Data sets and machine learning models for: Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates

The datasets and final machine learning model files for the manuscript "Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates". Citation should refer directly to the manuscript:

• Chung, Y.; Green, W. H. Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates. Chemical Science 2024, doi: 10.1039/D3SC05353A

To use the machine learning models, please refer to the sample files and instructions on https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML. 

Detailed information can be found in README.md file.

Details on the files

In the pretraining and finetuning set csv files, each column represents:

1. rxn_smiles: atom-mapped reaction SMILES
2. solvent_smiles: solvent SMILES
3. ddGsolv: solvation free energy of activation of a reaction-solvent pair at 298K in kcal/mol (main prediction target)
4. ddHsolv: solvation enthalpy of activation of a reaction-solvent pair at 298K in kcal/mol (main prediction target)
5. dGsolv_reactant: solvation free energy of reactant(s) at 298K in kcal/mol (additional feature)
6. dGsolv_product: solvation free energy of product(s) at 298K in kcal/mol (additional feature)
7. dHsolv_reactant: solvation enthalpy of reactant(s) at 298K in kcal/mol (additional feature)
8. dHsolv_product: solvation enthalpy of product(s) at 298K in kcal/mol (additional feature)

Data sets under 'RxnSolvKSE_dataset_v1.1.zip'

• pretraining_set: contains the dataset used for pre-training
  • all_data: contains all calculated data
    • pretraining_rxn_solvent_ddGsolv_ddHsolv_with_features_all.csv: contains both main prediction targets and additional feature for reaction-solvent pairs
    • pretraining_solvent_info.csv: list of all solvents
    • pretraining_unique_rxn.csv: list of all reactions, both forward and reverse directions
  • chosen_500k_data: contains the chosen 500k data
    • pretraining_rxn_solvent_ddGsolv_ddHsolv_500k.csv: contains main prediction targets for reaction-solvent pairs
    • pretraining_features_react_prod_dGsolv_dHsolv_500k.csv: contains additional features for reaction-solvent pairs
    • train_test_split: contains the 5-fold random split training and test sets.
• finetuning_set: contains the dataset used for fine-tuning
  • all_data: contains all calculated data
    • finetuning_rxn_solvent_ddGsolv_ddHsolv_with_features_all.csv: constains both main prediction targets and additional features for reaction-solvent pairs. The rxn_key column indicates whether the reaction is bimolecular hydrogen abstraction (bihabs), unimolecular hydrogen migration (intrahabs), or radical addition to a multiple bond (raddition). The 'fwd' and 'rev' each indicate forward and reverse reactions.
    • finetuning_solvent_info.csv: list of all solvents
    • finetuning_unique_rxn.csv: list of all reactions, both forward and reverse directions
  • chosen_data: contains chosen data
    • finetuning_rxn_solvent_ddGsolv_ddHsolv_chosen.csv: contains main prediction targets for reaction-solvent pairs
    • finetuning_features_react_prod_dGsolv_dHsolv_chosen.csv: contains additional features for reaction-solvent pairs
• experimental_set: contains the experimental rate constant data used to test the model. The original experimental data can be found at https://zenodo.org/record/7747557.
  •  expt_rxn_atom_mapped_smiles.csv: contains the atom-mapped reaction SMILES used for the experimental data.
  • expt_data_collected.xlsx: contains all experimental data and detailed information
  • expt_rxn_solv_smiles_with_features_all.csv: contains the computed additional features for the experimental reaction-solvent pairs.

Machine learning model files under 'RxnSolvKSE_ML_model_files.zip'

• Contains the Chemprop machine learning model files for predicting ddGsolv and ddHsolv for a reaction-solvent pair. It takes atom-mapped reaction SMILES and solvent SMILES as inputs.
• To use these ML models, please refer to the sample files and instructions on https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML