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A revised formulation of the generalized subsystem vibrational analysis (GSVA)
In this work, a simplified formulation of our recently developed generalized subsystem vibrational analysis (GSVA) for obtaining intrinsic fragmental vibrations (J Chem Theory Comput 14:2558, 2018) is presented. In contrast to the earlier implementation, which requires the explicit definition of a n...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7942689/ https://www.ncbi.nlm.nih.gov/pubmed/33716564 http://dx.doi.org/10.1007/s00214-021-02727-y |
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author | Tao, Yunwen Zou, Wenli Nanayakkara, Sadisha Freindorf, Marek Kraka, Elfi |
author_facet | Tao, Yunwen Zou, Wenli Nanayakkara, Sadisha Freindorf, Marek Kraka, Elfi |
author_sort | Tao, Yunwen |
collection | PubMed |
description | In this work, a simplified formulation of our recently developed generalized subsystem vibrational analysis (GSVA) for obtaining intrinsic fragmental vibrations (J Chem Theory Comput 14:2558, 2018) is presented. In contrast to the earlier implementation, which requires the explicit definition of a non-redundant set of internal coordinate parameters to be constructed for the subsystem, the new implementation circumvents this process by employing massless Eckart conditions to the subsystem fragment paired with a Gram–Schmidt orthogonalization to span the same internal vibration space indirectly. This revised version of GSVA (rev-GSVA) can be applied to equilibrium structure as well as transition state structure, and it has been incorporated into the open-source package UniMoVib (https://github.com/zorkzou/UniMoVib). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00214-021-02727-y. |
format | Online Article Text |
id | pubmed-7942689 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-79426892021-03-10 A revised formulation of the generalized subsystem vibrational analysis (GSVA) Tao, Yunwen Zou, Wenli Nanayakkara, Sadisha Freindorf, Marek Kraka, Elfi Theor Chem Acc Letter In this work, a simplified formulation of our recently developed generalized subsystem vibrational analysis (GSVA) for obtaining intrinsic fragmental vibrations (J Chem Theory Comput 14:2558, 2018) is presented. In contrast to the earlier implementation, which requires the explicit definition of a non-redundant set of internal coordinate parameters to be constructed for the subsystem, the new implementation circumvents this process by employing massless Eckart conditions to the subsystem fragment paired with a Gram–Schmidt orthogonalization to span the same internal vibration space indirectly. This revised version of GSVA (rev-GSVA) can be applied to equilibrium structure as well as transition state structure, and it has been incorporated into the open-source package UniMoVib (https://github.com/zorkzou/UniMoVib). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00214-021-02727-y. Springer Berlin Heidelberg 2021-03-09 2021 /pmc/articles/PMC7942689/ /pubmed/33716564 http://dx.doi.org/10.1007/s00214-021-02727-y Text en © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Letter Tao, Yunwen Zou, Wenli Nanayakkara, Sadisha Freindorf, Marek Kraka, Elfi A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title | A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title_full | A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title_fullStr | A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title_full_unstemmed | A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title_short | A revised formulation of the generalized subsystem vibrational analysis (GSVA) |
title_sort | revised formulation of the generalized subsystem vibrational analysis (gsva) |
topic | Letter |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7942689/ https://www.ncbi.nlm.nih.gov/pubmed/33716564 http://dx.doi.org/10.1007/s00214-021-02727-y |
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