Dynamics of water at DNA interfaces: The objective of this project is to characterize water dynamics at DNA interfaces. While it is well established that hydration is essential to the stability and function of biomolecules, its role as an active player in important biological processes, such as allosteric regulation, folding, reaction mechanisms, and molecular recognition, is not fully understood. We are investigating the solvation response in DNA of Hoechst 33258, a minor-groove binder, and Coumarin 102 a guanine-cytosine base-pair analogue. Decompositions of the computed solvation response into contributions from water, DNA, and ions will greatly aid in the interpretation of time-dependent fluorescence measurements for these systems.

Infrared probes of biomolecular environment and structure: We are developing robust computational protocols for the simulation of infrared spectra of site-specific carbon-deuterium (C-D) and nitrile (C≡N) probes in biological contexts. The objective of these studies is to connect the information contained in the experimentally measured infrared absorption spectra to local conformational structure and flexibility. We are also ultimately interested in developing methods to calculate chemical-exchange two-dimensional infrared spectra to aid in the interpretation of novel experiments that employ C≡N labels as probes of hydrogen-bond dynamics. Such probes could be used to measure local hydration dynamics at biomolecular interfaces.

Computer simulations of metal-oxide water interfaces: Transition metal oxides, such as TiO₂ and ZrO₂, are essential elements in most, if not all, chemical and photochemical energy conversion processes, including: environmental catalysis, solar energy cells, and photocatalysis. The dearth in our understanding of the factors that influence the thermodynamics, kinetics, and mechanisms of chemical reactions at liquid-solid interfaces presents a fundamental impediment to the rational design of improved low-temperature catalysts. Accurate computer simulations of reactivity at liquid-solid interfaces would offer tremendous insight and guidance into improvement of these systems. The long-term goal of this project is to develop, validate, and apply efficient computational models to predict the structure and reactivity of transition metal oxides in contact with water.

Nonadiabatic transition path sampling (NAPS): We are developing a new theoretical and computational framework for the study of charge transfer reactions in the condensed-phase. This new method, nonadiabatic transition path sampling (NAPS), combines features of transition path sampling (TPS) and the molecular dynamics with quantum transitions (MDQT) surface-hopping algorithm. By combining TPS with MDQT, chemical reactions involving multiple electronic states that are dominated by rare but important events can be studied within the powerful TPS framework. By focusing specifically on reactive trajectories, TPS can infer detailed reaction mechanisms for processes whose timescales are outside of the range of direct simulation.