Is MD Geometry Sampling Sufficient for Nucleobase Electronic Structure Analysis of ET Reactions? Comparing Classical MD and QM/MM Methods
journal contributionposted on 2010-12-09, 00:00 authored by Shahar Keinan, Ravindra Venkatramani, Alexander Balaeff, David N. Beratan
It has been shown in many experimental studies that one of the major charge-transfer mechanisms in nucleic acids is that by positive charge carriers (holes), residing predominantly on G bases. Theoretical charge-transfer calculations often use Koopmans’ theorem to approximate the relaxed doublet cation hole energies from simulations of the neutral ground state (GS). An assumption in these calculations is that the geometry and interactions of the doublet cation (DC) hole with the solvent is the same as that for the neutral GS. Here, we simulate the DC hole on solvated G and A nucleobases using combined quantum mechanics/molecular mechanics (QM/MM) methods and compare the geometries and electronic structure of the charged bases to those of the neutral bases. We also study the effects of the solvent environment on the nucleobase electronic structure and estimate the size of the smallest solvent shell that needs to be included in order to achieve convergence of the nucleobase energy levels. We find that Koopmans’ theorem based methods provide a satisfactory description of the nucleobase energy levels, with the largest deviation (∼0.1eV) for charged bases in explicit water. We also find that the size of the solvent shell is crucial for describing the nucleobase electronic structure. When the solvent is properly accounted for, we find that the average energy separation between the hole energy levels on isolated G and A is ∼0.2 eV, and the hole energy levels fluctuate by ∼0.3 eV. These findings suggest important corrections to earlier theoretical studies that overestimated the hole energy separation among nucleobases and underestimated or neglected the base energy distribution due to thermal fluctuations of the nucleobases and their environment. Our results further suggest that hopping charge transport plays an important role even at short distances.
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Classical MDDC holeMD Geometry SamplingGScharge carriersdoublet cationhole energy separationeVenergy separationnucleobase energy levelsdoublet cation hole energieshole energy levelsbase energy distributionG basescharge transportground statesolvated GET ReactionsNucleobase Electronic Structure AnalysisQM