No project ever really ends, but at least these projects have reached some conclusions. Most of these have produced publications.
Variable Radii for Implicit Solvation
My first project during my graduate career was the development for implicit solvent models. Implicit solvation plays an important role in computational chemistry because it provides a fast way to get first order approximation of solvation effects. A similar characteristic of the many implicit solvation models is the need for dividing surface for the solute and solvent. These surfaces are usually constructed from overlapping spheres centered at each atom. This leads to a static solvation surface even as atoms change electronic structure.
QCRNA Database
The QCRNA Database is a large collection of high-level density-functional electronic structure calculations of molecules, complexes and reactions relevant to RNA Catalysis. This is part of a 5-year project funded by the NIH to study the molecular mechanisms of RNA enzymes, or ribozymes. A detailed understanding of RNA catalysis is fundamental to biology, and has important implications toward the design of new medical therapies that target genetic disorders as well as the development of new biotechnology. The DFT Database for RNA Catalysis can be used to derive information about molecular structure, complexes and reactions. Moreover, the design of the database with a careful and consistent theoretical level opens the door to the design of new, highly accurate and efficient quantum models able to be applied in large-scale hybrid quantum mechanical/molecular mechanical simulations of ribozyme reactions.
Methylated CG DNA & DNA Adenine lesions
This work was in collaboration with the Tretyakova lab at the Cancer Research Center at the University of Minnesota. DNA methylation plays an important role in your bodies mechanism for deciding what genes to express. It turns out these methylations are hot spots for tobacco carcinogens. The work investigated the role of methylation in the increased carcinogen susceptibility.
Benchmark Proton Affinities and Gas Phase Basicities
Much of chemistry is driven by proton transfers and this work attempted to benchmark the enthalpy and Gibbs energy of various protonations and deprotonations on important biological molecules in the gas phase. This quantum chemical benchmark included both various density functionals as well as multi-level methods in the gas phase. This work is support for future parameterization of semi-empirical quantum models for biophysics.