def find_ts():
"""Find the transition state for the [4+2] Diels-Alder reaction between
ethene and butadiene"""
ade.Config.n_cores = 8
ade.Config.ORCA.keywords.set_functional('PBE')
rxn = ade.Reaction('C=CC=C.C=C>>C1=CCCCC1', name='DA')
rxn.locate_transition_state()
rxn.ts.print_xyz_file(filename='ts.xyz')
return None
def add_smiles_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:
solvent = None if len(line.split()) < 3 else line.split()[2]
rxn = ade.Reaction(smiles=line.split()[1],
name=line.split()[0],
solvent_name=solvent)
reactions.append(rxn)
return None
def test_prune_small_rings2():
reaction = ade.Reaction('CCCC=C>>C=C.C=CC')
reaction.find_complexes()
ade.Config.skip_small_ring_tss = False
bond_rearrs = br.get_bond_rearrangs(reactant=reaction.reactant,
product=reaction.product,
name='tmp',
save=False)
assert len(bond_rearrs) > 2
ade.Config.skip_small_ring_tss = True
br.prune_small_ring_rearrs(bond_rearrs, reaction.reactant)
assert len(bond_rearrs) == 2
# Should find the 6-membered TS
assert (bond_rearrs[0].n_membered_rings(reaction.reactant) == [6]
or bond_rearrs[1].n_membered_rings(reaction.reactant) == [6])
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
reaction = ade.Reaction('C=CC=C.C=C>>C1C=CCCC1', name='diels_alder')
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
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
ade.Config.n_cores = 8
# Use a basis set with diffuse functions this reaction involving anionic CN-
ade.Config.ORCA.keywords.set_opt_basis_set('ma-def2-SVP')
ade.Config.ORCA.keywords.sp.basis_set = 'ma-def2-TZVP'
# Define a reaction as a single string, with reactants and products seperated
# by '>>'
reaction = ade.Reaction('CC(C)=O.[C-]#N>>CC([O-])(C#N)C', solvent_name='water')
reaction.calculate_reaction_profile()
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()