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

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 -H 2 O 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 -H 2 O. The direct AIMD calculation of ionization process of (U) 2 -H 2 O showed that the rate of PT is affected even by a single water molecule, while it was dependent on the position of H 2 O 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 H 2 O molecule. The effects of one H 2 O molecule on the PT process were discussed on the basis of theoretical results.

Effect of water on excited‐state double proton transfer in 7‐azaindole‐H2O complex: A theoretical study

“…They concluded that the rate constant of ESPT was larger when water took place of the H‐bonded ether since the H‐bond formation with water strengthened the proton‐accepting ability of the water chain. Tachikawa studied the ionization dynamics of uracil dimer and its water complex (U) 2 ‐H 2 O by using direct ab initio molecular dynamics (AIMD) method for expounding the effect of single water on the rate of PT. Their results showed that the reaction rate of PT was evidently influenced by the position of H 2 O around U 2 .…”