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Conformational dependence of electron transfer through molecular media: Hydrocarbons, proteins, and interfacial solvent.

机译：电子通过分子介质的构象依赖性：碳氢化合物，蛋白质和界面溶剂。

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Four parts are included in this dissertation: Chapter 1 is introduction and background of our research; Chapter 2 is a study of the dependence of tunneling currents on conformation and end-to-end distance while pulling a flexible molecule; Chapter 3 is a simulation of electron transfer between cytchrome c2 and the bacterial photosynthetic reaction center using Brownian dynamics; Chapter 4 is a detailed study of solvent effects on interprotein electron transfer.; Most molecules access a broad range of conformations at room temperature. To study the conformational dependence of electron transfer through various media. We explored the influence of conformational freedom on tunneling currents using a simple model for tunneling mediated by a single floppy small molecule that bridges between a model tip and substrate. The tip and substrate are described as semi-infinite structures. The bridge molecule and the metals are all described with tight-binding Hamiltonians. We vary the sulfur-to-sulfur separation distance in -S- (CH2)8 -S- and, at each of these separations, compute the family of thermally accessible conformrs. The tunneling current is predicted to decay exponentially with a decay parameter of ∼1.0 A-1 based on the tip to substrate distance. This observation supports the notion that the most strongly coupled conformers in the ensemble dominate the STM tunneling currents.; We also studied interprotein electron transfer from cytochrome c2 of Rhodobacter capsulatus to the photosynthetic reaction center of Rhodobacter sphaeroides in native and mutated systems. Brownian dynamics, which is used to sample the docking geometories of the two-protein system, is used with an exponential distance-dependent electron-transfer rate model to compute biomolecular rate constants. And the results are consistent with experimental data when reasonable prefactors and decay constants are used.; Finally; we modeled electron tunneling between proteins across an aqueous interface. Molecular dynamics is used to sample the conformations of a cytochrome b5 self-exchange system. The conformation ally averaged electronic couplings are calculated at the extended-Huckel level. The results indicate three distinct tunneling-mediation regimes: a protein-coupled regime at contact, a structured water mediated regime at small inter-protein distances, and a bulk-water regime at larger distances. Each regime has a characteristic dependence of coupling on distance. This multi-exponential coupling strongly impacts observable rates.
机译：本文共分四个部分：第一章是绪论和研究背景。第2章研究了在牵引柔性分子时隧穿电流对构象和端对端距离的依赖性。第3章利用布朗动力学模拟了细胞色素c2与细菌光合作用反应中心之间的电子转移。第4章详细研究了溶剂对蛋白质间电子转移的影响。多数分子在室温下可进入各种构象。研究电子通过各种介质传输的构象依赖性。我们使用由一个在模型尖端和基质之间架桥的单个软小分子介导的简单隧道模型，探索了构象自由度对隧道电流的影响。尖端和基底被描述为半无限结构。用紧密结合的哈密顿量描述了桥分子和金属。我们在-S-（CH2）8 -S-中改变硫与硫的分离距离，并在每个分离中计算出热可及构象族。预测隧道电流将基于尖端到基板的距离以〜1.0 A-1的衰减参数呈指数衰减。该观察结果支持这样的观点，即整体中耦合最强的构象异构体支配着STM隧道电流。我们还研究了从荚膜红细菌的细胞色素c2到球形和球形系统中球形红细菌的光合反应中心的蛋白间电子转移。布朗动力学用于采样两种蛋白质系统的对接几何，与指数距离相关的电子传输速率模型一起用于计算生物分子速率常数。当使用合理的前置因子和衰减常数时，结果与实验数据一致。最后;我们模拟了跨水界面的蛋白质之间的电子隧穿。分子动力学用于对细胞色素b5自交换系统的构象进行采样。构型平均电子耦合在扩展的Huckel级别上计算。结果表明三种截然不同的隧穿调节机制：接触时的蛋白质偶联机制，较小的蛋白质间距离的结构化水介导机制和较大距离的散装水机制。每种方式都具有耦合对距离的特征依赖性。这种多指数耦合强烈影响可观察速率。

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