alexa Localization of a hole on an adenine-thymine radical cation in B-form DNA in water.
Chemistry

Chemistry

Journal of Physical Chemistry & Biophysics

Author(s): Kravec SM, KinzThompson CD, Conwell EM

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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. © 2011 American Chemical Society This article was published in J Phys Chem B and referenced in Journal of Physical Chemistry & Biophysics

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