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Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization

[Image: see text] Finding low-energy conformers of organic molecules is a complex problem due to the flexibilities of the molecules and the high dimensionality of the search space. When such molecules are on nanoclusters, the search complexity is exacerbated by constraints imposed by the presence of...

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Autores principales: Fang, Lincan, Guo, Xiaomi, Todorović, Milica, Rinke, Patrick, Chen, Xi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930108/
https://www.ncbi.nlm.nih.gov/pubmed/36642891
http://dx.doi.org/10.1021/acs.jcim.2c01120
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author Fang, Lincan
Guo, Xiaomi
Todorović, Milica
Rinke, Patrick
Chen, Xi
author_facet Fang, Lincan
Guo, Xiaomi
Todorović, Milica
Rinke, Patrick
Chen, Xi
author_sort Fang, Lincan
collection PubMed
description [Image: see text] Finding low-energy conformers of organic molecules is a complex problem due to the flexibilities of the molecules and the high dimensionality of the search space. When such molecules are on nanoclusters, the search complexity is exacerbated by constraints imposed by the presence of the cluster and other surrounding molecules. To address this challenge, we modified our previously developed active learning molecular conformer search method based on Bayesian optimization and density functional theory. Especially, we have developed and tested strategies to avoid steric clashes between a molecule and a cluster. In this work, we chose a cysteine molecule on a well-studied gold–thiolate cluster as a model system to test and demonstrate our method. We found that cysteine conformers in a cluster inherit the hydrogen bond types from isolated conformers. However, the energy rankings and spacings between the conformers are reordered.
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spelling pubmed-99301082023-02-16 Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization Fang, Lincan Guo, Xiaomi Todorović, Milica Rinke, Patrick Chen, Xi J Chem Inf Model [Image: see text] Finding low-energy conformers of organic molecules is a complex problem due to the flexibilities of the molecules and the high dimensionality of the search space. When such molecules are on nanoclusters, the search complexity is exacerbated by constraints imposed by the presence of the cluster and other surrounding molecules. To address this challenge, we modified our previously developed active learning molecular conformer search method based on Bayesian optimization and density functional theory. Especially, we have developed and tested strategies to avoid steric clashes between a molecule and a cluster. In this work, we chose a cysteine molecule on a well-studied gold–thiolate cluster as a model system to test and demonstrate our method. We found that cysteine conformers in a cluster inherit the hydrogen bond types from isolated conformers. However, the energy rankings and spacings between the conformers are reordered. American Chemical Society 2023-01-16 /pmc/articles/PMC9930108/ /pubmed/36642891 http://dx.doi.org/10.1021/acs.jcim.2c01120 Text en © 2023 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 Fang, Lincan
Guo, Xiaomi
Todorović, Milica
Rinke, Patrick
Chen, Xi
Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title_full Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title_fullStr Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title_full_unstemmed Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title_short Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization
title_sort exploring the conformers of an organic molecule on a metal cluster with bayesian optimization
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930108/
https://www.ncbi.nlm.nih.gov/pubmed/36642891
http://dx.doi.org/10.1021/acs.jcim.2c01120
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