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

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...

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Main Authors: Kungwan,N., Ogata,Y., Hannongbua,S., Tachikawa,M.
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Published: Springer New York 2015
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http://cmuir.cmu.ac.th/handle/6653943832/38747
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Institution: Chiang Mai University
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spelling th-cmuir.6653943832-387472015-06-16T07:54:08Z Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer Kungwan,N. Ogata,Y. Hannongbua,S. Tachikawa,M. Physical and Theoretical Chemistry 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. © 2014 Springer-Verlag Berlin Heidelberg. 2015-06-16T07:54:07Z 2015-06-16T07:54:07Z 2014-08-09 Article in Press 1432881X 2-s2.0-84905294428 10.1007/s00214-014-1553-y http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84905294428&origin=inward http://cmuir.cmu.ac.th/handle/6653943832/38747 Springer New York
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Physical and Theoretical Chemistry
spellingShingle Physical and Theoretical Chemistry
Kungwan,N.
Ogata,Y.
Hannongbua,S.
Tachikawa,M.
Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
description 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. © 2014 Springer-Verlag Berlin Heidelberg.
format Article
author Kungwan,N.
Ogata,Y.
Hannongbua,S.
Tachikawa,M.
author_facet Kungwan,N.
Ogata,Y.
Hannongbua,S.
Tachikawa,M.
author_sort Kungwan,N.
title Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
title_short Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
title_full Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
title_fullStr Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
title_full_unstemmed Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
title_sort nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer
publisher Springer New York
publishDate 2015
url http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84905294428&origin=inward
http://cmuir.cmu.ac.th/handle/6653943832/38747
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