Reactions¶

Because the cure chemistry here is identical to example 3 — epoxy + amine step-growth — the reactions block is a near-rename of tutorial 3’s: DFA plays the role of PAC, FDE plays the role of DGE, and the bond label N1-C1 is the same.

The three directives in this YAML are:

Primary-to-secondary amine¶

- name:        'Primary-to-secondary-amine'
  stage:       cure
  reactants:
    1: DFA
    2: FDE
  product:     DFA~N1-C1~FDE
  probability: 1.0
  atoms:
    A: {reactant: 1, resid: 1, atom: N1, z: 2}
    B: {reactant: 2, resid: 1, atom: C1, z: 1}
  bonds:
    - atoms: [A, B]
      order: 1

z: 2 on the nitrogen says it must still be primary (two H’s available); z: 1 on the carbon says it has one sacrificial methyl H to donate.

Secondary-to-tertiary amine¶

- name:        'Secondary-to-tertiary-amine'
  reactants:
    1: DFA~N1-C1~FDE
    2: FDE
  product:     DFA~N1-C1~FDE-C1~FDE
  stage:       cure
  probability: 0.5
  atoms:
    A: {reactant: 1, resid: 1, atom: N1, z: 1}
    B: {reactant: 2, resid: 1, atom: C1, z: 1}
  bonds:
    - atoms: [A, B]
      order: 1

The probability: 0.5 is the same intrinsic-rate weighting used in example 3 — secondary-to-tertiary amine formation is empirically slower than primary-to-secondary.

Oxirane-formation cap¶

- name:        'Oxirane-formation'
  reactants:
    1: FDE
  product:     FDEC
  stage:       cap
  probability: 1.0
  atoms:
    A: {reactant: 1, resid: 1, atom: O1, z: 1}
    B: {reactant: 1, resid: 1, atom: C1, z: 1}
  bonds:
    - atoms: [A, B]
      order: 1

Same intra-monomer ring-closure as in example 3: any FDE that still has a sacrificial-methyl H at the end of CURE gets its three-membered oxirane ring re-formed by bonding the hydroxyl oxygen O1 to the reactive carbon C1.

How these expand¶

Through the symmetry_equivalent_atoms declarations on the constituents, these three directives expand into:

4 primary-to-secondary cure templates (FDE.{C1,C2} × DFA.{N1,N2});
8 secondary-to-tertiary cure templates (one per primary-stage product × which FDE carbon reacts next);
2 cap templates (one per FDE carbon).

The diagnostic log at the start of a run lists the full expanded set.

The next page covers the configuration file.