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We estimate solvent reorganization energies λsof 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 λsdue 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 ε̃∞= 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 Å. 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 λs. Among these DNA-related systems, the effective parameter ε̃∞is remarkably constant over a broad range of donor−acceptor distances. [ABSTRACT FROM AUTHOR]

The electronic coupling is one of the key parameters governing electron hole transfer along DNA helices. In this study, we established the first comprehensive data base of electronic coupling elements, calculated at the ab initiolevel. The data set comprises allpossible Watson−Crick base pair dimers, both in standard A-DNA and B-DNA geometries. We also quantified the sensitivity of the coupling elements with respect to geometry changes by varying each of the six standard base step parameters, which specify the relative orientation of neighboring base pairs. We compare the couplings in a systematic way by discussing variations in the coupling magnitude due to geometry or nucleotide sequence in the dimer, and we analyze how the structure affects the electronic coupling in terms of general and dimer-specific trends. Furthermore, we studied how the coupling changes when one introduces the chemically modified base 7-deazaguanine in the corresponding base-pair dimers. Finally, on the basis of the calculated coupling elements, we suggest a model duplex with an enhanced capacity for hole transfer. [ABSTRACT FROM AUTHOR]

Chromophore−DNA complexes are useful for understanding charge transport along -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. [ABSTRACT FROM AUTHOR]

Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3‘-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol. [ABSTRACT FROM AUTHOR]

Atomistic modeling of insoluble monolayers is currently used to inspect their organization and electric characteristics, providing a link between theory and experiment. Extensive molecular dynamics simulations at 300 K were carried out for model films of the lipids dipalmitoylphosphatidylcholine (DPPC) and dicaprin (DC) at the air/water interface. Surface concentrations corresponding to a set of points along the surface pressure/area isotherms of the surfactants were considered. The models contained 25 or 81 lipid molecules in hexagonal arrangement and explicit aqueous media (TIP3P) treated in periodic boundary conditions. Molecular dynamics simulations based on a classical force field (CHARMM27) were carried out and key characteristics of the studied films were estimated. The dielectric properties of the films in normal and tangential direction were quantified by means of dipole moment magnitude and orientation analysis and by monolayer dielectric permittivity. The contributions of lipids and interfacial water to each component of the considered characteristics were assessed and their variations upon film compression were discussed and compared for the two monolayers and to earlier results. The dielectric permittivity tensors were analyzed. Electrostatic potential profiles across the layers and surface pressure values were used for more detailed clarification of experimental measurements. The results show dissimilar behavior of the two lipids at the air−water interface. While the average electric and dielectric properties of DPPC monolayers result from opposite surfactant and water contributions, the two subsystems are synergetic in the DC films. The anisotropy of the monolayer dipole moment and dielectric permittivity is explained by domination of a different subsystem in the various components. Tangential characteristics turn out to be more sensitive to the size of the model and to the degree of film compression. [ABSTRACT FROM AUTHOR]

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided. [ABSTRACT FROM AUTHOR]