def add_xyz_rxns_from_file(filename):
"""Add reactions from a file with lines in the format:
name XX.YY>>ZZ"""
with open(filename, 'r') as rxn_file:
for line in rxn_file:
name, rxn_str = line.split()
reac_names, prod_names = rxn_str.split('>>')
reacs = [
ade.Reactant(os.path.join(data_path, f'{name}.xyz'))
for name in reac_names.split('.')
]
prods = [
ade.Product(os.path.join(data_path, f'{name}.xyz'))
for name in prod_names.split('.')
]
rxn = ade.Reaction(*reacs, *prods, name=name)
reactions.append(rxn)
return None
import autode as ade
ade.Config.n_cores = 8
reactant = ade.Reactant(name='3,4-dimethylhexa-1,5-diene',
smiles='C=C[C@H](C)[C@@H](C)C=C')
product = ade.Product(name='octa-2,6-diene', smiles='C/C=C/CC/C=C/C')
reaction = ade.Reaction(reactant, product, name='cope_rearrangement')
reaction.calculate_reaction_profile()
import autode as ade
ade.Config.n_cores = 8
ade.Config.ORCA.keywords.set_opt_basis_set('ma-def2-SVP')
ade.Config.ORCA.keywords.sp.basis_set = 'ma-def2-TZVP'
methoxide = ade.Reactant(name='methoxide', smiles='C[O-]')
propyl_chloride = ade.Reactant(name='propyl_chloride', smiles='CCCCl')
chloride = ade.Product(name='Cl-', smiles='[Cl-]')
propene = ade.Product(name='propene', smiles='CC=C')
methanol = ade.Product(name='methanol', smiles='CO')
reaction = ade.Reaction(methoxide,
propyl_chloride,
chloride,
propene,
methanol,
name='E2',
solvent_name='water')
reaction.calculate_reaction_profile()
import autode as ade
reac = ade.Reactant('claisen_r.xyz')
prod = ade.Product('claisen_p.xyz')
# Create an 8 image nudged elastic band with intermediate images interpolated
# from the final points, thus they must be structurally similar
neb = ade.neb.CINEB(initial_species=reac, final_species=prod, num=8)
# minimise with XTB
neb.calculate(method=ade.methods.XTB(), n_cores=4)
# print the geometry of the peak species
peak_species = neb.get_species_saddle_point()
peak_species.print_xyz_file(filename='peak.xyz')
import autode as ade
ade.Config.n_cores = 8
ade.Config.hcode = 'g09' # Use Gaussian09 as the high-level method
# For hydroxide to be not too reactive requires diffuse functions; set all the
ade.Config.G09.keywords.set_opt_basis_set('6-31+G(d)')
ade.Config.G09.keywords.sp.basis_set = '6-311+G(d,p)'
# Set up the first step in the hydrolysis of the ester, attack of OH- to get a
# tetrahedral intermediate
r1 = ade.Reactant(name='ester', smiles='CC(OC)=O')
r2 = ade.Reactant(name='hydroxide', smiles='[OH-]')
tet_int = ade.Product(name='tet_intermediate', smiles='CC([O-])(OC)O')
step1 = ade.Reaction(r1, r2, tet_int, solvent_name='water')
# Second step is collapse of the tetrahedral intermediate to the acid and
# methoxide
tet_int = ade.Reactant(name='tet_intermediate', smiles='CC([O-])(OC)O')
p1 = ade.Product(name='acid', smiles='CC(O)=O')
p2 = ade.Product(name='methodixe', smiles='[O-]C')
step2 = ade.Reaction(tet_int, p1, p2, solvent_name='water')
# Calculate the reactions in sequence, so the conformers of the tetrahedral
# intermediate do not need to be found again
reaction = ade.MultiStepReaction(step1, step2)
reaction.calculate_reaction_profile()
import autode as ade
import numpy as np
ade.Config.n_cores = 4
reac = ade.Reactant('DA_r.xyz')
prod = ade.Product('DA_p.xyz')
pes = ade.pes.PES2d(reac,
prod,
r1s=np.linspace(1.45, 3.0, 10),
r1_idxs=(0, 5),
r2s=np.linspace(1.45, 3.0, 10),
r2_idxs=(3, 4))
pes.calculate(name='da_surface',
method=ade.methods.XTB(),
keywords=ade.OptKeywords([]))
# Save the matrix of energies (Ha) over the grid
np.savetxt('da_surface.txt', pes.energies())
# and print the 2D surface
pes.print_plot()
import autode as ade
ade.Config.n_cores = 8
flouride = ade.Reactant(name='F-', smiles='[F-]')
methyl_chloride = ade.Reactant(name='CH3Cl', smiles='ClC')
chloride = ade.Product(name='Cl-', smiles='[Cl-]')
methyl_flouride = ade.Product(name='CH3F', smiles='CF')
reaction = ade.Reaction(flouride,
methyl_chloride,
chloride,
methyl_flouride,
name='sn2',
solvent_name='water')
reaction.calculate_reaction_profile()