COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

电子转移反应的计算机模拟

• 批准号: 6018732
• 负责人: ARIEH WARSHEL
• 金额: $ 14.05万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 1988
• 资助国家: 美国
• 起止时间: 1988-07-01 至 2001-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6018732
• 关键词: bioenergetics; chemical models; computer graphics /printing; computer program /software; computer simulation; electron transport; hydrogen transport; iron sulfur protein; oxidation reduction reaction; oxidizing agents; photosynthesis; photosynthetic reaction centers; quantum chemistry; reducing agents; solutions

The advance in structural studies of biological electron transfer (ET) presents the exciting opportunity of progressing towards a more molecular level in correlaring structure and function of electron transport proteins. The overall aim of this project is to advance the understanding of ET processes in biological and chemical systems to a more niicroscopie level using the available structural information and computer simulation approaches. During the past grant periods we developed, refined and examined a wide range of strategies for studies of ET processes. These approaches were used in studies of the energetics and dynamics of the primary event in bacterial RC, in evaluating redox potentials of proteins, and in studies of other aspects of ET in proteins. Although our studies were very useful they did not resolve all of the fundamental problems in the field and actually in some cases they presented new and exciting questions. In order to fiirther progress in this important field we propose the following projects: (i) We will conduct a systematic evaluation of the redox potential of proteins, focusing on iron sulfiir proteins. We will concentrate on all-atom models trying to understand the role of water penetration and the effect of averaging over differet configurations with different degrees of penetation. We will use our understanding in refining computationally efficient models with simplified solvent representation. (ii) We will attack the nalin open questions about the primary ET in bacterial RC using microscopic simulations. This will include (a) exaznination of the time dependence of the dielectric screening, (b)analyzing the local dielectric constant in the sites of the electron- transporting chromophores and relating it to a recent interpretation of Stark effects, (c) determining the energetics of the charge transfer-states of the special pair, (d) studying the energetics of mutatin~charged residues and (e) exploring the origin of the oscillations in the time dependent spectra of P*. (iii) We will study the reorganization energies of biological donor-acceptor complexes. (iv) We will simulate ET reactions in solution focusing on the following: (a) evaluating reorganization energies of covalently linked donor-acceptor pairs, (b) studying the effect of solvent dynamics while representing the solute by consistent quantum mechanical approaches, (c) developing density matrix methods, and (d) pushing the frontiers of calculations of electronic coupling matrix element by treating the solvent quantum mechanically.

生物电子传递结构研究进展 （ET）提供了一个令人兴奋的机会，可以朝着 更多分子水平的相关结构和功能 电子传递蛋白。该项目的总体目标是 促进对生物和环境领域的 ET 过程的理解 使用现有技术将化学系统提升到更微观的水平 结构信息和计算机模拟方法。期间 在过去的资助期内，我们制定、完善并审查了广泛的 ET 过程研究的一系列策略。这些方法 用于初级能量学和动力学的研究 细菌 RC 事件，评估蛋白质的氧化还原电位， 以及蛋白质中 ET 其他方面的研究。虽然我们的 研究非常有用，但并没有解决所有问题 该领域的基本问题，实际上在某些情况下 提出了新的、令人兴奋的问题。为了进一步进步 在这一重要领域，我们提出以下项目： (i) 我们将对氧化还原电位进行系统评估 蛋白质，重点关注铁硫蛋白。我们将集中精力 在试图理解水的作用的全原子模型上 渗透率和平均不同的效果 具有不同渗透程度的配置。 我们将使用 我们对精炼的理解 具有简化溶剂表示的计算高效模型。 (ii) 我们将攻击关于主要 ET 的 nalin 开放问题 使用微观模拟进行细菌 RC。这将包括（一） 检查介电屏蔽的时间依赖性， (b)分析电子位置的局部介电常数 运输发色团并将其与最近的解释联系起来 斯塔克效应，(c) 确定电荷转移态的能量 特殊对的一部分，(d) 研究突变~带电的能量学 残差和（e）探索时间振荡的起源 P* 的相关光谱。 （三）研究重组能量 生物供体-受体复合物。 (iv) 我们将模拟 ET 反应 解决方案重点关注以下方面： (a) 评估重组 共价连接的供体-受体对的能量，(b) 研究效果 溶剂动力学，同时用一致的量子表示溶质 机械方法，(c) 开发密度矩阵方法，以及 (d) 推动电子耦合矩阵元计算的前沿 通过量子力学处理溶剂。