在水中 B 型 DNA 中腺嘌呤-胸腺嘧啶自由基阳离子上的孔的定位。
Localization of a hole on an adenine-thymine radical cation in B-form DNA in water.
机构信息
Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
出版信息
J Phys Chem B. 2011 May 19;115(19):6166-71. doi: 10.1021/jp110062y. Epub 2011 Apr 14.
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.
采用 CP2K 对水相中一个由 10 个腺嘌呤-胸腺嘧啶（A/T）对组成的 B 型 DNA 分子中的一个空穴进行了量子力学/分子力学（QM/MM）分子动力学（MD）模拟。在模拟开始时，空穴波函数扩展到几个腺嘌呤上。在 20-25 fs 内，空穴波函数收缩，从而使其定域在单个 A 上。在 300 K 下，空穴在这个 A 上停留的模拟时间长达几百 fs，波函数几乎没有变化。在低于 300 K 的一系列温度下，观察到空穴从 A 到 T 的质子转移发生在空穴占据的 A/T 中；在收缩后约 40 fs 完成。我们表明，收缩是由于空穴对水的极化引起的。这种极化也在质子转移中起作用。考虑了对输运的影响。
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