The Configuration File

We previously described an example configuration file for making a system of polystyrene, where all the directives were explained in detail. Here we will only highlight the constituents directive.

We’ll use a very small, stoichiometric system of only 200 DGEBA’s and 100 PACM’s.

constituents:
  DGE:
    count: 200
    symmetry_equivalent_atoms: [[C1,C2],[C3,C4],[O1,O2]]
    stereocenters: [C3]
  PAC:
    count: 100
    symmetry_equivalent_atoms: [[N1,N2],[C1,C2]]
    stereocenters: [C1]

Notice that the contituents directive is where we specify both symmetry-equivalent atoms and stereocenters in each monomer by referencing atom names. DGEBA has three sets of symmetry-equivalent atoms and one symmetry-unique stereocenter, for example. HTPolyNet uses information on symmetry-equivalent atoms to “expand” the set of reactions to include all possible combinations of reactants that symmetry allows. In the case of a general diepoxy with both C1 and C2 atoms designated as reactive and a general diamine with both N1 and N2 atoms designated as reactive, HTPolyNet expands the single primary-to-seconary amine reaction that generates DGE~C1-N1~PAC, which is explicitly specified in the configuration file, into a set of four reactions with distinct products:

  1. PAC~N1-C1~DGE

  2. PAC~N1-C2~DGE

  3. PAC~N2-C1~DGE

  4. PAC~N2-C2~DGE

HTPolyNet only does this because we stipulate that atoms C1 and C2 in DGE be treated as symmetric, and that atoms N1 and N2 on PACM be treated as symmetric. Now, from the standpoint of chemical structure, these atoms are strictly symmetry-equivalent, since the molecules themselves are symmetric. However, HTPolyNet does not recognize symmetry; the user can instead use symmetry-equivalence as a shortcut to automatically build all possible intermolecular interactions. This guarantees that all possible reactions are templated correctly during a cure.

Note also that since PAC~N1-C1~DGE is the product of the primary-to-secondary amine reaction and a reactant in the secondary-to-tertiary reaction, HTPolyNet must also expand the secondary-to-tertiary amine reactions into a set of eight distinct reactions whose products are:

  1. PAC~N1-C1~DGE~N1-C1~DGE

  2. PAC~N1-C2~DGE~N1-C1~DGE

  3. PAC~N2-C1~DGE~N2-C1~DGE

  4. PAC~N2-C2~DGE~N2-C1~DGE

  5. PAC~N1-C1~DGE~N1-C2~DGE

  6. PAC~N1-C2~DGE~N1-C2~DGE

  7. PAC~N2-C1~DGE~N2-C2~DGE

  8. PAC~N2-C2~DGE~N2-C2~DGE

Note that each of these reactions indicates a product where only N1 or N2 of a PACM is reacted with either a C1 or C2 of two distinct DGEBAs. Because the two nitrogens are so far apart on PACM, there is no need to parameterize an oligomer in which both N1 and N2 are simultaneously bound to DGEBA carbons. So we see that during cure, HTPolyNet will search for atoms that satisfy one of twelve possible reactions, all because we specified two reactions among reactants that have several sets of symmetry-equivalent atoms and the product of the first reaction is a reactant in the second.

Stereocenters are used by HTPolyNet to generate enantiomers strictly for building initial liquid systems that are racemic by default. That is, HTPolyNet assumes that any monomer structure provided by an input mol2 or pdb file is a single enantiomer (if it has one or more stereocenters), and instead of copying only this structure to build the liquid, it instead generates all possible enantiomers by flipping stereocenters and then randomly selects among these to build a liquid. HTPolyNet does brute force enumeration of enantiomers, meaning that a molecule with N stereocenters will have 2Nenantiomers.

In the case of of DGEBA, two atoms are designated by stereocenters, and since they each also belong to distinct groups of symmetry-equivalent atoms, a DGEBA has four unique stereocenters. This means 16 unique DGEBA diastereomers are used to build the liquid. Two of those atoms are not strictly chiral in the activated form, since they each have two methyl ligands, but only one of those methyl ligands contains the reactive C1 (or by symmetry, C2) atom that will form a bond, at which point they become chiral. Since we don’t want polymerization to introduce handedness, we make sure we have a racemic mixture to begin with with respect to all potentially chiral atoms.

PACM has only two relevant stereocenters, which are the carbons in the cyclohexyl rings to which the amine nitrogens are attached, so four distinct PACM diastereomers are used in building the initial liquid.

Now we can turn to actually running the build.