Modeling Charge Transport Through Biological Molecules with Transition Metals

Abstract

In this work the electronic structure of nucleic acids (modified DNA) and proteins are modeled with a focus on incorporation of transition metals. Building on previous work, experimental data has been combined with molecular mechanics methods, density functional theory calculations, and Green’s function methods to model charge transport through these structures as well as electronic behavior in varying environments. Addition of transition metals poses new challenges at each one of these steps, owing to the d-orbital interactions with coordinating ligands and the possibility of ground states with unpaired spin, which was explored in the analysis of two different systems. The first system was a metal-modified DNA structure, using modified base pairs to intercalate silver, mercury, and gold ions. Electronic structure calculations show that the intercalated metals create isolated valence states that can assist electron transport along the DNA strand. For structure generation in this system, a combination of ab-initio methods and generated molecular dynamics force fields were used to model interactions with the coordinated metal. The second system modeled was the OmcS cytochrome, which contains heme-coordinated Fe centers that can exist at multiple oxidation states. Therefore, a spin-dependent model must be used, resulting in spin-dependence of charge transport in the oxidized state, shown in both hopping models and Green’s function decoherent models. A non-collinear spin model was also developed, showing that the spin-orbit coupling from the contact influences the spin-dependence of transport.