Page - 86 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inMicrohydratedDNA Figure6.4: Reorganization energy for hole transfer from one nucleobase to another across 0–3 intervening ones in theAAoligo in the various environments. (Shaded area – std. dev.) next neighbor transfer may be an undersampling artifact. It is truly astonishing to see that the RE is little affected by the removal of certain (large) amounts of water around theDNA. Still, the removal of the innermost hydration shellwould presumably have a large impact on the RE.However, this is a setup forwhich it seems tobenearly impossible to achieve sufficient sampling inanMDsimulation. Therefore, driedDNA (as long as not toomuchwater is removed so that a stable helical structure is retained) seems tohaveverysimilar charge transportproperties as fully solvatedDNA.TheECand the IP are nearly identical, and theRE is very similar. Therefore,averysimilarconductivity(chargemobility)ofDNAforeither transport mechanism, tunnelingorhopping, is expected. 6.4 DirectDynamicsofChargeTransfer To prove this point, charge transfer simulations using a time-dependent scheme, were performed, thereby extending Landauer’s coherent transport picture. See chapter2.6.2 fordetails on theusedcharge transfermethods. Here,hole transfer in thecentralpentanucleotideof theAGoligowasstudied. Ten simulations of 1 nswere performed for the fully hydrated and theDry1 systems 86