TCBG Seminar

“A coarse grained QM/MM approach for the description of charge transfer in DNA and E. coli Photolyase”

Prof. Dr. Marcus Elstner
Karlsruhe Institute of Technology
Institute of Physical Chemistry
Karlsruhe, Germany

Friday, June 7, 2013
3:00 pm (CT)
3269 Beckman Institute


Charge transfer in DNA has received much attention in the last years due to its role in oxidative damage and repair in DNA, but also due to possible applications of DNA in nano- electronics. Despite intense experimental and theoretical efforts, the mechanism underlying long range hole transport is still unresolved. This is in particular due to the fact, that charge transfer sensitively depends on the complex structure and dynamics of DNA and the interaction with the solvent environment, which could not be addressed adequately in the modeling approaches up to now. We present a new computational strategy to evaluate the charge-transfer (CT) parameters for hole transfer in complex systems. Based on a fragment orbital approach, site energies and coupling integrals for a coarse grained tight binding description of the electronic structure can be rapidly calculated using the approximate Density Functional method SCC-DFTB . Environmental effects are captured using a combined quantum mechanics/molecular mechanics (QM/MM) coupling scheme and dynamical effects are included by evaluating these CT parameters along extensive classical molecular dynamics (MD) simulations. This methodology allows to analyze in detail several factors responsible for CT in DNA. Using this methodology, the time course of the hole can be followed by propagating the hole wave function using the time dependent Schrödinger equation for the coarse grained Hamiltonian. The photoactivation of E. coli Photolyase involves, after photoexcitation of the chromophor and energy transfer to FAD, a long range hole transfer along a chain of Trp residues. Since this process could not be modeled using Marcus theory with parameters computed with classical equilibrium MD simulations, we used fully coupled nonadiabatic (Ehrenfest) quantum mechanics/molecular mechanics (QM/MM) simulations. Charge transfer rates are in excellent agreement with experimental data and the simulations provide a more detailed picture of electron transfer than a classical analysis of Marcus parameters. The protein and solvent both strongly influence the localization and transport properties of a positive charge, but the directionality of the process is mainly caused by solvent polarization. The time scales of charge movement, delocalization, protein relaxation and solvent reorganization overlap and lead to nonequilibrium reaction conditions.

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