Influence of water and ions on the electronic structure and charge transfer in DNA and PNA

PHYS 269

Shahar Keinan, shahar@duke.edu1, Alexander Balaeff, abalaeff@duke.edu1, Ravindra Venkatramani, ravindra.venkatramani@duke.edu1, Elizabeth R Hatcher, ehatcher@outerbanks.umaryland.edu2, and David N. Beratan, david.beratan@duke.edu1. (1) Department of Chemistry, Duke University, Durham, NC 27708, (2) Department of Pharmaceutical Sciences, University of Maryland, 20 Penn St., Baltimore, MD 21201
Understanding charge transfer in deoxyribonucleic acid (DNA) and peptide nucleic acid (PNA) may be useful in future nanotechnology applications, as well as in understanding biological DNA damage and repair mechanisms. The dynamical nature of DNA and its environment (water, counterions) complicates the charge transfer mechanism. Molecular dynamics simulations were used to generate ensembles of double-stranded DNA and PNA conformations. The electronic structure of the generated conformations was calculated using QM methods, and the role of solvent and ions was investigated. It was found that including solvent is crucial for calculating the coupling element, but insufficient amount of water can incur very large errors, Figure 1. We also study the influence of the water model (implicit, as point charges or explicit) and the importance of including ions.