COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

电子转移（ET）反应在许多生物学和化学反应中起着重要作用。 化学过程。 早期的实验和理论研究 确定了ET反应的关键因素，并导致了定性的 使用连续溶剂模型。 然而，最近的实验 提供的信息在一个层次上， 供体和受体周围的环境可能是重要的。 这是 特别是在生物ET的研究中， 反应中心（RC），其中蛋白质结构已知， 挑战是使用这种结构再现实验事实。 的 本项目的总体目标是促进对ET的理解 生物和化学系统中的过程， 计算机模拟方法。 在上一个资助期内，我们 开发，检查和完善了广泛的模拟策略， 蛋白质和溶液中的ET过程，包括自由能 微扰/伞形采样方法，半经典轨道， 色散极化子和密度矩阵方法。 这些应用于 研究细菌RC和溶液中的ET过程。 我们的研究和那些 其他小组的研究证明了计算机模拟的有用性。 在 特别是，我们能够在细菌RC中模拟ET， 不同的可行机制。 在目前的资助期内，我们希望 在描述蛋白质中的ET时， 和解决方案。 这将涉及以下项目： (i)细菌RC的进一步研究。 早期的模拟结果显示， 令人鼓舞的结果，但关于电荷分离的独特结论 机制没有达到。 使用更长的模拟与改进的长- 范围治疗，同时侧重于突变的影响，预计将给予 关于电荷转移态的能量学的有价值的信息。 (ii)通过对突变效应的广泛研究进行误差范围评估 对细胞色素和其他蛋白质的氧化还原电位的影响 已知结构。 几种方法的性能，包括本地 反应场增强的自由能扰动，将被检查。 (iii)细菌的时间分辨信息分析 光合作用的各种模拟方法。 (iv)电子转移和质子转移的能量学探讨 醌位点。 (v)模拟Ru-cyt c中的ET以估计固有依赖性 的速率常数的电子耦合项，通过因式分解 蛋白质波动和重组能量的可能影响。 (vi)模拟溶液中的ET，使用显式表示 供体和受体，试图重现良好的实验结果 定义测试用例。

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.