Page - 25 - in Charge Transport in DNA - Insights from Simulations

2.4DynamicsofExcessCharge inDNA Figure2.1: Typical QM/MM system of DNA in water environment. The water molecules (blue spheres), the ions (orange spheres) and the backbone of the DNAare calculated classicallywith force fieldmethods. Thepurinenucle- obases involved in the CT process (shown in green) are treated quantum chemically. 2.4.1 TheMulti-ScaleFramework The general issue of computation of CT in large systems is that QCmethods are needed todescribe thedynamics of thewave functionof the excess charge. High- level electronic structure calculations can only describe tens of atoms over short periodson thepicosecondtimescale. QCmethods likeDFTaremorecomputation- allyefficientandthereforecandescribelargersystemsuptohundredsofatoms,but still only forvery shortperiodsof time. So, a reasonableapproach in thisquest for computational efficiency is to use approximativeQCmethods likeDFTB2, which areable todescribehundredsofatomsonthenanosecondtimescale. Still, for large molecular systems likeDNAinasolventorawholeprotein, thepartof the system which is described with these QCmethods has to be restricted. A sophisticated solution to this is a QM/MM scheme where a small QM region is defined and treatedwithQC,while the rest of the system is treated classicallywithMMforce fieldmethods. Figure 2.1 shows aDNAdouble helix inwater environment. Thewater, the ions and the DNA backbone are treated classically, while the purine bases (shown in green) are treatedwithQMmethods. This way, the QM region is being influenced by the MM environment and vice versa. See figure 2.2 for an overview of the computational framework. Shown are theQMandMMcalculation steps and theparameters communicatedbetween 25