Halogens-N bond (not in Parm99/Parm@Frosst)

[bannanc]

I'm looking up GAFF2 parameters:

br-n1  141.51   1.860                     SOUECE3       1
br-n2   88.47   2.038                     SOURCE3       5    0.1082
br-n   136.53   1.873                     SOURCE3       4    0.0046
br-n3  110.41   1.952                     SOURCE3       2
br-n4  118.29   1.926                     SOURCE3       3    0.0013
br-na   96.95   2.002                     SOURCE3       7    0.2156
br-nh  112.77   1.944                     SOURCE3       1
br-no   75.65   2.101                     SOURCE3       1

Where these are the nitrogen types:

n  14.01         0.530               Sp2 nitrogen in amide groups
n1 14.01         0.530               Sp N
n2 14.01         0.530               aliphatic Sp2 N with two connected atoms
n3 14.01         0.530               Sp3 N with three connected atoms
n4 14.01         0.530               Sp3 N with four connected atoms
na 14.01         0.530               Sp2 N with three connected atoms
nh 14.01         0.530               Amine N connected one or more aromatic rings
no 14.01         0.530               Nitro N

I propose we use a rough average for coverage's sake:

[#35:1]~[#7:2]   110.   2.0

[davidlmobley]

Sounds good to me.

How are you actually adding these? Adding to the smirffishFrcmod, hopefully, with comments on source?

[bannanc]

YES! Adding to smirffishFrcmod with a comment on source then I'll convert to smirff99Frosst. Once I've actually typed anything into the smirffFrcmod file I'll make a pull request.

[davidlmobley]

OK. Probably obvious but just wanted to make sure. :)

[bannanc]

I realized we should do this for F, Cl, I too, I'll add the GAFF2 parameters for those in a minute.

[bannanc]

Chlorine

cl-n1  217.59   1.630                     SOUECE3       1
cl-n2  123.81   1.819                     SOURCE3       6    0.1020
cl-n3  139.52   1.777             SOURCE4_SOURCE5      16    0.0044
cl-n   167.01   1.716             SOURCE4_SOURCE5      17    0.0049
cl-n4  149.71   1.753                     SOURCE3       4    0.0098
cl-na  118.36   1.835                     SOURCE3       7    0.2083
cl-nh  145.39   1.763                     SOURCE3       1
cl-no  116.71   1.840                     SOURCE2       1

N-Cl with k=150. r=1.8

Fluorine

f -n1  167.33   1.410                     SOUECE3       1
f -n2  148.04   1.444                     SOURCE3       5    0.0377
f -n3  169.79   1.406                     SOURCE1       9
f -n   175.49   1.397                     SOURCE3       3    0.0112
f -n4  246.14   1.308                     SOURCE3       2
f -na  166.72   1.411                     SOURCE3       7    0.0611
f -nh  157.90   1.426                     SOURCE3       3    0.0085
f -no  136.49   1.467                     SOURCE2       1

N-F with k=170. r=1.4

Iodine

i -n1  105.51   2.060                     SOUECE3       1
i -n2   59.35   2.304                     SOURCE3       6    0.1186
i -n    96.05   2.098                     SOURCE3       5    0.0156
i -n3   77.95   2.185                     SOURCE3       3    0.0437
i -n4   83.69   2.155                     SOURCE3       3    0.0168
i -na   89.07   2.129                     SOURCE3       8    0.1276
i -nh   84.69   2.150                     SOURCE3       1
i -no   70.03   2.231                     SOURCE3       1

N-I with k=80. r = 2.1

[bannanc]

Final: Add a "N-halogen" section with the following:

[#7:1]-[#9:2]    170.   1.4
[#7:1]-[#17:2]    150.   1.8
[#7:1]-[#35:2]   110.   2.0
[#7:1]-[#53:2]    80.    2.1

[davidlmobley]

Lots of fun chemistry here to follow up on, and the great thing is that we (a) know exactly where to find example molecules, and (b) can easily find and/or build more.

These proposals look like good starting points.

[bannanc]

covered in pull request #43