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Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field
[Image: see text] A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are present...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2014
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325604/ https://www.ncbi.nlm.nih.gov/pubmed/25691830 http://dx.doi.org/10.1021/ct500799g |
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author | Giese, Timothy J. Panteva, Maria T. Chen, Haoyuan York, Darrin M. |
author_facet | Giese, Timothy J. Panteva, Maria T. Chen, Haoyuan York, Darrin M. |
author_sort | Giese, Timothy J. |
collection | PubMed |
description | [Image: see text] A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pK(a). Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. |
format | Online Article Text |
id | pubmed-4325604 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-43256042015-12-24 Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field Giese, Timothy J. Panteva, Maria T. Chen, Haoyuan York, Darrin M. J Chem Theory Comput [Image: see text] A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pK(a). Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. American Chemical Society 2014-12-24 2015-02-10 /pmc/articles/PMC4325604/ /pubmed/25691830 http://dx.doi.org/10.1021/ct500799g Text en Copyright © 2014 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Giese, Timothy J. Panteva, Maria T. Chen, Haoyuan York, Darrin M. Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field |
title | Multipolar
Ewald Methods, 2: Applications Using a
Quantum Mechanical Force Field |
title_full | Multipolar
Ewald Methods, 2: Applications Using a
Quantum Mechanical Force Field |
title_fullStr | Multipolar
Ewald Methods, 2: Applications Using a
Quantum Mechanical Force Field |
title_full_unstemmed | Multipolar
Ewald Methods, 2: Applications Using a
Quantum Mechanical Force Field |
title_short | Multipolar
Ewald Methods, 2: Applications Using a
Quantum Mechanical Force Field |
title_sort | multipolar
ewald methods, 2: applications using a
quantum mechanical force field |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325604/ https://www.ncbi.nlm.nih.gov/pubmed/25691830 http://dx.doi.org/10.1021/ct500799g |
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