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Molecular Manipulation

Molecular Manipulation#

autodE provides some simple methods for molecular manipulation and more functionality when combined with molfunc.

Fragmentation#

From a molecular graph representation of a molecule its fragmentation is relatively straightforward. For example, to fragment methane to CH3• + H•

>>> import autode as ade
>>> methane = ade.Molecule(smiles='C')
>>> [atom.atomic_symbol for atom in methane.atoms]
['C', 'H', 'H', 'H', 'H']

>>> from autode.mol_graphs import split_mol_across_bond
>>> ch3_nodes, h_nodes = split_mol_across_bond(methane.graph, bond=(0, 1))
>>> ch3 = ade.Molecule(name='CH3', mult=2, atoms=[methane.atoms[i] for i in ch3_nodes])
>>> ch3.atoms
Atoms(n_atoms=4, [Atom(C,  0.0009,  0.0041, -0.0202),
                  Atom(H, -0.4585,  0.9752, -0.3061),
                  Atom(H,  0.0853, -0.0253,  1.0804),
                  Atom(H,  1.0300, -0.1058, -0.4327)])
>>> h = ade.Molecule(name='H', mult=2, atoms=[methane.atoms[i] for i in h_nodes])
>>> h.atoms
Atoms(n_atoms=1, [Atom(H, -0.6577, -0.8481, -0.3214)])

Functionalisation#

../_images/functionalisation.png

Swapping fragments on a structure (e.g. H → Me) can be achieved using SMILES concatenation. For example to stitch two methyl fragments to generate an ethane molecule

>>> ethane = ade.Molecule(name='C2H6', smiles='C%99.C%99')
>>> ethane.n_atoms
8

Multiple fragments can be added to the same core by specifying multiple sites on a single atom

>>> propane = ade.Molecule(name='C3H8', smiles='C%99%98.C%99.C%98')
>>> propane.n_atoms
11

This method regenerates the whole structure which may not be desirable if the molecule is a transition state (TS) or a particular conformation of interest.

molfunc#

Adding a fragment to a fixed core structure can be achieved with molfunc and can be installed with: pip install molfunc. molfunc requires a xyz file to initialise a molecule and indexes atoms from 1 so that atom 2 is the first hydrogen atom in methane

>>> from molfunc import CoreMolecule, CombinedMolecule
>>> methane.print_xyz_file()
>>> methane_core = CoreMolecule(xyz_filename='CH4.xyz', atoms_to_del=[2])
>>> ethane = CombinedMolecule(methane_core, frag_smiles='C[*]', name='C2H6')
>>> ethane.n_atoms
8

A set of fragments can be iterated through using molfunc to generate a library rapidly e.g.

from molfunc import CoreMolecule, CombinedMolecule

fragments = {
    "NMe2": "CN([Fr])C",
    "NH2": "N[Fr]",
    "OH": "O[Fr]",
    "Me": "C[Fr]",
    "F": "F[Fr]",
}

methane = CoreMolecule(xyz_filename="CH4.xyz", atoms_to_del=[2])

for name, smiles in fragments.items():
    combined = CombinedMolecule(
        core_mol=methane, frag_smiles=smiles, name=f"CH3_{name}"
    )
    combined.print_xyz_file()

Out (visualised):

../_images/molfunc_functionalisation.png
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