Reactions

The YAML has three groups of reactions: two param-stage reactions that assemble bisGMA from BPA + 2×HIE at runtime, four cure-stage reactions that polymerize STY and HIE radicals, and two cap-stage reactions that restore vinyl double bonds on any monomer that did not react.

Building bisGMA at runtime

Fig. 11 Bisphenol-A (BPA)

Fig. 12 2-hydroxypropyl isopropyl ester (HIE)

Fig. 13 bisGMA (active form)

The first reaction esterifies one HIE onto one of BPA’s two phenolic hydroxyls:

- name: B1
  stage: param
  reactants:
    1: BPA
    2: HIE
  product: GM1
  atoms:
    A:
      reactant: 1
      resid: 1
      atom: O1
      z: 1
    B:
      reactant: 2
      resid: 1
      atom: C4
      z: 2
  bonds:
    - atoms: [A, B]
      order: 1

The intermediate GM1 then reacts with a second HIE on the other phenolic hydroxyl:

- name: B2
  stage: param
  reactants:
    1: GM1
    2: HIE
  product: GMA
  atoms:
    A:
      reactant: 1
      resid: 1
      atom: O2
      z: 1
    B:
      reactant: 2
      resid: 1
      atom: C4
      z: 1
  bonds:
    - atoms: [A, B]
      order: 1

Both reactions are stage: param because the product needs to be GAFF-parameterized. Once both run, the system has a fully parameterized GMA template ready to be inserted into the initial liquid.

Why build GMA at runtime rather than supply a pre-made GMA.mol2? The reason is that the two HIE moieties in a GMA each house a reactive C=C double bond, and we want htpolynet to treat them as equivalent HIE sites during cure. By keeping HIE as the canonical reactive species in the cure reactions, the chain-expanded template set is much smaller than it would be if GMA itself appeared on either side of a cure bond.

Cure reactions

Cure proceeds by C=C double-bond opening: C1 of one radical bonds to C2 of another, with each side donating a sacrificial H. On both STY and HIE, C1 is the radical carbon and C2 is the terminal methyl. We need to cover all four reactant combinations:

Table 1 Monomer–monomer reactions in the bisGMA/styrene system

Attacker (C1 owner)	Attackee (C2 owner)
HIE	HIE
STY	STY
STY	HIE
HIE	STY

Each row gets a single C1-attacks-C2 cure reaction in the YAML (four reactions total; see 2-bisgma-styrene-thermoset.yaml for the full block — they all have the same structure as the polystyrene example, just with the appropriate reactant pair).

Cap reactions

Any STY or HIE monomer that didn’t react during CURE still carries its saturated “active” form. The cap reactions convert the leftover C1–C2 single bonds back to the natural 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
- name:         hieCC
  stage:        cap
  reactants:    {1: HIE}
  product:      HIECC
  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

Chain expansion

htpolynet automatically generates the trimer and tetramer templates needed to cover the dihedral environments that arise as polymer chains grow. Because the four cure reactions span 2 monomer types × 2 attacker roles, there are 8 distinct trimer sequences, with the templated bond in one of two positions in each sequence → 16 trimer templates. For tetramers, only the middle (second–third) bond position is needed (the other positions are already covered by the trimer templates), giving 16 tetramer templates. Total chain-expanded cure templates: 32.

You do not list these explicitly; htpolynet reports the expanded set in the diagnostic log at the start of a run.

The next page walks through the full configuration file.