Nonadiabatic Ring Polymer Molecular Dynamics for the Description of Biological Electron and Proton Transfer Processes

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Nonadiabatic processes, such as electron and proton coupled electron transfers, are ubiquitous in chemical and biological energy conversion reactions. The theoretical description of these processes in realistic, multidimensional condensed phase systems requires molecular dynamics methods that incorporate quantum effects, including nonadiabatic transitions, tunneling and zero-point motion. This research proposal aims to develop and apply a novel method for approximate nonadiabatic quantum molecular dynamics in the condensed phase. Path integral-based approaches like ring polymer molecular dynamics have proved successful for condensed-phase quantum dynamics and there have been significant interest in extending these approaches to the nonadiabatic regime. The kinetically-constrained ring polymer molecular dynamics method has demonstrated excellent performance for nonadiabatic donor-acceptor chemistries, which involve only two electronic states, and I propose to generalize the method to nonadiabatic dynamics that takes place on multiple potential energy surfaces. Azurin is an important test system for biological electron and proton transfer with a wealth of available experimental data. I will apply the new method to describe in full atomistic detail electron hopping and electron hopping coupled with proton transfer in azurin, both of which involve three or more potential energy surfaces. I will address the detailed mechanism of multistep long-range electron transfer, the influence of the protein and the surrounding medium, and the coupling of the electron transfer with the proton motion. This work will benefit from close collaborations with experimental groups at Caltech and will pave the way to the simulation of biological electron, proton, and proton coupled electron transfers in redox active proteins and protein complexes with numerous follow-up applications to ribonucleotide reductase, non-heme iron oxidoreductases, cytochromes P450, and photosystem II.