Conformer search - eChem book

import veloxchem as vlx

We define a structure in terms of a SMILES string.

molecule = vlx.Molecule.read_smiles("OC=CC=O")
molecule.show(atom_indices=True)

We also define the electronic structure theory method to be used as well as an VeloxChem optimization driver.

scf_drv = vlx.XtbDriver()
scf_drv.ostream.mute()

opt_drv = vlx.OptimizationDriver(scf_drv)
opt_drv.ostream.mute()

Conformer optimization¶

Optimize the structures of all conformers.

conformer_energies = []
conformer_structures = []

cis, trans = 0.0, 180.0

hocc, occc, ccco = (6, 1, 2, 3), (1, 2, 3, 4), (2, 3, 4, 5)

for i in (cis, trans):
    for j in (cis, trans):
        for k in (cis, trans):

            molecule = vlx.Molecule.read_smiles("OC=CC=O")

            molecule.set_dihedral_in_degrees(hocc, i)
            molecule.set_dihedral_in_degrees(occc, j)
            molecule.set_dihedral_in_degrees(ccco, k)

            opt_results = opt_drv.compute(molecule)
            conformer_energies.append(opt_results["opt_energies"][-1])
            conformer_structures.append(opt_results["final_geometry"])

Find the conformer with the lowest energy.

import numpy as np

conformer_energies = np.array(conformer_energies)

idx_lowest_conformer = np.argmin(conformer_energies)

lowest_conformer = vlx.Molecule.read_xyz_string(
    conformer_structures[idx_lowest_conformer]
)
lowest_conformer.show()

We find the most stable conformer to be the cis–cis–cis conformer.

print("Conformer  Energy (kcal/mol)\n" + 27 * "-")
for i, conformer_energy in enumerate(
    (conformer_energies - np.min(conformer_energies)) * vlx.hartree_in_kcalpermol()
):
    print(f"{i+1:>2d} {conformer_energy:14.2f}")

Conformer  Energy (kcal/mol)
---------------------------
 1           0.00
 2           7.43
 3           5.81
 4           5.78
 5          12.97
 6          10.24
 7           8.44
 8           9.34