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NERSC Initiative for Scientific Exploration (NISE) 2011 Awards

Coupled Electronic and Nuclear Dynamics in Enzymes and Photocatalysts

Thomas Miller, California Institute of Technology

Associated NERSC Project: Sampling diffusive dynamics on long timescales, and simulating the coupled dynamics of electrons and nuclei (m822)

NISE Award: 750,000 Hours
Award Date: March 2011

We aim to design and employ novel simulation techniques to provide crucial insights and new methodologies that further the understanding of fundamental chemical processes, which are relevant to the chemistries of energy and health. These simulations will yield breakthroughs in our fundamental understanding of the reaction dynamics of energy-related chemical processes.

Charge transfer processes, including electron transfer, hydrogen/proton/hydride transfer and proton-coupled electron transfer (PCET) reactions, are central to the chemistry of energy conversion, respiration, and enzyme kinetics. But key aspects of such reactions remain poorly understood due to the coupling of intrinsically quantum motions to the slower, classical motions of the surrounding environment. We propose to employ the large-scale NERSC computational resources to perform direct simulations of these processes to reveal the detailed mechanisms and the nature of the dynamic coupling between the environment and the transferred quantum particle(s). These simulations will yield breakthroughs in our fundamental understanding of the reaction dynamics of energy-related chemical processes, a key NERSC research goal. In particular, it will open the door for future simulation studies of PCET reactions in energy-related materials and enzymes.

The specific research objectives of this proposal are (1) to extend path-integral simulation techniques to study dynamical coupling between the reaction center and enzyme environment in the hydride transfer reaction catalyzed by dihydrofolate reductase, and (2) to discover the mechanism and to explain the kinetics of a prototypical PCET reaction in biomimetic inorganic chemistry, namely the transfer of a proton and electron in the tyrosine reduction step of photosystem II (PSII). These systems pose outstanding mechanistic questions that demand detailed simulation studies.

The Miller group has recently extended the ring polymer molecular dynamics (RPMD) method to directly simulate the coupled dynamics of electrons and nuclei in complex systems. The RPMD method uses the Feynman path integral formulation of statistical mechanics to map quantum mechanical particles onto an isomorphic classical mechanical system. In a series of proof-of-principle studies, we have demonstrated the model provides an accurate description of excess electron diffusion in liquids, the dynamics of electron localization and trapping following high-energy injection, and the dynamics and kinetics of electron transfer between explicitly solvated metal ions. By combining RPMD with conventional classical molecular dynamics technology, as well as well-established rare-event sampling methods such as transition path sampling and transition interface sampling methods, we have demonstrated that the massively parallel computational resources can be efficiently utilized to extract the mechanism and kinetics of reactions involving coupled electronic and nuclear degrees of freedom.

RPMD is a method for describing the dynamics of a quantum mechanical system, given an underlying potential energy surface. In the proposed simulation studies, we will employ conventional atomistic force-fields (such as SPC/E and CHARMM) for the interactions among solvent molecules and for interactions within the enzyme or inorganic compounds. We will employ previously developed one-electron pseudopotentials for the interactions of the transferring electron with the solvent environment and the metal centers on the inorganic compounds, and we will employ the empirical valence bond method or analytical potentials to describe the interactions of the transferring proton with its donor and acceptor atoms.

Given adequate computational resources such as those available on the NERSC systems, we are ready to begin using our new methodology to investigate breakthrough applications, such as those described above. The NERSC Initiative for Scientific Exploration award is thus instrumental to the elucidation of biological and synthetic pathways for solar energy conversion and catalysis.