Abstract
Proton transfer in DNA has attracted much attention because of its close relationship with charge transfer and DNA base damage. In the present study, the relationship between proton transfer and water polarization at a certain temperature in the radical cation stack of adenine-thymine is investigated by QM/MM molecular dynamics simulations. By analyzing the polarization of aqueous solution, it is found that at low temperature water molecules promote proton transfer by means of displacement polarization and oriented polarization, while at high temperature, water molecules promote proton transfer only by displacement polarization.
Highlights
DNA charge transport (CT) has received considerable attention over the past decades for its potential applications in molecular electronic devices and its relationship with DNA damage and repair.1–6 In the study of DNA, an electron or a hole carrier is usually generated by trapping or exciting an electron in theoretical simulations7–11 which will change the pH value, proton transfer (PT) will take place.12–14 It is shown that there is a certain relationship between proton transfer and charge transport
With one electron removed to introduce a hole5 continuous base pairs (No 4-8 and its complementary bases No 13-17) including the phosphates and sugar were dealt with Quantum Mechanics (QM), and the remaining parts were calculated with Molecular Mechanics (MM)
It should be noted that, in agreement with previous model calculations, the hole localization is in the QM region; due to the influence of water molecules and temperature, the it will appear at the edge of the QM region, which does not influence the calculation of the effect of water on PT.31,32
Summary
DNA charge transport (CT) has received considerable attention over the past decades for its potential applications in molecular electronic devices and its relationship with DNA damage and repair. In the study of DNA, an electron or a hole carrier is usually generated by trapping or exciting an electron in theoretical simulations which will change the pH value, proton transfer (PT) will take place. It is shown that there is a certain relationship between proton transfer and charge transport. In the study of DNA, an electron or a hole carrier is usually generated by trapping or exciting an electron in theoretical simulations which will change the pH value, proton transfer (PT) will take place.. It is shown that there is a certain relationship between proton transfer and charge transport. Theoretical and experimental studies on proton transfer have become one of the attractive topics in recent years. Whether proton transfer promotes CT in DNA has not been solved.. In the PT study of DNA, the proton transfer of guanine-cytosine (GC) has been paid more and more attention, and the theoretical calculation is in good agreement with the experimental results.. According to the pka experiment, proton transfer in adenine-thymine (AT) can not take place Whether proton transfer promotes CT in DNA has not been solved. In the PT study of DNA, the proton transfer of guanine-cytosine (GC) has been paid more and more attention, and the theoretical calculation is in good agreement with the experimental results. According to the pka experiment, proton transfer in adenine-thymine (AT) can not take place
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