Solvent reorganization energies in A-DNA, B-DNA, and rhodamine 6G-DNA complexes from molecular dynamics simulations with a polarizable force field.
We estimate solvent reorganization energies lambda(s) of electron transfer (ET) in DNA stacks between positively charged guanine (acceptor) and neutral guanine (donor), as well as in rhodamine 6G (R6G)-DNA complexes between R6G (acceptor) and neutral guanine (donor) from molecular dynamics simulations that used a polarizable force field in combination with a polarizable water model. We compare results from the polarizable scheme with those from a common nonpolarizable analogue. We also discuss the influence of charge sets, separate contributions of solute and solvent electronic polarizations, and partial contributions of different molecular groups to changes of lambda(s) due to electronic polarization. Independent of donor-acceptor distances, solvent reorganization energies of ET processes in DNA duplexes from a polarizable force field are about 30% smaller than the corresponding results from a nonpolarizable force field. The effective optical dielectric constant epsilon(infinity) = 1.5, extracted from pertinent scaling factors, is also independent of the donor-acceptor separation over a wide range of distances, from 3.4 to 50.0 A. Reorganization energies calculated with the polarizable force field agree satisfactorily with experimental data for DNA duplexes. Comparison of results for A-DNA and B-DNA forms as well as for the conformational alignment of the dye relative to the duplex in R6G-DNA complexes demonstrates that the conformation of a duplex hardly affects lambda(s). Among these DNA-related systems, the effective parameter epsilon(infinity) is remarkably constant over a broad range of donor-acceptor distances.
Vladimirov
Egor
E
Department Chemie, Technische Universitat Munchen, Garching, Germany.
Ivanova
Anela
A
Rösch
Notker
N
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D012235:Rhodamines / Q000737:chemistry*; D012680:Sensitivity and Specificity; D012997:Solvents / Q000737:chemistry*
D012235:Rhodamines; D012997:Solvents; C026188:rhodamine 6G; D004247:DNA