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: ジャーナルへの寄稿記事

4 引用 (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.

元の言語英語
記事番号104111
ジャーナルJournal of Chemical Physics
142
発行部数10
DOI
出版物ステータス出版済み - 3 14 2015

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elongation
Elongation
Alkylation
interactions
energy
DNA
deoxyribonucleic acid
alkylation
strands
Guanine
Error correction
Hydrogen bonds
Stabilization
guanines
Atoms
sliding
stabilization
hydrogen bonds
scaling
causes

All Science Journal Classification (ASJC) codes

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

これを引用

Ab initio O (N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems. / Orimoto, Yuuichi; Yamamoto, Ryohei; Xie, Peng; Liu, Kai; Imamura, Akira; Aoki, Yuriko.

:: Journal of Chemical Physics, 巻 142, 番号 10, 104111, 14.03.2015.

研究成果: ジャーナルへの寄稿記事

Orimoto, Yuuichi ; Yamamoto, Ryohei ; Xie, Peng ; Liu, Kai ; Imamura, Akira ; Aoki, Yuriko. / Ab initio O (N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems. :: Journal of Chemical Physics. 2015 ; 巻 142, 番号 10.
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abstract = "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.",
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