Designing Cross-Linking Reactions

Programming cross-linking reactions can be very tedious because it requires consistent numbering, accurate chemistry and adding and subtracting bonds, dihedrals, angles, virtual sites etc. The classes in xlink_schemes.py attempt to simplify the process so that minimal work is required to cross-link a new system. As of now, only the diene scheme used for the QI phase is implemented. In order to implement new reaction schemes, one should follow this reaction as an example.

In addition to designing reactions, different monomers, even those with the same cross-linkable groups, may be number differently. This is hard to avoid without manually renumbering everything. Instead of manually renumbering, one can define a class for a monomer which defines all of the necessary monomer attributes. Follow the recommendations in the docstring for the QI monomer Dibrpyr14 as an example.

Classes

__init__(monomer)

Define the cross-linking reaction scheme based on the monomer.

Parameters:monomer (str) – name of monomer being cross-linked. It should have its own class defined with attributes.
Attributes:
scheme: a class that defines the reaction scheme followed by the monomer
__init__(monomer)

Define the cross-linking reaction of a monomer with terminal diene tails

Parameters:monomer (str) – name of monomer
Attributes:

monomer: a class defining the constituent atoms. The name of the class is the same as the monomer

weights: dictionary with the relative weights of one type of reaction. For example, a C1 and C2 atom may be chosen to bond but there may be multiple types of addition (e.g. head-to-tail and 1,4 addition)

reaction_weights: the relative weights of all types of reactions. For example, a C1 and C2 may be eligible to react and perhaps another C2 is eligible to react with a C3. These weights control the number of each type of distinct reaction so that head-to-tail dominates over 13 addition for example.

radical_reaction_weights: the same as reaction weights, but applied to the radical reactions.

Determine the type of reaction based on which carbons are bonding

Parameters:
  • c1 (str) – name of carbon in first chain
  • c2 (str) – name of carbon in second chain
  • radical (bool) – True if this reaction involves a radical

Define the head-to-tail addition of the terminal double bonds (c1 – c2)

Parameters:atoms (dict) – dictionary of atom names (keys) and their index (values) in the context of an entire unit cell
Returns:atom indices and their corresponding types after reaction

Define the reaction of a radical c2 with unreacted c1

Parameters:atoms (dict) – dictionary of atom names (keys) and their index (values) in the context of an entire unit cell
Returns:reacted_types, dummy_bonds, radicals, rm_improper, terminated

Define the termination reaction. i.e. a dummy atom attaches to a radical carbon atoms. The hybridization of the carbon changes to sp3

Parameters:atoms (dict) – dictionary with atom name (key) and its index (value) in the context of an entire unit cell
Returns:reacted_types, dummy_bonds, radicals, rm_improper, terminated
__init__()

Define monomer attributes necessary for cross-linking TODO: clean this up! Some attributes can be combined or written more intuitively Attributes:

chains: a dictionary of dictionaries of the form {‘a’: {‘C’: ‘C1’, ‘C1’: ‘C2 …}, ‘b’: {‘C45’: ‘C1, ‘C44’: ‘C2’ …}}. This monomer contains two alkane chain tails. ‘a’ and ‘b’ are labels referring to each chain respectively. Each sub-dictionary is used to map the names of relevant monomer atoms to generalized atom names that are recognized by the reaction schemes. For a diene tail, C1 refers to the terminal carbon atom, C2 refers to the second-to-last carbon atom and so on. H1 and H2 refer to hydrogen atoms attached to C1. H3 is attached to C2, H4 to C3 and H5 to C4. These generalized names are the values in each sub-dictionary. The keys are the names of the carbon atoms in the context of the monomer, so the names as they appear in the .gro file. Take a look at Dibrpyr14.gro if this is still unclear.

nchains: the number of chains that a monomer has. This makes code more readable elsewhere

chain_numbers: Each chain should have its own number starting from 0. This is used to determine whether a given chain has already been involved in a reaction.

indices: this dictionary of dictionaries stores the indices of relevant monomer atoms in the context of a single monomer. It is constructed in a similar way to self.chains, but the generalized carbon atoms names are the keys (instead of the values) and the index is the index of generalized carbon atom. For example, C1 in chain ‘b’ is index 49, meaning it is the 50th atom in the topology file for a single Dibrpyr14 residue. (See Dibrpyr14.gro or Dibrpyr14.itp to confirm this and all other entries). The indices include those corresponding to the dummy atoms (D1, D2, D3, D4).

dummy_connectivity: this dictionary of dictionaries defines the connectivity between carbon atoms and the dummy atoms. For each chain, the sub-dictionary contains the name of each carbon atom (in the context of the monomer) as keys and the generalized name of the attached dummy atom as the value. In general, for the diene reaction, D1 is attached to C1, D2 to C2 and so on.

hydrogen_connectivity: similar to dummy_connectivity, this defines which hydrogen atoms are bonded to which carbon. This dictionary does not distinguish between chains. Each key is the name of a carbon atom, as you’d find in the corresponding Dibrpyr14 .gro or .itp file, with a list of generalized hydrogen atoms that are attached to that carbon.

dummy_mass: the mass of the dummy atom (hydrogen)

carbons: a dictionary with keys that are the generalized carbon atom names and values that are a list of the actual carbon atom names as you’d find them in the .gro or .itp file.

bonds_with: a list of carbon pairs. Each sub-list contains two lists: a list of carbon atoms in the 1st entry that can bond with carbon atoms in the second list entry.

impropers: a dictionary of dictionaries. Each sub-dictionary refers to a chain. The sub-directories contain keys corresponding to each carbon atom. Each value is a list of atoms that make up the improper dihedral which holds the originally sp2 carbon in a planar configuration. When an sp2 carbon is converted to sp3, the improper must be removed. The order of the improper is written in the same way that you’d find it in Dibrpyr14.itp. Required ordering was a choice that I made to speed up some calculations. Be very careful defining this attribute.