Page - 83 - in Charge Transport in DNA - Insights from Simulations

6.2ChargeTransferParameters Figure6.2: Distributions of the distances ofNa+ ions and phosphate groups from the nucleobases in theAAoligo. To explain this, the distances of theNa+ ions aswell as of the phosphate groups in thebackbones (whichare theonlychargedgroups in thesystem) fromtheDNA helical axiswere calculated. Thehelical axiswas obtained for everyMDsnapshot with the SCHNAaP algorithm implemented in 3DNA.[107, 126] The probability distributions of these distances are shown in Fig. 6.2. See appendix B.5 for val- ues of all groups asmeanvalues over time andatoms for thedifferent sequences. Apparently, as the amount of water in the system decreases, both the ions and thephosphategroups approach closer to theprobednucleobase. This is notunex- pected for theNa+ ions as these are confined to theDNAhydration shell, which becomesmore restricted spatially upon thepartial removal ofwater. Remarkably, the structure of the DNA changes in away that the phosphate groups approach closer to thenucleobases, too, contributing to the overall ESP in the oppositeway. As for theESP component due towater,which reduces effectively upondehydra- tion, themost likely interpretation is that theDNAhydration shell is affected by theapproachingNa+ ions. Thus, thewatermoleculeshavea largerpositivecharge to shield, and the decreasing ESP corresponds actually to increasing negative po- larization rather thandepolarization. Summarizing the findings so far, there are two distinct effects of dehydration on the electronic structure. First, the change of geometrical structure of DNA due to desolvation leads to a change of the EC,which are not affected by the solvent substantially. On the other hand, the IP are affected largely not by the structure of nucleobases andbasepairs, rathermostly by thefluctuations of theESPdue to solvent dynamics. These solvent fluctuationswere shown to have amajor impact onDNA conductivity,[44] therefore, a similar solvent effect onDry1 andDry2 is expectedas found for the fullyhydratedDNA.[44] 83