Page - 26 - in Charge Transport in DNA - Insights from Simulations

TheoreticalBackground Figure2.2: Overview of the steps in the multi-scale approach. The MM simula- tion generates the structure of the molecule. This is passed to the QM calculation, performed with DFTB2, which generates the Hamiltonian. This Hamiltonian can be used for charge transport calculations with the Landauer–Büttiker theory. Or, thewave-function is propagated by the the mean-field (Ehrenfest) or the surface hoppingmethod. Finally, the atomic charges in theMMsystemareupdated according to thewave-function. the calculations. This interaction is crucial for the description of charge transfer in biomolecular systems and cannot be neglected. The next step in this approach is to reduce the necessary amount of computation time for the still largeQM re- gion. Charge transfer is supposed to occur only via the frontier orbitals of the in- volvedmolecules. In thecaseofholemigration inDNA,only thehighest-occupied molecular-orbitals (HOMO) of the purine bases are treated explicitly. This can be seen as a fragment-orbital approach where a part of the electronic structure is frozen and treated implicitly like the σ and π separation in theHückel theory [74,75]. 2.4.2 TheFragmentOrbitalApproach To achieve a reasonable computational efficiency, aQM/MMmodel is introduced where only the excess charge is calculatedwithQMmethodswhile the rest of the molecule is treatedwith classicalMMmethods. Thegeneral idea is todecompose the system into M spatially non-overlapping fragments. With this assumption, it ispossible toperformseparateQMcalculationsof every fragment. Thisprocedure 26