Estimate of the reorganization energy for charge transfer in DNA

The solvent reorganization energy lambda(s) can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)-acceptor (A) distance R-DA. To estimate lambda(s) and the resulting effective contribution beta(5) to the falloff parameter beta for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5'-GGGT(n)GGG-3', in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on As were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of lambda(s) were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. lambda(s) was calculated to increase rapidly at small RDA values (< 15 A), and accordingly the falloff parameter lambda(s) (defined as a local function of R-DA) decreases appreciably with increasing R-DA (from 1.0 Angstrom(-1) with only one intermediate base pair between D and A to 0.15 Angstrom(-1) for systems with five intervening pairs). Calculated As values were accurately fitted (standard deviation of similar to0.5 kcal/mol) to a linear function of 1/R-DA, including all cases except contact (R-DA = 3.4 Angstrom), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(-beta(s)R(DA))) gave comparable accuracy for the entire R-DA range. lambda(s) based on D and A holes delocalized over two adjacent guanine bases was uniformly similar to12 kcal/mol smaller than the corresponding results for holes localized on single guanines, almost independent of R-DA. The internal reorganization energy for hole transfer between GC pairs was calculated at 16.6 kcal/mol at the B3LYP/6-31G* level.