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Teaching a neural network to attach and detach electrons from molecules
Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were par...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357920/ https://www.ncbi.nlm.nih.gov/pubmed/34381051 http://dx.doi.org/10.1038/s41467-021-24904-0 |
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author | Zubatyuk, Roman Smith, Justin S. Nebgen, Benjamin T. Tretiak, Sergei Isayev, Olexandr |
author_facet | Zubatyuk, Roman Smith, Justin S. Nebgen, Benjamin T. Tretiak, Sergei Isayev, Olexandr |
author_sort | Zubatyuk, Roman |
collection | PubMed |
description | Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions. |
format | Online Article Text |
id | pubmed-8357920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83579202021-08-30 Teaching a neural network to attach and detach electrons from molecules Zubatyuk, Roman Smith, Justin S. Nebgen, Benjamin T. Tretiak, Sergei Isayev, Olexandr Nat Commun Article Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions. Nature Publishing Group UK 2021-08-11 /pmc/articles/PMC8357920/ /pubmed/34381051 http://dx.doi.org/10.1038/s41467-021-24904-0 Text en © The Author(s) 2021 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 Zubatyuk, Roman Smith, Justin S. Nebgen, Benjamin T. Tretiak, Sergei Isayev, Olexandr Teaching a neural network to attach and detach electrons from molecules |
title | Teaching a neural network to attach and detach electrons from molecules |
title_full | Teaching a neural network to attach and detach electrons from molecules |
title_fullStr | Teaching a neural network to attach and detach electrons from molecules |
title_full_unstemmed | Teaching a neural network to attach and detach electrons from molecules |
title_short | Teaching a neural network to attach and detach electrons from molecules |
title_sort | teaching a neural network to attach and detach electrons from molecules |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357920/ https://www.ncbi.nlm.nih.gov/pubmed/34381051 http://dx.doi.org/10.1038/s41467-021-24904-0 |
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