Page - 28 - in Charge Transport in DNA - Insights from Simulations

TheoreticalBackground Inthesimplestapproachtopropagatethiswave-functionnowistoperformaBorn– Oppenheimer simulation.Here theHamiltonian isdiagonalized toyield thewave- function coefficients am directly. But, thewave-function can also be propagatedwithmore sophisticated non-adia- batic schemes,whichwill bedescribed in the followingchapter2.6. Application toDNA Thepartof theDNAwhichis theeasiest tooxidizearethenucleobases,particularly thepurinesadenine (A)andguanine (G).Guaninehas the lowest ionizationpoten- tialofallnucleobaseswhile theIPofadenine is0.4eVhigher[77,78]. Sincecytosine (C) and thymine (T) have an ionization potential about 1 eV higher, G andA are supposed tobe thechargecarryingsites inDNAincaseofhole transport/transfer. Therefore, the hole transfer inDNA in thismodel occurs between theHOMOof guanine and adenine nucleobases, which form a linear chain of charge carrying sites. Issueswith thisQM/MMapproach Thismulti-scale approach suffers from certain issues. Someof themare resulting fromtheassumptionsmade, andsomeare inherent to theappliedmethods. Firstly, the treatment of the single fragments involves approximations that require discussion. When thepoint charges of theMMsystemareupdated after a stepof dynamics, theCoulomb interactions of those atomsdo change. But, these interac- tions are not evaluated for neighbors andnext-neighbors in theMMcalculations. Thisway, thechangeofCoulombinteractions isneglectednearlycompletely.More- over, theparametersof thebondsandanglesdonot changeeitheras theyarefixed values of the used force-field. This way, the inner-sphere reorganization energy (RE, see also chapter 2.6.1) is neglected completely. To account for this essential flaw, the inner-sphereRE is introduced as an empirical contribution to the energy of the system.Quantumchemical calculationsyieldavalue forλi of about0.23 eV for adenineandguanine [79]. 28