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Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths
The accurate prediction of aqueous pK(a) values for tautomerizable compounds is a formidable task, even for the most established in silico tools. Empirical approaches often fall short due to a lack of pre-existing knowledge of dominant tautomeric forms. In a rigorous first-principles approach, calcu...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814527/ https://www.ncbi.nlm.nih.gov/pubmed/36703356 http://dx.doi.org/10.1038/s42004-020-0264-7 |
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author | Caine, Beth A. Bronzato, Maddalena Fraser, Torquil Kidley, Nathan Dardonville, Christophe Popelier, Paul L. A. |
author_facet | Caine, Beth A. Bronzato, Maddalena Fraser, Torquil Kidley, Nathan Dardonville, Christophe Popelier, Paul L. A. |
author_sort | Caine, Beth A. |
collection | PubMed |
description | The accurate prediction of aqueous pK(a) values for tautomerizable compounds is a formidable task, even for the most established in silico tools. Empirical approaches often fall short due to a lack of pre-existing knowledge of dominant tautomeric forms. In a rigorous first-principles approach, calculations for low-energy tautomers must be performed in protonated and deprotonated forms, often both in gas and solvent phases, thus representing a significant computational task. Here we report an alternative approach, predicting pK(a) values for herbicide/therapeutic derivatives of 1,3-cyclohexanedione and 1,3-cyclopentanedione to within just 0.24 units. A model, using a single ab initio bond length from one protonation state, is as accurate as other more complex regression approaches using more input features, and outperforms the program Marvin. Our approach can be used for other tautomerizable species, to predict trends across congeneric series and to correct experimental pK(a) values. |
format | Online Article Text |
id | pubmed-9814527 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-98145272023-01-10 Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths Caine, Beth A. Bronzato, Maddalena Fraser, Torquil Kidley, Nathan Dardonville, Christophe Popelier, Paul L. A. Commun Chem Article The accurate prediction of aqueous pK(a) values for tautomerizable compounds is a formidable task, even for the most established in silico tools. Empirical approaches often fall short due to a lack of pre-existing knowledge of dominant tautomeric forms. In a rigorous first-principles approach, calculations for low-energy tautomers must be performed in protonated and deprotonated forms, often both in gas and solvent phases, thus representing a significant computational task. Here we report an alternative approach, predicting pK(a) values for herbicide/therapeutic derivatives of 1,3-cyclohexanedione and 1,3-cyclopentanedione to within just 0.24 units. A model, using a single ab initio bond length from one protonation state, is as accurate as other more complex regression approaches using more input features, and outperforms the program Marvin. Our approach can be used for other tautomerizable species, to predict trends across congeneric series and to correct experimental pK(a) values. Nature Publishing Group UK 2020-02-12 /pmc/articles/PMC9814527/ /pubmed/36703356 http://dx.doi.org/10.1038/s42004-020-0264-7 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Caine, Beth A. Bronzato, Maddalena Fraser, Torquil Kidley, Nathan Dardonville, Christophe Popelier, Paul L. A. Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title | Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title_full | Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title_fullStr | Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title_full_unstemmed | Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title_short | Aqueous pK(a) prediction for tautomerizable compounds using equilibrium bond lengths |
title_sort | aqueous pk(a) prediction for tautomerizable compounds using equilibrium bond lengths |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814527/ https://www.ncbi.nlm.nih.gov/pubmed/36703356 http://dx.doi.org/10.1038/s42004-020-0264-7 |
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