Chemistry and Biochemistry Department, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
J Phys Chem B. 2010 May 6;114(17):5886-94. doi: 10.1021/jp9120723.
Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.; et al. J. Am. Chem. Soc. 2009, 131, 6460). In a first step, a high level of theory, CCSD(T)/aug-cc-pVDZ, was used to calculate the vertical IP of each of the four single bases isolated in the QM region while the remaining DNA fragment, counterions, and water solvent molecules were included in the MM region. The calculated vertical IPs show a large positive shift of 3.2-3.3 eV compared to the corresponding gas-phase values. This shift is similar for all four DNA bases. The origin of the large increase in vertical IPs of nucleobases is found to be the long-range electrostatic interactions with the solvation structure outside the DNA helix. Thermal fluctuations in the fluid can result in IP changes of roughly 1 eV on a picosecond time scale. IPs of pi-stacked and H-bonded clusters of DNA bases were also calculated using the same QM/MM model but with a lower level of theory, B3LYP/6-31G(d=0.2). An IP shift of 4.02 eV relative to the gas phase is found for a four-base-pair B-DNA duplex configuration. The primary goal of this work was to estimate the influence of long-range solvation interactions on the ionization properties of DNA bases rather than provide highly precise IP evaluations. The QM/MM model presented in this work provides an attractive method to treat the difficult problem of incorporating a detailed long-range structural model of physiological conditions into investigations of the electronic processes in DNA.
在完全溶剂化的 DNA 片段（12 -mer B-DNA 片段+22 个钠离子抗衡离子+5760 个水分子，在 298 K 下达到平衡）中嵌入的碱基的垂直电离势（IP）已使用组合量子力学分子力学（QM/MM）方法进行了计算。报告了阴离子 Cl(-)的垂直 IP 的计算结果，这支持了将 QM/MM 方法应用于该问题的准确性。结果表明，围绕 DNA 的水合结构使 DNA 中碱基的 π 核苷酸 HOMO 起源对于发射电子具有本地化作用，这与最近在水溶液中嘧啶核苷酸中观察到的方式相似（Slavicek，P.等人，J. Am. Chem. Soc.，2009 年，131，6460）。在第一步中，使用高水平的理论（CCSD(T)/aug-cc-pVDZ）计算了 QM 区域中每个孤立的四种单碱基的垂直 IP，而其余的 DNA 片段、抗衡离子和水溶剂分子则包含在 MM 区域中。计算出的垂直 IP 与相应的气相值相比显示出 3.2-3.3 eV 的大正位移。所有四种 DNA 碱基的这种位移都相似。碱基垂直 IP 大幅增加的原因是与 DNA 螺旋外的溶剂化结构的远程静电相互作用。在皮秒时间尺度上，流体中的热波动可导致 IP 变化约 1 eV。还使用相同的 QM/MM 模型但采用较低的理论（B3LYP/6-31G(d=0.2)）计算了 DNA 碱基的π-堆积和 H 键合簇的 IP。与气相相比，发现四碱基对 B-DNA 双链构象的 IP 偏移为 4.02 eV。这项工作的主要目标是估计远程溶剂化相互作用对 DNA 碱基电离特性的影响，而不是提供高度精确的 IP 评估。本文提出的 QM/MM 模型为处理将生理条件下详细的远程结构模型纳入 DNA 中电子过程研究的难题提供了一种有吸引力的方法。
