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

用于描述生物电子和质子转移过程的非绝热环聚合物分子动力学

基本信息

批准号：
364714289
负责人：
Dr. Philip Shushkov
金额：
--
依托单位：
Division of Chemistry and Chemical Engineering
依托单位国家：
德国
项目类别：
Research Fellowships
财政年份：
2017
资助国家：
德国
起止时间：
2016-12-31 至 2018-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/364714289?language=en
关键词：
Nonadiabatic Ring Polymer Molecular Dynamics

项目摘要

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.

非绝热过程，如电子和质子耦合的电子转移，在化学和生物能量转换反应中普遍存在。在现实的，多维凝聚相系统中的这些过程的理论描述需要分子动力学方法，将量子效应，包括非绝热跃迁，隧穿和零点运动。本研究计划旨在发展和应用一种新的近似非绝热凝聚相量子分子动力学方法。路径积分为基础的方法，如环聚合物分子动力学已被证明是成功的凝聚相量子动力学和有显着的兴趣，这些方法扩展到非绝热制度。动力学约束的环聚合物分子动力学方法已经证明了非绝热供体-受体化学，其中只涉及两个电子态的优异性能，我建议推广的方法，发生在多个势能面的非绝热动力学。天青蛋白是一种重要的生物电子和质子转移测试体系，具有丰富的实验数据。我将应用新的方法来描述在全原子的细节电子跳跃和电子跳跃与质子转移天青，这两个涉及三个或更多的势能面耦合。我将解决的详细机制的多步远程电子转移，蛋白质和周围介质的影响，以及耦合的电子转移与质子运动。这项工作将受益于与加州理工学院实验组的密切合作，并将为模拟氧化还原活性蛋白质和蛋白质复合物中的生物电子，质子和质子耦合电子转移铺平道路，并将其应用于核糖核苷酸还原酶，非血红素铁氧化还原酶，细胞色素P450和光系统II。