COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

生物电子转移的结构研究进展 (ET)提供了迈向 更多分子水平的相关结构和功能 电子传递蛋白。这个项目的总体目标是 促进对生物学和生物医学中的ET过程的理解 使用可用的化学系统将其提升到更微观的水平 结构信息和计算机模拟方法。在.期间 在过去的资助期间，我们制定、完善和审查了广泛的 研究ET过程的一系列策略。这些方法 都被用来研究初级的能量和动力学 事件在细菌RC，在评估蛋白质的氧化还原电位， 以及蛋白质中ET的其他方面的研究。虽然我们的 研究非常有用，它们并没有解决所有的 该领域的基本问题，实际上在某些情况下，它们 提出了新的令人兴奋的问题。为了更上一层楼 在这一重要领域，我们提出了以下项目： (一)我们将对氧化还原电势进行系统评估 蛋白质，重点是铁硫化物蛋白质。我们会集中精力 关于试图理解水的作用的全原子模型 渗透率与差值平均化的效果 具有不同穿透度的构型。我们将使用 我们对炼油的理解 简化的溶剂表示法在计算上有效的模型。 (Ii)我们将攻击纳林关于初选ET的公开问题 使用微观模拟的细菌RC。这将包括(A) 揭示了介电屏蔽的时间依赖性， (B)分析电子位置的局部介电常数- 生色团的运输及其与最近对 斯塔克效应，(C)确定电荷转移态的能级 (D)研究突变素荷电态的能量学 余数和(E)探索时间振荡的起源 P~*的相依谱。(三)研究重组能量 生物供体-受体复合体。(四)模拟外星人反应 重点解决以下问题：(A)评估重组 共价连接的给体-受体对的能量，(B)研究其影响 用一致量子表示溶质时的溶剂动力学 机械方法，(C)发展密度矩阵法，和(D) 推进电子耦合矩阵元计算的前沿 通过对溶剂进行量子力学处理。

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.