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Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer

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Abstract

The structure of 7-azaindole dimer (7AI2) as a model compound for DNA base pair has been studied by classical molecular dynamics (MD) and path integral molecular dynamics (PIMD) simulations on the semi-empirical PM6 potential energy surface at various temperatures, to investigate the nuclear quantum effect and temperature dependency on the hydrogen-bonded moiety of 7AI2. At 75 K, two H-bondings are maintained throughout a given simulation time in both classical and PIMD (quantum) simulations. At 150 K, these two H-bondings are maintained in only quantum simulation, while in classical simulation, the two H-bondings (or one H-bonding) are sometimes broken and reformed. For 225 K, these two H-bondings are broken in both classical and quantum simulations. We have also applied a principal component analysis to MD and PIMD simulations to analyze the intermolecular motions. We found that the ratio of the second lowest (dimer butterfly out-of-plane) vibrational mode from normal mode analysis which is the most dominant motion decreases with increasing temperature, whereas that of first lowest (dimer torsion out-of-plane) vibrational mode which is the second most dominant motion increases with increasing temperature from temperature 75 to 150 K and then decreases at 225 K due to the nuclear quantum effect. Moreover, the motions of two hydrogen-bonded structures are significantly different with increasing temperature. This difference is revealed by the principal component analysis which shows that the ratio of opening in-plane motion decreases and the ratio of stretching in-plane motion decreases.

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Acknowledgments

The present study has been supported by Grant-in-aid for Scientific Research by Ministry of Education, Culture, Spots, Science and Technology, Japan. N. Kungwan wishes to thank the Thailand Research Fund (TRG5680098) for financial support. Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand is also acknowledged.

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Authors and Affiliations

  1. Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand

    Nawee Kungwan

  2. Quantum Chemistry Division, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan

    Yudai Ogata & Masanori Tachikawa

  3. Department of Chemistry, Faculty of Science, Kasetsart University, Bangkhen Campus, Bangkok, 10930, Thailand

    Supa Hannongbua

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  1. Nawee Kungwan
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  2. Yudai Ogata
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  4. Masanori Tachikawa
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Correspondence to Nawee Kungwan or Masanori Tachikawa.

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Kungwan, N., Ogata, Y., Hannongbua, S. et al. Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer. Theor Chem Acc 133, 1553 (2014). https://doi.org/10.1007/s00214-014-1553-y

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