title: Localization of a hole on an adenine-thymine radical cation in B-form DNA in water.
abstract: A quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation has been carried out using CP2K for a hole introduced into a B-form DNA molecule consisting of 10 adenine-thymine (A/T) pairs in water. At the beginning of the simulation, the hole wave function is extended over several adenines. Within 20-25 fs, the hole wave function contracts so that it is localized on a single A. At 300 K, it stays on this A for the length of the simulation, several hundred fs, with the wave function little changed. In a range of temperatures below 300 K, proton transfer from A to T is seen to take place within the A/T occupied by the hole; it is completed by ∼40 fs after the contraction. We show that the contraction is due to polarization of the water by the hole. This polarization also plays a role in the proton transfer. Implications for transport are considered.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
authors.forename: S M
authors.initials: SM
authors.lastname: Kravec
authors.forename: C D
authors.initials: CD
authors.lastname: Kinz-Thompson
authors.forename: E M
authors.initials: EM
authors.lastname: Conwell
mesh_terms: D000225:Adenine / Q000737:chemistry*; D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005609:Free Radicals / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011522:Protons; D011789:Quantum Theory; D013696:Temperature; D013941:Thymine / Q000737:chemistry*; D013997:Time Factors; D014867:Water / Q000737:chemistry
chemical_list: D002412:Cations; D005609:Free Radicals; D011522:Protons; D014867:Water; D004247:DNA; D000225:Adenine; D013941:Thymine