Welcome
'Comistry' group works in the computational exploration of molecules and the discovery of innovative drugs. We merge the rich, century-long knowledge of chemistry with the prowess of Computational Chemistry, Computational Structural Biology, and Machine Learning.
Research Projects
Computer-assisted and Computer-driven Drug Discovery
We combine Molecular Docking (Docking) and Molecular Dynamics (MD) to study drug-like molecules, proteins, and protein-ligand complexes.
Explore how metabolites from medicinal herbs and plants interact with protein targets with high druggability.
Explore how DNA polymerase discriminate nucleotides and correct the mismatched ones when replicating DNA. This molecular level of understanding is essential in exploring the working mechanism of DNA- or RNA-replicating associated drugs such as Remdesivir which was authorized for emergency use to treat COVID‑19 in numerous countries. In collaboration with the Simmerling Lab at Stony Brook University.
Develop prediction tools for targeted covalent inhibitors. This is an emerging class of drugs that covalently binds to a protein, as compared to mostly Van der Waals interaction in most small molecule drugs. The computational methods involve Density Functional Theory (DFT) calculations, machine learning, and Docking. In collaboration with the Forli Lab at The Scripps Research Institute.
Exploring Molecules and Reactions with Quantum Chemistry and Machine Learning
We utilize the robust DFT to compute electronic structures of a molecule and its associated thermodynamics and kinetics properties such as changes in enthalpies and Gibb free energies, activation energies, and transition state structures. We also harness machine learning models, which predict properties based on historical data rather than physical laws, from traditional ones like Linear Regression, Artificial Neural Network, Random Forest, and Gradient Boosting, to sophisticated ones like Transformer.
Explore and predict properties of the adducts of Lewis bases (LB) and Lewis acids (LA). This is a classic yet exciting non-conventional chemical bond. In collaboration with Prof. Emily Jarvis at Loyola Marymount University.
Study mechanisms of organic reactions
DFT calculations to study Gibb free energy changes associated with a green condensation reaction catalyzed by Zn-based metal-organic-framework nanocrystals. In collaboration with Gachon University.
DFT for kinetics and stereochemistry of a Diels-Alder reaction using green bio-sourced reactants
Publications
Papers of Comistrylab
Full list of publications can be found here.
Synergy of Machine Learning and Density Functional Theory Calculations for Predicting Experimental Lewis Base Affinity and Lewis Polybase Binding Atoms, Journal of Computational Chemistry, 2024. Full-text.
Quantum Chemistry–Machine Learning Approach for Predicting Properties of Lewis Acid–Lewis Base Adducts, ACS Omega, 2023. Full-text.
Experimental and computational investigation of a green Knoevenagel condensation catalyzed by zeolitic imidazolate framework-8, Environmental Research, 2022. Full-text.
Selected papers of Hung Phan for research at UC Santa Barbara
Tuning Optical Properties of Conjugated Molecules by Lewis Acids: Insights from Electronic Structure Modeling, The Journal of Physical Chemistry Letters, 2019. Full-text.
Electrical Double-Slope Nonideality in Organic Field-Effect Transistors, Advanced Functional Materials, 2018. Full-text.
Improving Electrical Stability and Ideality in Organic Field-Effect Transistors by the Addition of Fullerenes: Understanding the Working Mechanism, Advanced Functional Materials, 2017. Full-text.
Biofilm as a redox conductor: a systematic study of the moisture and temperature dependence of its electrical properties, Physical Chemistry Chemical Physics, 2016. Full-text.
Electrical Instability Induced by Electron Trapping in Low-Bandgap Donor–Acceptor Polymer Field-Effect Transistors, Advanced Materials, 2015. Full-text.
Structural and optoelectronic properties of hybrid bulk-heterojunction materials based on conjugated small molecules and mesostructured TiO2, Applied Physics Letters, 2014. Full-text.
Direct Observation of Doping Sites in Temperature-Controlled, p-Doped P3HT Thin Films by Conducting Atomic Force Microscopy, Advanced Materials, 2014. Full-text.
Understanding TiO2 Size-Dependent Electron Transport Properties of a Graphene-TiO2 Photoanode in Dye-Sensitized Solar Cells Using Conducting Atomic Force Microscopy, Advanced Materials, 2013. Full-text.
Selected papers of Hung Phan for research at Gwangju Institute of Science and Technology
Reflection of the structural distinctions of source—different humic substances on organic fouling behaviors of SWRO membranes, Desalination, 2013. Full-text.
Behaviors of commercialized seawater reverse osmosis membranes under harsh organic fouling conditions, Desalination and Water Treatment, 2010. Full-text.
Prediction of boron transport through seawater reverse osmosis membranes using solution–diffusion model, Desalination, 2009. Full-text.