Combining mechanistic and statistical models for predicting reaction outcomes in organic synthesis
Gallegos, L. C. Colorado State University 2023
Regiodivergent Nucleophilic Fluorination under Hydrogen Bonding Catalysis: A Computational and Experimental Study
Horwitz, M. A.; Dürr, A. B.; Afratis, K.; Chen, Z.; Soika, J.; Christensen, K. E.; Fushimi, M.; Paton, R. S.; Gouverneur, V. J. Am. Chem. Soc. 2023, 145, 9708–9717
Multi-objective goal-directed optimization of de novo stable organic radicals for aqueous redox flow batteries
Sowndarya, S. S. V.; Law, J.; Tripp, C.; Duplyakin, D.; Skordilis, E.; Biagioni, D.; Paton, R. S.; St. John, P. C. Nat. Mach. Intell. 2022, 7, 720–730
Mechanistic Studies Yield Improved Protocols for Base-Catalyzed anti-Markovnikov Alcohol Addition Reactions
Luo, C.; Alegre-Requena, J. V.; Sujansky, S. J.; Pajk, S.; Gallegos, L. C.; Paton, R. S.; Bandar, J. S. J. Am. Chem. Soc. 2022, 144, 9586–9596
Homologation of Electron-Rich Benzyl Bromide Derivatives via Diazo C–C Bond Insertion
A Quantitative Metric for Organic Radical Persistence Using Thermodynamic and Kinetic Features
Sowndarya, S. S. V.; St. John, P. C.; Paton, R. S.Chem. Sci. 2021, 12, 13158-13166.
Real-time Prediction of 1H and 13C Chemical Shifts with DFT accuracy using a 3D Graph Neural Network
Guan, Y.; Sowndarya, S. S. V.; Gallegos, L. C.; St. John, P. C.; Paton, R. S. Chem. Sci. 2021, 12, 12012-12026.
CASCADE
CASCADE stands for ChemicAl Shift CAlculation with DEep learning. It is a stereochemically-aware graph network for the prediction of NMR chemical shifts. Model training was performed against 8,000 DFT structures followed by transfer learning with experimental spectra. A web-server has been created to access CASCADE predictions from SMILES or by drawing structures in the graphical interface. An automated workflow executes 3D structure embedding and MMFF conformer searching. The full ensemble of optimized conformations are passed to a trained graph neural network to predict the NMR chemical shifts (in ppm) for C and H atoms. The underlying datasets used for training and the Python code to run CASCADE from the command line have been made available.
DBSTEP
DBSTEP is a python package for obtaining DFT-Based Steric Parameters from 3-dimensional chemical structures. It can parse the outputs from most computational chemistry programs and other common molecular structure file formats. Steric properties can either be obtained exactly or by using a Cartesian grid, the latter approach being amenable to the featurization of a molecular isodensity surface (DBSTEP can process wavefunction files) rather than using classical atomic radii. Currently, traditional Sterimol parameters (L, Bmin, Bmax) and percent buried volume parameters are implemented, as well as our novel steric parameter vectors Sterimol2vec and vol2vec. This package is designed for use on the command line or alternatively implemented in a Python script for use in a computational workflow to collect steric parameters.
Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties
Gallegos, L. C.; Luchini, G.; St. John, P. C.; Kim, S.; Paton, R. S. Acc. Chem. Res. 2021, 54, 827–836
