Page - 24 - in Charge Transport in DNA - Insights from Simulations

TheoreticalBackground 2.4 DynamicsofExcessCharge inDNA Inspiteofexcessiveresearch in thefieldofchargemigrationthroughbiomolecules, especially through DNA, no unified explanation of the microscopic mechanisms has been found until now. Two basic concepts regarding the dynamics of charge have been established, the charge transport and the charge transfer. The former, is the physicist’s approachwhichdescribes the ability ofDNA to support electric current. The latter is the chemical (physics) approach of charge transfer inDNA involvingmulti-stephoppingprocesses. Eitherway, thecomputationalmodelusedforchargetransport/transferdescription in DNA has to fulfill several requirements. Firstly, the computational efficiency has to be high enough to take dynamic effects on the nanosecond timescale into account. Secondly, ithas tobeable toreproducetheresultsofhigher-levelmethods inaqualitativeway. Thefirst conceptused in thisworkwillbe thecalculationofcharge transportprop- ertieswithQMmethodsonstructuralensemblesoriginatingfromMDsimulations. In this case, themolecular structure is simulatedwithout the chargeactuallybeing in the system. Thus, the structure and dynamics of the molecule are unaffected by the charge in the system. TheCTproperties are calculated on these “neutral” structures over several thousand snapshots. This provides an insight into the dy- namics ofCT efficiency. This previously developedmulti-scale framework for the dynamic calculation of charge transport properties [45] has already been applied successfully to fullyhydratedDNAspecies ina free state.[44,69,70] In the secondpart,mechanismsof charge transferwill be introduced. Theclassical description of charge transfer inmolecular systems in apolarizablemediumgoes back to the theory ofMarcus [71]. First, the general concept and the neededCT parameterswill be introduced. Then, the computational approaches used in this work will be presented. The computation of charge transfer here is based on a direct combination of force field andquantummethods. TheMMenvironment is influenced by the charge residing on the nucleobases and reacts accordingly. To make such an approach computationally efficient, several assumptions have to be made, whichwill be described in detail. The basics of thismulti-scale approach have recently beendescribedbyT.Kubarˇ andM.Elstner[72, 73] andwill be sum- marized in this thesis. 24