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Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB
[Image: see text] A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increa...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400107/ https://www.ncbi.nlm.nih.gov/pubmed/35943747 http://dx.doi.org/10.1021/acs.jcim.2c00144 |
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author | Jha, Kunal Kumar Gruza, Barbara Sypko, Aleksandra Kumar, Prashant Chodkiewicz, Michał Leszek Dominiak, Paulina Maria |
author_facet | Jha, Kunal Kumar Gruza, Barbara Sypko, Aleksandra Kumar, Prashant Chodkiewicz, Michał Leszek Dominiak, Paulina Maria |
author_sort | Jha, Kunal Kumar |
collection | PubMed |
description | [Image: see text] A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules. Thus, the University at Buffalo Databank (UBDB) has been renamed to the Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank, broadened, restructured, and implemented into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms. MATTS2021 data bank now covers most of the small molecules, peptides, RNA, DNA, and some frequently occurring cations and anions in biological, pharmaceutical, and organic materials, including the majority of known crystal structures composed of the above elements. The multipole model parameters (P(val), κ, κ′, P(lm)) obtained for different atom types were greatly influenced by neighboring atom types, hybridization, geometrical strain in the ring system, and charges on the molecule. Contrary to previous findings, the atoms showing variable oxidation states and ions deviate from the linear dependence of monopole-derived charges on the expansion–contraction κ parameter. |
format | Online Article Text |
id | pubmed-9400107 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-94001072022-08-25 Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB Jha, Kunal Kumar Gruza, Barbara Sypko, Aleksandra Kumar, Prashant Chodkiewicz, Michał Leszek Dominiak, Paulina Maria J Chem Inf Model [Image: see text] A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules. Thus, the University at Buffalo Databank (UBDB) has been renamed to the Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank, broadened, restructured, and implemented into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms. MATTS2021 data bank now covers most of the small molecules, peptides, RNA, DNA, and some frequently occurring cations and anions in biological, pharmaceutical, and organic materials, including the majority of known crystal structures composed of the above elements. The multipole model parameters (P(val), κ, κ′, P(lm)) obtained for different atom types were greatly influenced by neighboring atom types, hybridization, geometrical strain in the ring system, and charges on the molecule. Contrary to previous findings, the atoms showing variable oxidation states and ions deviate from the linear dependence of monopole-derived charges on the expansion–contraction κ parameter. American Chemical Society 2022-08-09 2022-08-22 /pmc/articles/PMC9400107/ /pubmed/35943747 http://dx.doi.org/10.1021/acs.jcim.2c00144 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Jha, Kunal Kumar Gruza, Barbara Sypko, Aleksandra Kumar, Prashant Chodkiewicz, Michał Leszek Dominiak, Paulina Maria Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title | Multipolar Atom
Types from Theory and Statistical
Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title_full | Multipolar Atom
Types from Theory and Statistical
Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title_fullStr | Multipolar Atom
Types from Theory and Statistical
Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title_full_unstemmed | Multipolar Atom
Types from Theory and Statistical
Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title_short | Multipolar Atom
Types from Theory and Statistical
Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB |
title_sort | multipolar atom
types from theory and statistical
clustering (matts) data bank: restructurization and extension of ubdb |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400107/ https://www.ncbi.nlm.nih.gov/pubmed/35943747 http://dx.doi.org/10.1021/acs.jcim.2c00144 |
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