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Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry
[Image: see text] The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmenta...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8582257/ https://www.ncbi.nlm.nih.gov/pubmed/34666488 http://dx.doi.org/10.1021/acs.jctc.1c00788 |
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author | Ceselin, Giorgia Barone, Vincenzo Tasinato, Nicola |
author_facet | Ceselin, Giorgia Barone, Vincenzo Tasinato, Nicola |
author_sort | Ceselin, Giorgia |
collection | PubMed |
description | [Image: see text] The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. To this end, we have further enlarged the compilation of available semi-experimental (SE) equilibrium structures, now covering the most important fragments containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new SE100 database. Next, comparison with geometries optimized by methods rooted in the density functional theory showed that the already remarkable results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals can be further improved by a linear regression (LR) approach. Use of template fragments (taken from the SE100 library) together with LR estimates for the missing interfragment parameters paves the route toward accurate structures of large molecules, as witnessed by the very small deviations between computed and experimental rotational constants. The whole approach has been implemented in a user-friendly tool, termed nano-LEGO, and applied to a number of demanding case studies. |
format | Online Article Text |
id | pubmed-8582257 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-85822572021-11-12 Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry Ceselin, Giorgia Barone, Vincenzo Tasinato, Nicola J Chem Theory Comput [Image: see text] The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. To this end, we have further enlarged the compilation of available semi-experimental (SE) equilibrium structures, now covering the most important fragments containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new SE100 database. Next, comparison with geometries optimized by methods rooted in the density functional theory showed that the already remarkable results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals can be further improved by a linear regression (LR) approach. Use of template fragments (taken from the SE100 library) together with LR estimates for the missing interfragment parameters paves the route toward accurate structures of large molecules, as witnessed by the very small deviations between computed and experimental rotational constants. The whole approach has been implemented in a user-friendly tool, termed nano-LEGO, and applied to a number of demanding case studies. American Chemical Society 2021-10-20 2021-11-09 /pmc/articles/PMC8582257/ /pubmed/34666488 http://dx.doi.org/10.1021/acs.jctc.1c00788 Text en © 2021 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 | Ceselin, Giorgia Barone, Vincenzo Tasinato, Nicola Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry |
title | Accurate Biomolecular Structures by the Nano-LEGO
Approach: Pick the Bricks and Build Your Geometry |
title_full | Accurate Biomolecular Structures by the Nano-LEGO
Approach: Pick the Bricks and Build Your Geometry |
title_fullStr | Accurate Biomolecular Structures by the Nano-LEGO
Approach: Pick the Bricks and Build Your Geometry |
title_full_unstemmed | Accurate Biomolecular Structures by the Nano-LEGO
Approach: Pick the Bricks and Build Your Geometry |
title_short | Accurate Biomolecular Structures by the Nano-LEGO
Approach: Pick the Bricks and Build Your Geometry |
title_sort | accurate biomolecular structures by the nano-lego
approach: pick the bricks and build your geometry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8582257/ https://www.ncbi.nlm.nih.gov/pubmed/34666488 http://dx.doi.org/10.1021/acs.jctc.1c00788 |
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