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Cuesta SA, Moreno M, López RA, Mora JR, Paz JL, Márquez EA. ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms. J Chem Inf Model 2023; 63:507-521. [PMID: 36594600 DOI: 10.1021/acs.jcim.2c01367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Electrophilicity (E) is one of the most important parameters to understand the reactivity of an organic molecule. Although the theoretical electrophilicity index (ω) has been associated with E in a small homologous series, the use of w to predict E in a structurally heterogeneous set of compounds is not a trivial task. In this study, a robust ensemble model is created using Mayr's database of reactivity parameters. A combination of topological and quantum mechanical descriptors and different machine learning algorithms are employed for the model's development. The predictability of the model is assessed using different statistical parameters, and its validation is examined, including a training/test partition, an applicability domain, and a y-scrambling test. The global ensemble model presents a Q5-fold2 of 0.909 and a Qext2 of 0.912, demonstrating an excellent predictability performance of E values and showing that w is not a good descriptor for the prediction of E, especially for the case of neutral compounds. ElectroPredictor, a noncommercial Python application (https://github.com/mmoreno1/ElectroPredictor), is developed to predict E. QM9, a well-known large dataset containing 133885 neutral molecules, is used to perform a virtual screening (94.0% coverage). Finally, the 10 most electrophilic molecules are analyzed as possible new Mayr's electrophiles, which have not yet been experimentally tested. This study confirms the necessity to build an ensemble model using nonlinear machine learning algorithms, topographic descriptors, and separating molecules into charged and neutral compounds to predict E with precision.
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Affiliation(s)
- Sebastián A Cuesta
- Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito170901, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K
| | - Martín Moreno
- Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito170901, Ecuador
| | - Romina A López
- Colegio San Ignacio de Loyola─Fe y Alegría, Ministerio de Educación, Quito170901, Ecuador
| | - José R Mora
- Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito170901, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima, Lima15081, Peru
| | - Edgar A Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla081007, Colombia
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Mood A, Tavakoli M, Gutman E, Kadish D, Baldi P, Van Vranken DL. Methyl Anion Affinities of the Canonical Organic Functional Groups. J Org Chem 2020; 85:4096-4102. [PMID: 31995384 DOI: 10.1021/acs.joc.9b03187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calculated methyl anion affinities are known to correlate with experimentally determined Mayr E parameters for individual organic functional group classes but not between neutral and cationic organic electrophiles. We demonstrate that methyl anion affinities calculated with a solvation model (MAA*) give a linear correlation with Mayr E parameters for a broad range of functional groups. Methyl anion affinities (MAA*), plotted on the log scale of Mayr E, provide insights into the full range of electrophilicity of organic functional groups. On the Mayr E scale, the electrophilicity toward the methyl anion spans 180 orders of magnitude.
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Affiliation(s)
- Aaron Mood
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Mohammadamin Tavakoli
- Department of Computer Science, University of California Irvine, Irvine, California 92697, United States
| | - Eugene Gutman
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Dora Kadish
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Pierre Baldi
- Department of Computer Science, University of California Irvine, Irvine, California 92697, United States
| | - David L Van Vranken
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
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Berionni G, Kurouchi H, Eisenburger L, Mayr H. Nucleophilicity of Alkyl Zirconocene and Titanocene Precatalysts, and Kinetics of Activation by Carbenium Ions and by B(C6F5)3. Chemistry 2016; 22:11196-200. [DOI: 10.1002/chem.201602452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Guillaume Berionni
- Department Chemie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
| | - Hiroaki Kurouchi
- Department Chemie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
| | - Lucien Eisenburger
- Department Chemie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
| | - Herbert Mayr
- Department Chemie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
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