Non-covalent Interaction Complexes

autodE allows for the systematic search of a NCI complexes conformational space. For example, to find the lowest energy structure of the water trimer:

import autode as ade

xtb = ade.methods.XTB()

# Number of points on the surface of the sphere for each component
ade.Config.num_complex_sphere_points = 5  # N_s

# and the number of rotations to perform per point on the sphere
ade.Config.num_complex_random_rotations = 3  # N_r

# Total number of conformers ~(N_s × N_r)^(N-1) for N molecules => ~225

# Make a water molecule and optimise at the XTB level
water = ade.Molecule(name="water", smiles="O")
water.optimise(method=xtb)

# Make the NCI complex and find the lowest energy structure
trimer = ade.NCIComplex(water, water, water, name="water_trimer")
trimer.find_lowest_energy_conformer(lmethod=xtb)
trimer.print_xyz_file()

Out (visualised)

The parameters (num_complex_sphere_points and num_complex_random_rotations) define the number of generated conformers, up to ade.Config.max_num_complex_conformers.

By default, autodE will exclude any conformers with differing connectivity, thus may not generate any conformers of e.g. a [M(H₂O)_m]_n+ system. Complexes of systems with dative bonds can be generated by including allow_connectivity_changes=True. For example, with a [Na(H₂O)₃]⁺system:

import autode as ade

ade.Config.n_cores = 8


h2o = ade.Molecule(smiles="O")
na_ion = ade.Molecule(smiles="[Na+]")

# Initialise the [Na(H2O)3]+ complex and search 'conformers'
na_h2o_3 = ade.NCIComplex(na_ion, h2o, h2o, h2o)
na_h2o_3.find_lowest_energy_conformer(allow_connectivity_changes=True)

# Print .xyz files of all the generated conformers
for idx, conformer in enumerate(na_h2o_3.conformers):
    conformer.print_xyz_file(filename=f"conf{idx}.xyz")

Out (visualised)