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Rangel-Peña UJ, Zárate-Hernández LA, Camacho-Mendoza RL, Gómez-Castro CZ, González-Montiel S, Pescador-Rojas M, Meneses-Viveros A, Cruz-Borbolla J. Conceptual DFT, machine learning and molecular docking as tools for predicting LD 50 toxicity of organothiophosphates. J Mol Model 2023; 29:217. [PMID: 37380915 DOI: 10.1007/s00894-023-05630-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
CONTEXT Several descriptors from conceptual density functional theory (cDFT) and the quantum theory of atoms in molecules (QTAIM) were utilized in Random Forest (RF), LASSO, Ridge, Elastic Net (EN), and Support Vector Machines (SVM) methods to predict the toxicity (LD50) of sixty-two organothiophosphate compounds. The A-RF-G1 and A-RF-G2 models were obtained using the RF method, yielding statistically significant parameters with good performance, as indicated by R2 values for the training set (R2Train) and R2 values for the test set (R2Test), around 0.90. METHODS The molecular structure of all organothiophosphates was optimized via the range-separated hybrid functional ωB97XD with the 6-311 + + G** basis set. Seven hundred and eighty-seven descriptors have been processed using a variety of machine learning algorithms: RF LASSO, Ridge, EN and SVM to generate a predictive model. The properties were obtained with Multiwfn, AIMALL and VMD programs. Docking simulations were performed by using AutoDock 4.2 and LigPlot + programs. All the calculations in this work are carried out in Gaussian 16 program package.
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Affiliation(s)
- Uriel J Rangel-Peña
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México
| | - Luis A Zárate-Hernández
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México
| | - Rosa L Camacho-Mendoza
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México
| | - Carlos Z Gómez-Castro
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México
| | - Simplicio González-Montiel
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México
| | | | - Amilcar Meneses-Viveros
- Departamento de Computación, CINVESTAV-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, Ciudad de Mexico, 07360, México
| | - Julián Cruz-Borbolla
- Area Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, C.P. 42184, Mineral de La Reforma, Hidalgo, México.
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Acosta-Jiménez EH, Zárate-Hernández LA, Camacho-Mendoza RL, González-Montiel S, Alvarado-Rodríguez JG, Gómez-Castro CZ, Pescador-Rojas M, Meneses-Viveros A, Cruz-Borbolla J. QSTR Modeling to Find Relevant DFT Descriptors Related to the Toxicity of Carbamates. Molecules 2022; 27:molecules27175530. [PMID: 36080298 PMCID: PMC9457808 DOI: 10.3390/molecules27175530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
Compounds containing carbamate moieties and their derivatives can generate serious public health threats and environmental problems due their high potential toxicity. In this study, a quantitative structure–toxicity relationship (QSTR) model has been developed by using one hundred seventy-eight carbamate derivatives whose toxicities in rats (oral administration) have been evaluated. The QSRT model was rigorously validated by using either tested or untested compounds falling within the applicability domain of the model. A structure-based evaluation by docking from a series of carbamates with acetylcholinesterase (AChE) was carried out. The toxicity of carbamates was predicted using physicochemical, structural, and quantum molecular descriptors employing a DFT approach. A statistical treatment was developed; the QSRT model showed a determination coefficient (R2) and a leave-one-out coefficient (Q2LOO) of 0.6584 and 0.6289, respectively.
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Affiliation(s)
- Emma H. Acosta-Jiménez
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | - Luis A. Zárate-Hernández
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | - Rosa L. Camacho-Mendoza
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | - Simplicio González-Montiel
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | - José G. Alvarado-Rodríguez
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | - Carlos Z. Gómez-Castro
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
| | | | - Amilcar Meneses-Viveros
- Departamento de Computación, CINVESTAV-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, Ciudad de México 07360, Mexico
| | - Julián Cruz-Borbolla
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento, Mineral de la Reforma 42184, Mexico
- Correspondence: ; Tel.: +52-771-7172000 (ext. 2205)
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Moulandou-Koumba RD, Doggui MY, N'Sikabaka S, Ouamba JM, Arfaoui Y, Frapper G, Guégan F. Proposal of a Fermi-Dirac-Derived Reactivity Descriptor: Beyond the Frontier MO Model. J Phys Chem A 2021; 125:8090-8097. [PMID: 34473520 DOI: 10.1021/acs.jpca.1c04415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this paper, we derive a reactivity descriptor stemming from the Fermi-Dirac population scheme, applied to density functional calculations on molecular systems. Assuming that molecular orbitals only marginally change when temperature is slightly increased from 0 K, we study the response of electron density to a change in temperature. Connection with usual conceptual density functional theory descriptors is made, and the T-variation of electron density for some representative examples is given and discussed.
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Affiliation(s)
- R D Moulandou-Koumba
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - M Y Doggui
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - S N'Sikabaka
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - J-M Ouamba
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - Y Arfaoui
- Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - G Frapper
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
| | - F Guégan
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
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Munárriz J, Gallegos M, Contreras-García J, Martín Pendás Á. Energetics of Electron Pairs in Electrophilic Aromatic Substitutions. Molecules 2021; 26:513. [PMID: 33478091 PMCID: PMC7835785 DOI: 10.3390/molecules26020513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 11/16/2022] Open
Abstract
The interacting quantum atoms approach (IQA) as applied to the electron-pair exhaustive partition of real space induced by the electron localization function (ELF) is used to examine candidate energetic descriptors to rationalize substituent effects in simple electrophilic aromatic substitutions. It is first shown that inductive and mesomeric effects can be recognized from the decay mode of the aromatic valence bond basin populations with the distance to the substituent, and that the fluctuation of the population of adjacent bonds holds also regioselectivity information. With this, the kinetic energy of the electrons in these aromatic basins, as well as their mutual exchange-correlation energies are proposed as suitable energetic indices containing relevant information about substituent effects. We suggest that these descriptors could be used to build future reactive force fields.
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Affiliation(s)
- Julen Munárriz
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain;
| | - Miguel Gallegos
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain;
| | | | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain;
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Guégan F, Tognetti V, Martínez-Araya JI, Chermette H, Merzoud L, Toro-Labbé A, Morell C. A statistical thermodynamics view of electron density polarisation: application to chemical selectivity. Phys Chem Chem Phys 2020; 22:23553-23562. [PMID: 33073279 DOI: 10.1039/d0cp03228j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fundamental link between conceptual density functional theory and statistical thermodynamics is herein drawn, showing that intermolecular electrostatic interactions can be understood in terms of effective work and heat exchange. From a more detailed analysis of the heat exchange in a perturbation theory framework, an associated entropy can be subsequently derived, which appears to be a suitable descriptor for the local polarisability of the electron density. A general rule of thumb is evidenced: the more the perturbation can be spread, both through space and among the excited states, the larger the heat exchange and entropy.
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Affiliation(s)
- Frédéric Guégan
- IC2MP UMR 7285, Université de Poitiers - CNRS, 4, rue Michel Brunet TSA, 51106-86073 Cedex 9 Poitiers, France.
| | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 - FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont St Aignan, Cedex, France
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 498, Santiago, Chile
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1 - 5, rue de la Doua, F-69100 Villeurbanne, France.
| | - Lynda Merzoud
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1 - 5, rue de la Doua, F-69100 Villeurbanne, France.
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1 - 5, rue de la Doua, F-69100 Villeurbanne, France.
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