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Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions
[Image: see text] We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to...
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/PMC3985928/ https://www.ncbi.nlm.nih.gov/pubmed/24803856 http://dx.doi.org/10.1021/ct401035t |
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author | Giese, Timothy J. Chen, Haoyuan Huang, Ming York, Darrin M. |
author_facet | Giese, Timothy J. Chen, Haoyuan Huang, Ming York, Darrin M. |
author_sort | Giese, Timothy J. |
collection | PubMed |
description | [Image: see text] We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. |
format | Online Article Text |
id | pubmed-3985928 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-39859282015-02-11 Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions Giese, Timothy J. Chen, Haoyuan Huang, Ming York, Darrin M. J Chem Theory Comput [Image: see text] We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. American Chemical Society 2014-02-11 2014-03-11 /pmc/articles/PMC3985928/ /pubmed/24803856 http://dx.doi.org/10.1021/ct401035t Text en Copyright © 2014 American Chemical Society |
spellingShingle | Giese, Timothy J. Chen, Haoyuan Huang, Ming York, Darrin M. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions |
title | Parametrization of an Orbital-Based Linear-Scaling
Quantum Force Field for Noncovalent Interactions |
title_full | Parametrization of an Orbital-Based Linear-Scaling
Quantum Force Field for Noncovalent Interactions |
title_fullStr | Parametrization of an Orbital-Based Linear-Scaling
Quantum Force Field for Noncovalent Interactions |
title_full_unstemmed | Parametrization of an Orbital-Based Linear-Scaling
Quantum Force Field for Noncovalent Interactions |
title_short | Parametrization of an Orbital-Based Linear-Scaling
Quantum Force Field for Noncovalent Interactions |
title_sort | parametrization of an orbital-based linear-scaling
quantum force field for noncovalent interactions |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985928/ https://www.ncbi.nlm.nih.gov/pubmed/24803856 http://dx.doi.org/10.1021/ct401035t |
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