Monomers

DGEBA

../../_images/DGE-epoxy.png

Bisphenol A diglycidyl ether — we keep the historical abbreviation DGEBA (residue name DGE) — is bisphenol A with each phenolic oxygen extended into a glycidyl (epoxide) group. The natural SMILES for DGEBA is:

CC(C)(C1=CC=C(C=C1)OCC2CO2)C3=CC=C(C=C3)OCC4CO4

But htpolynet needs the active form: every reactive atom carries a sacrificial hydrogen that is deleted when a new bond forms. For epoxy-amine chemistry, the amine donates its H to the oxirane oxygen and the epoxide C–O bond breaks to form the new C–N bond. So the epoxide ring has to be pre-opened in our input structure into a methyl + hydroxyl pair: CC(O) replaces each oxirane ring.

In SMILES that becomes:

CC(C)(c1ccc(OC[CH:3]([OH:5])[CH3:1])cc1)c1ccc(OC[CH:4]([OH:6])[CH3:2])cc1

with atom-mapping tokens picking out the four reactive atoms. This is exactly what the YAML’s constituents.DGE block contains:

DGE:
  smiles: "CC(C)(c1ccc(OC[CH:3]([OH:5])[CH3:1])cc1)c1ccc(OC[CH:4]([OH:6])[CH3:2])cc1"
  reactive_atoms: {1: C1, 2: C2, 3: C3, 4: C4, 5: O1, 6: O2}
  count: 200
  symmetry_equivalent_atoms: [[C1, C2], [C3, C4], [O1, O2]]
  stereocenters: [C3]

Six atoms get explicit names:

../../_images/DGE-labelled.png

  • C1, C2 — the two reactive carbons (the sacrificial methyls). These are the atoms an amine nitrogen will bond to.

  • C3, C4 — the two stereocenters (the carbons bearing the hydroxyl). Opening the oxirane creates a chiral centre; we declare C3 and htpolynet produces the appropriate diastereomer pool via symmetry_equivalent_atoms.

  • O1, O2 — the two hydroxyl oxygens. They get explicit names because the cap reaction re-forms an epoxide three-ring (O–C bond) on any unreacted carbon.

PACM

../../_images/PAC-2d.png

PACM (4,4-diaminodicyclohexylmethane, residue name PAC) has two primary amines, one on each cyclohexyl ring. Because each amine has two N–H bonds, each can react twice (with two different epoxides), so a single PACM can crosslink up to four DGEBAs. Native SMILES:

C1CC(CCC1CC2CCC(CC2)N)N

The atom-mapped form (matching the YAML’s constituents.PAC block):

PAC:
  smiles: "C1C[CH:1](CCC1CC2CC[CH:2](CC2)[NH2:3])[NH2:4]"
  reactive_atoms: {1: C1, 2: C1, 3: N1, 4: N1}
  count: 100
  symmetry_equivalent_atoms: [[N1, N2], [C1, C2]]
  stereocenters: [C1]

Both amine carbons are named C1 and both nitrogens are named N1 in reactive_atoms — the symmetry_equivalent_atoms block is what tells htpolynet to internally relabel the second copies as C2 / N2 so the reactions block can refer to them unambiguously.

../../_images/PAC-labelled.png

The next page describes the reaction dictionaries that drive the cure.