Page - 101 - in Charge Transport in DNA - Insights from Simulations

7.4ChargeTransferExtensions Theobtainedrelaxationfunctiononlycoversadropof the IPofabout2.5eVwithin the initial100 fs followingaCTevent. Comparisonwiththedata intable7.4 reveals amissing portion of the relaxation amounting to 0.9 eV,which has to occur for a fully localized charge. Until now, the obtained relaxation function is scaled up to account for the larger decrease of the IP. This clearly is an issue in theCTmodel that requires a solution. Thework on thedescription of this additional relaxation ona longer time scale isunderwaypresently. TheHubbardMatrix Also, a Hubbard matrix is needed for CT simulations. This matrix contains the relevantparameters toestimate theenergychangeduetodifferenton-siteelectron– electrons interactions aswell as due to relaxation and rotation of orbitals. In this CTmodel, theHubbardmatrix dependsonly on the input sequence. Therefore, it is set uponlyonce at thebeginningand is kept for the rest of the simulation. It is built fromtwocomponents: First, thediagonal elementsare theHubbardparametersof eachnucleobase.Here, theHubbardparameters of guanine andadenine are implementedasfixedvalues obtained fromDFTB2 calculations; theyamount to5.66eVforguanineand5.58eV for adenine. Second, the off-diagonal elements take the form 1rij, where rij is the distance be- tween the centers of mass (COM) of the neighboring nucleobases. These off- diagonal elements have been calculated asmean values for every possible nucle- obase step. MD simulations of 20 ns were performed and the distances of the COMof the purine nucleobaseswere recorded. Table 7.5 shows themean values for the ten different base-pair steps. Notably, difference is found between intra- and interstranddistances. Table7.5: Mean values of theCOMdistances for the base-pair steps from 20nsMD simulations. X\Y–purine–pyrimidinestep,X/Y–pyrimidine–purinestep, X|Y–purine–purine step. Step A|A A/A A\A A|G G|A G/A A\G G|G G/G G\G Distance [nm] 0.3851 0.6940 0.5221 0.4144 0.3783 0.5238 0.6364 0.4142 0.6724 0.5109 101