Orimoto Yuuichi, Yamamoto Ryohei, Xie Peng, Liu Kai, Imamura Akira, Aoki Yuriko
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan.
Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan.
J Chem Phys. 2015 Mar 14;142(10):104111. doi: 10.1063/1.4913931.
An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs' inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10(-7)-10(-8) hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. -290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.
为了在生物系统中进行准确高效的相互作用能分析并校正基组叠加误差（BSSE），开发了一种伸长平衡（ELG-CP）方法。该方法是通过将我们开发的从头算O(N)伸长方法与为解决BSSE问题而提出的传统平衡方法相结合来实现的。作为测试，ELG-CP方法被应用于分析DNA链间相互作用能，该相互作用能与导致从G⋯C到A⋯T转变的烷基化诱导碱基对错配现象有关。结果发现，与传统的平衡处理方法相比，ELG-CP方法在总能量计算中显示出高效率（接近线性缩放）和高精度，能量误差小到可以忽略不计（约为10^(-7)-10^(-8)哈特里/原子）。此外，对于一个具有21个碱基对的DNA模型计算，发现BSSE的大小约为-290千卡/摩尔。这强调了在使用有限大小的基组研究DNA模型并比较它们之间的小能量差异时，校正BSSE的重要性。在这项工作中，我们通过ELG-CP方法定量估计了从G⋯C到A⋯T转变过程中每个可能步骤的链间相互作用能。结果发现，该过程中的碱基对替换仅影响错配位置周围有限区域以及少数相邻碱基对的相互作用能。从相互作用能的角度来看，我们的结果表明，鸟嘌呤烷基化后可能会发生碱基对滑动机制，以获得碱基之间尽可能多的氢键。此外，发现导致A⋯T替换并伴随复制的步骤是不利过程，对应于约10千卡/摩尔的稳定能损失。本研究表明，ELG-CP方法在生物系统中进行有效相互作用能分析方面具有前景。
