Research

Computational chemistry, molecular modeling, and chemical informatics.

Research using chemical theory, statistics, and computation to study molecular structure, activity, and design.

Research Overview

My research projects use computers to explore questions in modern chemistry that experimental methods often cannot answer. Specifically, I apply chemical theory, statistics, and informatics to study relationships between the structure of organic molecules and their biological activity.

This quantitative structure-activity relationship, or QSAR, approach can support the design of molecules with desired pharmacological properties, including possible therapeutic agents for infectious, inflammatory, and hyperproliferative diseases.

A Fragment-Based Search for HIV Inhibitors

This project involves the design and population of a fragment library for discovery of inhibitors of HIV-1 reverse transcriptase. The work focuses on heterocycles, linker groups, and derivatives that can be characterized individually and in combination.

The goal is to design drug candidates using complementary geometries, torsions, polarities, and hydrogen bonding, then dock candidates into the allosteric binding pocket of HIV-RT for quantitative ranking.

Continuum Solvation Models and Force Field Development

My graduate work involved development of a method for rapid free-energy calculations with continuum solvent models. The work implemented generalized Born/surface area solvation with free-energy perturbation and an approximation designed to reduce unnecessary pairwise Born energy recalculations.

This approach improved efficiency while producing minimal error, supporting the use of GB/SA as a viable solvent choice for free-energy perturbation of large systems.

E/Z Energetics for Molecular Modeling and Design

This work examined thermochemical data for prototypical organic molecules that exhibit E/Z conformational equilibria. The results help molecular design workflows, including evaluation of structures from protein-ligand docking.

Exploring Dihedral Torsion Profiles

This project examines dihedral torsion profiles of drug-like organic molecules in aqueous environments. Comparing torsional profiles with and without solvation provides insight into molecular shapes and conformational energetics under biological conditions.