distribution functions and ion−ion potentials of mean force appear to be only moderately sensitive to this change. These properties are similar for the two sets and, in the case of the ion−water radial distribution functions, in good agreement with available experimental data.}, langid = {english}, keywords = {ff}, - file = {/home/simon/Zotero/storage/7RKFMQMM/Reif et al. - 2012 - New Interaction Parameters for Charged Amino Acid .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7RKFMQMM/Reif et al. - 2012 - New Interaction Parameters for Charged Amino Acid .pdf} } @article{rimszaMolecularDynamicsSimulations2016, title = {Molecular Dynamics Simulations of Nanoporous Organosilicate Glasses Using {{Reactive Force Field}} ({{ReaxFF}})}, author = {Rimsza, J M and Deng, Lu and Du, Jincheng}, - year = {2016}, - abstract = {The structure and properties of nanoporous organosilicate glass (OSG) structure models with 30{\textendash}70\% porosities and different pore morphologies were simulated using molecular dynamics simulations with Reactive Force Field (ReaxFF) potential. The OSG structures were created from nanoporous silica structures generated using classical molecular dynamics (MD) simulations with partial charge pairwise potentials and a subsequent step of adding hydroxide and methyl groups to the dangling bonds and coordination defects. The nanoporous OSG systems were then fully relaxed using molecular dynamics simulations with ReaxFF and detailed structure analysis performed and properties calculated. Analysis of the OSG systems indicated that the structural features (bond distances and angles) as well as the Qn distribution of the nanoporous silica backbone structure are consistent with the features of dense silica and that the geometry of the added methyl groups is experimentally accurate, even after ReaxFF relaxation. The elastic modulus of the nanoporous silica was calculated and found to be 24{\textendash}31 GPa for system with 30\% porosity and 0.5{\textendash}2.5 GPa for those with 70\% porosity, consistent with previously reported experimental results.}, + date = {2016}, + abstract = {The structure and properties of nanoporous organosilicate glass (OSG) structure models with 30–70\% porosities and different pore morphologies were simulated using molecular dynamics simulations with Reactive Force Field (ReaxFF) potential. The OSG structures were created from nanoporous silica structures generated using classical molecular dynamics (MD) simulations with partial charge pairwise potentials and a subsequent step of adding hydroxide and methyl groups to the dangling bonds and coordination defects. The nanoporous OSG systems were then fully relaxed using molecular dynamics simulations with ReaxFF and detailed structure analysis performed and properties calculated. Analysis of the OSG systems indicated that the structural features (bond distances and angles) as well as the Qn distribution of the nanoporous silica backbone structure are consistent with the features of dense silica and that the geometry of the added methyl groups is experimentally accurate, even after ReaxFF relaxation. The elastic modulus of the nanoporous silica was calculated and found to be 24–31 GPa for system with 30\% porosity and 0.5–2.5 GPa for those with 70\% porosity, consistent with previously reported experimental results.}, langid = {english}, keywords = {MD,silica}, - file = {/home/simon/Zotero/storage/6ITFY92B/Rimsza et al. - 2016 - Molecular dynamics simulations of nanoporous organ.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6ITFY92B/Rimsza et al. - 2016 - Molecular dynamics simulations of nanoporous organ.pdf} } @article{robesonPolymerMembranesGas1999, title = {Polymer Membranes for Gas Separation}, author = {Robeson, L M}, - year = {1999}, - journal = {Current Opinion in Solid State and Materials Science}, + date = {1999}, + journaltitle = {Current Opinion in Solid State and Materials Science}, + shortjournal = {Curr Opin Solid State Mater Sci}, volume = {4}, number = {6}, - abstract = {In the past several decades, membrane separation has gone from a laboratory curiosity to commercial reality. These membranes often have a separating layer thickness ,100 nm and offer specific advantages in low energy costs, ease of operation, and compactness. Gas separation using polymeric membranes include many of the common gas pairs (i.e. O2 / N2; H2 / N2; CO2 / CH4) in a multiplicity of applications. The basic fundamentals of gas permeability and separation will be discussed along structure / property relationships. A brief discussion on fabrication of these membranes and various applications is included. {\textcopyright} 2000 Elsevier Science Ltd. All rights reserved.}, + abstract = {In the past several decades, membrane separation has gone from a laboratory curiosity to commercial reality. These membranes often have a separating layer thickness ,100 nm and offer specific advantages in low energy costs, ease of operation, and compactness. Gas separation using polymeric membranes include many of the common gas pairs (i.e. O2 / N2; H2 / N2; CO2 / CH4) in a multiplicity of applications. The basic fundamentals of gas permeability and separation will be discussed along structure / property relationships. A brief discussion on fabrication of these membranes and various applications is included. © 2000 Elsevier Science Ltd. All rights reserved.}, langid = {english}, - file = {/home/simon/Zotero/storage/8HXZPB5W/Robeson - 1999 - Polymer membranes for gas separation.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/8HXZPB5W/Robeson - 1999 - Polymer membranes for gas separation.pdf} } @article{robinNanofluidicsCrossroads2023, title = {Nanofluidics at the Crossroads}, - author = {Robin, Paul and Bocquet, Lyd{\'e}ric}, - year = {2023}, - month = apr, - journal = {The Journal of Chemical Physics}, + author = {Robin, Paul and Bocquet, Lydéric}, + date = {2023-04-28}, + journaltitle = {The Journal of Chemical Physics}, volume = {158}, number = {16}, pages = {160901}, issn = {0021-9606, 1089-7690}, doi = {10.1063/5.0143222}, + url = {https://pubs.aip.org/jcp/article/158/16/160901/2884974/Nanofluidics-at-the-crossroadsP-Robin-and-L}, urldate = {2023-04-28}, - abstract = {Nanofluidics, the field interested in flows at the smallest scales, has grown at a fast pace, reaching an ever finer control of fluidic and ionic transport at the molecular level. Until now, artificial pores are far from reaching the wealth of functionalities of biological channels that regulate sensory detection, biological transport, and neurostransmission{\textemdash}all while operating at energies comparable to thermal noise. Here, we argue that artificial ionic machines can be designed by harnessing the entire wealth of phenomena available at the nanoscales and exploiting techniques developed in various fields of physics. As they are generally based on solid-state nanopores, rather than soft membranes and proteins, they should, in particular, aim at taking advantage of their specific properties, such as their electronic structure or their ability to interact with light. These observations call for the design of new ways of probing nanofluidic systems. Nanofluidics is now at the crossroads, there are new avenues to build complex ionic machines, and this may allow to develop new functionalities inspired by nature.}, + abstract = {Nanofluidics, the field interested in flows at the smallest scales, has grown at a fast pace, reaching an ever finer control of fluidic and ionic transport at the molecular level. Until now, artificial pores are far from reaching the wealth of functionalities of biological channels that regulate sensory detection, biological transport, and neurostransmission—all while operating at energies comparable to thermal noise. Here, we argue that artificial ionic machines can be designed by harnessing the entire wealth of phenomena available at the nanoscales and exploiting techniques developed in various fields of physics. As they are generally based on solid-state nanopores, rather than soft membranes and proteins, they should, in particular, aim at taking advantage of their specific properties, such as their electronic structure or their ability to interact with light. These observations call for the design of new ways of probing nanofluidic systems. Nanofluidics is now at the crossroads, there are new avenues to build complex ionic machines, and this may allow to develop new functionalities inspired by nature.}, langid = {english}, keywords = {nanofluid}, - file = {/home/simon/Zotero/storage/CZ6J5KHM/Robin and Bocquet - 2023 - Nanofluidics at the crossroads.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/CZ6J5KHM/Robin and Bocquet - 2023 - Nanofluidics at the crossroads.pdf} } @article{rorschachProteinDynamicsNMR1986, title = {Protein Dynamics and the {{NMR}} Relaxation Time {{T1}} of Water in Biological Systems}, author = {Rorschach, H.E and Hazlewood, C.F}, - year = {1986}, - month = oct, - journal = {Journal of Magnetic Resonance (1969)}, + date = {1986-10}, + journaltitle = {Journal of Magnetic Resonance (1969)}, + shortjournal = {Journal of Magnetic Resonance (1969)}, volume = {70}, number = {1}, pages = {79--88}, issn = {00222364}, doi = {10.1016/0022-2364(86)90364-1}, + url = {https://linkinghub.elsevier.com/retrieve/pii/0022236486903641}, urldate = {2023-07-09}, langid = {english}, keywords = {bio,NMR}, - file = {/home/simon/Zotero/storage/2RAQE3D7/1-s2.0-0022236486903641-main.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2RAQE3D7/1-s2.0-0022236486903641-main.pdf} } @article{salazar-canoHydrogenBondsMethane2016, - title = {Hydrogen Bonds in Methane{\textendash}Water Clusters}, - author = {{Salazar-Cano}, Juan-Ram{\'o}n and {Guevara-Garc{\'i}a}, Alfredo and Vargas, Rubicelia and Restrepo, Albeiro and Garza, Jorge}, - year = {2016}, - journal = {Physical Chemistry Chemical Physics}, + title = {Hydrogen Bonds in Methane–Water Clusters}, + author = {Salazar-Cano, Juan-Ramón and Guevara-García, Alfredo and Vargas, Rubicelia and Restrepo, Albeiro and Garza, Jorge}, + date = {2016}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {18}, number = {34}, pages = {23508--23515}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C6CP04086A}, + url = {http://xlink.rsc.org/?DOI=C6CP04086A}, urldate = {2023-03-24}, - abstract = {Water{\textendash}methane clusters are stable at low temperatures as those found in Mars. Water cages enveloping methane are stable, although they present small probability to occur. , Characterization of hydrogen bonds in CH 4 {\textendash}(H 2 O) 12 clusters was carried out by using several quantum chemistry tools. An initial stochastic search provided around 2\,500\,000 candidate structures, then, using a convex-hull polygon criterion followed by gradient based optimization under the Kohn{\textendash}Sham scheme, a total of 54 well defined local minima were located in the Potential Energy Surface. These structures were further analyzed through second-order many-body perturbation theory with an extended basis set at the MP2/6-311++G(d,p) level. Our analysis of Gibbs energies at several temperatures clearly suggests a structural preference toward compact water clusters interacting with the external methane molecule, instead of the more commonly known clathrate-like structures. This study shows that CH 4 {\textendash}(H 2 O) 12 clusters may be detected at temperatures up to 179 K, this finding provides strong support to a recently postulated hypothesis that suggests that methane{\textendash}water clusters could be present in Mars at these conditions. Interestingly, we found that water to water hydrogen bonding is strengthened in the mixed clusters when compared to the isolated water dimer, which in turn leads to a weakening of the methane to water hydrogen bonding when compared to the CH 4 {\textendash}(H 2 O) dimer. Finally, our evidence places a stern warning about the abilities of popular geometrical criteria to determine the existence of hydrogen bonds.}, + abstract = {Water–methane clusters are stable at low temperatures as those found in Mars. Water cages enveloping methane are stable, although they present small probability to occur. , Characterization of hydrogen bonds in CH 4 –(H 2 O) 12 clusters was carried out by using several quantum chemistry tools. An initial stochastic search provided around 2\,500\,000 candidate structures, then, using a convex-hull polygon criterion followed by gradient based optimization under the Kohn–Sham scheme, a total of 54 well defined local minima were located in the Potential Energy Surface. These structures were further analyzed through second-order many-body perturbation theory with an extended basis set at the MP2/6-311++G(d,p) level. Our analysis of Gibbs energies at several temperatures clearly suggests a structural preference toward compact water clusters interacting with the external methane molecule, instead of the more commonly known clathrate-like structures. This study shows that CH 4 –(H 2 O) 12 clusters may be detected at temperatures up to 179 K, this finding provides strong support to a recently postulated hypothesis that suggests that methane–water clusters could be present in Mars at these conditions. Interestingly, we found that water to water hydrogen bonding is strengthened in the mixed clusters when compared to the isolated water dimer, which in turn leads to a weakening of the methane to water hydrogen bonding when compared to the CH 4 –(H 2 O) dimer. Finally, our evidence places a stern warning about the abilities of popular geometrical criteria to determine the existence of hydrogen bonds.}, langid = {english}, keywords = {HB,mixture}, - file = {/home/simon/Zotero/storage/QFCXGSJB/Salazar-Cano et al. - 2016 - Hydrogen bonds in methane–water clusters.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QFCXGSJB/Salazar-Cano et al. - 2016 - Hydrogen bonds in methane–water clusters.pdf} } @article{sannHighlyHydrophobicZIF82018, title = {Highly Hydrophobic {{ZIF-8}} Particles and Application for Oil-Water Separation}, author = {Sann, Ei Ei and Pan, Yong and Gao, Zhongfeng and Zhan, Shenshan and Xia, Fan}, - year = {2018}, - month = nov, - journal = {Separation and Purification Technology}, + date = {2018-11}, + journaltitle = {Separation and Purification Technology}, + shortjournal = {Separation and Purification Technology}, volume = {206}, pages = {186--191}, issn = {13835866}, doi = {10.1016/j.seppur.2018.04.027}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1383586617340984}, urldate = {2023-05-23}, - abstract = {ZIF-8(zinc-methylimidazolate framework-8), one of the zeolitic imidazolate frameworks (ZIFs), was put into a tea bag for selective removal of oils from water surface, and exhibits strong hydrophobicity with a water contact angle of 142{\textdegree}, ZIF-8 particles combined with highly hydrophobic and superoleophilic properties. Our Experiment results showed that the highly hydrophobic ZIF-8 particles and the ZIF-8/tea bag could be reused in oil-water separation for twenty cycles. More importantly, the oil could be readily removed from the surfaces of particles by heating combined with reduced pressure treatment whereas the particles still kept highly hydrophobic and superolephilic characteristics, which render its potential applications in the cleanup of oil spills and the removal of organic pollutants on water surface.}, + abstract = {ZIF-8(zinc-methylimidazolate framework-8), one of the zeolitic imidazolate frameworks (ZIFs), was put into a tea bag for selective removal of oils from water surface, and exhibits strong hydrophobicity with a water contact angle of 142°, ZIF-8 particles combined with highly hydrophobic and superoleophilic properties. Our Experiment results showed that the highly hydrophobic ZIF-8 particles and the ZIF-8/tea bag could be reused in oil-water separation for twenty cycles. More importantly, the oil could be readily removed from the surfaces of particles by heating combined with reduced pressure treatment whereas the particles still kept highly hydrophobic and superolephilic characteristics, which render its potential applications in the cleanup of oil spills and the removal of organic pollutants on water surface.}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/G7GIMDNU/Sann et al. - 2018 - Highly hydrophobic ZIF-8 particles and application.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/G7GIMDNU/Sann et al. - 2018 - Highly hydrophobic ZIF-8 particles and application.pdf} } @article{satoCooperativeMolecularDynamics2005, title = {Cooperative and Molecular Dynamics of Alcohol/Water Mixtures: The View of Dielectric Spectroscopy}, shorttitle = {Cooperative and Molecular Dynamics of Alcohol/Water Mixtures}, author = {Sato, Takaaki and Buchner, Richard}, - year = {2005}, - month = mar, - journal = {Journal of Molecular Liquids}, + date = {2005-03}, + journaltitle = {Journal of Molecular Liquids}, + shortjournal = {Journal of Molecular Liquids}, volume = {117}, number = {1-3}, pages = {23--31}, issn = {01677322}, doi = {10.1016/j.molliq.2004.08.015}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0167732204002272}, urldate = {2023-05-02}, - abstract = {This contribution reviews our recent investigations into the dielectric relaxation behavior of methanol/water (MW), ethanol/water (EW), 1-propanol/water (1PW), and 2-propanol/water (2PW) mixtures. The analysis of the complex permittivity spectra measured in the frequency range 0.1Vm/GHzV89 reveals that in the alcohol-rich region of {\textasciitilde}0.3VXAV1.0, where XA is the mole fraction of alcohol, a three-step relaxation model is most appropriate for the description of the spectra whereas at low XA the intermediate process becomes too small to be resolved. The dominating low-frequency Cole{\textendash}Cole (CC) dispersion ( j=1) is assigned to the cooperative dynamics of the H-bond system where the motions of alcohol and water molecules cannot be distinguished. Its time scale is largely governed by the number density of H-bond acceptor and donor sites but steric effects also contribute. Two additional Debye (D) terms ( j=2 and j=3) with relaxation times of s2{\textasciitilde}10{\textendash}20 ps and s3{\textasciitilde}1{\textendash}2 ps are required to reproduce the high-frequency part of the spectrum. These small-amplitude dispersion steps can be assigned to the motion of singly H-bonded alcohol monomers at the ends of the chain structure ( j=2) and to the flipping motion of free OH ( j=3). The increase of the amplitude De2 and the simultaneous decrease of the (effective) dipole{\textendash}dipole correlation factor with decreasing XA in {\textasciitilde}0.5VXAV1.0 suggests insertion of water molecules into the zigzag structure of H-bonded alcohol chains inducing a reduction of the average chain length and an increase of the number of end-standing alcohol molecules that can contribute to the s2-mode.}, + abstract = {This contribution reviews our recent investigations into the dielectric relaxation behavior of methanol/water (MW), ethanol/water (EW), 1-propanol/water (1PW), and 2-propanol/water (2PW) mixtures. The analysis of the complex permittivity spectra measured in the frequency range 0.1Vm/GHzV89 reveals that in the alcohol-rich region of \textasciitilde 0.3VXAV1.0, where XA is the mole fraction of alcohol, a three-step relaxation model is most appropriate for the description of the spectra whereas at low XA the intermediate process becomes too small to be resolved. The dominating low-frequency Cole–Cole (CC) dispersion ( j=1) is assigned to the cooperative dynamics of the H-bond system where the motions of alcohol and water molecules cannot be distinguished. Its time scale is largely governed by the number density of H-bond acceptor and donor sites but steric effects also contribute. Two additional Debye (D) terms ( j=2 and j=3) with relaxation times of s2\textasciitilde 10–20 ps and s3\textasciitilde 1–2 ps are required to reproduce the high-frequency part of the spectrum. These small-amplitude dispersion steps can be assigned to the motion of singly H-bonded alcohol monomers at the ends of the chain structure ( j=2) and to the flipping motion of free OH ( j=3). The increase of the amplitude De2 and the simultaneous decrease of the (effective) dipole–dipole correlation factor with decreasing XA in \textasciitilde 0.5VXAV1.0 suggests insertion of water molecules into the zigzag structure of H-bonded alcohol chains inducing a reduction of the average chain length and an increase of the number of end-standing alcohol molecules that can contribute to the s2-mode.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/GF64SVRM/Sato and Buchner - 2005 - Cooperative and molecular dynamics of alcoholwate.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/GF64SVRM/Sato and Buchner - 2005 - Cooperative and molecular dynamics of alcoholwate.pdf} } @article{schmidComputingChemicalPotentials2023, title = {Computing Chemical Potentials of Adsorbed or Confined Fluids}, author = {Schmid, Rochus and Cheng, Bingqing}, - year = {2023}, - month = apr, - journal = {The Journal of Chemical Physics}, + date = {2023-04-28}, + journaltitle = {The Journal of Chemical Physics}, volume = {158}, number = {16}, pages = {161101}, issn = {0021-9606, 1089-7690}, doi = {10.1063/5.0146711}, + url = {https://pubs.aip.org/jcp/article/158/16/161101/2884975/Computing-chemical-potentials-of-adsorbed-or}, urldate = {2023-11-24}, abstract = {The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.}, langid = {english}, - file = {/home/simon/Zotero/storage/RL7PYJDL/Schmid and Cheng - 2023 - Computing chemical potentials of adsorbed or confi.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/RL7PYJDL/Schmid and Cheng - 2023 - Computing chemical potentials of adsorbed or confi.pdf} } @article{segaGeneralizedIdentificationTruly2013, title = {The Generalized Identification of Truly Interfacial Molecules ({{ITIM}}) Algorithm for Nonplanar Interfaces}, - author = {Sega, Marcello and Kantorovich, Sofia S. and Jedlovszky, P{\'a}l and Jorge, Miguel}, - year = {2013}, - month = jan, - journal = {The Journal of Chemical Physics}, + author = {Sega, Marcello and Kantorovich, Sofia S. and Jedlovszky, Pál and Jorge, Miguel}, + date = {2013-01-28}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {138}, number = {4}, pages = {044110}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4776196}, + url = {https://pubs.aip.org/aip/jcp/article/193226}, urldate = {2023-06-16}, langid = {english}, - file = {/home/simon/Zotero/storage/BG25PPSB/Sega et al. - 2013 - The generalized identification of truly interfacia.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/BG25PPSB/Sega et al. - 2013 - The generalized identification of truly interfacia.pdf} } @article{segaPytimPythonPackage2018, title = {Pytim: {{A}} Python Package for the Interfacial Analysis of Molecular Simulations}, shorttitle = {Pytim}, - author = {Sega, Marcello and Hantal, Gy{\"o}rgy and F{\'a}bi{\'a}n, Bal{\'a}zs and Jedlovszky, P{\'a}l}, - year = {2018}, - month = sep, - journal = {Journal of Computational Chemistry}, + author = {Sega, Marcello and Hantal, György and Fábián, Balázs and Jedlovszky, Pál}, + date = {2018-09-30}, + journaltitle = {Journal of Computational Chemistry}, + shortjournal = {J Comput Chem}, volume = {39}, number = {25}, pages = {2118--2125}, issn = {01928651}, doi = {10.1002/jcc.25384}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.25384}, urldate = {2023-06-21}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/FQKRW6WN/Sega et al. - 2018 - Pytim A python package for the interfacial analys.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/FQKRW6WN/Sega et al. - 2018 - Pytim A python package for the interfacial analys.pdf} } @article{semiatEnergyIssuesDesalination2008, title = {Energy {{Issues}} in {{Desalination Processes}}}, author = {Semiat, Raphael}, - year = {2008}, - month = nov, - journal = {Environmental Science \& Technology}, + date = {2008-11-15}, + journaltitle = {Environmental Science \& Technology}, + shortjournal = {Environ. Sci. Technol.}, volume = {42}, number = {22}, pages = {8193--8201}, issn = {0013-936X, 1520-5851}, doi = {10.1021/es801330u}, + url = {https://pubs.acs.org/doi/10.1021/es801330u}, urldate = {2023-07-12}, langid = {english}, - file = {/home/simon/Zotero/storage/7B9D47R7/Semiat - 2008 - Energy Issues in Desalination Processes.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7B9D47R7/Semiat - 2008 - Energy Issues in Desalination Processes.pdf} } @article{severinDynamicsEthanolWater2014, title = {Dynamics of {{Ethanol}} and {{Water Mixtures Observed}} in a {{Self-Adjusting Molecularly Thin Slit Pore}}}, author = {Severin, N. and Sokolov, I. M. and Rabe, J. P.}, - year = {2014}, - month = apr, - journal = {Langmuir}, + date = {2014-04-01}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {30}, number = {12}, pages = {3455--3459}, issn = {0743-7463, 1520-5827}, doi = {10.1021/la404818a}, + url = {https://pubs.acs.org/doi/10.1021/la404818a}, urldate = {2023-07-10}, - abstract = {The structure of multicomponent fluids in confined geometries is a key to understanding their properties. However, it remains an experimental challenge to gain molecular-scale resolution information on this structure. Here we show that mono- and multilayers of graphene, conforming to heterogeneous monolayers of molecules in a flexible slit pore between a mica surface and the graphene layers, allow for mapping the phase separation of water and ethanol within such a slit pore. Employing scanning force microscopy, we readily distinguish clusters of ethanol and water molecules due their different sizes, and we show that the phase separated water-ethanol structures become coarser under thicker graphenes. Moreover, we obtain a lower bound for the two-dimensional diffusion coefficient of ethanol in water of D {$\geq$} 2 {\texttimes} 10-14 m2 s-1. Thus, the molecularly thin slit pore provides a powerful tool to control and to investigate mixed fluids in self-adjusting nanopores.}, + abstract = {The structure of multicomponent fluids in confined geometries is a key to understanding their properties. However, it remains an experimental challenge to gain molecular-scale resolution information on this structure. Here we show that mono- and multilayers of graphene, conforming to heterogeneous monolayers of molecules in a flexible slit pore between a mica surface and the graphene layers, allow for mapping the phase separation of water and ethanol within such a slit pore. Employing scanning force microscopy, we readily distinguish clusters of ethanol and water molecules due their different sizes, and we show that the phase separated water−ethanol structures become coarser under thicker graphenes. Moreover, we obtain a lower bound for the two-dimensional diffusion coefficient of ethanol in water of D ≥ 2 × 10−14 m2 s−1. Thus, the molecularly thin slit pore provides a powerful tool to control and to investigate mixed fluids in self-adjusting nanopores.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/2UEP2DM9/Severin et al. - 2014 - Dynamics of Ethanol and Water Mixtures Observed in.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2UEP2DM9/Severin et al. - 2014 - Dynamics of Ethanol and Water Mixtures Observed in.pdf} } @article{severinNanophaseSeparationMonomolecularly2015, - title = {Nanophase {{Separation}} in {{Monomolecularly Thin Water}}{\textendash}{{Ethanol Films Controlled}} by {{Graphene}}}, + title = {Nanophase {{Separation}} in {{Monomolecularly Thin Water}}–{{Ethanol Films Controlled}} by {{Graphene}}}, author = {Severin, N. and Gienger, J. and Scenev, V. and Lange, P. and Sokolov, I. M. and Rabe, J. P.}, - year = {2015}, - month = feb, - journal = {Nano Letters}, + date = {2015-02-11}, + journaltitle = {Nano Letters}, + shortjournal = {Nano Lett.}, volume = {15}, number = {2}, pages = {1171--1176}, issn = {1530-6984, 1530-6992}, doi = {10.1021/nl5042484}, + url = {https://pubs.acs.org/doi/10.1021/nl5042484}, urldate = {2023-07-10}, - abstract = {Control over nanoscale patterning of ultrathin molecular films plays an important role both in natural as well as artificial nanosystems. Here we report on nanophase separated patterns of water and ethanol within monomolecularly thin films confined between the cleavage plane of mica and single or a few layers of graphene. Employing scanning force microscopy of the graphene layers conforming to the molecular films we quantify the patterns using the ethanol-water cross correlation and the autocorrelation of domain wall directions. They reveal that lateral pattern dimensions grow and the domain walls stiffen upon increasing the thickness of the graphene multilayers. We attribute the control of the patterns through the graphene layers to the competition between the mechanical deformation energy of the graphene sheets and the electrostatic repulsion of dipoles normal to the interface. The latter results from charge transfer between graphene and the molecules confined between mica and graphene.}, + abstract = {Control over nanoscale patterning of ultrathin molecular films plays an important role both in natural as well as artificial nanosystems. Here we report on nanophase separated patterns of water and ethanol within monomolecularly thin films confined between the cleavage plane of mica and single or a few layers of graphene. Employing scanning force microscopy of the graphene layers conforming to the molecular films we quantify the patterns using the ethanol−water cross correlation and the autocorrelation of domain wall directions. They reveal that lateral pattern dimensions grow and the domain walls stiffen upon increasing the thickness of the graphene multilayers. We attribute the control of the patterns through the graphene layers to the competition between the mechanical deformation energy of the graphene sheets and the electrostatic repulsion of dipoles normal to the interface. The latter results from charge transfer between graphene and the molecules confined between mica and graphene.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/698SZXXG/Severin et al. - 2015 - Nanophase Separation in Monomolecularly Thin Water.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/698SZXXG/Severin et al. - 2015 - Nanophase Separation in Monomolecularly Thin Water.pdf} } -@article{shenCryogenicTechnologyProgress2022a, +@article{shenCryogenicTechnologyProgress2022, title = {Cryogenic Technology Progress for {{CO2}} Capture under Carbon Neutrality Goals: {{A}} Review}, shorttitle = {Cryogenic Technology Progress for {{CO2}} Capture under Carbon Neutrality Goals}, author = {Shen, Minghai and Tong, Lige and Yin, Shaowu and Liu, Chuanping and Wang, Li and Feng, Wujun and Ding, Yulong}, - year = {2022}, - month = oct, - journal = {Separation and Purification Technology}, + date = {2022-10-15}, + journaltitle = {Separation and Purification Technology}, + shortjournal = {Separation and Purification Technology}, volume = {299}, pages = {121734}, issn = {1383-5866}, doi = {10.1016/j.seppur.2022.121734}, + url = {https://www.sciencedirect.com/science/article/pii/S1383586622012904}, urldate = {2023-11-06}, - abstract = {This review discusses the cryogenic capture system from the perspective of constructing new cryogenic capture system structures, exploring the optimal system parameters, and analyzing the challenges faced by different cryogenic capture systems. The gas that needs to remove CO2 undergoes desulfurization, denitrification and dust removal treatment, which can effectively reduce impurities and remove, and ensure the progress of the subsequent carbon capture process. Among the cryogenic technologies of carbon capture, cryogenic distillation is restricted by the concentration of carbon dioxide (CO2) in the gas and cost, and it cannot be widely popularized. Cryogenic condensation offers a wide range of industrial applications because it may immediately liquefy CO2 for oil displacement. Currently, the most concerned cryogenic sublimation can capture low-concentration CO2 at a rate of 99.9\% at 13.5~vol\%, and energy consumption and annual investment costs can also be effectively reduced. In general, cryogenic CO2 capture technology provides remarkable cost and efficiency benefits compared with other carbon capture technologies. By 2030, China's CO2 capture cost will be 13{\textendash}57\$/t, and it will be 3{\textendash}19\$/t in 2060. Combining fixed costs and operating costs, the total abatement cost is 65\$/t CO2, which is similar to the cost of 54\$/ton CO2 in Japan and 60{\textendash}193\$/t CO2 in Australia. By 2060, the carbon emission reduction ratio of carbon capture, utilization, and storage (CCUS) will account for about 10\% of the total emission reduction, so the research on CCUS is very urgent. It must break through the extreme utilization of cold energy and energy consumption barriers as well as increase the efficiency of the system.}, + abstract = {This review discusses the cryogenic capture system from the perspective of constructing new cryogenic capture system structures, exploring the optimal system parameters, and analyzing the challenges faced by different cryogenic capture systems. The gas that needs to remove CO2 undergoes desulfurization, denitrification and dust removal treatment, which can effectively reduce impurities and remove, and ensure the progress of the subsequent carbon capture process. Among the cryogenic technologies of carbon capture, cryogenic distillation is restricted by the concentration of carbon dioxide (CO2) in the gas and cost, and it cannot be widely popularized. Cryogenic condensation offers a wide range of industrial applications because it may immediately liquefy CO2 for oil displacement. Currently, the most concerned cryogenic sublimation can capture low-concentration CO2 at a rate of 99.9\% at 13.5~vol\%, and energy consumption and annual investment costs can also be effectively reduced. In general, cryogenic CO2 capture technology provides remarkable cost and efficiency benefits compared with other carbon capture technologies. By 2030, China’s CO2 capture cost will be 13–57\$/t, and it will be 3–19\$/t in 2060. Combining fixed costs and operating costs, the total abatement cost is 65\$/t CO2, which is similar to the cost of 54\$/ton CO2 in Japan and 60–193\$/t CO2 in Australia. By 2060, the carbon emission reduction ratio of carbon capture, utilization, and storage (CCUS) will account for about 10\% of the total emission reduction, so the research on CCUS is very urgent. It must break through the extreme utilization of cold energy and energy consumption barriers as well as increase the efficiency of the system.}, keywords = {CO capture,Condensation,Cryogenic,Distillation,Sublimation}, - file = {/home/simon/Zotero/storage/4F4IUZKS/Shen et al. - 2022 - Cryogenic technology progress for CO2 capture unde.pdf;/home/simon/Zotero/storage/MCSFLAMR/S1383586622012904.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4F4IUZKS/Shen et al. - 2022 - Cryogenic technology progress for CO2 capture unde.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/MCSFLAMR/S1383586622012904.html} } -@article{shiHierarchicallyNanoporousCarbon2023a, +@article{shiHierarchicallyNanoporousCarbon2023, title = {Hierarchically {{Nanoporous Carbon}} for {{CO2 Capture}} and {{Separation}}: {{Roles}} of {{Morphology}}, {{Porosity}}, and {{Surface Chemistry}}}, shorttitle = {Hierarchically {{Nanoporous Carbon}} for {{CO2 Capture}} and {{Separation}}}, author = {Shi, Weiwei and Yu, Jiao and Liu, Huili and Gao, Defeng and Yuan, Aili and Chang, Binbin}, - year = {2023}, - month = may, - journal = {ACS Applied Nano Materials}, + date = {2023-05-12}, + journaltitle = {ACS Applied Nano Materials}, + shortjournal = {ACS Appl. Nano Mater.}, volume = {6}, number = {9}, pages = {7887--7900}, publisher = {{American Chemical Society}}, doi = {10.1021/acsanm.3c01040}, + url = {https://doi.org/10.1021/acsanm.3c01040}, urldate = {2023-11-06}, - abstract = {Nanoporous carbons, as promising adsorbents for CO2 capture and separation from flue gas, span the major challenge of optimizing the physicochemical property to meet the need of CO2 capture and separation. Herein, we rationally engineered sustainable nanoporous carbons with tailorable porosity and rich surface chemistry using an activating agent of small-molecule organic acids. The porosity could be easily tailored by varying the activation temperature and activator dosage. The surface chemistry and morphology could be tuned by changing the dopant concentration. In detail, porosity played a determinant role in CO2 adsorption capacity, especially ultramicroporosity. Narrow micropores brought major contributions to CO2 uptake at low pressure, while mesopores played a great role at high adsorption pressure. Surface chemistry played a critical role in CO2 capture, especially adsorption selectivity and the isosteric heat of adsorption when the ultramicroporosity was optimal. We revealed that the C{\textendash}OH group (one type of oxygen-containing species) made a relatively high contribution for improving CO2 capture by hydrogen bonding. For nitrogen-containing groups, the pyridinic-N, pyrrolic-N, and amine groups provoked more improvements in CO2 capture by offering more basic CO2-philic sites, while the oxidized-N group made a weak influence. Sheet-like structures exhibited more accessible affine sites for fast CO2 capture and separation. We proposed a valuable reference for rationally engineering nanoporous carbons with the optimal texture to meet the different requirements of CO2 capture. More importantly, the conversion of biowaste into high-added-value adsorbents for effective CO2 capture and separation opened up an elegant route of killing two birds with one stone.}, - file = {/home/simon/Zotero/storage/4QTVPK2I/Shi et al. - 2023 - Hierarchically Nanoporous Carbon for CO2 Capture a.pdf} + abstract = {Nanoporous carbons, as promising adsorbents for CO2 capture and separation from flue gas, span the major challenge of optimizing the physicochemical property to meet the need of CO2 capture and separation. Herein, we rationally engineered sustainable nanoporous carbons with tailorable porosity and rich surface chemistry using an activating agent of small-molecule organic acids. The porosity could be easily tailored by varying the activation temperature and activator dosage. The surface chemistry and morphology could be tuned by changing the dopant concentration. In detail, porosity played a determinant role in CO2 adsorption capacity, especially ultramicroporosity. Narrow micropores brought major contributions to CO2 uptake at low pressure, while mesopores played a great role at high adsorption pressure. Surface chemistry played a critical role in CO2 capture, especially adsorption selectivity and the isosteric heat of adsorption when the ultramicroporosity was optimal. We revealed that the C–OH group (one type of oxygen-containing species) made a relatively high contribution for improving CO2 capture by hydrogen bonding. For nitrogen-containing groups, the pyridinic-N, pyrrolic-N, and amine groups provoked more improvements in CO2 capture by offering more basic CO2-philic sites, while the oxidized-N group made a weak influence. Sheet-like structures exhibited more accessible affine sites for fast CO2 capture and separation. We proposed a valuable reference for rationally engineering nanoporous carbons with the optimal texture to meet the different requirements of CO2 capture. More importantly, the conversion of biowaste into high-added-value adsorbents for effective CO2 capture and separation opened up an elegant route of killing two birds with one stone.}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4QTVPK2I/Shi et al. - 2023 - Hierarchically Nanoporous Carbon for CO2 Capture a.pdf} } @article{shollSevenChemicalSeparations2016, title = {Seven Chemical Separations to Change the World}, author = {Sholl, David S. and Lively, Ryan P.}, - year = {2016}, - month = apr, - journal = {Nature}, + date = {2016-04}, + journaltitle = {Nature}, + shortjournal = {Nature}, volume = {532}, number = {7600}, pages = {435--437}, issn = {0028-0836, 1476-4687}, doi = {10.1038/532435a}, + url = {https://www.nature.com/articles/532435a}, urldate = {2023-06-23}, langid = {english}, - file = {/home/simon/Zotero/storage/ESAB7NDC/Sholl and Lively - 2016 - Seven chemical separations to change the world.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ESAB7NDC/Sholl and Lively - 2016 - Seven chemical separations to change the world.pdf} } @article{singerElucidatingNMRRelaxation2020, title = {Elucidating the {\textsuperscript{1}} {{H NMR Relaxation Mechanism}} in {{Polydisperse Polymers}} and {{Bitumen Using Measurements}}, {{MD Simulations}}, and {{Models}}}, author = {Singer, Philip M. and Valiya Parambathu, Arjun and Wang, Xinglin and Asthagiri, Dilip and Chapman, Walter G. and Hirasaki, George J. and Fleury, Marc}, - year = {2020}, - month = may, - journal = {The Journal of Physical Chemistry B}, + date = {2020-05-21}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {124}, number = {20}, pages = {4222--4233}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.0c01941}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.0c01941}, urldate = {2023-05-26}, langid = {english}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/U5AXHAQ2/Singer et al. - 2020 - Elucidating the 1 H NMR Relaxation Mech.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/U5AXHAQ2/Singer et al. - 2020 - Elucidating the 1 H NMR Relaxation Mech.pdf} } @article{singerMolecularDynamicsSimulations2017, title = {Molecular Dynamics Simulations of {{NMR}} Relaxation and Diffusion of Bulk Hydrocarbons and Water}, author = {Singer, Philip M. and Asthagiri, Dilip and Chapman, Walter G. and Hirasaki, George J.}, - year = {2017}, - month = apr, - journal = {Journal of Magnetic Resonance}, + date = {2017-04}, + journaltitle = {Journal of Magnetic Resonance}, + shortjournal = {Journal of Magnetic Resonance}, volume = {277}, pages = {15--24}, issn = {10907807}, doi = {10.1016/j.jmr.2017.02.001}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1090780717300319}, urldate = {2023-05-16}, - abstract = {Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1;2 in the fast motion regime where T1 {$\frac{1}{4}$} T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.}, + abstract = {Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1;2 in the fast motion regime where T1 ¼ T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.}, langid = {english}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/ZVXYXNKX/Singer et al. - 2017 - Molecular dynamics simulations of NMR relaxation a.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/ZVXYXNKX/Singer et al. - 2017 - Molecular dynamics simulations of NMR relaxation a.pdf} } @article{singerNMRSpinrotationRelaxation2018, title = {{{NMR}} Spin-Rotation Relaxation and Diffusion of Methane}, author = {Singer, P. M. and Asthagiri, D. and Chapman, W. G. and Hirasaki, G. J.}, - year = {2018}, - month = may, - journal = {The Journal of Chemical Physics}, + date = {2018-05-22}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {148}, number = {20}, pages = {204504}, issn = {0021-9606}, doi = {10.1063/1.5027097}, + url = {https://doi.org/10.1063/1.5027097}, urldate = {2023-07-09}, - abstract = {The translational diffusion-coefficient and the spin-rotation contribution to the 1H NMR relaxation rate for methane (CH4) are investigated using MD (molecular dynamics) simulations, over a wide range of densities and temperatures, spanning the liquid, supercritical, and gas phases. The simulated diffusion-coefficients agree well with measurements, without any adjustable parameters in the interpretation of the simulations. A minimization technique is developed to compute the angular velocity for non-rigid spherical molecules, which is used to simulate the autocorrelation function for spin-rotation interactions. With increasing diffusivity, the autocorrelation function shows increasing deviations from the single-exponential decay predicted by the Langevin theory for rigid spheres, and the deviations are quantified using inverse Laplace transforms. The 1H spin-rotation relaxation rate derived from the autocorrelation function using the ``kinetic model'' agrees well with measurements in the supercritical/gas phase, while the relaxation rate derived using the ``diffusion model'' agrees well with measurements in the liquid phase. 1H spin-rotation relaxation is shown to dominate over the MD-simulated 1H-1H dipole-dipole relaxation at high diffusivity, while the opposite is found at low diffusivity. At high diffusivity, the simulated spin-rotation correlation time agrees with the kinetic collision time for gases, which is used to derive a new expression for 1H spin-rotation relaxation, without any adjustable parameters.}, + abstract = {The translational diffusion-coefficient and the spin-rotation contribution to the 1H NMR relaxation rate for methane (CH4) are investigated using MD (molecular dynamics) simulations, over a wide range of densities and temperatures, spanning the liquid, supercritical, and gas phases. The simulated diffusion-coefficients agree well with measurements, without any adjustable parameters in the interpretation of the simulations. A minimization technique is developed to compute the angular velocity for non-rigid spherical molecules, which is used to simulate the autocorrelation function for spin-rotation interactions. With increasing diffusivity, the autocorrelation function shows increasing deviations from the single-exponential decay predicted by the Langevin theory for rigid spheres, and the deviations are quantified using inverse Laplace transforms. The 1H spin-rotation relaxation rate derived from the autocorrelation function using the “kinetic model” agrees well with measurements in the supercritical/gas phase, while the relaxation rate derived using the “diffusion model” agrees well with measurements in the liquid phase. 1H spin-rotation relaxation is shown to dominate over the MD-simulated 1H-1H dipole-dipole relaxation at high diffusivity, while the opposite is found at low diffusivity. At high diffusivity, the simulated spin-rotation correlation time agrees with the kinetic collision time for gases, which is used to derive a new expression for 1H spin-rotation relaxation, without any adjustable parameters.}, keywords = {MD,NMR}, - file = {/home/simon/Zotero/storage/8T4YWT65/Singer et al. - 2018 - NMR spin-rotation relaxation and diffusion of meth.pdf;/home/simon/Zotero/storage/3LLY6NL5/NMR-spin-rotation-relaxation-and-diffusion-of.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/8T4YWT65/Singer et al. - 2018 - NMR spin-rotation relaxation and diffusion of meth.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/3LLY6NL5/NMR-spin-rotation-relaxation-and-diffusion-of.html} } @article{siracusaBiodegradablePolymersFood2008, title = {Biodegradable Polymers for Food Packaging: A Review}, shorttitle = {Biodegradable Polymers for Food Packaging}, author = {Siracusa, Valentina and Rocculi, Pietro and Romani, Santina and Rosa, Marco Dalla}, - year = {2008}, - month = dec, - journal = {Trends in Food Science \& Technology}, + date = {2008-12}, + journaltitle = {Trends in Food Science \& Technology}, + shortjournal = {Trends Food Sci Technol}, volume = {19}, number = {12}, pages = {634--643}, issn = {09242244}, doi = {10.1016/j.tifs.2008.07.003}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0924224408002185}, urldate = {2023-10-17}, langid = {english}, - file = {/home/simon/Zotero/storage/7X95WEE4/Siracusa et al. - 2008 - Biodegradable polymers for food packaging a revie.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7X95WEE4/Siracusa et al. - 2008 - Biodegradable polymers for food packaging a revie.pdf} } @article{sitaramanImpactLargescaleEffects2022, title = {Impact of Large-Scale Effects on Mass Transfer and Concentration Polarization in {{Reverse Osmosis}} Membrane Systems}, author = {Sitaraman, Hariswaran and Battiato, Ilenia}, - year = {2022}, - month = dec, - journal = {Separation and Purification Technology}, + date = {2022-12}, + journaltitle = {Separation and Purification Technology}, + shortjournal = {Sep. Purif. Technol.}, volume = {303}, pages = {122121}, issn = {13835866}, doi = {10.1016/j.seppur.2022.122121}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1383586622016768}, urldate = {2023-10-12}, - abstract = {We present well-resolved computational fluid dynamics simulations of a large-scale reverse osmosis membranespacer configuration ({$\sim$} 1 m). Our computational model solves the flow and transport equations with variable solute-dependent properties. We utilize a high resolution computational mesh to resolve all relevant length scales associated with spacer-induced mixing and thin concentration boundary layers. An important contribution of this work is the development of a modified mass-transfer correlation that accounts for the development of the concentration boundary layer along the channel. A set of 2D axisymmetric simulations were performed for a spiral wound module layer with varying cross-flow conditions and spacer diameters which indicate a significant entrance length effect for concentration profile development at lower flow rates while mixing effects dominate at higher flow rates. The mass-transfer correlations at higher flow rates compare well with published correlations while a surrogate model for Sherwood number was obtained that depends on an additional similarity variable that accounted for entrance length effects at lower flow rates. Finally, a large-scale membrane-spacer design relevant to high-pressure reverse osmosis is studied with a non-uniform arrangement of spacers, which indicate a substantial saving in pressure drop ({$\sim$} 40\%) compared to traditional uniformly spaced pattern with minor variations ({$\sim$} 2\%) in concentration polarization, product water quality ({$\sim$} 1\%) and water recovery ({$\sim$} 7\%) compared to a uniform spacer pattern.}, + abstract = {We present well-resolved computational fluid dynamics simulations of a large-scale reverse osmosis membranespacer configuration (∼ 1 m). Our computational model solves the flow and transport equations with variable solute-dependent properties. We utilize a high resolution computational mesh to resolve all relevant length scales associated with spacer-induced mixing and thin concentration boundary layers. An important contribution of this work is the development of a modified mass-transfer correlation that accounts for the development of the concentration boundary layer along the channel. A set of 2D axisymmetric simulations were performed for a spiral wound module layer with varying cross-flow conditions and spacer diameters which indicate a significant entrance length effect for concentration profile development at lower flow rates while mixing effects dominate at higher flow rates. The mass-transfer correlations at higher flow rates compare well with published correlations while a surrogate model for Sherwood number was obtained that depends on an additional similarity variable that accounted for entrance length effects at lower flow rates. Finally, a large-scale membrane-spacer design relevant to high-pressure reverse osmosis is studied with a non-uniform arrangement of spacers, which indicate a substantial saving in pressure drop (∼ 40\%) compared to traditional uniformly spaced pattern with minor variations (∼ 2\%) in concentration polarization, product water quality (∼ 1\%) and water recovery (∼ 7\%) compared to a uniform spacer pattern.}, langid = {english}, - file = {/home/simon/Zotero/storage/X254HHMT/Sitaraman and Battiato - 2022 - Impact of large-scale effects on mass transfer and.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/X254HHMT/Sitaraman and Battiato - 2022 - Impact of large-scale effects on mass transfer and.pdf} } @article{smithFreeEnergyEntropy1993, title = {Free Energy, Entropy, and Internal Energy of Hydrophobic Interactions: {{Computer}} Simulations}, shorttitle = {Free Energy, Entropy, and Internal Energy of Hydrophobic Interactions}, author = {Smith, David E. and Haymet, A. D. J.}, - year = {1993}, - month = apr, - journal = {The Journal of Chemical Physics}, + date = {1993-04-15}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {The Journal of Chemical Physics}, volume = {98}, number = {8}, pages = {6445--6454}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.464809}, + url = {https://pubs.aip.org/aip/jcp/article/98/8/6445-6454/784711}, urldate = {2023-07-04}, langid = {english}, - file = {/home/simon/Zotero/storage/AKUGUIKD/Smith and Haymet - 1993 - Free energy, entropy, and internal energy of hydro.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/AKUGUIKD/Smith and Haymet - 1993 - Free energy, entropy, and internal energy of hydro.pdf} } @article{snurrPredictionAdsorptionAromatic1993, title = {Prediction of Adsorption of Aromatic Hydrocarbons in Silicalite from Grand Canonical {{Monte Carlo}} Simulations with Biased Insertions}, author = {Snurr, Randall Q. and Bell, Alexis T. and Theodorou, Doros N.}, - year = {1993}, - month = dec, - journal = {The Journal of Physical Chemistry}, + date = {1993-12}, + journaltitle = {The Journal of Physical Chemistry}, + shortjournal = {J. Phys. Chem.}, volume = {97}, number = {51}, pages = {13742--13752}, issn = {0022-3654, 1541-5740}, doi = {10.1021/j100153a051}, + url = {https://pubs.acs.org/doi/abs/10.1021/j100153a051}, urldate = {2023-07-13}, langid = {english}, keywords = {heat,MD}, - file = {/home/simon/Zotero/storage/YXIUNUWF/Snurr et al. - 1993 - Prediction of adsorption of aromatic hydrocarbons .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YXIUNUWF/Snurr et al. - 1993 - Prediction of adsorption of aromatic hydrocarbons .pdf} } -@misc{StepCarbonCapture, +@online{StepCarbonCapture, title = {A {{Step}} in {{Carbon Capture}} from {{Wet Gases}}: {{Understanding}} the {{Effect}} of {{Water}} on {{CO2 Adsorption}} and {{Diffusion}} in {{UiO-66}}}, shorttitle = {A {{Step}} in {{Carbon Capture}} from {{Wet Gases}}}, doi = {10.1021/acs.jpcc.1c09914}, + url = {https://pubs.acs.org/doi/epdf/10.1021/acs.jpcc.1c09914}, urldate = {2023-10-20}, - howpublished = {https://pubs.acs.org/doi/epdf/10.1021/acs.jpcc.1c09914}, langid = {english}, - file = {/home/simon/Zotero/storage/634QXGM4/A Step in Carbon Capture from Wet Gases Understan.pdf;/home/simon/Zotero/storage/DBZXD76V/acs.jpcc.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/634QXGM4/A Step in Carbon Capture from Wet Gases Understan.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/DBZXD76V/acs.jpcc.html} } @article{strioloSimulatedWaterAdsorption2005, title = {Simulated {{Water Adsorption Isotherms}} in {{Hydrophilic}} and {{Hydrophobic Cylindrical Nanopores}}}, author = {Striolo, Alberto and Naicker, Pavanandan K. and Chialvo, Ariel A. and Cummings, Peter T. and Gubbins, Keith E.}, - year = {2005}, - month = jul, - journal = {Adsorption}, + date = {2005-07}, + journaltitle = {Adsorption}, + shortjournal = {Adsorption}, volume = {11}, number = {S1}, pages = {397--401}, issn = {0929-5607, 1572-8757}, doi = {10.1007/s10450-005-5957-9}, + url = {http://link.springer.com/10.1007/s10450-005-5957-9}, urldate = {2023-07-18}, abstract = {Grand canonical Monte Carlo simulations are performed to study the adsorption of water in singlewalled carbon nanotubes (SWCNs). At room temperature the resulting adsorption isotherms in (10:10) and wider SWCNs are characterized by negligible amount of water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption/desorption hysteresis loops. The width of these loops decreases as pore diameter narrows. Adsorption/desorption hysteresis loops are not observed for water adsorption in (6:6) SWCNs. When the nanotubes are doped with small amounts of oxygenated sites it is possible to obtain adsorption isotherms in which the water uptake increases gradually as the pressure increases. Simulated X-ray diffraction patterns for confined water are also reported.}, langid = {english}, keywords = {heat,MD}, - file = {/home/simon/Zotero/storage/4NTERIZY/Striolo et al. - 2005 - Simulated Water Adsorption Isotherms in Hydrophili.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4NTERIZY/Striolo et al. - 2005 - Simulated Water Adsorption Isotherms in Hydrophili.pdf} } @article{suarezDirectMethodsComputing2015, title = {Direct Methods for Computing Single-Molecule Entropies from Molecular Simulations}, - author = {Su{\'a}rez, Dimas and D{\'i}az, Natalia}, - year = {2015}, - month = jan, - journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science}, + author = {Suárez, Dimas and Díaz, Natalia}, + date = {2015-01}, + journaltitle = {Wiley Interdisciplinary Reviews: Computational Molecular Science}, + shortjournal = {WIREs Comput Mol Sci}, volume = {5}, number = {1}, pages = {1--26}, issn = {17590876}, doi = {10.1002/wcms.1195}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/wcms.1195}, urldate = {2023-05-02}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/QULMKWQN/Suárez and Díaz - 2015 - Direct methods for computing single-molecule entro.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QULMKWQN/Suárez and Díaz - 2015 - Direct methods for computing single-molecule entro.pdf} } @article{surblysMolecularDynamicsAnalysis2014, title = {Molecular Dynamics Analysis on Wetting and Interfacial Properties of Water-Alcohol Mixture Droplets on a Solid Surface}, author = {Surblys, D. and Yamaguchi, Y. and Kuroda, K. and Kagawa, M. and Nakajima, T. and Fujimura, H.}, - year = {2014}, - month = jan, - journal = {The Journal of Chemical Physics}, + date = {2014-01-21}, + journaltitle = {The Journal of Chemical Physics}, volume = {140}, number = {3}, pages = {034505}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.4861039}, + url = {https://pubs.aip.org/jcp/article/140/3/034505/601484/Molecular-dynamics-analysis-on-wetting-and}, urldate = {2023-07-18}, abstract = {Molecular dynamics simulations of single water, water-methanol, or water-IPA (isopropyl-alcohol) mixture droplets on a solid surface were performed with various mixture ratios. An increase in alcohol fraction generally gave an increase in droplet wettability. Both methanol and IPA molecules showed a strong preference to gather at various interfaces, with methanol molecules also showing a tendency to diffuse into the droplet bulk. Specific interfacial tensions were investigated using quasi-one-dimensional simulation systems, and liquid-vapor and solid-liquid interfacial tensions were found to decrease greatly due to the presence of interfacial alcohol, while solid-vapor interfacial tensions were proved to have little influence on wettability. Young's relation was found to hold quantitatively well for both water-methanol and water-IPA droplets. The validity of using Bakker's equation on solid-liquid interfaces was also investigated, and it was shown that for tightly spaced crystal surfaces, the introduced uncertainly is small.}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/JTF79HEQ/Surblys et al. - 2014 - Molecular dynamics analysis on wetting and interfa.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/JTF79HEQ/Surblys et al. - 2014 - Molecular dynamics analysis on wetting and interfa.pdf} } @article{szlufarskaRecentAdvancesSingleasperity2008, title = {Recent Advances in Single-Asperity Nanotribology}, author = {Szlufarska, Izabela and Chandross, Michael and Carpick, Robert W}, - year = {2008}, - month = jun, - journal = {Journal of Physics D: Applied Physics}, + date = {2008-06-21}, + journaltitle = {Journal of Physics D: Applied Physics}, + shortjournal = {J. Phys. D: Appl. Phys.}, volume = {41}, number = {12}, pages = {123001}, issn = {0022-3727, 1361-6463}, doi = {10.1088/0022-3727/41/12/123001}, + url = {https://iopscience.iop.org/article/10.1088/0022-3727/41/12/123001}, urldate = {2023-07-03}, abstract = {As the size of electronic and mechanical devices shrinks to the nanometre regime, performance begins to be dominated by surface forces. For example, friction, wear and adhesion are known to be central challenges in the design of reliable micro- and nano-electromechanical systems (MEMS/NEMS). Because of the complexity of the physical and chemical mechanisms underlying atomic-level tribology, it is still not possible to accurately and reliably predict the response when two surfaces come into contact at the nanoscale. Fundamental scientific studies are the means by which these insights may be gained. We review recent advances in the experimental, theoretical and computational studies of nanotribology. In particular, we focus on the latest developments in atomic force microscopy and molecular dynamics simulations and their application to the study of single-asperity contact.}, langid = {english}, keywords = {tribo}, - file = {/home/simon/Zotero/storage/YBATLQ3N/Szlufarska et al. - 2008 - Recent advances in single-asperity nanotribology.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YBATLQ3N/Szlufarska et al. - 2008 - Recent advances in single-asperity nanotribology.pdf} } @article{tanConsistencyNVTNPT2020, - title = {Consistency of {{NVT}}, {{NPT}}, {{{\textmu}VT}} and {{Gibbs}} ({{NV2T}} and {{NPT}}) with Kinetic {{Monte Carlo}} Schemes}, + title = {Consistency of {{NVT}}, {{NPT}}, {{µVT}} and {{Gibbs}} ({{NV2T}} and {{NPT}}) with Kinetic {{Monte Carlo}} Schemes}, author = {Tan, Shiliang (Johnathan) and Do, D.D. and Nicholson, D.}, - year = {2020}, - month = dec, - journal = {Chemical Engineering Journal}, + date = {2020-12}, + journaltitle = {Chemical Engineering Journal}, + shortjournal = {Chemical Engineering Journal}, volume = {401}, pages = {126056}, issn = {13858947}, doi = {10.1016/j.cej.2020.126056}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1385894720321847}, urldate = {2023-07-25}, - abstract = {We investigate the consistency of the simulation methodology for fluid phase equilibria and mixture adsorption from various ensembles [NVT (canonical), NPT (isothermal-isobaric systems), {\textmu}VT (grand canonical) and Gibbs NV2T and Gibbs NPT] with the kinetic Monte Carlo (kMC) scheme. kMC is an alternative to Metropolis Monte Carlo (MC), in which chemical potential can be determined accurately. This is a major advantage in dense phases where the Widom method, usually employed in Metropolis MC, fails to provide sufficient accuracy. We have studied binary mixtures of methane with ethane to illustrate the consistency between the simulation methods for bulk fluids, and mixtures of ethanol{\textendash}water and ammonia-water as examples of adsorption systems. The adsorption systems exhibit cooperative effects between water and ethanol and between water and ammonia: water by itself does not wet a carbon surface, but it adsorbs in large quantities when either ethanol or ammonia are present. Microscopic configurations taken from the simulations show a distinct difference between the adsorption mechanism in the water/ethanol mixtures and the water/ammonia mixtures.}, + abstract = {We investigate the consistency of the simulation methodology for fluid phase equilibria and mixture adsorption from various ensembles [NVT (canonical), NPT (isothermal-isobaric systems), µVT (grand canonical) and Gibbs NV2T and Gibbs NPT] with the kinetic Monte Carlo (kMC) scheme. kMC is an alternative to Metropolis Monte Carlo (MC), in which chemical potential can be determined accurately. This is a major advantage in dense phases where the Widom method, usually employed in Metropolis MC, fails to provide sufficient accuracy. We have studied binary mixtures of methane with ethane to illustrate the consistency between the simulation methods for bulk fluids, and mixtures of ethanol–water and ammonia-water as examples of adsorption systems. The adsorption systems exhibit cooperative effects between water and ethanol and between water and ammonia: water by itself does not wet a carbon surface, but it adsorbs in large quantities when either ethanol or ammonia are present. Microscopic configurations taken from the simulations show a distinct difference between the adsorption mechanism in the water/ethanol mixtures and the water/ammonia mixtures.}, langid = {english}, keywords = {MD,mu,water-ethanol}, - file = {/home/simon/Zotero/storage/WCY56GRG/Tan et al. - 2020 - Consistency of NVT, NPT, µVT and Gibbs (NV2T and N.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WCY56GRG/Tan et al. - 2020 - Consistency of NVT, NPT, µVT and Gibbs (NV2T and N.pdf} } @article{taylorMoleculardynamicsSimulationsEthanol2003, - title = {Molecular-Dynamics Simulations of the Ethanol Liquid{\textendash}Vapor Interface}, + title = {Molecular-Dynamics Simulations of the Ethanol Liquid–Vapor Interface}, author = {Taylor, Ramona S. and Shields, Roseanne L.}, - year = {2003}, - month = dec, - journal = {The Journal of Chemical Physics}, + date = {2003-12-15}, + journaltitle = {The Journal of Chemical Physics}, volume = {119}, number = {23}, pages = {12569--12576}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.1625643}, + url = {https://pubs.aip.org/jcp/article/119/23/12569/534599/Molecular-dynamics-simulations-of-the-ethanol}, urldate = {2023-07-25}, - abstract = {Molecular-dynamics computer simulations have been utilized to study the thermodynamic, structural, and dynamical properties of the liquid{\textendash}vapor interface of ethanol as a function of temperature. Both the ethanol united-atom and the ethanol all-atom optimized potential models for liquid simulations (OPLS) have been investigated. For both potentials, the calculated ethanol surface tensions as a function of temperature and the orientation of ethanol molecules at the liquid{\textendash}vapor interface are in agreement with the corresponding experimental data. However, given the degree of agreement between the experimental and simulation data, the OPLS all-atom model better represents the types of interactions present at the liquid{\textendash}vapor interface of ethanol. In addition, for both potentials the self-diffusion constant of ethanol is found to be larger at the surface than in the bulk of the liquid.}, + abstract = {Molecular-dynamics computer simulations have been utilized to study the thermodynamic, structural, and dynamical properties of the liquid–vapor interface of ethanol as a function of temperature. Both the ethanol united-atom and the ethanol all-atom optimized potential models for liquid simulations (OPLS) have been investigated. For both potentials, the calculated ethanol surface tensions as a function of temperature and the orientation of ethanol molecules at the liquid–vapor interface are in agreement with the corresponding experimental data. However, given the degree of agreement between the experimental and simulation data, the OPLS all-atom model better represents the types of interactions present at the liquid–vapor interface of ethanol. In addition, for both potentials the self-diffusion constant of ethanol is found to be larger at the surface than in the bulk of the liquid.}, langid = {english}, keywords = {ff,water-ethanol}, - file = {/home/simon/Zotero/storage/5YMGPLWN/Taylor and Shields - 2003 - Molecular-dynamics simulations of the ethanol liqu.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5YMGPLWN/Taylor and Shields - 2003 - Molecular-dynamics simulations of the ethanol liqu.pdf} } @article{thompsonLAMMPSFlexibleSimulation2022, title = {{{LAMMPS}} - a Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales}, author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and In 'T Veld, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.}, - year = {2022}, - month = feb, - journal = {Computer Physics Communications}, + date = {2022-02}, + journaltitle = {Computer Physics Communications}, + shortjournal = {Computer Physics Communications}, volume = {271}, pages = {108171}, issn = {00104655}, doi = {10.1016/j.cpc.2021.108171}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0010465521002836}, urldate = {2023-05-12}, langid = {english}, - file = {/home/simon/Zotero/storage/U7RJB45S/Thompson et al. - 2022 - LAMMPS - a flexible simulation tool for particle-b.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/U7RJB45S/Thompson et al. - 2022 - LAMMPS - a flexible simulation tool for particle-b.pdf} } @article{tsimpanogiannisSelfdiffusionCoefficientBulk2019, title = {Self-Diffusion Coefficient of Bulk and Confined Water: A Critical Review of Classical Molecular Simulation Studies}, shorttitle = {Self-Diffusion Coefficient of Bulk and Confined Water}, - author = {Tsimpanogiannis, Ioannis N. and Moultos, Othonas A. and Franco, Lu{\'i}s F. M. and Spera, Marcelle B. De M. and Erd{\H o}s, M{\'a}t{\'e} and Economou, Ioannis G.}, - year = {2019}, - month = mar, - journal = {Molecular Simulation}, + author = {Tsimpanogiannis, Ioannis N. and Moultos, Othonas A. and Franco, Luís F. M. and Spera, Marcelle B. De M. and Erdős, Máté and Economou, Ioannis G.}, + date = {2019-03-24}, + journaltitle = {Molecular Simulation}, + shortjournal = {Molecular Simulation}, volume = {45}, number = {4-5}, pages = {425--453}, issn = {0892-7022, 1029-0435}, doi = {10.1080/08927022.2018.1511903}, + url = {https://www.tandfonline.com/doi/full/10.1080/08927022.2018.1511903}, urldate = {2023-12-12}, abstract = {We present a detailed overview of classical molecular simulation studies examining the self-diffusion coefficient of water. The self-diffusion coefficient is directly associated with the calculations of tracer or mutual diffusion coefficient of mixtures and, therefore, is a fundamental transport property, essential for an accurate description of mass transfer processes in biological, geological (i.e. energy or environmentally related), and chemical systems. In the current review we explore two distinct research areas. Namely, we discuss the self-diffusion of water in the bulk phase and under confinement. Different aspects that affect the diffusion process, including the molecular models, the system-size effects, the temperature and pressure conditions and the type of confinement are discussed. Finally, possible directions for future research are outlined.}, langid = {english}, - file = {/home/simon/Zotero/storage/X948U963/Tsimpanogiannis et al. - 2019 - Self-diffusion coefficient of bulk and confined wa.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/X948U963/Tsimpanogiannis et al. - 2019 - Self-diffusion coefficient of bulk and confined wa.pdf} } @article{vanossRoleVanWaals1986, - title = {The Role of van Der {{Waals}} Forces and Hydrogen Bonds in ``Hydrophobic Interactions'' between Biopolymers and Low Energy Surfaces}, + title = {The Role of van Der {{Waals}} Forces and Hydrogen Bonds in “Hydrophobic Interactions” between Biopolymers and Low Energy Surfaces}, author = {Van Oss, C.J and Good, R.J and Chaudhury, M.K}, - year = {1986}, - month = jun, - journal = {Journal of Colloid and Interface Science}, + date = {1986-06}, + journaltitle = {Journal of Colloid and Interface Science}, + shortjournal = {Journal of Colloid and Interface Science}, volume = {111}, number = {2}, pages = {378--390}, issn = {00219797}, doi = {10.1016/0021-9797(86)90041-X}, + url = {https://linkinghub.elsevier.com/retrieve/pii/002197978690041X}, urldate = {2023-07-04}, langid = {english}, keywords = {HB}, - file = {/home/simon/Zotero/storage/Y4IRWQ9C/Van Oss et al. - 1986 - The role of van der Waals forces and hydrogen bond.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Y4IRWQ9C/Van Oss et al. - 1986 - The role of van der Waals forces and hydrogen bond.pdf} } @article{walker-gibbonsRoleSurfaceChemistry2022, title = {The {{Role}} of {{Surface Chemistry}} in the {{Orientational Behavior}} of {{Water}} at an {{Interface}}}, - author = {{Walker-Gibbons}, Rowan and Kubincov{\'a}, Al{\v z}beta and H{\"u}nenberger, Philippe H. and Krishnan, Madhavi}, - year = {2022}, - month = jun, - journal = {The Journal of Physical Chemistry B}, + author = {Walker-Gibbons, Rowan and Kubincová, Alžbeta and Hünenberger, Philippe H. and Krishnan, Madhavi}, + date = {2022-06-30}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {126}, number = {25}, pages = {4697--4710}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.2c01752}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.2c01752}, urldate = {2023-04-19}, abstract = {Molecular dynamics studies have demonstrated that molecular water at an interface, with either a gas or a solid, displays anisotropic orientational behavior in contrast to its bulk counterpart. This effect has been recently implicated in the like-charge attraction problem for colloidal particles in solution. Here, negatively charged particles in solution display a long-ranged attraction where continuum electrostatic theory predicts monotonically repulsive interactions, particularly in solutions with monovalent salt ions at low ionic strength. Anisotropic orientational behavior of solvent molecules at an interface gives rise to an excess interfacial electrical potential which we suggest generates an additional solvation contribution to the total free energy that is traditionally overlooked in continuum descriptions of interparticle interactions in solution. In the present investigation we perform molecular dynamics simulation based calculations of the interfacial potential using realistic surface models representing various chemistries as well as different solvents. Similar to previous work that focused on simple model surfaces constructed by using oxygen atoms, we find that solvents at more realistic model surfaces exhibit substantial anisotropic orientational behavior. We explore the dependence of the interfacial solvation potential on surface properties such as surface group chemistry and group density at silica and carboxylated polystyrene interfaces. For water, we note surprisingly good agreement between results obtained for a simple O-atom wall and more complex surface models, suggesting a general qualitative consistency of the interfacial solvation effect for surfaces in contact with water. In contrast, for an aprotic solvent such as DMSO, surface chemistry appears to exert a stronger influence on the sign and magnitude of the interfacial solvation potential. The study carries broad implications for molecular-scale interactions and may find relevance in explaining a range of phenomena in softmatter physics and cell biology.}, langid = {english}, keywords = {HB,MD}, - file = {/home/simon/Zotero/storage/I6X5LB59/Walker-Gibbons et al. - 2022 - The Role of Surface Chemistry in the Orientational.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/I6X5LB59/Walker-Gibbons et al. - 2022 - The Role of Surface Chemistry in the Orientational.pdf} } @article{wangMOFGlassMembrane2020, title = {A {{MOF Glass Membrane}} for {{Gas Separation}}}, author = {Wang, Yuhan and Jin, Hua and Ma, Qiang and Mo, Kai and Mao, Haizhuo and Feldhoff, Armin and Cao, Xingzhong and Li, Yanshuo and Pan, Fusheng and Jiang, Zhongyi}, - year = {2020}, - month = mar, - journal = {Angewandte Chemie}, + date = {2020-03-09}, + journaltitle = {Angewandte Chemie}, + shortjournal = {Angew. Chem.}, volume = {132}, number = {11}, pages = {4395--4399}, issn = {0044-8249, 1521-3757}, doi = {10.1002/ange.201915807}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/ange.201915807}, urldate = {2023-07-21}, - abstract = {Metal{\textendash}organic framework (MOF) glasses are promising candidates for membrane fabrication due to their significant porosity, the ease of processing, and most notably, the potential to eliminate the grain boundary that is unavoidable for polycrystalline MOF membranes. Herein, we developed a ZIF-62 MOF glass membrane and exploited its intrinsic gas-separation properties. The MOF glass membrane was fabricated by melt-quenching treatment of an in situ solvothermally synthesized polycrystalline ZIF-62 MOF membrane on a porous ceramic alumina support. The molten ZIF-62 phase penetrated into the nanopores of the support and eliminated the formation of intercrystalline defects in the resultant glass membrane. The molecular sieving ability of the MOF membrane is remarkably enhanced via vitrification. The separation factors of the MOF glass membrane for H2/CH4, CO2/N2 and CO2/CH4 mixtures are 50.7, 34.5, and 36.6, respectively, far exceeding the Robeson upper bounds.}, + abstract = {Metal–organic framework (MOF) glasses are promising candidates for membrane fabrication due to their significant porosity, the ease of processing, and most notably, the potential to eliminate the grain boundary that is unavoidable for polycrystalline MOF membranes. Herein, we developed a ZIF-62 MOF glass membrane and exploited its intrinsic gas-separation properties. The MOF glass membrane was fabricated by melt-quenching treatment of an in situ solvothermally synthesized polycrystalline ZIF-62 MOF membrane on a porous ceramic alumina support. The molten ZIF-62 phase penetrated into the nanopores of the support and eliminated the formation of intercrystalline defects in the resultant glass membrane. The molecular sieving ability of the MOF membrane is remarkably enhanced via vitrification. The separation factors of the MOF glass membrane for H2/CH4, CO2/N2 and CO2/CH4 mixtures are 50.7, 34.5, and 36.6, respectively, far exceeding the Robeson upper bounds.}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/NAQLZQ9V/Wang et al. - 2020 - A MOF Glass Membrane for Gas Separation.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NAQLZQ9V/Wang et al. - 2020 - A MOF Glass Membrane for Gas Separation.pdf} } @article{weiImpactsEthanolWater2019, title = {Impacts of {{Ethanol}} and {{Water Adsorptions}} on {{Thermal Conductivity}} of {{ZIF-8}}}, author = {Wei, Wei and Huang, Jun and Li, Wei and Peng, Haiyan and Li, Song}, - year = {2019}, - month = nov, - journal = {The Journal of Physical Chemistry C}, + date = {2019-11-14}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {123}, number = {45}, pages = {27369--27374}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.9b08187}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.9b08187}, urldate = {2023-05-23}, - abstract = {Metal-organic frameworks are promising nanoporous materials for adsorption heat pumps (AHPs) using water and alcohols as working fluids due to their ultrahigh surface area. The heat transfer in porous crystals containing adsorbed gases is vital for their performance in adsorbed natural gas storage or AHPs. However, limited attention has been paid to their thermal properties. In this study, equilibrium molecular dynamics simulations were performed to investigate the impacts of ethanol/water adsorption on the thermal conductivity of zeolitic imidazolate framework-8 (ZIF-8). The results demonstrated that the thermal conductivity of ZIF-8 increased from 0.165 to 0.319 W m-1 K-1 with the increased number of adsorbed ethanol molecules. On the contrary, the thermal conductivity of ZIF-8 upon water adsorption is approximately 0.190 W m-1 K-1, which is not significantly affected by the number of adsorbed water molecules. Such a different tendency may be ascribed to the different interaction strengths between ZIF-8 and gas molecules. In addition, the larger overlap energy in the vibrational density of state of ZIF-8/ethanol than that of ZIF-8/ water also correlates with the higher thermal conductivity of the ZIF-8/ethanol system. This work provides molecular insights into the effects of ethanol/water adsorption on the thermal conductivity of ZIF-8, which may inspire further exploration of novel techniques to improve the heat transfer performance of practical applications.}, + abstract = {Metal−organic frameworks are promising nanoporous materials for adsorption heat pumps (AHPs) using water and alcohols as working fluids due to their ultrahigh surface area. The heat transfer in porous crystals containing adsorbed gases is vital for their performance in adsorbed natural gas storage or AHPs. However, limited attention has been paid to their thermal properties. In this study, equilibrium molecular dynamics simulations were performed to investigate the impacts of ethanol/water adsorption on the thermal conductivity of zeolitic imidazolate framework-8 (ZIF-8). The results demonstrated that the thermal conductivity of ZIF-8 increased from 0.165 to 0.319 W m−1 K−1 with the increased number of adsorbed ethanol molecules. On the contrary, the thermal conductivity of ZIF-8 upon water adsorption is approximately 0.190 W m−1 K−1, which is not significantly affected by the number of adsorbed water molecules. Such a different tendency may be ascribed to the different interaction strengths between ZIF-8 and gas molecules. In addition, the larger overlap energy in the vibrational density of state of ZIF-8/ethanol than that of ZIF-8/ water also correlates with the higher thermal conductivity of the ZIF-8/ethanol system. This work provides molecular insights into the effects of ethanol/water adsorption on the thermal conductivity of ZIF-8, which may inspire further exploration of novel techniques to improve the heat transfer performance of practical applications.}, langid = {english}, keywords = {MD,water-ethanol,zif}, - file = {/home/simon/Zotero/storage/4E8JQQTE/Wei et al. - 2019 - Impacts of Ethanol and Water Adsorptions on Therma.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/4E8JQQTE/Wei et al. - 2019 - Impacts of Ethanol and Water Adsorptions on Therma.pdf} } @article{weinerAllAtomForce1986, title = {An All Atom Force Field for Simulations of Proteins and Nucleic Acids: {{An All Atom Force Field}}}, shorttitle = {An All Atom Force Field for Simulations of Proteins and Nucleic Acids}, author = {Weiner, Scott J. and Kollman, Peter A. and Nguyen, Dzung T. and Case, David A.}, - year = {1986}, - month = apr, - journal = {Journal of Computational Chemistry}, + date = {1986-04}, + journaltitle = {Journal of Computational Chemistry}, + shortjournal = {J. Comput. Chem.}, volume = {7}, number = {2}, pages = {230--252}, issn = {01928651}, doi = {10.1002/jcc.540070216}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.540070216}, urldate = {2023-07-26}, langid = {english}, keywords = {ff}, - file = {/home/simon/Zotero/storage/6WDUNZYD/Weiner et al. - 1986 - An all atom force field for simulations of protein.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/6WDUNZYD/Weiner et al. - 1986 - An all atom force field for simulations of protein.pdf} } @article{wilsonAdsorptionSolvationEthanol1997, - title = {Adsorption and {{Solvation}} of {{Ethanol}} at the {{Water Liquid}}-{{Vapor Interface}}: {{A Molecular Dynamics Study}}}, - shorttitle = {Adsorption and {{Solvation}} of {{Ethanol}} at the {{Water Liquid}}-{{Vapor Interface}}}, + title = {Adsorption and {{Solvation}} of {{Ethanol}} at the {{Water Liquid}}−{{Vapor Interface}}: {{A Molecular Dynamics Study}}}, + shorttitle = {Adsorption and {{Solvation}} of {{Ethanol}} at the {{Water Liquid}}−{{Vapor Interface}}}, author = {Wilson, Michael A. and Pohorille, Andrew}, - year = {1997}, - month = apr, - journal = {The Journal of Physical Chemistry B}, + date = {1997-04-01}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {101}, number = {16}, pages = {3130--3135}, issn = {1520-6106, 1520-5207}, doi = {10.1021/jp962629n}, + url = {https://pubs.acs.org/doi/10.1021/jp962629n}, urldate = {2023-07-18}, langid = {english}, - file = {/home/simon/Zotero/storage/D7IT7XB7/Wilson and Pohorille - 1997 - Adsorption and Solvation of Ethanol at the Water L.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/D7IT7XB7/Wilson and Pohorille - 1997 - Adsorption and Solvation of Ethanol at the Water L.pdf} } @article{woessnerDenseGasDiffusion1969, title = {Dense {{Gas Diffusion Coefficients}} for the {{Methane-Propane System}}}, author = {Woessner, D. E. and Snowden, B. S. and George, R. A. and Melrose, J. C.}, - year = {1969}, - month = nov, - journal = {Industrial \& Engineering Chemistry Fundamentals}, + date = {1969-11}, + journaltitle = {Industrial \& Engineering Chemistry Fundamentals}, + shortjournal = {Ind. Eng. Chem. Fund.}, volume = {8}, number = {4}, pages = {779--786}, issn = {0196-4313, 1541-4833}, doi = {10.1021/i160032a029}, + url = {https://pubs.acs.org/doi/abs/10.1021/i160032a029}, urldate = {2023-05-30}, langid = {english}, keywords = {NMR,propane}, - file = {/home/simon/Zotero/storage/PEKRTNAB/Woessner et al. - 1969 - Dense Gas Diffusion Coefficients for the Methane-P.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/PEKRTNAB/Woessner et al. - 1969 - Dense Gas Diffusion Coefficients for the Methane-P.pdf} } @article{wolde-kidanInfluencePolarCosolutes2019, title = {Influence of Polar Co-Solutes and Salt on the Hydration of Lipid Membranes}, - author = {{Wolde-Kidan}, Amanuel and Pham, Quoc Dat and Schlaich, Alexander and Loche, Philip and Sparr, Emma and Netz, Roland R. and Schneck, Emanuel}, - year = {2019}, - journal = {Physical Chemistry Chemical Physics}, + author = {Wolde-Kidan, Amanuel and Pham, Quoc Dat and Schlaich, Alexander and Loche, Philip and Sparr, Emma and Netz, Roland R. and Schneck, Emanuel}, + date = {2019}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, volume = {21}, number = {31}, pages = {16989--17000}, issn = {1463-9076, 1463-9084}, doi = {10.1039/C9CP01953G}, + url = {http://xlink.rsc.org/?DOI=C9CP01953G}, urldate = {2023-05-12}, - abstract = {The influence of the co-solutes TMAO, urea, and NaCl on the hydration repulsion between lipid membranes is investigated in a combined experimental/simulation approach. , The influence of the co-solutes TMAO, urea, and NaCl on the hydration repulsion between lipid membranes is investigated in a combined experimental/simulation approach. Pressure{\textendash}hydration curves obtained via sorption experiments reveal that the repulsion significantly increases when the membranes are loaded with co-solutes, most strongly for TMAO. As a result, the co-solutes retain additional water molecules and therefore provide membranes with a fluid and more physiological environment. The experimental data are quantitatively reproduced in complementary solvent-explicit atomistic molecular dynamics simulations, which yield the chemical potential of water. Simulation analysis reveals that the additional repulsion arises from the osmotic pressure generated by the co-solutes, an effect which is maximal for TMAO, due to its unfavorable interactions with the lipid headgroup layer and its extraordinarily high osmotic coefficient.}, + abstract = {The influence of the co-solutes TMAO, urea, and NaCl on the hydration repulsion between lipid membranes is investigated in a combined experimental/simulation approach. , The influence of the co-solutes TMAO, urea, and NaCl on the hydration repulsion between lipid membranes is investigated in a combined experimental/simulation approach. Pressure–hydration curves obtained via sorption experiments reveal that the repulsion significantly increases when the membranes are loaded with co-solutes, most strongly for TMAO. As a result, the co-solutes retain additional water molecules and therefore provide membranes with a fluid and more physiological environment. The experimental data are quantitatively reproduced in complementary solvent-explicit atomistic molecular dynamics simulations, which yield the chemical potential of water. Simulation analysis reveals that the additional repulsion arises from the osmotic pressure generated by the co-solutes, an effect which is maximal for TMAO, due to its unfavorable interactions with the lipid headgroup layer and its extraordinarily high osmotic coefficient.}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/HCEU5CMW/Wolde-Kidan et al. - 2019 - Influence of polar co-solutes and salt on the hydr.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/HCEU5CMW/Wolde-Kidan et al. - 2019 - Influence of polar co-solutes and salt on the hydr.pdf} } @article{wolde-kidanInterplayInterfacialViscosity2021, title = {Interplay of {{Interfacial Viscosity}}, {{Specific-Ion}}, and {{Impurity Adsorption Determines Zeta Potentials}} of {{Phospholipid Membranes}}}, - author = {{Wolde-Kidan}, Amanuel and Netz, Roland R.}, - year = {2021}, - month = jul, - journal = {Langmuir}, + author = {Wolde-Kidan, Amanuel and Netz, Roland R.}, + date = {2021-07-20}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {37}, number = {28}, pages = {8463--8473}, issn = {0743-7463, 1520-5827}, doi = {10.1021/acs.langmuir.1c00868}, + url = {https://pubs.acs.org/doi/10.1021/acs.langmuir.1c00868}, urldate = {2023-05-19}, - abstract = {Ion-specific induced changes of the {$\zeta$}-potential of phospholipid vesicles are commonly used to quantify the affinity of different ions to the lipid interface. The negative {$\zeta$}-potential of zwitterionic net-neutral phospholipid vesicles in neat water, which changes sign and increases in solutions of NaCl or KCl, is a phenomenon consistently observed in experiments but not fully understood theoretically. Using atomistic molecular dynamics simulations in the presence of applied electric fields which drive electroosmotic flows, in combination with an electrostatic continuum model based on the modified Poisson-Boltzmann and Helmholtz-Smoluchowski equations, we study the electrokinetic and electrostatic properties as well as the specific ion affinities to the phospholipid-water interface, in order to resolve these puzzling observations. Our modified continuum equations account for the dielectric profile at the lipid-water interface, ion-specific interactions between ions and the lipid-water interface, and the interfacial viscosity profile, which are all extracted from our atomistic simulations and rather accurately predict ion-density and electrostatic-potential distributions as well as {$\zeta$}-potentials in comparison with our atomistic simulations. Our continuum model can explain experimental {$\zeta$}-potentials only when we assume minute amounts of surface-active anionic impurities in the aqueous solution. In fact, the amount of impurities needed to explain the experimental data increases linearly with the salt concentration, suggesting that surface-active species, which might be already present in the lab water or lipid samples, could further be introduced through the added salt.}, + abstract = {Ion-specific induced changes of the ζ-potential of phospholipid vesicles are commonly used to quantify the affinity of different ions to the lipid interface. The negative ζ-potential of zwitterionic net-neutral phospholipid vesicles in neat water, which changes sign and increases in solutions of NaCl or KCl, is a phenomenon consistently observed in experiments but not fully understood theoretically. Using atomistic molecular dynamics simulations in the presence of applied electric fields which drive electroosmotic flows, in combination with an electrostatic continuum model based on the modified Poisson−Boltzmann and Helmholtz−Smoluchowski equations, we study the electrokinetic and electrostatic properties as well as the specific ion affinities to the phospholipid−water interface, in order to resolve these puzzling observations. Our modified continuum equations account for the dielectric profile at the lipid−water interface, ion-specific interactions between ions and the lipid−water interface, and the interfacial viscosity profile, which are all extracted from our atomistic simulations and rather accurately predict ion-density and electrostatic-potential distributions as well as ζ-potentials in comparison with our atomistic simulations. Our continuum model can explain experimental ζ-potentials only when we assume minute amounts of surface-active anionic impurities in the aqueous solution. In fact, the amount of impurities needed to explain the experimental data increases linearly with the salt concentration, suggesting that surface-active species, which might be already present in the lab water or lipid samples, could further be introduced through the added salt.}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/PEHAPUE4/Wolde-Kidan and Netz - 2021 - Interplay of Interfacial Viscosity, Specific-Ion, .pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/PEHAPUE4/Wolde-Kidan and Netz - 2021 - Interplay of Interfacial Viscosity, Specific-Ion, .pdf} } @article{wuEnergyLandscapeWater2015, title = {Energy {{Landscape}} of {{Water}} and {{Ethanol}} on {{Silica Surfaces}}}, author = {Wu, Di and Guo, Xiaofeng and Sun, Hui and Navrotsky, Alexandra}, - year = {2015}, - month = jul, - journal = {The Journal of Physical Chemistry C}, + date = {2015-07-09}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {119}, number = {27}, pages = {15428--15433}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.5b04271}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.5b04271}, urldate = {2023-06-09}, - abstract = {Fundamental understanding of small molecule-silica surface interactions at their interfaces is essential for the scientific, technological, and medical communities. We report direct enthalpy of adsorption ({$\Delta$}hads) measurements for ethanol and water vapor on porous silica glass (CPG-10), in both hydroxylated and dehydroxylated (hydrophobic) forms. The results suggest a spectrum of energetics as a function of coverage, stepwise for ethanol but continuous for water. The zero-coverage enthalpy of adsorption for hydroxylated silica shows the most exothermic enthalpies for both water (-72.7 {$\pm$} 3.1 kJ/mol water) and ethanol (-78.0 {$\pm$} 1.9 kJ/mol ethanol). The water adsorption enthalpy becomes less exothermic gradually until reaching its only plateau (-20.7 {$\pm$} 2.2 kJ/mol water) reflecting water clustering on a largely hydrophobic surface, while the enthalpy of ethanol adsorption profile presents two well separated plateaus, corresponding to strong chemisorption of ethanol on adsorbate-free silica surface (-66.4 {$\pm$} 4.8 kJ/mol ethanol), and weak physisorption of ethanol on ethanol covered silica (-4.0 {$\pm$} 1.6 kJ/mol ethanol). On the other hand, dehydroxylation leads to missing water-silica interactions, whereas the number of ethanol binding sites is not impacted. The isotherms and partial molar properties of adsorption suggest that water may only bind strongly onto the silanols (which are a minor species on silica glass), whereas ethanol can interact strongly with both silanols and the hydrophobic areas of the silica surface.}, + abstract = {Fundamental understanding of small molecule−silica surface interactions at their interfaces is essential for the scientific, technological, and medical communities. We report direct enthalpy of adsorption (Δhads) measurements for ethanol and water vapor on porous silica glass (CPG-10), in both hydroxylated and dehydroxylated (hydrophobic) forms. The results suggest a spectrum of energetics as a function of coverage, stepwise for ethanol but continuous for water. The zero-coverage enthalpy of adsorption for hydroxylated silica shows the most exothermic enthalpies for both water (−72.7 ± 3.1 kJ/mol water) and ethanol (−78.0 ± 1.9 kJ/mol ethanol). The water adsorption enthalpy becomes less exothermic gradually until reaching its only plateau (−20.7 ± 2.2 kJ/mol water) reflecting water clustering on a largely hydrophobic surface, while the enthalpy of ethanol adsorption profile presents two well separated plateaus, corresponding to strong chemisorption of ethanol on adsorbate-free silica surface (−66.4 ± 4.8 kJ/mol ethanol), and weak physisorption of ethanol on ethanol covered silica (−4.0 ± 1.6 kJ/mol ethanol). On the other hand, dehydroxylation leads to missing water−silica interactions, whereas the number of ethanol binding sites is not impacted. The isotherms and partial molar properties of adsorption suggest that water may only bind strongly onto the silanols (which are a minor species on silica glass), whereas ethanol can interact strongly with both silanols and the hydrophobic areas of the silica surface.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/7SX36EIE/Wu et al. - 2015 - Energy Landscape of Water and Ethanol on Silica Su.pdf;/home/simon/Zotero/storage/VX67W7IV/acs.jpcc.html} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7SX36EIE/Wu et al. - 2015 - Energy Landscape of Water and Ethanol on Silica Su.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/VX67W7IV/acs.jpcc.html} } @article{wuForceFieldZIF82014, title = {Force Field for {{ZIF-8}} Flexible Frameworks: Atomistic Simulation of Adsorption, Diffusion of Pure Gases as {{CH}} {\textsubscript{4}} , {{H}} {\textsubscript{2}} , {{CO}} {\textsubscript{2}} and {{N}} {\textsubscript{2}}}, shorttitle = {Force Field for {{ZIF-8}} Flexible Frameworks}, author = {Wu, Xuanjun and Huang, Jin and Cai, Weiquan and Jaroniec, Mietek}, - year = {2014}, - journal = {RSC Adv.}, + date = {2014}, + journaltitle = {RSC Adv.}, + shortjournal = {RSC Adv.}, volume = {4}, number = {32}, pages = {16503--16511}, issn = {2046-2069}, doi = {10.1039/C4RA00664J}, + url = {http://xlink.rsc.org/?DOI=C4RA00664J}, urldate = {2023-05-23}, - abstract = {A full set of flexible force field parameters for ZIF-8, applied for its gas adsorption and diffusion, has been presented. , A full set of flexible force field parameters for ZIF-8 is presented, based on the AMBER, UFF parameters and the partial charges computed by the density-derived electrostatic and chemical charge method (DDEC). The parameters for the 2-methyl imidazole (MeIM) ring are adopted from the AMBER force field, while the van der Waals (VDW) parameters for organic linkers and metal centers were determined by rescaling the UFF parameters as {$\epsilon$} = 0.635 {$\epsilon$} UFF and {$\sigma$} = 1.0 {$\sigma$} UFF to fit the CH 4 adsorption isotherms obtained by Grand Canonical Monte Carlo (GCMC) simulations with the force field parameters to the experimental ones. The CH 4 adsorption isotherms on four different structures of ZIF-8 at 298 K obtained by GCMC simulations are compared with the experimental data. The results show that the simulated CH 4 adsorption isotherms on the ZIF-8 structure reported from the Cambridge Crystallographic Data Centre (CCDC) are closest to the ones on the ZIF-8 structure from the report of Moggach et al. To test our model, adsorption isotherms of CH 4 , H 2 , CO 2 and N 2 at different temperatures were computed using GCMC simulations, and the results were found to be in a good agreement with the experimental data. In the case of H 2 , the equilibrium configurations obtained by GCMC simulations were statistically analyzed with ad hoc code to get probability density distribution profiles. These profiles were transformed to visual slice images, which indicate that the preferential adsorption sites of H 2 molecules in ZIF-8 are located close to the MeIM rings, where the host{\textendash}guest VDW or electrostatic interactions are maximal, as revealed by the potential energy surfaces (PES). In addition, these force field parameters were confirmed to well reproduce the ZIF-8 structural properties including lattice constants, bond lengths and angles over a wide range of temperatures. The self-diffusivities at the specific loadings of adsorbed gases (CH 4 , H 2 and CO 2 ) in ZIF-8 were calculated by the mean squared displacement (MSD) method. It was found that our self-diffusivities of H 2 are slightly higher than the ones in the literature, and our self-diffusivity of CO 2 is as about three times as the one in the literature, due to the different partial charges and the effect of different force field parameters on framework shape and flexibility in our simulations.}, + abstract = {A full set of flexible force field parameters for ZIF-8, applied for its gas adsorption and diffusion, has been presented. , A full set of flexible force field parameters for ZIF-8 is presented, based on the AMBER, UFF parameters and the partial charges computed by the density-derived electrostatic and chemical charge method (DDEC). The parameters for the 2-methyl imidazole (MeIM) ring are adopted from the AMBER force field, while the van der Waals (VDW) parameters for organic linkers and metal centers were determined by rescaling the UFF parameters as ε = 0.635 ε UFF and σ = 1.0 σ UFF to fit the CH 4 adsorption isotherms obtained by Grand Canonical Monte Carlo (GCMC) simulations with the force field parameters to the experimental ones. The CH 4 adsorption isotherms on four different structures of ZIF-8 at 298 K obtained by GCMC simulations are compared with the experimental data. The results show that the simulated CH 4 adsorption isotherms on the ZIF-8 structure reported from the Cambridge Crystallographic Data Centre (CCDC) are closest to the ones on the ZIF-8 structure from the report of Moggach et al. To test our model, adsorption isotherms of CH 4 , H 2 , CO 2 and N 2 at different temperatures were computed using GCMC simulations, and the results were found to be in a good agreement with the experimental data. In the case of H 2 , the equilibrium configurations obtained by GCMC simulations were statistically analyzed with ad hoc code to get probability density distribution profiles. These profiles were transformed to visual slice images, which indicate that the preferential adsorption sites of H 2 molecules in ZIF-8 are located close to the MeIM rings, where the host–guest VDW or electrostatic interactions are maximal, as revealed by the potential energy surfaces (PES). In addition, these force field parameters were confirmed to well reproduce the ZIF-8 structural properties including lattice constants, bond lengths and angles over a wide range of temperatures. The self-diffusivities at the specific loadings of adsorbed gases (CH 4 , H 2 and CO 2 ) in ZIF-8 were calculated by the mean squared displacement (MSD) method. It was found that our self-diffusivities of H 2 are slightly higher than the ones in the literature, and our self-diffusivity of CO 2 is as about three times as the one in the literature, due to the different partial charges and the effect of different force field parameters on framework shape and flexibility in our simulations.}, langid = {english}, keywords = {MD,zif}, - file = {/home/simon/Zotero/storage/5NHJ2AFM/Wu et al. - Force Field for ZIF-8 Flexible Frameworks Atomist.pdf;/home/simon/Zotero/storage/Q9RCD5TS/Wu et al. - 2014 - Force field for ZIF-8 flexible frameworks atomist.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5NHJ2AFM/Wu et al. - Force Field for ZIF-8 Flexible Frameworks Atomist.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/Q9RCD5TS/Wu et al. - 2014 - Force field for ZIF-8 flexible frameworks atomist.pdf} } @article{xiongAlcoholAdsorptionSilicalite2011, title = {Alcohol {{Adsorption}} onto {{Silicalite}} from {{Aqueous Solution}}}, author = {Xiong, Ruichang and Sandler, Stanley I. and Vlachos, Dionisios G.}, - year = {2011}, - month = sep, - journal = {The Journal of Physical Chemistry C}, + date = {2011-09-29}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {115}, number = {38}, pages = {18659--18669}, issn = {1932-7447, 1932-7455}, doi = {10.1021/jp205312k}, + url = {https://pubs.acs.org/doi/10.1021/jp205312k}, urldate = {2023-07-31}, - abstract = {A methodology based on the combination of grand canonical Monte Carlo (GCMC) and expanded ensemble (EE) simulations has been used to study the adsorption of alcohols from dilute aqueous solution onto the silicalite zeolite. The chemical potential of the guest alcohol molecules in bulk aqueous solutions is calculated by the EE method, and the adsorption isotherms of the alcohols are calculated using GCMC simulations. This approach results in adsorption isotherms that relate the loadings to external concentrations without using an equation of state, experimental data, or performing computationally expensive simulations such as two-phase Gibbs ensemble Monte Carlo (GEMC). Also, the method is ``force-field-consistent'', in that the same force field is used for the bulk fluid and the adsorption calculations, and the resulting isotherms can be directly compared with experimental data. We have established the validity of the method used by comparing the calculated adsorption isotherms with experimental data for methanol and ethanol on silicalite, both from aqueous solution and from the vapor phase. Calculated heats of adsorption are also in reasonable agreement with experimental data. In addition, these simulations provide information on the location of the alcohol adsorption sites. We also observe that the presence of water increases the adsorption of alcohols at dilute concentrations onto silicalite; therefore, an accurate estimate of amount of water adsorbed in the nanoporous substrate is important to the prediction of alcohol adsorption from aqueous solution. The method presented here can be used to study the adsorption of any molecular species on any nanoporous adsorbent.}, + abstract = {A methodology based on the combination of grand canonical Monte Carlo (GCMC) and expanded ensemble (EE) simulations has been used to study the adsorption of alcohols from dilute aqueous solution onto the silicalite zeolite. The chemical potential of the guest alcohol molecules in bulk aqueous solutions is calculated by the EE method, and the adsorption isotherms of the alcohols are calculated using GCMC simulations. This approach results in adsorption isotherms that relate the loadings to external concentrations without using an equation of state, experimental data, or performing computationally expensive simulations such as two-phase Gibbs ensemble Monte Carlo (GEMC). Also, the method is “force-field-consistent”, in that the same force field is used for the bulk fluid and the adsorption calculations, and the resulting isotherms can be directly compared with experimental data. We have established the validity of the method used by comparing the calculated adsorption isotherms with experimental data for methanol and ethanol on silicalite, both from aqueous solution and from the vapor phase. Calculated heats of adsorption are also in reasonable agreement with experimental data. In addition, these simulations provide information on the location of the alcohol adsorption sites. We also observe that the presence of water increases the adsorption of alcohols at dilute concentrations onto silicalite; therefore, an accurate estimate of amount of water adsorbed in the nanoporous substrate is important to the prediction of alcohol adsorption from aqueous solution. The method presented here can be used to study the adsorption of any molecular species on any nanoporous adsorbent.}, langid = {english}, keywords = {MD}, - file = {/home/simon/Zotero/storage/A6SBQXIH/Xiong et al. - 2011 - Alcohol Adsorption onto Silicalite from Aqueous So.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/A6SBQXIH/Xiong et al. - 2011 - Alcohol Adsorption onto Silicalite from Aqueous So.pdf} } @article{yaacobiHydrophobicInteractionWaterethanol1973, title = {Hydrophobic Interaction in Water-Ethanol Mixtures}, - author = {Yaacobi, M. and {Ben-Naim}, A.}, - year = {1973}, - month = oct, - journal = {Journal of Solution Chemistry}, + author = {Yaacobi, M. and Ben-Naim, A.}, + date = {1973-10}, + journaltitle = {Journal of Solution Chemistry}, + shortjournal = {J Solution Chem}, volume = {2}, number = {5}, pages = {425--443}, issn = {0095-9782, 1572-8927}, doi = {10.1007/BF00651005}, + url = {http://link.springer.com/10.1007/BF00651005}, urldate = {2023-04-26}, langid = {english}, keywords = {water-ethanol}, - file = {/home/simon/Zotero/storage/7J5QVMVP/Yaacobi and Ben-Naim - 1973 - Hydrophobic interaction in water-ethanol mixtures.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/7J5QVMVP/Yaacobi and Ben-Naim - 1973 - Hydrophobic interaction in water-ethanol mixtures.pdf} } @article{yangNMRMeasurementBitumen2008, title = {{{NMR}} Measurement of Bitumen at Different Temperatures}, author = {Yang, Zheng and Hirasaki, George J.}, - year = {2008}, - month = jun, - journal = {Journal of Magnetic Resonance (San Diego, Calif.: 1997)}, + date = {2008-06}, + journaltitle = {Journal of Magnetic Resonance (San Diego, Calif.: 1997)}, + shortjournal = {J Magn Reson}, volume = {192}, number = {2}, + eprint = {18387325}, + eprinttype = {pmid}, pages = {280--293}, issn = {1090-7807}, doi = {10.1016/j.jmr.2008.03.007}, abstract = {Heavy oil (bitumen) is characterized by its high viscosity and density, which is a major obstacle to both well logging and recovery. Due to the lost information of T2 relaxation time shorter than echo spacing (TE) and interference of water signal, estimation of heavy oil properties from NMR T2 measurements is usually problematic. In this work, a new method has been developed to overcome the echo spacing restriction of NMR spectrometer during the application to heavy oil (bitumen). A FID measurement supplemented the start of CPMG. Constrained by its initial magnetization (M0) estimated from the FID and assuming log normal distribution for bitumen, the corrected T2 relaxation time of bitumen sample can be obtained from the interpretation of CPMG data. This new method successfully overcomes the TE restriction of the NMR spectrometer and is nearly independent on the TE applied in the measurement. This method was applied to the measurement at elevated temperatures (8-90 degrees C). Due to the significant signal-loss within the dead time of FID, the directly extrapolated M0 of bitumen at relatively lower temperatures ({$<$}60 degrees C) was found to be underestimated. However, resulting from the remarkably lowered viscosity, the extrapolated M0 of bitumen at over 60 degrees C can be reasonably assumed to be the real value. In this manner, based on the extrapolation at higher temperatures ({$>$} or = 60 degrees C), the M0 value of bitumen at lower temperatures ({$<$}60 degrees C) can be corrected by Curie's Law. Consequently, some important petrophysical properties of bitumen, such as hydrogen index (HI), fluid content and viscosity were evaluated by using corrected T2.}, langid = {english}, - pmid = {18387325}, keywords = {NMR} } -@misc{yanInteractivePolymerBuilding2022, +@online{yanInteractivePolymerBuilding2022, title = {An {{Interactive Polymer Building Toolkit}} for {{Molecular Dynamics Simulations}}: {{PolyMAPS}}}, shorttitle = {An {{Interactive Polymer Building Toolkit}} for {{Molecular Dynamics Simulations}}}, author = {Yan, Xiaoli and Chaudhuri, Santanu}, - year = {2022}, - month = apr, - number = {arXiv:2204.14218}, + date = {2022-04-28}, eprint = {2204.14218}, - primaryclass = {cond-mat, physics:physics}, - publisher = {{arXiv}}, + eprinttype = {arxiv}, + eprintclass = {cond-mat, physics:physics}, doi = {10.48550/arXiv.2204.14218}, + url = {http://arxiv.org/abs/2204.14218}, urldate = {2023-09-26}, abstract = {PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter notebook. PolyMAPS enables users to build small or polymeric molecules in a user-friendly interactive 3D plotting system that supports reading and writing systems in LAMMPS data file format. Hence, PolyMAPS demonstrates the potential of reducing the learning difficulties of new users of the LAMMPS software.}, - archiveprefix = {arxiv}, - file = {/home/simon/Zotero/storage/3DREJGMV/Yan and Chaudhuri - 2022 - An Interactive Polymer Building Toolkit for Molecu.pdf;/home/simon/Zotero/storage/VH36ZVXT/2204.html} + pubstate = {preprint}, + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3DREJGMV/Yan and Chaudhuri - 2022 - An Interactive Polymer Building Toolkit for Molecu.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/VH36ZVXT/2204.html} } @article{yanoCorrelationSurfaceBulk2005, - title = {Correlation between Surface and Bulk Structures of Alcohol{\textendash}Water Mixtures}, + title = {Correlation between Surface and Bulk Structures of Alcohol–Water Mixtures}, author = {Yano, Yohko F.}, - year = {2005}, - month = apr, - journal = {Journal of Colloid and Interface Science}, + date = {2005-04}, + journaltitle = {Journal of Colloid and Interface Science}, + shortjournal = {Journal of Colloid and Interface Science}, volume = {284}, number = {1}, pages = {255--259}, issn = {00219797}, doi = {10.1016/j.jcis.2004.09.059}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021979704009907}, urldate = {2023-06-21}, - abstract = {Adsorption isotherms of binary aqueous solutions of methanol, ethanol, 1-propanol, 2-propanol, tert-butanol, and 1-butanol are demonstrated, being calculated by using the Gibbs adsorption equation with experimental data of surface tension and vapor pressure found in the literature. For all of the alcohol{\textendash}water mixtures, the maximum value in the adsorption isotherm, namely, the maximum surface excess is about that expected for the formation of a monolayer. Furthermore, the composition of the mixture for the maximum surface excess coincides with that corresponding to the minimum in the excess partial molar volume of the solutes. These results indicate that the hydrophobic hydration in bulk induces the surface excess of the alcohols and after a monolayer is formed, the hydrophobic hydration itself is no longer retained.}, + abstract = {Adsorption isotherms of binary aqueous solutions of methanol, ethanol, 1-propanol, 2-propanol, tert-butanol, and 1-butanol are demonstrated, being calculated by using the Gibbs adsorption equation with experimental data of surface tension and vapor pressure found in the literature. For all of the alcohol–water mixtures, the maximum value in the adsorption isotherm, namely, the maximum surface excess is about that expected for the formation of a monolayer. Furthermore, the composition of the mixture for the maximum surface excess coincides with that corresponding to the minimum in the excess partial molar volume of the solutes. These results indicate that the hydrophobic hydration in bulk induces the surface excess of the alcohols and after a monolayer is formed, the hydrophobic hydration itself is no longer retained.}, langid = {english}, keywords = {mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/2GD9HME9/Yano - 2005 - Correlation between surface and bulk structures of.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/2GD9HME9/Yano - 2005 - Correlation between surface and bulk structures of.pdf} } @article{zangiRefinementOPLSAAForceField2018, title = {Refinement of the {{OPLSAA Force-Field}} for {{Liquid Alcohols}}}, author = {Zangi, Ronen}, - year = {2018}, - month = dec, - journal = {ACS Omega}, + date = {2018-12-31}, + journaltitle = {ACS Omega}, + shortjournal = {ACS Omega}, volume = {3}, number = {12}, pages = {18089--18099}, issn = {2470-1343, 2470-1343}, doi = {10.1021/acsomega.8b03132}, + url = {https://pubs.acs.org/doi/10.1021/acsomega.8b03132}, urldate = {2023-07-25}, - abstract = {We employ the popular all-atom optimized potential for liquid simulations, OPLSAA, force-field to model 17 different alcohols in the liquid state. Using the standard simulation protocol for few hundred nanosecond time periods, we find that 1-octanol, 1-nonanol, and 1-decanol undergo spontaneous transition to a crystalline state at temperatures which are 35-55 K higher than the experimental melting temperatures. Nevertheless, the crystal structures obtained from the simulations are very similar to those determined by X-ray powder diffraction data for several n-alcohols. Although some degree of deviations from the experimental freezing points are to be expected, for 1-nonanol and 1-decanol, the elevation of the freezing temperature warrants special attention because at room temperature, these alcohols are liquids; however, if simulated by the OPLSAA force-field, they will crystallize. This behavior is likely a consequence of exaggerated attractive interactions between the alkane chains of the alcohols. To circumvent this problem, we combined the OPLSAA model with the L-OPLS force-field. We adopted the L-OPLS parameters to model the hydrocarbon tail of the alcohols, whereas the hydroxyl head group remained as in the original OPLSAA force-field. The resulting alcohols stayed in the liquid state at temperatures above their experimental melting points, thus, resolving the enhanced freezing observed with the OPLSAA force-field. In fact, the mixed-model alcohols did not exhibit any spontaneous freezing even at temperatures much lower than the experimental values. However, a series of simulations in which these mixed-OPLSAA alcohols started from a coexistence configuration of the liquid and solid phases resulted in freezing transitions at temperatures 14-25 K lower than the experimental values, confirming the validity of the proposed model. For all of the other alcohols, the mixed model yields results very similar to the OPLSAA force-field and is in good agreement with the experimental data. Thus, for simulating alcohols in the liquid phase, the mixed-OPLSAA model is necessary for large (7 carbons and above) hydrocarbon chains.}, + abstract = {We employ the popular all-atom optimized potential for liquid simulations, OPLSAA, force-field to model 17 different alcohols in the liquid state. Using the standard simulation protocol for few hundred nanosecond time periods, we find that 1-octanol, 1-nonanol, and 1-decanol undergo spontaneous transition to a crystalline state at temperatures which are 35−55 K higher than the experimental melting temperatures. Nevertheless, the crystal structures obtained from the simulations are very similar to those determined by X-ray powder diffraction data for several n-alcohols. Although some degree of deviations from the experimental freezing points are to be expected, for 1-nonanol and 1-decanol, the elevation of the freezing temperature warrants special attention because at room temperature, these alcohols are liquids; however, if simulated by the OPLSAA force-field, they will crystallize. This behavior is likely a consequence of exaggerated attractive interactions between the alkane chains of the alcohols. To circumvent this problem, we combined the OPLSAA model with the L-OPLS force-field. We adopted the L-OPLS parameters to model the hydrocarbon tail of the alcohols, whereas the hydroxyl head group remained as in the original OPLSAA force-field. The resulting alcohols stayed in the liquid state at temperatures above their experimental melting points, thus, resolving the enhanced freezing observed with the OPLSAA force-field. In fact, the mixed-model alcohols did not exhibit any spontaneous freezing even at temperatures much lower than the experimental values. However, a series of simulations in which these mixed-OPLSAA alcohols started from a coexistence configuration of the liquid and solid phases resulted in freezing transitions at temperatures 14−25 K lower than the experimental values, confirming the validity of the proposed model. For all of the other alcohols, the mixed model yields results very similar to the OPLSAA force-field and is in good agreement with the experimental data. Thus, for simulating alcohols in the liquid phase, the mixed-OPLSAA model is necessary for large (7 carbons and above) hydrocarbon chains.}, langid = {english}, keywords = {ff}, - file = {/home/simon/Zotero/storage/IEJWMB73/ao8b03132_si_001.pdf;/home/simon/Zotero/storage/P8G6MN9E/Zangi - 2018 - Refinement of the OPLSAA Force-Field for Liquid Al.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/IEJWMB73/ao8b03132_si_001.pdf;/home/simon/snap/zotero-snap/common/Zotero/storage/P8G6MN9E/Zangi - 2018 - Refinement of the OPLSAA Force-Field for Liquid Al.pdf} } @article{zhangAdsorptionWaterEthanol2012, title = {Adsorption of {{Water}} and {{Ethanol}} in {{MFI-Type Zeolites}}}, author = {Zhang, Ke and Lively, Ryan P. and Noel, James D. and Dose, Michelle E. and McCool, Benjamin A. and Chance, Ronald R. and Koros, William J.}, - year = {2012}, - month = jun, - journal = {Langmuir}, + date = {2012-06-12}, + journaltitle = {Langmuir}, + shortjournal = {Langmuir}, volume = {28}, number = {23}, pages = {8664--8673}, issn = {0743-7463, 1520-5827}, doi = {10.1021/la301122h}, + url = {https://pubs.acs.org/doi/10.1021/la301122h}, urldate = {2023-07-30}, - abstract = {Water and ethanol vapor adsorption phenomena are investigated systematically on a series of MFI-type zeolites: silicalite-1 samples synthesized via both alkaline (OH-) and fluoride (F-) routes, and ZSM-5 samples with different Si/Al ratios as well as different chargebalancing cations. Full isotherms (0.05-0.95 activity) over the range 25- 55 {\textdegree}C are presented, and the lowest total water uptake ever reported in the literature is shown for silicalite-1 made via a fluoride-mediated route wherein internal silanol defects are significantly reduced. At a water activity level of 0.95 (35 {\textdegree}C), the total water uptake by silicalite-1 (F-) was found to be 0.263 mmol/g, which was only 12.6\%, 9.8\%, and 3.3\% of the capacity for silicalite-1 (OH-), H-ZSM-5 (Si/Al:140), and H-ZSM-5 (Si/Al:15), respectively, under the same conditions. While water adsorption shows distinct isotherms for different MFI-type zeolites due to the difference in the concentration, distribution, and types of hydrophilic sites, the ethanol adsorption isotherms present relatively comparable results because of the overall organophilic nature of the zeolite framework. Due to the dramatic differences in the sorption behavior with the different sorbate-sorbent pairs, different models are applied to correlate and analyze the sorption isotherms. An adsorption potential theory was used to fit the water adsorption isotherms on all MFI-type zeolite adsorbents studied. The Langmuir model and Sircar's model are applied to describe ethanol adsorption on silicalite-1 and ZSM-5 samples, respectively. An ideal ethanol/water adsorption selectivity ({$\alpha$}) was estimated for the fluoride-mediated silicalite-1. At 35 {\textdegree}C, {$\alpha$} was estimated to be 36 for a 5 mol \% ethanol solution in water increasing to 53 at an ethanol concentration of 1 mol \%. The adsorption data demonstrate that silicalite-1 made via the fluoride-mediated route is a promising candidate for ethanol extraction from dilute ethanol-water solutions.}, + abstract = {Water and ethanol vapor adsorption phenomena are investigated systematically on a series of MFI-type zeolites: silicalite-1 samples synthesized via both alkaline (OH−) and fluoride (F−) routes, and ZSM-5 samples with different Si/Al ratios as well as different chargebalancing cations. Full isotherms (0.05−0.95 activity) over the range 25− 55 °C are presented, and the lowest total water uptake ever reported in the literature is shown for silicalite-1 made via a fluoride-mediated route wherein internal silanol defects are significantly reduced. At a water activity level of 0.95 (35 °C), the total water uptake by silicalite-1 (F−) was found to be 0.263 mmol/g, which was only 12.6\%, 9.8\%, and 3.3\% of the capacity for silicalite-1 (OH−), H-ZSM-5 (Si/Al:140), and H-ZSM-5 (Si/Al:15), respectively, under the same conditions. While water adsorption shows distinct isotherms for different MFI-type zeolites due to the difference in the concentration, distribution, and types of hydrophilic sites, the ethanol adsorption isotherms present relatively comparable results because of the overall organophilic nature of the zeolite framework. Due to the dramatic differences in the sorption behavior with the different sorbate−sorbent pairs, different models are applied to correlate and analyze the sorption isotherms. An adsorption potential theory was used to fit the water adsorption isotherms on all MFI-type zeolite adsorbents studied. The Langmuir model and Sircar’s model are applied to describe ethanol adsorption on silicalite-1 and ZSM-5 samples, respectively. An ideal ethanol/water adsorption selectivity (α) was estimated for the fluoride-mediated silicalite-1. At 35 °C, α was estimated to be 36 for a 5 mol \% ethanol solution in water increasing to 53 at an ethanol concentration of 1 mol \%. The adsorption data demonstrate that silicalite-1 made via the fluoride-mediated route is a promising candidate for ethanol extraction from dilute ethanol−water solutions.}, langid = {english}, keywords = {ff,MD,zif}, - file = {/home/simon/Zotero/storage/3VPHG6VG/Zhang et al. - 2012 - Adsorption of Water and Ethanol in MFI-Type Zeolit.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/3VPHG6VG/Zhang et al. - 2012 - Adsorption of Water and Ethanol in MFI-Type Zeolit.pdf} } @article{zhangAlcoholWaterAdsorption2013, title = {Alcohol and Water Adsorption in Zeolitic Imidazolate Frameworks}, author = {Zhang, Ke and Lively, Ryan P. and Dose, Michelle E. and Brown, Andrew J. and Zhang, Chen and Chung, Jaeyub and Nair, Sankar and Koros, William J. and Chance, Ronald R.}, - year = {2013}, - journal = {Chemical Communications}, + date = {2013}, + journaltitle = {Chemical Communications}, + shortjournal = {Chem. Commun.}, volume = {49}, number = {31}, pages = {3245}, issn = {1359-7345, 1364-548X}, doi = {10.1039/c3cc39116g}, + url = {http://xlink.rsc.org/?DOI=c3cc39116g}, urldate = {2023-07-19}, langid = {english}, keywords = {zif}, - file = {/home/simon/Zotero/storage/Q6H743DF/Zhang et al. - 2013 - Alcohol and water adsorption in zeolitic imidazola.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/Q6H743DF/Zhang et al. - 2013 - Alcohol and water adsorption in zeolitic imidazola.pdf} } @article{zhangInvestigatingIntrinsicEthanol2013, title = {Investigating the {{Intrinsic Ethanol}}/{{Water Separation Capability}} of {{ZIF-8}}: {{An Adsorption}} and {{Diffusion Study}}}, shorttitle = {Investigating the {{Intrinsic Ethanol}}/{{Water Separation Capability}} of {{ZIF-8}}}, author = {Zhang, Ke and Lively, Ryan P. and Zhang, Chen and Koros, William J. and Chance, Ronald R.}, - year = {2013}, - month = apr, - journal = {The Journal of Physical Chemistry C}, + date = {2013-04-11}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {117}, number = {14}, pages = {7214--7225}, issn = {1932-7447, 1932-7455}, doi = {10.1021/jp401548b}, + url = {https://pubs.acs.org/doi/10.1021/jp401548b}, urldate = {2023-05-23}, - abstract = {Intrinsic ethanol/water separation capability of ZIF-8 is characterized by a detailed study of adsorption and diffusion of ethanol and water vapor in dodecahedral crystals with principle axis dimension of 324, 15.8, and 0.4 {$\mu$}m. ZIF-8 exhibits extremely low water uptakes. At 35 {\textdegree}C and a relative pressure (P/Po) of 0.95, the water uptakes for 324, 15.8, and 0.4 {$\mu$}m ZIF-8 are 0.184, 0.197, and 0.503 mmol/g, respectively, all of which are less than 1 wt \% increase relative to original sorbent mass (0.33, 0.35, 0.91 wt \%). For ethanol adsorption, ZIF-8 exhibits an S-shape isotherm with low ethanol uptakes at P/Po up to 0.08 and the cage filling phenomenon occurs at P/Po higher than 0.08. The ethanol saturation uptake in ZIF-8 is as high as 30\% of the sorbent weight. Because of the existence of the hydrophilic -N-H functionality introduced by the terminating imidazolate (Im) linker and the overall hydrophobicity of the inner network, the effect of outer surface area of ZIF-8 crystals is proved to be non-negligible as ZIF-8 crystals becomes smaller despite the extremely large inner surface area and pore volume, especially for water sorption. The variation of isosteric heats of adsorption for water reveals the existence of structural defect of ZIF-8 framework. Transport diffusivity and corrected diffusivity for water and ethanol in ZIF-8 are determined within the entire P/Po range. The ethanol/water separation performance in ZIF-8 is evaluated in terms of vaporphase sorption selectivity and permselectivity. While ZIF-8 exhibits ample ethanol/water sorption selectivity, it is not effective for ethanol extraction as a membrane material from dilute ethanol aqueous solutions due to the unfavorable diffusion selectivity and the competitive water uptakes in the adsorbed ethanol phase.}, + abstract = {Intrinsic ethanol/water separation capability of ZIF-8 is characterized by a detailed study of adsorption and diffusion of ethanol and water vapor in dodecahedral crystals with principle axis dimension of 324, 15.8, and 0.4 μm. ZIF-8 exhibits extremely low water uptakes. At 35 °C and a relative pressure (P/Po) of 0.95, the water uptakes for 324, 15.8, and 0.4 μm ZIF-8 are 0.184, 0.197, and 0.503 mmol/g, respectively, all of which are less than 1 wt \% increase relative to original sorbent mass (0.33, 0.35, 0.91 wt \%). For ethanol adsorption, ZIF-8 exhibits an S-shape isotherm with low ethanol uptakes at P/Po up to 0.08 and the cage filling phenomenon occurs at P/Po higher than 0.08. The ethanol saturation uptake in ZIF-8 is as high as 30\% of the sorbent weight. Because of the existence of the hydrophilic −N−H functionality introduced by the terminating imidazolate (Im) linker and the overall hydrophobicity of the inner network, the effect of outer surface area of ZIF-8 crystals is proved to be non-negligible as ZIF-8 crystals becomes smaller despite the extremely large inner surface area and pore volume, especially for water sorption. The variation of isosteric heats of adsorption for water reveals the existence of structural defect of ZIF-8 framework. Transport diffusivity and corrected diffusivity for water and ethanol in ZIF-8 are determined within the entire P/Po range. The ethanol/water separation performance in ZIF-8 is evaluated in terms of vaporphase sorption selectivity and permselectivity. While ZIF-8 exhibits ample ethanol/water sorption selectivity, it is not effective for ethanol extraction as a membrane material from dilute ethanol aqueous solutions due to the unfavorable diffusion selectivity and the competitive water uptakes in the adsorbed ethanol phase.}, langid = {english}, keywords = {water-ethanol,zif}, - file = {/home/simon/Zotero/storage/WJEU2MGY/Zhang et al. - 2013 - Investigating the Intrinsic EthanolWater Separati.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WJEU2MGY/Zhang et al. - 2013 - Investigating the Intrinsic EthanolWater Separati.pdf} } @article{zhangMolecularDynamicsInvestigation2023, title = {Molecular {{Dynamics Investigation}} of {{Nanoscale Hydrophobicity}} of {{Polymer Surfaces}}: {{What Makes Water Wet}}?}, shorttitle = {Molecular {{Dynamics Investigation}} of {{Nanoscale Hydrophobicity}} of {{Polymer Surfaces}}}, author = {Zhang, Hang and Sundaresan, Sankaran and Webb, Michael A.}, - year = {2023}, - month = jun, - journal = {The Journal of Physical Chemistry B}, + date = {2023-06-08}, + journaltitle = {The Journal of Physical Chemistry B}, + shortjournal = {J. Phys. Chem. B}, volume = {127}, number = {22}, pages = {5115--5127}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.3c00616}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.3c00616}, urldate = {2023-06-10}, - abstract = {The wettability of a polymer surface{\dbend}related to its hydrophobicity or tendency to repel water{\dbend}can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating the relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon-66, and poly(vinyl alcohol). We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation{\dbend}even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. These results provide new insights into how polymer chemistry specifically impacts water-polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.}, + abstract = {The wettability of a polymer surface�related to its hydrophobicity or tendency to repel water�can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating the relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon-66, and poly(vinyl alcohol). We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation�even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. These results provide new insights into how polymer chemistry specifically impacts water−polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.}, langid = {english}, keywords = {favorite,MD}, - file = {/home/simon/Zotero/storage/XBSYSSWM/Zhang et al. - 2023 - Molecular Dynamics Investigation of Nanoscale Hydr.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/XBSYSSWM/Zhang et al. - 2023 - Molecular Dynamics Investigation of Nanoscale Hydr.pdf} } @article{zhangOILGASNMR, @@ -3775,94 +4042,100 @@ @article{zhangOILGASNMR abstract = {Relaxation times of intermediate viscosity dead oils show a linear correlation with viscosity/temperature on a log-log plot. In contrast, dissolved methane at the low end and heavy crude oils at the other extreme fail to follow this correlation. It is well known that the presence of these components in an oil complicates analysis and interpretation.}, langid = {english}, keywords = {NMR,propane}, - file = {/home/simon/Zotero/storage/YIRETWT4/Zhang et al. - OIL AND GAS NMR PROPERTIES THE LIGHT AND HEAVY EN.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/YIRETWT4/Zhang et al. - OIL AND GAS NMR PROPERTIES THE LIGHT AND HEAVY EN.pdf} } @article{zhangQuantificationSolventContribution2013, title = {Quantification of {{Solvent Contribution}} to the {{Stability}} of {{Noncovalent Complexes}}}, - author = {Zhang, Haiyang and Tan, Tianwei and Het{\'e}nyi, Csaba and Van Der Spoel, David}, - year = {2013}, - month = oct, - journal = {Journal of Chemical Theory and Computation}, + author = {Zhang, Haiyang and Tan, Tianwei and Hetényi, Csaba and Van Der Spoel, David}, + date = {2013-10-08}, + journaltitle = {Journal of Chemical Theory and Computation}, + shortjournal = {J. Chem. Theory Comput.}, volume = {9}, number = {10}, pages = {4542--4551}, issn = {1549-9618, 1549-9626}, doi = {10.1021/ct400404q}, + url = {https://pubs.acs.org/doi/10.1021/ct400404q}, urldate = {2023-07-05}, - abstract = {We introduce an indirect approach to estimate the solvation contributions to the thermodynamics of noncovalent complex formation through molecular dynamics simulation. This estimation is demonstrated by potential of mean force and entropy calculations on the binding process between {$\beta$}-cyclodextrin (host) and four drug molecules puerarin, daidzin, daidzein, and nabumetone (guest) in explicit water, followed by a stepwise extraction of individual enthalpy ({$\Delta$}H) and entropy ({$\Delta$}S) terms from the total free energy. Detailed analysis on the energetics of the host-guest complexation demonstrates that flexibility of the binding partners and solvation-related {$\Delta$}H and {$\Delta$}S need to be included explicitly for accurate estimation of the binding thermodynamics. From this, and our previous work on the solvent dependency of binding energies (Zhang et al. J. Phys. Chem. B 2012, 116, 12684-12693), it follows that calculations neglecting host or guest flexibility, or those employing implicit solvent, will not be able to systematically predict binding free energies. The approach presented here can be readily adopted for obtaining a deeper understanding of the mechanisms governing noncovalent associations in solution.}, + abstract = {We introduce an indirect approach to estimate the solvation contributions to the thermodynamics of noncovalent complex formation through molecular dynamics simulation. This estimation is demonstrated by potential of mean force and entropy calculations on the binding process between β-cyclodextrin (host) and four drug molecules puerarin, daidzin, daidzein, and nabumetone (guest) in explicit water, followed by a stepwise extraction of individual enthalpy (ΔH) and entropy (ΔS) terms from the total free energy. Detailed analysis on the energetics of the host−guest complexation demonstrates that flexibility of the binding partners and solvation-related ΔH and ΔS need to be included explicitly for accurate estimation of the binding thermodynamics. From this, and our previous work on the solvent dependency of binding energies (Zhang et al. J. Phys. Chem. B 2012, 116, 12684−12693), it follows that calculations neglecting host or guest flexibility, or those employing implicit solvent, will not be able to systematically predict binding free energies. The approach presented here can be readily adopted for obtaining a deeper understanding of the mechanisms governing noncovalent associations in solution.}, langid = {english}, keywords = {PMF}, - file = {/home/simon/Zotero/storage/VSGIUVUV/Zhang et al. - 2013 - Quantification of Solvent Contribution to the Stab.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/VSGIUVUV/Zhang et al. - 2013 - Quantification of Solvent Contribution to the Stab.pdf} } @article{zhangTinyChargeScaling2022, - title = {A Tiny Charge-scaling in the {{{\textsc{OPLS}}}}{\textsc{-}}{{{\textsc{AA}}}} + {{{\textsc{L}}}}{\textsc{-}}{{{\textsc{OPLS}}}} Force Field Delivers the Realistic Dynamics and Structure of Liquid Primary Alcohols}, - shorttitle = {A Tiny Charge-scaling in The}, + title = {A Tiny Charge‐scaling in the {{{\textsc{OPLS}}}}{\textsc{‐}}{{{\textsc{AA}}}} + {{{\textsc{L}}}}{\textsc{‐}}{{{\textsc{OPLS}}}} Force Field Delivers the Realistic Dynamics and Structure of Liquid Primary Alcohols}, + shorttitle = {A Tiny Charge‐scaling in The}, author = {Zhang, Xuan and Wang, Yongtao and Yao, Jia and Li, Haoran and Mochizuki, Kenji}, - year = {2022}, - month = mar, - journal = {Journal of Computational Chemistry}, + date = {2022-03-05}, + journaltitle = {Journal of Computational Chemistry}, + shortjournal = {J Comput Chem}, volume = {43}, number = {6}, pages = {421--430}, issn = {0192-8651, 1096-987X}, doi = {10.1002/jcc.26802}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.26802}, urldate = {2023-07-25}, abstract = {We carry out molecular dynamics simulations for pure liquid primary alcohols ranging from methanol to 1-decanol under ambient conditions. Based on the OPLS-AA force field with the L-OPLS correction, we demonstrate that a few \% increases in the partial charges deliver the realistic dynamics (self-diffusion coefficient and shear viscosity) and structure (density and X-ray scattering intensity) as well as enthalpy of vaporization and isothermal compressibility. The validity against thermal expansion coefficient, isobaric heat capacity, and static dielectric constant are also discussed.}, langid = {english}, keywords = {ff}, - file = {/home/simon/Zotero/storage/QUCAWU6C/Zhang et al. - 2022 - A tiny charge‐scaling in the span style=font-var.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/QUCAWU6C/Zhang et al. - 2022 - A tiny charge‐scaling in the span style=font-var.pdf} } @article{zhaoSegregationStructuresMiscellaneous2015, title = {Segregation {{Structures}} and {{Miscellaneous Diffusions}} for {{Ethanol}}/{{Water Mixtures}} in {{Graphene-Based Nanoscale Pores}}}, author = {Zhao, Mengyao and Yang, Xiaoning}, - year = {2015}, - month = sep, - journal = {The Journal of Physical Chemistry C}, + date = {2015-09-17}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {119}, number = {37}, pages = {21664--21673}, issn = {1932-7447, 1932-7455}, doi = {10.1021/acs.jpcc.5b03307}, + url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.5b03307}, urldate = {2023-03-27}, - abstract = {Molecular dynamics simulation was conducted to study ethanol-water mixtures and the corresponding pure species, confined within slit-shaped graphene nanopores. Extensive structural and dynamical properties of the confined fluids, including hydrogen-bonding behavior, were investigated. The effects of pore width and mixture composition on the confined behavior were illustrated. It is observed that a layered structure is formed within the confined spaces and the ethanol- water mixtures show segregation at larger pores, with ethanol molecules preferentially adsorbing on graphene surfaces. This microphase demixing behavior stems from the competitive effect of the solid-fluid and fluid-fluid interactions. Moreover, miscellaneous diffusion mechanisms have been revealed for the hydrogen-bonding mixtures within the graphene pores. In the mixtures, water and ethanol generally display analogous diffusion mechanism due to ethanol-water association, converting from short-time subdiffusion to long-time Fickian diffusion in the larger nanopores. In the smaller pore (7 {\AA}), both ethanol and water show a suppressed single-file diffusion behavior at the initial time and then display subdiffusion or single-file diffusion behavior. The complex diffusion behavior of ethanol-water mixtures can be described by the collaborating effects of pore confinement and enhanced interaction in the hydrogen-bonding mixtures.}, + abstract = {Molecular dynamics simulation was conducted to study ethanol−water mixtures and the corresponding pure species, confined within slit-shaped graphene nanopores. Extensive structural and dynamical properties of the confined fluids, including hydrogen-bonding behavior, were investigated. The effects of pore width and mixture composition on the confined behavior were illustrated. It is observed that a layered structure is formed within the confined spaces and the ethanol− water mixtures show segregation at larger pores, with ethanol molecules preferentially adsorbing on graphene surfaces. This microphase demixing behavior stems from the competitive effect of the solid−fluid and fluid−fluid interactions. Moreover, miscellaneous diffusion mechanisms have been revealed for the hydrogen-bonding mixtures within the graphene pores. In the mixtures, water and ethanol generally display analogous diffusion mechanism due to ethanol−water association, converting from short-time subdiffusion to long-time Fickian diffusion in the larger nanopores. In the smaller pore (7 Å), both ethanol and water show a suppressed single-file diffusion behavior at the initial time and then display subdiffusion or single-file diffusion behavior. The complex diffusion behavior of ethanol−water mixtures can be described by the collaborating effects of pore confinement and enhanced interaction in the hydrogen-bonding mixtures.}, langid = {english}, keywords = {MD,mixture,water-ethanol}, - file = {/home/simon/Zotero/storage/NV74PGD3/Zhao and Yang - 2015 - Segregation Structures and Miscellaneous Diffusion.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/NV74PGD3/Zhao and Yang - 2015 - Segregation Structures and Miscellaneous Diffusion.pdf} } @article{zhengForceFieldMolecular2012, title = {Force {{Field}} for {{Molecular Dynamics Computations}} in {{Flexible ZIF-8 Framework}}}, author = {Zheng, Bin and Sant, Marco and Demontis, Pierfranco and Suffritti, Giuseppe B.}, - year = {2012}, - month = jan, - journal = {The Journal of Physical Chemistry C}, + date = {2012-01-12}, + journaltitle = {The Journal of Physical Chemistry C}, + shortjournal = {J. Phys. Chem. C}, volume = {116}, number = {1}, pages = {933--938}, issn = {1932-7447, 1932-7455}, doi = {10.1021/jp209463a}, + url = {https://pubs.acs.org/doi/10.1021/jp209463a}, urldate = {2023-07-29}, abstract = {Correct modeling of framework flexibility plays a major role in obtaining accurate results when performing atomistic simulations of guest molecule diffusion within ZIF crystal structures. Here we present a full set of force field parameters, based on the AMBER database and on previously computed partial charges, well reproducing the ZIF-8 structural properties over a wide range of temperatures and pressures. To test our model, the self-diffusivity for sorbed carbon-dioxide is computed and is found to be in good agreement with experimental measurements. Our results are also compared to the ones obtained with other charge models and are found to be more accurate. Finally, an estimate of the influence on self-diffusion of various simulation details is given.}, langid = {english}, keywords = {ff,MD,zif}, - file = {/home/simon/Zotero/storage/5LVT6FXP/Zheng et al. - 2012 - Force Field for Molecular Dynamics Computations in.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/5LVT6FXP/Zheng et al. - 2012 - Force Field for Molecular Dynamics Computations in.pdf} } @article{zouExploringPotentialDesign2018, title = {Exploring the Potential and Design of Zeolite Nanosheets as Pervaporation Membranes for Ethanol Extraction}, author = {Zou, Changlong and Lin, Li-Chiang}, - year = {2018}, - journal = {Chemical Communications}, + date = {2018}, + journaltitle = {Chemical Communications}, + shortjournal = {Chem. Commun.}, volume = {54}, number = {94}, pages = {13200--13203}, issn = {1359-7345, 1364-548X}, doi = {10.1039/C8CC06587J}, + url = {http://xlink.rsc.org/?DOI=C8CC06587J}, urldate = {2023-07-26}, abstract = {Demonstrate the potential of zeolite nanosheets as pervaporation membranes for ethanol extraction and shed light on their key design components. , Molecular dynamics simulations are employed to demonstrate the potential of zeolite nanosheets as pervaporation membranes for ethanol extraction. Our results show that zeolite nanosheets can provide orders of magnitude higher fluxes compared to currently available membranes and achieve outstanding separation factors. The dominant role of membrane surfaces in determining the separation performance is also identified and explored at an atomic level. Developing nanosheet membranes with hydrophobic surfaces and/or with a minimal surface silanol density represents the keys to enable highly selective separation processes.}, langid = {english}, - file = {/home/simon/Zotero/storage/KSX35HZ5/Zou and Lin - 2018 - Exploring the potential and design of zeolite nano.pdf} + file = {/home/simon/snap/zotero-snap/common/Zotero/storage/KSX35HZ5/Zou and Lin - 2018 - Exploring the potential and design of zeolite nano.pdf} } diff --git a/docs/source/theory/best-practice.rst b/docs/source/theory/best-practice.rst index 6774d9ca..c60a42a2 100644 --- a/docs/source/theory/best-practice.rst +++ b/docs/source/theory/best-practice.rst @@ -11,11 +11,21 @@ Choosing the force field force fields lead to excellent agreement with experimental data, as for instance for water, hydrocarbons, or polymer melts :cite:`singerMolecularDynamicsSimulations2017,gravelleNMRInvestigationWater2023,gravelleAssessingValidityNMR2023`, - it is important to keep in mind that force fields are usually parametrized - based on thermodynamic quantities. Since NMR relaxation quantities - depend on both structural and dynamical quantities, differences between experiments + it is important to keep in mind that force fields are often parametrized + to reproduce thermodynamic quantities, such as solvation energy. + However, NMR relaxation times depend on both structural + and dynamical quantities, differences between experiments and simulations can be expected for the less accurate force field. +.. container:: justify + + Here, as an illustration, the NMR relaxation time :math:`T_1` + of bulk water was measured as a function of the temperature + for three different water models: + :math:`\text{TIP4P}-\epsilon` :cite:`fuentes-azcatlNonPolarizableForceField2014`, + :math:`\text{SPC/E}-\epsilon` :cite:`berendsenMissingTermEffective1987`, + and :math:`\text{TIP3P}` :cite:`jorgensenComparisonSimplePotential1983`, + .. image:: ../figures/illustrations/bulk-water/experimental_comparison-dark.png :class: only-dark :alt: NMR results obtained from the LAMMPS simulation of water