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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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 |
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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 |
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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. |
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Kungwan,N. Ogata,Y. Hannongbua,S. Tachikawa,M. |
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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 |
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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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