COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

电子转移反应的计算机模拟

• 批准号: 6180342
• 负责人: ARIEH WARSHEL
• 金额: $ 14.47万
• 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/6180342
• 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.

生物电子转移结构研究的进步 （ET）提出了朝着一个进展的激动人心的机会 相关结构和功能的分子水平更高 电子传输蛋白。该项目的总体目的是 促进对生物学和生物学的ET过程的理解 化学系统使用可用的 结构信息和计算机模拟方法。期间 我们开发，完善和检查了过去的赠款期 ET过程研究策略范围。这些方法 用于研究主要的能量和动力学 在细菌RC中的事件，评估蛋白质的氧化还原电位时， 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，他们无法解决所有 该领域的根本问题，实际上在某些情况下它们 提出了新的令人兴奋的问题。为了进步 在这个重要领域，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，专注于铁硫蛋白。我们将集中精力 在所有原子模型上试图了解水的作用 渗透和平均效果 具有不同程度的benetation的配置。 我们将使用 我们的理解 具有简化溶剂表示的计算有效模型。 （ii）我们将攻击Nalin关于主要ET的纳林开放问题 使用微观模拟的细菌RC。这将包括（a） 介电筛选时间依赖性的依赖性， （b）分析电子位点的局部介电常数 运输发色团并将其与最近的解释有关 鲜明的效果，（c）确定电荷传输状态的能量学 在特殊对中，（d）研究肌蛋白的能量学 残留物和（e）探索振荡的起源 p*的依赖光谱。 （iii）我们将研究重组能量 生物捐赠者 - 受体复合物。 （iv）我们将模拟ET反应 在关注以下内容的解决方案中：（a）评估重组 共价连接的供体 - 受体对的能量，（b）研究效果 溶剂动力学的同时通过一致的量子代表溶质 机械方法，（c）开发密度矩阵方法，（d） 推动电子耦合矩阵元件计算的边界 通过机械处理溶剂量子。