Static and dynamic aspects of DNA charge transfer: a theoretical perspective

Abstract

In this work, we approach the impact of dynamic and static disorder on DNA charge transfer from a theoretical and numerical perspective. Disordered or defect geometries are either realized via molecular dynamics simulations using a classical force field or by experimentally determined DNA bulge structures. We apply a chemically specific, atomically resolved extended Su-Schrieffer-Heeger model to compute the energy parameters relevant to DNA charge transfer. For both models studied here, the effective donor-acceptor couplings--and hence the charge transfer rates--significantly depend upon the geometry. Dynamic disorder leads to a correlation time in this quantity of the order of 30 fs, and the transfer rates universally exhibit a broad, yet well-defined, exponential distribution. For DNA bulges, the angle characterizing the defect controls the charge transfer efficiency. The results are discussed and extensively compared to experimental findings and other calculations.

Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

“…The effects of DNA conformational dynamics on the efficiency of HT have also been considered from different points of view. [10][11][12][13][14][15][16][17][18][19][20] The obtained results suggest that the electronic couplings found for idealized B-DNA ͑Refs. 21-23͒ may substantially differ from the corresponding values averaged over thermally accessible DNA configurations, and therefore, a combined quantum mechanical/ molecular dynamic ͑QM/MD͒ approach should be used to obtain more accurate estimates of the electronic couplings.…”

Charge dynamics through pi-stacked arrays of conjugated molecules: effect of dynamic disorder in different transport/transfer regimes

“…The large amplitude of the computed fluctuations in the Hamiltonian makes it difficult to consider the electronic structure of DNA anyhow related to that of an idealized or 'averaged' structure. A similar observation was made also in other studies [14][15][16] and it is consistent with the variability of the intermolecular coupling computed using a set of crystallographic (static) structures. [11] The effect of these fluctuations on the electron dynamics depends on the charge transport mechanism, but there is not a consensus on the actual transport mechanism of positive charge in DNA and several contrasting hypotheses have been formulated.…”

“…Several authors [16,29,30,40] have evaluated (0) k and (2) k from eq. 10-11 and found that the correction is typically very small ( (2) k <0.1 (0) k ).…”

Direct Simulation of Electron Transfer Reactions in DNA Radical Cations

“…The Δ ij are tight binding hopping matrix elements, which are non-zero only for atoms bonded to each other. Tight-binding parameters from the previous work of Cramer et al were used in this study (Table 1),36 together with their description of base stacking interactions based on empirical functions for the overlap of p z -orbitals in arbitrary spatial relationships 26…”