Ab initio O (N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

Yuuichi Orimoto, Ryohei Yamamoto, Peng Xie, Kai Liu, Akira Imamura, Yuriko Aoki

    研究成果: Contribution to journalArticle査読

    5 被引用数 (Scopus)

    抄録

    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.

    本文言語英語
    論文番号104111
    ジャーナルJournal of Chemical Physics
    142
    10
    DOI
    出版ステータス出版済み - 3 14 2015

    All Science Journal Classification (ASJC) codes

    • Physics and Astronomy(all)
    • Physical and Theoretical Chemistry

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