Page - 29 - in Charge Transport in DNA - Insights from Simulations

2.5ChargeTransport inDNA Secondly, the interactions between the single fragments should changewhen the point chargesareupdated.Here, theCoulomb interactionsare coveredby theMM calculation. What ismissing is the change in the van-der-Waals parameters of the fragments. Thesearefixedvalues inaforce-fieldmethodanddonotchangeduring asimulation. As theseeffectsareverysmall, it is likely that this effect isnegligible. Andfinally, the polarization of the environment is not covered completely by the reorientationof themolecules alone. The electric-chargedensity is representedby the MM point charges, while the electronic polarization is not considered in the force-field used. This is a crucial point, because the fluctuations of the IP of the fragments are overestimated in such a non-polarizable force-field. As an efficient and reliable implementation of a polarizable force-field is not available, a simple scaling of the electronic interaction is performed to reduce the energy barriers of CT. In theusedTIP3Pwater environment, these interactions are overestimatedby 26-34%[80], thereforeQM/MMinteractionsarescaleddownbya factorof1.5 [73]. 2.5 ChargeTransport inDNA 2.5.1 Landauer–BüttikerFramework The method for charge transport calculations used in this work is based on the Landauer–Büttiker framework. This method represents the physicist’s view of a coherent charge transport throughasystem. TheCTparameters areobtainedwith thepresentedmulti-scale framework andused to calculate transmission functions for singleMDsnapshot structures. Toaccount fordynamicfluctuations, thousands ofsnapshotsfromMDsimulationswillbeaveragedover.Withthissetup,aninsight into the dynamic charge transport properties of the investigated systems will be obtained. Asdescribedpreviously, only thehighest occupiedmolecular orbitals (HOMO)of the purine baseswere considered as states participating in hole transport. While this choice isa justifiedfirstapproximation, theapplicationofhighervoltagecould makeother states accessible, for instance loweroccupiedorbitals of thepurines or orbitals of thepyrimidines [81,82]Note further that transport of excess electron is not taken intoaccountwith this approach. 29