Monomers

FDE

FDE — furfurylmethylenediepoxide, name FDE — is the diepoxide hardener. Its skeleton is a tertiary nitrogen with three arms:

  • one furfuryl arm (a furan ring with a methylene bridge to the N);

  • two opened-oxirane arms (each a -CH2-CH(OH)-CH3 chain).

The native, closed oxirane form would have each arm end in a three-membered C-O-C ring. As in example 3, htpolynet expects the active form with the oxirane already opened into -CH(OH)-CH3, so each reactive carbon carries a sacrificial H that gets removed when a new C–N bond forms. The YAML’s constituents.FDE block carries that active-form SMILES with atom-mapping tokens:

FDE:
  smiles: "N(Cc1occc1)(C[CH:3]([OH:5])[CH3:1])C[CH:4]([OH:6])[CH3:2]"
  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]

The six named atoms map one-for-one onto the DGE atoms from tutorial 3:

  • C1, C2 — the two reactive (sacrificial-methyl) carbons.

  • C3, C4 — the two stereocenters (the carbons bearing the hydroxyl).

  • O1, O2 — the two hydroxyl oxygens, used by the cap reaction to re-form the oxirane ring on any unreacted carbon.

The symmetry_equivalent_atoms and stereocenters declarations have the same effect as in DGEBA: the two opened-oxirane arms are treated as chemically equivalent, and the diastereomer pool is built from flipping the chiral carbons.

DFA

DFA — difurfuryl diamine — is the diamine that plays the role of PACM. Two furfurylmethylamine units are joined by a central methylene bridge. Each amine is primary, so each can react twice — a single DFA can crosslink up to four FDE molecules through its two nitrogens.

DFA:
  smiles: "C(c1oc([CH2][NH2:1])cc1)c1oc([CH2][NH2:2])cc1"
  reactive_atoms: {1: N1, 2: N2}
  count: 100
  symmetry_equivalent_atoms: [[N1, N2]]

Only the two nitrogens need explicit names; the cure reactions reference them as N1 (and via the symmetry pairing, N2). No stereocenters: the furan rings are planar aromatic and the central methylene is not chiral.

A note on the SMILES

For the FDE arms, [CH:3] and [CH:4] are written with an explicit H rather than the bare [C:3] / [C:4]. This is the same valence-conservation gotcha noted in example 2: a SMILES bracket atom without an explicit H count defaults to zero implicit Hs, which would leave the carbon at valence 3, and antechamber would then mistype it (and the adjacent atoms) so badly that tleap fails. Writing [CH:3] keeps the carbon at valence 4 and AmberTools handles it cleanly.

Historically, this example was awkward because openbabel’s mol2 writer produced inconsistent atom numbering for fused heterocycles, so the original workflow used PDB inputs with manual atom renaming via sed. Atom-mapped SMILES sidesteps that entirely: the mapping tokens encode which atom gets which name, so the mol2 atom-ordering never matters.

The next page describes the reaction dictionaries.