# Import necessary modules from utils import * from py3Dmol_utils import MolTo3DView from utils import CIRconvert from nbo_parser import nbo_parser import pandas as pd import autode as ade import os # Get the dataframe from task0 task_0_df = pd.read_csv('task_0_20220125_16_04.csv') # Let's focus on Tyrosine, since it should be able to exhibity both conjugation and hyperconjugation # We will re-optimize the configuration from task_0 with xtb (coarse-grained), then ORCA HF-3c level of theory and # finally perform a single point with a more robust level of theory (hybrid functional) HF_3c_opt_nbo_orca = ade.methods.ORCA() HF_3c_opt_nbo_orca.keywords.opt = ade.OptKeywords(['HF-3c', 'NBO']) PBE0_sp_nbo_orca = ade.methods.ORCA() PBE0_sp_nbo_orca.keywords.sp = ade.SinglePointKeywords(['PBE0', 'NBO', 'def2-SV(P)', 'def2/J', 'D3BJ', 'RIJCOSX']) def run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(name, smiles): amino_acid = ade.Molecule(name = name, smiles = smiles) amino_acid.optimise(method=ade.methods.XTB()) # coarse-grained amino_acid.optimise(method=HF_3c_opt_nbo_orca) # HF amino_acid.single_point(method=PBE0_sp_nbo_orca) # Hybrid print(name, amino_acid.energy) # Call the optimization function # smiles = task_0_df[task_0_df['amino acid name'] == "Tyrosine"]['non_canonical_SMILES_L_amino_acid'].iloc[0] # name_label = "Tyrosine_hw1" # run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(name=name_label, smiles=smiles) # From the Tyrosine_hw1_sp_orca.out file, we can see in the

hyperconjugation_types_examples_mols_id = [0, 1, 2] hyperconjugation_types_examples_mols_names = ['ethane', 'methyl_amine', 'methyl_borane'] hyperconjugation_types_examples_mols_smiles = ['CC', 'CN', 'CB'] for i in hyperconjugation_types_examples_mols_id: run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(hyperconjugation_types_examples_mols_names[i], hyperconjugation_types_examples_mols_smiles[i])

conjugation_types_examples_mols_id = [0, 1, 2] conjugation_types_examples_mols_names = ['ethene', 'MA_conj', 'MB_conj'] conjugation_types_examples_mols_smiles = ['C=C', 'C=[N+]', 'C=[B+]'] for i in conjugation_types_examples_mols_id: run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(conjugation_types_examples_mols_names[i], conjugation_types_examples_mols_smiles[i])