Reactions

Cure reaction

The single inter-monomer cure reaction forms a bond between C1 of one styrene and C2 of another:

reactions:
  - name:        sty1_1
    stage:       cure
    reactants:
      1: STY
      2: STY
    product:     STY~C1-C2~STY
    probability: 1.0
    atoms:
      A:
        reactant: 1
        resid: 1
        atom: C1
        z: 1
      B:
        reactant: 2
        resid: 1
        atom: C2
        z: 1
    bonds:
      - atoms: [A, B]
        order: 1

The product name STY~C1-C2~STY is used internally by htpolynet to build and parameterize the dimer template. That template provides atom types, charges, and bonded interactions which get mapped back onto the growing polymer every time a new C1–C2 bond is formed during CURE.

Chain expansion

Because styrene polymerizes by C=C double-bond opening, C1 and C2 can extend into chains of arbitrary length through the polymer backbone. htpolynet automatically expands the dimer reaction above into all trimer and tetramer combinations needed to correctly parameterize the dihedral environments that arise as chains grow. You do not list these explicitly; htpolynet reports the expanded set in the diagnostic log at the start of a run.

Cap reaction

Once CURE finishes, any monomer that did not react still carries its two sacrificial hydrogens and its C1–C2 atoms are in the saturated (ethylbenzene-like) “active” form. The cap reaction converts these back to the true C=C double bond:

- name:         styCC
  stage:        cap
  reactants:
    1: STY
  product:      STYCC
  probability:  1.0
  atoms:
    A:
      reactant: 1
      resid: 1
      atom: C1
      z: 1
    B:
      reactant: 1
      resid: 1
      atom: C2
      z: 1
  bonds:
    - atoms: [A, B]
      order: 2

The stage: cap label is what tells htpolynet to defer this reaction until after CURE has converged; the bond order: 2 is what restores the double bond and strips the two sacrificial Hs.

The next page walks through the full configuration file.