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| Original file line number | Diff line number | Diff line change |
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| from autode import * | ||
| from autode.molecule import product_to_reactant | ||
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| Config.n_cores = 8 | ||
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| # For hydroxide to be not too reactive in solution requires diffuse functions | ||
| Config.ORCA.keywords.low_opt = ['PBE0', 'D3BJ', 'LooseOpt', 'ma-def2-SVP'] | ||
| Config.ORCA.keywords.hess = ['PBE0', 'D3BJ', 'Freq', 'ma-def2-SVP'] | ||
| Config.ORCA.keywords.opt = ['PBE0', 'D3BJ', 'LooseOpt', 'ma-def2-SVP'] | ||
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| # Set up the first step in the hydrolysis of the ester, attack of OH- to get a tetrahedral intermediate | ||
| r1 = Reactant(name='ester', smiles='CC(OC)=O') | ||
| r2 = Reactant(name='hydroxide', smiles='[OH-]') | ||
| tet_int = Product(name='tet_intermediate', smiles='CC([O-])(OC)O') | ||
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| step1 = Reaction(r1, r2, tet_int, solvent_name='water') | ||
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| # Second step is collapse of the tetrahedral intermediate to the acid and methoxide | ||
| tet_int = product_to_reactant(tet_int) | ||
| p1 = Product(name='acid', smiles='CC(O)=O') | ||
| p2 = Product(name='methodixe', smiles='[O-]C') | ||
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| step2 = Reaction(tet_int, p1, p2, solvent_name='water') | ||
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| # Calculate the reactions in sequence, so the conformers of the tetrahedral | ||
| # intermediate do not need to be found again | ||
| reaction = MultiStepReaction(step1, step2) | ||
| reaction.calculate_reaction_profile() |
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| from autode import Reactant, Product, Reaction, Config | ||
| Config.n_cores = 4 | ||
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| r1 = Reactant(smiles='CC(C)=O', name='acetone') | ||
| r2 = Reactant(smiles='[C-]#N', name='cn-') | ||
| p = Product(smiles='CC([O-])(C#N)C', name='prod') | ||
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| reaction = Reaction(r1, r2, p, solvent_name='water') | ||
| reaction.calculate_reaction_profile() |
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| from autode import * | ||
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| Config.n_cores = 8 | ||
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| reactant = Reactant(name='3,4-dimethylhexa-1,5-diene', smiles='C=C[C@H](C)[C@@H](C)C=C') | ||
| product = Product(name='octa-2,6-diene', smiles='C/C=C/CC/C=C/C') | ||
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| reaction = Reaction(reactant, product, name='cope_rearrangement') | ||
| reaction.calculate_reaction_profile() |
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| from autode import * | ||
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| Config.n_cores = 2 | ||
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| butadiene = Reactant(name='butadiene', smiles='C=CC=C') | ||
| ethene = Reactant(name='ethene', smiles='C=C') | ||
| cyclohexene = Product(name='cyclohexene', smiles='C1C=CCCC1') | ||
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| reaction = Reaction(butadiene, ethene, cyclohexene, name='diels_alder') | ||
| reaction.calculate_reaction_profile() |
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| from autode import * | ||
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| Config.n_cores = 2 | ||
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| methoxide = Reactant(name='methoxide', smiles='C[O-]') | ||
| propyl_chloride = Reactant(name='propyl_chloride', smiles='CCCCl') | ||
| chloride = Product(name='Cl-', smiles='[Cl-]') | ||
| propene = Product(name='propene', smiles='CC=C') | ||
| methanol = Product(name='methanol', smiles='CO') | ||
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| reaction = Reaction(methoxide, propyl_chloride, chloride, propene, methanol, | ||
| name='elimination', solvent_name='water') | ||
| reaction.calculate_reaction_profile() |
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| @@ -0,0 +1,11 @@ | ||
| from autode import * | ||
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| Config.n_cores = 2 | ||
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| flouride = Reactant(name='F-', smiles='[F-]') | ||
| methyl_chloride = Reactant(name='CH3Cl', smiles='ClC') | ||
| chloride = Product(name='Cl-', smiles='[Cl-]') | ||
| methyl_flouride = Product(name='CH3F', smiles='CF') | ||
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| reaction = Reaction(flouride, methyl_chloride, chloride, methyl_flouride, name='sn2', solvent_name='water') | ||
| reaction.calculate_reaction_profile() |