Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details.

Abstract

The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an "on-the-fly" calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical-molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor-bridge-acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the "full" atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.