Predictive Models for Kinetic Parameters of Cycloaddition Reactions
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This paper reports SVR (Support Vector Regression) and GTM (Generative Topographic Mapping) modeling of three kinetic properties of cycloaddition reactions: rate constant (log k), activation energy (Ea) and pre‐exponential factor (logA). A data set of 1849 reactions, comprising (4+2), (3+2) and (2+2) cycloadditions (CA) were studied in different solvents and at different temperatures. The reactions were encoded by the ISIDA fragment descriptors generated for Condensed Graph of Reaction (CGR). For a given reaction, a CGR condenses structures of all the reactants and products into one single molecular graph, described both by conventional chemical bonds and “dynamical” bonds characterizing chemical transformations. Different scenarios of log k assessment were exploited: direct modeling, application of the Arrhenius equation and temperature‐scaled GTM landscapes. The log k models with optimal cross‐validated statistics (Q 2=0.78–0.94 RMSE=0.45–0.86) have been challenged to predict rates for the external test set of 200 reactions, comprising both reactions that were not present in the training set, and training set transformations performed under different reaction conditions. The models are freely available on our web‐server: http://cimm.kpfu.ru/models.
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Fragment descriptors generated for CGRs were concatenated with solvent and temperature descriptors and used to train logk models for bimolecular nucleophilic substitution, bimolecular elimination, and different types of cycloaddition.
“Fragment descriptors generated for CGRs were concatenated with solvent and temperature descriptors and used to train logk models for bimolecular nucleophilic substitution,159 bimolecular elimination, and different types of cycloaddition.160”
From QSAR without borders (2020) · cites this paper as [160]
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Expert System for Predicting Reaction Conditions: The Michael Reaction Case
Marcou, G., Aires de Sousa, J., Latino, D. A. R. S., de Luca, A., Horvath, D., Rietsch, V., & Varnek, A. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500698a · Cited by 86 · see citing works
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Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., Oprea, T. I., Baskin, I. I., Varnek, A., Roitberg, A., et al. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00098a · Cited by 913 · see citing works
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- Authors
- Glavatskikh, M., Madzhidov, T., Horvath, D., Nugmanov, R., Gimadiev, T., Malakhova, D., Marcou, G., & Varnek, A.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Kazan Federal University (RU)
- Laboratory of Chemoinformatics and Molecular Modeling Butlerov Institute of Chemistry Kazan Federal University Kremlyovskaya str. 18 Kazan Russia
- Corresponding author
- Varnek, Alexandre
- ORCID
- Venue
- Molecular Informatics
- Publisher
- Wiley
- Published
- 2018-08-22
- Volume
- 38
- Issue
- 1-2
- Pages
- e1800077-e1800077
- ISSN
- 1868-1743 (ISSN-L)
- 1868-1751
- OpenAlex
- W2888302950
- Cited by
- 36
- References
- 1
- Citations by year
- 2026: 1 · 2025: 4 · 2023: 7 · 2022: 3 · 2021: 7 · 2020: 7 · 2019: 6 · 2018: 1
- FWCI
- 3.93
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Molecular Informatics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Russian Science Foundation (14-43-00024)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
- Physical Sciences › Chemistry › Organic Chemistry › Organic Chemistry Cycloaddition Reactions
- Keywords
- cycloaddition, reaction kinetics, rate constant prediction, activation energy, pre-exponential factor, support vector regression, generative topographic mapping, Diels-Alder reaction, [3+2] cycloaddition, [2+2] cycloaddition, solvent effects, temperature effects, reaction rate prediction
- MeSH terms
- Kinetics, Models, Chemical, Cycloaddition Reaction
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