Creating EPDM copolymer chain

EMC
1

Dear Dr. Veld,

Hi! I am trying to creating a EPDM (Ethylene Propylene Diene Monomer) copolymer chain using EMC.
At the present, I am assuming there are only 1 ethyl, 1 propyl and 1 enb (5-Ethylidene-2-norbornene) in such a chain. Terminators are 2 methyls. My input script goes like this:

ITEM OPTIONS

field pcff
ntotal 44
mass true
replace true
density 0.87

ITEM END

ITEM GROUPS

ethyl *CC*,1,ethyl:2,2,propyl:1
propyl *CC(C)*,1,propyl:2,2,enb:1
enb CC=C1CC2CC1C(*)C2*,1,enb:2,2,ethyl:1 # the Diene Monomer part
methyl *C,1,ethyl:1,1,ethyl:2,1,propyl:1,1,propyl:2,1,enb:1,1,enb:2

ITEM END

ITEM CLUSTERS

poly random 1

ITEM END

ITEM POLYMERS

poly
100 ethyl,1,propyl,1,enb,1,methyl,2

ITEM END

This would work, but when visualizing the lammps data file (or pdb file) generated from this script, it seems like there are geometrical mistakes. So I am not sure if I put the asterisks at the right location in the SMILES string of enb monomer.

So I would like to know:

  1. If my ‘enb’ part in the ITEM GROUPS section comes with correct expression
  2. Is there any method that can assign ratios (x:y:z) for these three types of monomers? Because normally ethyl comes with largest portion, then propyl, and enb is the least.
  3. Can I create crosslinks between chains in EMC?

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Thank you very much Dr. Veld.
Your advice and reply are highly appreciated! Thanks!

2

Dear Shengjie,

Your script goes into the right direction. To answer your questions:

  1. Your ENB is correct. I took the liberty of using the canonical SMILES instead, but that does not change the final structure.
  2. There are two ways to deal with controlling the number of monomers in your example: you can either set the number of monomers by ethyl,5,propyl,4,enb,1,methyl,2, or you can set the ratio by ethyl:propyl:enb=5:4:1,10,methyl,2 (see below). The former always creates exactly 5 ethyls, 4 propyls, and 1 ENB, while the latter creates these numbers on average based on the provided frequencies. My polymer always consists of 10 monomers in both cases. You can enter a distribution by adding more entries to the ITEM POLYMER section.
  3. Unfortunately, EMC currently does not allow for crosslinks, since EMC constructs polymer connectivity before actually creating its coordinates; EMC does not use directed regrowth, which would be needed for adding crosslinks; a possibility is to create a dendrimer, which has the right cross linking density.

My version of your script reads:

#!/usr/bin/env emc_setup.pl

# Options section

ITEM	OPTIONS

field		pcff

#density		0.87
#mass		true
#ntotal		44

density		0.1
number		true
focus		true

replace		true
emc_execute	true

ITEM	END	# OPTIONS

# Groups section

ITEM	GROUPS

ethyl		*CC*, &
		1,ethyl:2, 1,propyl:2, 1,enb:2, 1,methyl:1, &
		2,ethyl:1, 2,propyl:1, 2,enb:1, 2,methyl:1
	      
propyl		*CC(C)*, &
		1,ethyl:2, 1,propyl:2, 1,enb:2, 1,methyl:1, &
		2,ethyl:1, 2,propyl:1, 2,enb:1, 2,methyl:1
	      
enb		*C1C(*)C2CC(=CC)C1C2, &
		1,ethyl:2, 1,propyl:2, 1,enb:2, 1,methyl:1, &
		2,ethyl:1, 2,propyl:1, 2,enb:1, 2,methyl:1
	      
methyl		*C

ITEM	END	# GROUPS

# Clusters section

ITEM	CLUSTERS

poly		random, 1

ITEM	END	# CLUSTERS

# Polymers section

ITEM	POLYMERS

poly
#100		ethyl,5,propyl,4,enb,1,methyl,2
100		ethyl:propyl:enb=5:4:1,10,methyl,2

ITEM	END	# POLYMERS

The monomer connectivity was under-defined, assuming one monomer can react with all others. As you see, I have over-defined monomer connectivity, which allows me to copy each entry and swap out monomer name and SMILES afterwards. For demonstration purposes, I build only one polymer at low density by setting number true and density 0.1. The option number true builds the number of molecules as specified by the numbers in the ITEM CLUSTERS section.

3

Thank you very much for your detailed and thorough explainations, which made it whole lot more clear!