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

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.