Estimate of the Reorganization Energy for Charge Transfer in DNA

Abstract

The solvent reorganization energy λs 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 λs and the resulting effective contribution β s to the falloff parameter β 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 λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs 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. λs was calculated to increase rapidly at small R DA values (<15 Å), and accordingly the falloff parameter β s (defined as a local function of R DA) decreases appreciably with increasing R DA (from 1.0 Å-1 with only one intermediate base pair between D and A to 0.15 Å-1 for systems with five intervening pairs). Calculated λs values were accurately fitted (standard deviation of ∼0.5 kcal/mol) to a linear function of 1/R DA, including all cases except contact (R DA = 3.4 Å), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(−βs R DA)) gave comparable accuracy for the entire R DA range. λs based on D and A holes delocalized over two adjacent guanine bases was uniformly ∼12 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.

Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects

“…This model appears to be rather crude, and it is not supported by the results of moleculardynamics simulations of DNA 18,19 or even by the more extended electrostatic models using a heterogeneous dielectric medium. 2,[6][7][8] As expected, the calculation carried out using 0 = 1 = 2 = 1.0 leads to quite delocalized hole states in ͑GC͒ n . For instance, we obtain that in ͑GC͒ 5 q 0 = 0.476, q ±1 = 0.251, q ±2 = 0.011.…”

“…For instance, to estimate the reorganization energy for hole transfer in DNA, one applied the Poisson equation solver 6 to heterogeneous dielectric models consisting of several different dielectric zones surrounding the hole donor and acceptor sites. 2,5,7,8 The calculation results are quite different because of uncertainties concerning the construction of the dielectric model. 8 The surrounding polar medium affects also the delocalization of an electron hole in DNA over adjacent base pairs.…”

“…2,5,7,8 The calculation results are quite different because of uncertainties concerning the construction of the dielectric model. 8 The surrounding polar medium affects also the delocalization of an electron hole in DNA over adjacent base pairs. There has been an interesting discussion as to whether the hole charge in DNA is confined to a single base pair or delocalized over several adjacent base pairs ͑see, for instance, Ref.…”

Activation entropy of electron transfer reactions

“…The heterogeneous nature of the solvent in the vicinity of a redox site can in principle * E-mail:dmitrym@asu.edu. † E-mail:newton@bnl.gov be included by assigning different dielectric constants to its heterogeneous parts [8]. Two fundamental problems inevitably arise in this algorithm.…”

The Kinetics of Charge Recombination in DNA Hairpins Controlled by Counterions

“…In principle, based on the ionization potentials of DNA bases calculated in a vacuum [14,15,16], one should expect that the hole tunnels through the adjacent adenine bases rather than the thymine bases because the adenine ionization potential is lower by about 1eV. However, the real situation is complicated by the dissolution of DNA in water, which can affect ionization potential.…”