Computation of electron transfer in proteins: Method development and applications to cytochrome c oxidase and DNA photolyase

In this thesis, theoretical and computational methods are presented that are being developed and used for the analysis of long-range electron transfer reactions in chemical and biological systems with complex structural organization. Applications are given for electron transfer reactions in proteins. In part I we discuss importance of electron and proton transfer reactions. In part II, we give a short introduction to the general theory of electron transfer reactions. In part III, we discuss some theoretical methods and their computational implementation for the calculation of the electronic coupling matrix element in proteins within a one-electron picture. Further, results of molecular dynamics simulations of the protein medium during the tunneling event are presented which show that the tunneling matrix element is a sensitive function of the atomic configuration of the part of the protein matrix in which tunneling currents are localized (non-Condon effects). It is shown that knowledge of electron transfer matrix element may lead to conclusions about other aspects of structure and functioning of systems in question, in our example we are able to draw conclusions about geometry of a complex system which is not known otherwise. It is also demonstrated that traditional methods of theoretical physical chemistry can be successfully combined with methods of seemingly unrelated disciplines, in our case genomics, to give better insight into complex biochemical processes. Finally, in part IV some recent theoretical developments in the theory of electron transfer are presented, while in part V efficient methods of solution of partial differential equations important for electron and proton transfer are described.