Generation of a sulfonated polymer using EMC

EMC
1

Hi everyone,
I am trying to generate a sulfonated polymer based on the pcff forcefield. I am using v9.4.4. I have attached the input .esh file, debug.emc file, and output file. The error says that:

Warning: no rule found for {group, site} = {poly1, 15}.

Warning: no rule found for {group, site} = {poly1, 16}.

Warning: no rule found for {group, site} = {poly1, 17}.

,where 15,16,17 indices refer to the oxygen atoms bonded to sulfur atoms in the sulfonate group. Upon further investigation of these indices in the EMC output, type[15(16,17)] is stated to be empty. In the output, site=14 (sulfur) is indicated to be type “s” ({type → 174, comment → “sp3 sulfur”, element → “S”}). I had thought that this should be type “sf” since it a sulfonate group.

I checked the ${EMC_ROOT}/field/pcff/pcff.frc file to find a type for the sulfur atom in a sulfonate group, which is listed as “sf”. However, this “sf” type is listed to have only 1 connection and virtually the same to " s’ ", when I checked the equivalences.

I checked the debug.emc file in the groups section, which states that site=14 (sulfur atom) has 4 connections.

Finally, I checked the ${EMC_ROOT}/field/pcff/pcff_templates.dat to find type “sf” :

type: sf
! S in sulfonate group
template: (>S(=O)(=O)(-)(-))
atom_test:1
hybridization:SP3
aromaticity:NON_AROMATIC
end_test
atom_test:4
disallowed_elements:S
end_test
atom_test:5
disallowed_elements:S
end_test
end_type

From this type assignment, it seems to be that the type “sf” should have 4 connections. This contradicts pcff.frc file and the debug.emc file, which I found confusing.

I am hoping someone could point me in the right direction in order to generate the sulfonated polymer. Thank you in advance.

p5PhSH_test_pcff.esh (627 Bytes)
output_emc.txt (163.8 KB)
debug.emc (21.3 KB)

2

Dear user,

EMC internally converts your monomer SMILES from

*CCC(c1ccc(S(=O)(=O)[O-])cc1)CC*

into

*CCC(c1ccc(S(:O)(:O):O)cc1)CC*

since all connected oxygen are de facto partially bonded. Rules for oxygens with this bond type are not part of the PCFF template file. For type sf one would have to add

type: sf
   ! S in sulfonate group
   template: (>S(:O)(:O)(:O)(-*))
    atom_test:1
      hybridization:SP3
      aromaticity:NON_AROMATIC
    end_test
  atom_test:4
    disallowed_elements:S
  end_test
  atom_test:5
    disallowed_elements:S
  end_test
end_type

for type o

type:o
   ! generic SP3 oxygen in alcohol, ether, or acid group
   template (>O(:*))
   atom_test:1
   end_test
end_type

and added (sf) at the end of precedence line

  (s(sc(s'(sf))(sp)(s3e)(s4e)(sh(s'(sf))(s3e)(s4e))(s1(s3e)(s4e)))(sf))

This will type without errors. The eventual group is charge neutral though. I checked typing with Materials Studio as a sanity check, which types the sulfonate group with

-[s](:[o])(:[o](:[o])

The resulting molecule is also charge neutral. Upon further inspection of the available bond increments in pcff.frc, I come to the conclusion, that a type for sulfonates sf was added, but corresponding entries for bond increments are missing. Hence, it seems that PCFF would not type sulfonates correctly, neither in EMC, nor in MS, due to the simple fact of missing parameters. You would have to perform quantum mechanical ESP calculations to determine the correct bond increment contributions.