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.

Effect of solvent polarization on the reorganization energy of electron transfer from molecular dynamics simulations.

The solvent contribution lambda(s) to the reorganization energy of electron transfer can be estimated from averages of the potential energy gaps between neutral-pair and ion-pair states over an ensemble of structures generated from molecular dynamics simulations. Invoking a Marcus-type two-sphere model for charge separation and recombination in an aqueous environment, we explored the effect of a polarizable force field and noted a strong reduction of lambda(s) (by approximately 45%) compared to the corresponding value obtained with a standard nonpolarizable force field. Both types of force fields yield lambda(s) values that in agreement with the Marcus theory, vary strictly linearly with the inverse of the donor-acceptor distance; the corresponding slopes translate into appropriate effective optical dielectric constants, epsilon(infinity) approximately 1.0+/-0.2 for a nonpolarizable and epsilon(infinity) approximately 1.7+/-0.4 for a polarizable force field. The reduction in the solvent reorganization energy due to a polarizable force field translates into a scaling factor that is essentially independent of the donor-acceptor distance. The corresponding effective optical dielectric constant, epsilon(infinity) approximately 1.80, is in excellent agreement with experiment for water.

Structure of rhodamine 6G-DNA complexes from molecular dynamics simulations.

Chromophore-DNA complexes are useful for understanding charge transport along pi-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other.

Molecular-dynamics simulations of pyronine 6G and rhodamine 6G dimers in aqueous solution.

We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.