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Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network()
Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicat...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990454/ https://www.ncbi.nlm.nih.gov/pubmed/24748697 http://dx.doi.org/10.1016/j.molliq.2013.05.033 |
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author | Kaiser, Alexander Ismailova, Oksana Koskela, Antti Huber, Stefan E. Ritter, Marcel Cosenza, Biagio Benger, Werner Nazmutdinov, Renat Probst, Michael |
author_facet | Kaiser, Alexander Ismailova, Oksana Koskela, Antti Huber, Stefan E. Ritter, Marcel Cosenza, Biagio Benger, Werner Nazmutdinov, Renat Probst, Michael |
author_sort | Kaiser, Alexander |
collection | PubMed |
description | Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. |
format | Online Article Text |
id | pubmed-3990454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-39904542014-04-18 Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() Kaiser, Alexander Ismailova, Oksana Koskela, Antti Huber, Stefan E. Ritter, Marcel Cosenza, Biagio Benger, Werner Nazmutdinov, Renat Probst, Michael J Mol Liq Article Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. Elsevier 2014-01 /pmc/articles/PMC3990454/ /pubmed/24748697 http://dx.doi.org/10.1016/j.molliq.2013.05.033 Text en © 2013 The Authors https://creativecommons.org/licenses/by-nc-sa/3.0/This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (https://creativecommons.org/licenses/by-nc-sa/3.0/) . |
spellingShingle | Article Kaiser, Alexander Ismailova, Oksana Koskela, Antti Huber, Stefan E. Ritter, Marcel Cosenza, Biagio Benger, Werner Nazmutdinov, Renat Probst, Michael Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title | Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title_full | Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title_fullStr | Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title_full_unstemmed | Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title_short | Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
title_sort | ethylene glycol revisited: molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network() |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990454/ https://www.ncbi.nlm.nih.gov/pubmed/24748697 http://dx.doi.org/10.1016/j.molliq.2013.05.033 |
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