{"title":"用基于图的机器学习方法预测氧化还原电位","authors":"Linlin Jia, Éric Brémond, Larissa Zaida, Benoit Gaüzère, Vincent Tognetti, Laurent Joubert","doi":"10.1002/jcc.27380","DOIUrl":null,"url":null,"abstract":"<p>The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoretical chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic compounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol<span></span><math>\n <mrow>\n <msup>\n <mrow></mrow>\n <mrow>\n <mo>−</mo>\n <mn>1</mn>\n </mrow>\n </msup>\n </mrow></math> for reduction and 7.2 kcal mol<span></span><math>\n <mrow>\n <msup>\n <mrow></mrow>\n <mrow>\n <mo>−</mo>\n <mn>1</mn>\n </mrow>\n </msup>\n </mrow></math> for oxidation potentials, which paves a way toward efficient <i>in silico</i> design of new electrochemical systems.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 28","pages":"2383-2396"},"PeriodicalIF":3.4000,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27380","citationCount":"0","resultStr":"{\"title\":\"Predicting redox potentials by graph-based machine learning methods\",\"authors\":\"Linlin Jia, Éric Brémond, Larissa Zaida, Benoit Gaüzère, Vincent Tognetti, Laurent Joubert\",\"doi\":\"10.1002/jcc.27380\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoretical chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic compounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol<span></span><math>\\n <mrow>\\n <msup>\\n <mrow></mrow>\\n <mrow>\\n <mo>−</mo>\\n <mn>1</mn>\\n </mrow>\\n </msup>\\n </mrow></math> for reduction and 7.2 kcal mol<span></span><math>\\n <mrow>\\n <msup>\\n <mrow></mrow>\\n <mrow>\\n <mo>−</mo>\\n <mn>1</mn>\\n </mrow>\\n </msup>\\n </mrow></math> for oxidation potentials, which paves a way toward efficient <i>in silico</i> design of new electrochemical systems.</p>\",\"PeriodicalId\":188,\"journal\":{\"name\":\"Journal of Computational Chemistry\",\"volume\":\"45 28\",\"pages\":\"2383-2396\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2024-06-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27380\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/jcc.27380\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jcc.27380","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Predicting redox potentials by graph-based machine learning methods
The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoretical chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic compounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol for reduction and 7.2 kcal mol for oxidation potentials, which paves a way toward efficient in silico design of new electrochemical systems.
期刊介绍:
This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.