An illustration is provided to help get a very basic grasp of what this analysis is used for. NBO helps you identify natural orbital populations, as well as quantify charge-transfer between atoms, as depicted below.
This tutorial has been written for NBO version 7.0.8. For any further details see the manual.
0. Gaining Access
For CSF, you must request access to NBO 7.0.8.
1. File generation
Run single point calculation on previously optimised system with Gaussian (submission scripts available for ICHEC and CSF3-4 (No need for first 2 lines) found in trujillo_group_resources/scripts directory). Ensure that you include keyword "pop=nbo7", as shown below.
%nprocshared=40
%mem=100GB
# wb97xd def2svp scrf=(smd,solvent=dichloromethane) pop=nbo7
filename
2 1
C -2.84087900 -0.13629700 0.83103500
C -2.46248200 0.28464400 -0.44227700
N.B. It is highly advised to use the same basis set as used for optimisation.
2. Data analysis
Once the single point calculation is complete, you may analyse the filename.log output file using the following commands. The examples below are studying the charge transfer from the lone pairs (LP) of electrons of the oxygen atom to the antibonding orbitals BD* of the iodine atom.
This command will extract all the charge transfer data from all the lone pairs (LP) of electrons to the antibonding orbitals (BD*) in the system.
grep 'LP' B2_cat6b_ts1_product.log | grep 'BD\*'
In order to narrow this data set down for ease of analysis, we will use the following command, grep -v eliminates irrelevant atoms, in this case the hydrogen and fluorine.
grep 'LP' B2_cat6b_ts1_product.log | grep 'BD\*' | grep -v F | grep -v H
Adding > filename.txt as shown below will extract all the specified data in a textfile name "filename.txt"
grep 'LP' B2_cat6b_ts1_product.log | grep 'BD\*' | grep -v F | grep -v H > filename.txt