COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

电子转移(ET)反应在许多生物和生物反应中发挥着重要作用。 化学过程。早期的实验和理论研究已经 确定了ET反应中的关键因素，并导致了定性 使用连续介质溶剂模型的图片。然而，最近的实验已经 提供了某种程度上的信息，在这种程度上， 供体和受体周围的环境可能很重要。这是 尤其与细菌等生物内毒素的研究有关 已知蛋白质结构的反应中心(RC)和 挑战在于如何利用这种结构再现实验事实。这个 本项目的总体目标是促进对ET的理解 将生物和化学系统中的过程提高到微观水平 计算机模拟方法。在之前的授权期内，我们 开发、检查和改进了广泛的模拟策略 蛋白质和溶液中的ET过程，包括自由能 摄动/伞形采样法，半经典轨迹， 分散极化子和密度矩阵方法。这些都被应用于 研究细菌RC和溶液中的ET过程。我们的研究和那些 证明了计算机模拟的用处。在……里面 特别是，我们能够在细菌RC中模拟ET并检查 不同的可行机制。在目前的授权期内，我们希望 将蛋白质中ET的描述提高到一个更定量的水平 和解决方案。这将涉及以下项目： (I)对细菌RC的进一步研究。早期的模拟产生了 令人鼓舞的结果，但关于电荷分离的独特结论 机制尚未达成。使用更长的模拟和改进的Long- 集中在突变影响上的范围治疗预计将给出 关于电荷转移态的能量学的有价值的信息。 (2)通过对突变影响的广泛研究来评估误差范围 突变体对细胞色素等蛋白质氧化还原电位的影响 已知的结构。几种方法的性能，包括局部 将考察反应场的增广自由能微扰。 (3)关于细菌的时间分辨信息分析 通过各种模拟方法进行光合作用。 (Iv)探索电子对撞机的能量学和质子转移 对苯二酚站点。 (V)在Ru-cyt c中模拟ET以估计固有依赖性 电子耦合项的速率常数，通过因式分解 蛋白质波动和重组能量的可能影响。 (Vi)使用显式表示法模拟溶液中的ET 供体和受体，试图重现Well的实验结果 已定义的测试用例。

Electron Transfer (ET) reactions play a major role in many biological and chemical processes. Early experimental and theoretical studies have identified the key factors in ET reactions and led to a qualitative picture using continuum solvent models. However, recent experiments have provided information at a level where the microscopic nature of the environment around donor and acceptor might be important. this is particularly relevant in studies of biological ET such as bacterial reaction centers (RC's) where the protein structure is known and the challenge is to reproduce experimental facts using this structure. The overall objective of this project is to advance the understanding of ET processes in biological and chemical systems to a microscopic level using computer simulation approaches. During the previous grant period we developed, examined and refined a wide range of simulation strategies for ET processes in proteins and solution, including a free energy perturbation/umbrella sampling method, semiclassical trajectory, dispersed polaron and density matrix approaches. These were applied to study ET processes in bacterial RC's and solution. Our studies and those of other groups demonstrated the usefulness of computer simulations. In particular, we were able to simulate ET in bacterial RC's and to examine different feasible mechanisms. In the current grant period we would like to move to a more quantitative level in the description of ET in proteins and solution. This will involve the following projects: (i) Further study of bacterial RC's. Earlier simulations yielded encouraging results but unique conclusions about the charge separation mechanism were not reached. Using longer simulations with improved long- range treatment while focussing on mutation effects is expected to give valuable information about the energetics of charge transfer states. (ii) Error range evaluation through extensive study of mutation effects on the redox potential of cytochromes and other proteins with mutants of known structure. The performance of several methods, including local reaction field augmented free energy perturbation, will be examined. (iii) Analysis of time resolved information about bacterial photosynthesis by various simulation methods. (iv) Exploration of the energetics of ET and proton transfer in the quinone sites. (v) Simulation of ET in Ru-cyt c to estimate the inherent dependence of the rate constant on the electronic coupling term, by factoring out the possible effect of protein fluctuations and reorganization energy. (vi) Simulation of ET in solution, using an explicit representation of donor and acceptor, trying to reproduce experimental results of well defined test cases.