Monomer: Styrene

../../_images/styrene-polymerization.png

Fig. 7 Polymerization of styrene via carbon–carbon double-bond opening. The two reactive carbons we will name C1 (the internal, phenyl-bearing carbon) and C2 (the terminal methylene carbon).

Styrene polymerizes by radical addition: the C=C double bond opens so that each radical carbon bonds to a radical carbon on an adjacent monomer (Fig. 7). htpolynet needs to be able to refer to those two carbons by name in the reactions block, so they get explicit labels (C1 and C2); the remaining atoms keep generic names.

Valence-conservation and the active form

As described in the user guide, htpolynet requires each reactive atom to carry a sacrificial hydrogen that is deleted when a new bond forms. The natural, “inactive” form of styrene has a C=C double bond and so the would-be reactive carbons don’t have an H to spare:

../../_images/STYCC.png

Fig. 8 Styrene (inactive form).

The active form we hand to htpolynet is ethylbenzene, which carries two extra hydrogens on what will become the reactive carbons:

../../_images/STY.png

Fig. 9 Ethylbenzene (active form of styrene, monomer name STY).

In-config SMILES generation

The constituents block of 1-polystyrene.yaml carries the SMILES string and, via the SMILES atom-mapping syntax ([CH2:1], [CH3:2]), the names of the two carbons referenced by the cure and cap reactions:

constituents:
  STY:
    smiles: "c1ccccc1[CH2:1][CH3:2]"
    reactive_atoms: {1: C1, 2: C2}
    count: 1000

When htpolynet run starts, it sees the smiles key, invokes RDKit to generate lib/molecules/inputs/STY.mol2 with atom names C1 and C2 substituted at the mapped positions, then proceeds with the usual AmberTools parameterization (antechamber → parmchk2 → tleap). The mol2 it writes looks something like this, with the two reactive carbons named:

@<TRIPOS>ATOM
      1 C       ...  C.ar  1  STY  ...
      2 C       ...  C.ar  1  STY  ...
      3 C       ...  C.ar  1  STY  ...
      4 C       ...  C.ar  1  STY  ...
      5 C       ...  C.ar  1  STY  ...
      6 C       ...  C.ar  1  STY  ...
      7 C1      ...  C.3   1  STY  ...
      8 C2      ...  C.3   1  STY  ...
      9 H       ...  H     1  STY  ...
     ...

Users without RDKit can instead supply a pre-built mol2 in lib/molecules/inputs/ and use the rename_atoms key in the config to assign atom names by index — see Molecular Structure Inputs for the full alternative path.

The next page covers the reaction dictionaries that tell htpolynet how to glue these monomers together.