title: Effect of structural dynamics on charge transfer in DNA hairpins.
abstract: We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studied by a combination of molecular dynamics simulations of the structural dynamics and density functional theory calculations of charge transfer integrals and orbital energies. The fluctuations in both parameters were found to be substantial and to occur on subpicosecond time scales. Tight-binding calculations of the dynamics of charge transfer show that for short DNA hairpins (<4 base pairs) the charge moves by a single-step superexchange mechanism with a relatively strong distance dependence. For longer hairpins, a crossover to a fluctuation-assisted incoherent mechanism was found. Analysis of the charge distribution during the charge transfer process indicates that for longer bridges substantial charge density builds up on the bridge, but this charge density is mostly confined to the adenine next to the hole donor. This is caused by the electrostatic interaction between the hole on the AT bridge and the negative charge on the hole donor. We conclude both that the relatively strong distance dependence for short bridges is mostly due to this electrostatic interaction and that structural fluctuations play a critical role in the charge transfer, especially for longer bridge lengths.
authors.affiliation: Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands. f.c.grozema@tudelft.nl
authors.forename: Ferdinand C
authors.initials: FC
authors.lastname: Grozema
authors.forename: Stefano
authors.initials: S
authors.lastname: Tonzani
authors.forename: Yuri A
authors.initials: YA
authors.lastname: Berlin
authors.forename: George C
authors.initials: GC
authors.lastname: Schatz
authors.forename: Laurens D A
authors.initials: LD
authors.lastname: Siebbeles
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ratner
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D011336:Probability; D055672:Static Electricity; D013267:Stilbenes / Q000737:chemistry
chemical_list: D007477:Ions; D013267:Stilbenes; D004247:DNA