PCFF Atom type of Nitrogen in amide

EMC
1

In PCFF, should the atomic type of nitrogen in the amide be n (similar to CFF91), nb or n_ 2? And is the hydrogen connected to it hn or hn2? I found a simplest amide in EMC, such as CC (=O) NC atom type recognition failure,so how can I fix it?

2

Maybe I can modify pcff_ template.dat to identify the atomic type I want, but the specific modification method is not yet determined.

3

It seems that in aramid, the N of the amide bond is preferentially recognized as nb rather than n_ 2 or n

4

Could you share an example SMILES of a structure that you are intending to type?

5

Thank you very much. The example is an aromatic system containing amide bonds，like this：c1ccccc1C(=O)/N(c2ccccc2)

6

The correct type for an SP3 nitrogen in an amide moiety should be na. The following type explanations are provided in pcff.frc:

1.0  1   n_2  ...   nitrogen of urethane
1.0  1   na   ...   sp3 nitrogen in amines
1.0  1   nb   ...   sp2 nitrogen in aromatic amines

However, pcff_templates.dat states

type: n_2
   ! nitrogen in carbamate

with carbamate being a *OC(=O)N(*)* moiety. This implies that both n_2 and nb are unsuitable as type for a SP3 nitrogen in amides. Note that you might experience a message like

Warning: increment pair {c_1, na} not found.

EMC applies stricter error messaging than for instance Materials Studio does. The latter assumes a zero contribution upon missing bond increments. This behavior can be duplicated in EMC by adding

field_increment  warn

to your ITEM OPTIONS paragraph in your .esh. This will still provide a warning, but no error is generated. You can also silence the warning by using ignore instead of warn.

My version of PCFF generates results using your SMILES and the above discussed settings. I used the following .esh:

ITEM	OPTIONS

replace		true
field		pcff
field_increment	warn
number		true
focus		true
density		0.1
emc_execute	true

ITEM	END

ITEM	SHORTHAND

molecule	c1ccccc1C(=O)Nc1ccccc1,1

ITEM	END
7

Thanks for your reply :), but here I tend to handle it in a sp2 hybrid manner. I have blocked the na type section in the template. After that, N is recognized as nb, but in Materials studio, it is recognized as n_ 2. I am not sure which type is more reasonable yet.

8

The nitrogen in this case is not an SP2 though. It would be SP2 if it is part of the aromatic ring, which in this case it is not. This is also not an n_2, since no *OC(=O)N* moieties (i.e. carbamate/urethane patterns) are part of this chemistry. Now you are of course free to use what you see fit as typing, which indeed you can influence by modifying the templates file. I personally would type this with an na based on the provided documentation and typing rules as part of the original PCFF files.

9

Thank you for your answer! I will give it a try in the way you mentioned