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Effects of single water molecule on proton transfer reaction in uracil dimer cation

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Abstract

Ionizing radiation to DNA induces sometimes the DNA damage. In this report, the ionization dynamics of uracil dimer (U)2 and its water complex (U)2–H2O have been investigated by means of direct ab initio molecular dynamics (AIMD) method in order to elucidate the effects of single water molecule on the reaction rate of proton transfer (PT) in DNA model base pair. The (U)2 dimer is widely used as a simplified mimetic model of Watson–Crick base pair. The static ab initio calculation showed that two conformers exist as neutral complex of (U)2–H2O. The direct AIMD calculation of ionization process of (U)2–H2O showed that the rate of PT is affected even by a single water molecule, while it was dependent on the position of H2O around (U)2. The interaction of water molecule with (U)2 affected the potential energy curve for PT. Especially, the activation barrier along the PT coordinate was significantly changed by the interaction with one H2O molecule. The effects of one H2O molecule on the PT process were discussed on the basis of theoretical results.

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Acknowledgments

The author acknowledges partial support from JSPS KAKENHI Grant Number 15K05371 and MEXT KAKENHI Grant Number 25108004.

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Authors and Affiliations

  1. Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, 060-8628, Japan

    Hiroto Tachikawa

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  1. Hiroto Tachikawa
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Correspondence to Hiroto Tachikawa.

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Tachikawa, H. Effects of single water molecule on proton transfer reaction in uracil dimer cation. Theor Chem Acc 135, 55 (2016). https://doi.org/10.1007/s00214-016-1807-y

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  • DOI: https://doi.org/10.1007/s00214-016-1807-y

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