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Zhang Z, Ma Y, Chen C, Bondarchuk SV, Liu Y. A General Model of Impact Sensitivity for Nitrogen-Rich Energetic Materials: A Combined Incremental Theory and Genetic Function Approximation Study. Chemphyschem 2024; 25:e202400014. [PMID: 38388960 DOI: 10.1002/cphc.202400014] [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: 01/05/2024] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 02/24/2024]
Abstract
In this paper, we report the first example of impact sensitivity prediction based on the genetic function approximation (GFA) as a regression method. The prediction is applicable for a wide variety of chemical families, which include nitro compounds, peroxides, nitrogen-rich salts, heterocycles, etc. Within this work, we have obtained 7 empirical models (with 27-32 basis functions), which all provide 0.80≤R2≤0.83 and 7.2 J≤RMSE≤7.8 J (for 450 training set compounds) and 0.64≤R2≤0.70 and 11.2 J≤RMSE≤12.4 J (for 170 test set compounds). The models were developed using Friedman Lack-of-Fit as a scoring function, which allows avoiding an overfitting. All the models have simple descriptors as basis functions and include linear splines. Furthermore, the applied descriptors do not require expensive calculation procedures, namely, non-empirical quantum-chemical calculations, complex iterative procedures, real space electron density analysis, etc. Most descriptors are based on structural and topological analysis and a part of them require very cheap semi-empirical PM6 calculations. The prediction takes a few minutes as an average, and most of the time is for the structure preparation and manual calculation of the descriptor "Increment", which is based on our recent incremental theory.
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Affiliation(s)
- Zhixiang Zhang
- Xi'an Modern Chemistry Research Institute, Xi'an, 710065, P. R. China
- Xi'an Key Laboratory of Liquid Crystal and Organic Photovoltaic Materials, Xi'an, 710065, P. R. China
| | - Yiding Ma
- Xi'an Modern Chemistry Research Institute, Xi'an, 710065, P. R. China
- Xi'an Key Laboratory of Liquid Crystal and Organic Photovoltaic Materials, Xi'an, 710065, P. R. China
| | - Chao Chen
- Xi'an Modern Chemistry Research Institute, Xi'an, 710065, P. R. China
- Xi'an Key Laboratory of Liquid Crystal and Organic Photovoltaic Materials, Xi'an, 710065, P. R. China
| | - Sergey V Bondarchuk
- Department of Chemistry and Nanomaterials Science, The Bohdan Khmelnytsky National University of Cherkasy, blvd. Shevchenko, 81, Cherkasy, 18031, Ukraine
| | - Yingzhe Liu
- Xi'an Modern Chemistry Research Institute, Xi'an, 710065, P. R. China
- National Key Laboratory of Energetic Materials, Xi'an, 710065, P. R. China
- Xi'an Key Laboratory of Liquid Crystal and Organic Photovoltaic Materials, Xi'an, 710065, P. R. China
- State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an, 710065, P. R. China
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Martinez-Mayorga K, Rosas-Jiménez JG, Gonzalez-Ponce K, López-López E, Neme A, Medina-Franco JL. The pursuit of accurate predictive models of the bioactivity of small molecules. Chem Sci 2024; 15:1938-1952. [PMID: 38332817 PMCID: PMC10848664 DOI: 10.1039/d3sc05534e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Property prediction is a key interest in chemistry. For several decades there has been a continued and incremental development of mathematical models to predict properties. As more data is generated and accumulated, there seems to be more areas of opportunity to develop models with increased accuracy. The same is true if one considers the large developments in machine and deep learning models. However, along with the same areas of opportunity and development, issues and challenges remain and, with more data, new challenges emerge such as the quality and quantity and reliability of the data, and model reproducibility. Herein, we discuss the status of the accuracy of predictive models and present the authors' perspective of the direction of the field, emphasizing on good practices. We focus on predictive models of bioactive properties of small molecules relevant for drug discovery, agrochemical, food chemistry, natural product research, and related fields.
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Affiliation(s)
- Karina Martinez-Mayorga
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José G Rosas-Jiménez
- Department of Theoretical Biophysics, IMPRS on Cellular Biophysics Max-von-Laue Strasse 3 Frankfurt am Main 60438 Germany
| | - Karla Gonzalez-Ponce
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
| | - Edgar López-López
- Department of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute Mexico City 07000 Mexico
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
| | - Antonio Neme
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
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3
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Keshavarz MH, Shirazi Z, Barghahi A, Mousaviazar A, Zali A. A novel model for prediction of stability constants of the thiosemicarbazone ligands with different types of toxic heavy metal ions using structural parameters and multivariate linear regression method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37084-37095. [PMID: 35031996 DOI: 10.1007/s11356-021-17714-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
A novel model is presented for reliable estimation of the stability constants of the thiosemicarbazone ligands with different types of toxic heavy metal ions (log β11) in an aqueous solution, which has wide usage in environmental safety and ecotoxicology applications. The biggest reported data of log β11 for 120 metalthiosemicarbazone complexes are used for deriving and testing the novel model. In contrast to available methods where they need the two-dimensional (2D) and three-dimensional (3D) complex molecular descriptors as well as expert users and computer codes, the novel correlation uses four additive and two non-additive structural parameters of thiosemicarbazone ligands. The calculated results of the novel correlation are compared with the outputs of the genetic algorithm with multivariate linear regression method (GA-MLR) as one of the best existing methods, which requires seven complex descriptors. The estimated results for 78 of training as well as 42 of two different test sets were established by external and internal validations. The values of statistical parameters comprising average deviation, average absolute deviation, average absolute relative deviation, absolute maximum deviation, and the coefficient of determination for 73 data of training set of New model/GA-MLR are 0.04/ - 0.25, 1.06/1.31, 14.4/18.7, 3.18/7.92, and 0.830/0.652, respectively. Thus, the predicted results of the new model are worthy as compared to the complex GA-MLR model. Moreover, assessments of various statistical parameters confirm that the new model provides great reliability, goodness-of-fit, accuracy, and precision.
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Affiliation(s)
| | - Zeinab Shirazi
- Faculty of Applied Sciences, Malek Ashtar University of Technology, Shahin Shahr, Iran
| | - Asileh Barghahi
- Faculty of Applied Sciences, Malek Ashtar University of Technology, Shahin Shahr, Iran
| | - Ali Mousaviazar
- Faculty of Applied Sciences, Malek Ashtar University of Technology, Shahin Shahr, Iran
| | - Abbas Zali
- Faculty of Applied Sciences, Malek Ashtar University of Technology, Shahin Shahr, Iran
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4
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Keshavarz MH, Hasani R. Simple Approach for Reliable Prediction of the Flash Point of Organosilicon Compounds as Compared to the Best Available Methods. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c03327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Ronak Hasani
- Faculty of Applied Sciences, Malek Ashtar University of Technology, Shahin Shahr 8315713115, Iran
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Fayet G, Rotureau P. Chemoinformatics for the Safety of Energetic and Reactive Materials at Ineris. Mol Inform 2020; 41:e2000190. [PMID: 33283975 DOI: 10.1002/minf.202000190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/06/2020] [Indexed: 11/07/2022]
Abstract
The characterization of physical hazards of substances is a key information to manage the risks associated to their use, storage and transport. With decades of work in this area, Ineris develops and implements cutting-edge experimental facilities allowing such characterizations at different scales and under various conditions to study all of the dreaded accident scenarios. This review presents the efforts engaged by Ineris more recently in the field of chemoinformatics to develop and use new predictive methods for the anticipation and management of industrials risks associated to energetic and reactive materials as a complement to experiments. An overview of the methods used for the development of Quantitative Structure-Property Relationships for physical hazards are presented and discussed regarding the specificities associated to this class of properties. A review of models developed at Ineris is also provided from the first tentative models on the explosivity of nitro compounds to the successful application to the flammability of organic mixtures. Then, a discussion is proposed on the use of QSPR models. Good practices for robust use for QSPR models are recalled with specific comments related to physical hazards, notably for regulatory purpose. Dissemination and training efforts engaged by Ineris are also presented. The potential offered by these predictive methods in terms of in silico design and for the development of new intrinsically safer technologies in safety-by-design strategies is finally discussed. At last, challenges and perspectives to extend the application of chemoinformatics in the field of safety and in particular for the physical hazards of energetic and reactive substances are proposed.
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Affiliation(s)
- Guillaume Fayet
- Ineris, Accidental Risk Division, Parc Technologique Alata, 60550, Verneuil-en-Halatte, France
| | - Patricia Rotureau
- Ineris, Accidental Risk Division, Parc Technologique Alata, 60550, Verneuil-en-Halatte, France
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A simple model for the assessment of the agonistic activity of dibenzazepine derivatives by molecular moieties. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02654-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Jafari M, Keshavarz MH, Ebadpour R. A Simple Approach to Assess the Performance of Non‐ideal Aluminum/Ammonium Perchlorate Composite Explosives as Compared to the Best Available Methods. Z Anorg Allg Chem 2020. [DOI: 10.1002/zaac.202000269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mohammad Jafari
- Faculty of Sciences Malek‐ashtar University of Technology Shahin‐Shahr Iran
| | | | - Reza Ebadpour
- Faculty of Sciences Malek‐ashtar University of Technology Shahin‐Shahr Iran
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8
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Keshavarz MH, Bagheri V. A Simple Correlation for Assessment of the Shock Wave Energy in Underwater Detonation. Z Anorg Allg Chem 2019. [DOI: 10.1002/zaac.201900221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Vahid Bagheri
- Department of Chemistry; Malek-ashtar University of Technology; P.O. Box 83145/115 Shahin-Shahr Iran
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Du M, Han T, Liu F, Wu H. Theoretical investigation of the structure, detonation properties, and stability of bicyclo[3.2.1]octane derivatives. J Mol Model 2019; 25:253. [DOI: 10.1007/s00894-019-4116-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/02/2019] [Indexed: 11/24/2022]
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Abstract
A comprehensive theoretical study of 18 metal azides is reported.
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Affiliation(s)
- Sergey V. Bondarchuk
- Department of Chemistry and Nanomaterials Science
- Bogdan Khmelnitsky Cherkasy National University
- 18031 Cherkasy
- Ukraine
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Bondarchuk SV. Quantification of Impact Sensitivity Based on Solid-State Derived Criteria. J Phys Chem A 2018; 122:5455-5463. [PMID: 29851488 DOI: 10.1021/acs.jpca.8b01743] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergey V. Bondarchuk
- Department of Chemistry and Nanomaterials Science, Bogdan Khmelnitsky Cherkasy National University, blvd. Shevchenko 81, 18031 Cherkasy, Ukraine
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12
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Computational study of the structure and properties of bicyclo[3.1.1]heptane derivatives for new high-energy density compounds with low impact sensitivity. J Mol Model 2017; 24:17. [PMID: 29256012 DOI: 10.1007/s00894-017-3540-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022]
Abstract
To design new high-energy density compounds (HEDCs), a series of new bicyclo[2.2.1]heptane derivatives containing an aza nitrogen atom and nitro substituent were designed and studied theoretically. The density, heat of sublimation and impact sensitivity were estimated by electrostatic potential analysis of the molecular surface. Based on the designed isodesmic reaction, and the reliable heat of formation (HOF) of the reference compounds, HOFs were calculated and compared at B3LYP/6-311G(d,p) and B3P86/6-311G(d,p), respectively. The detonation performances, bond dissociation energies (BDE) and impact sensitivity were calculated to evaluate the designed compounds. The calculated results show that the number of aza nitrogen atoms and NO2 groups are two important factors for improving HOF, density and detonation properties. Thermal stability generally decreases with increasing nitro groups. And the N-NO2 bond is the trigger bond for all designed compounds except B8, whose trigger bond is C-NO2. Importantly, the BDE values are between 86.95 and 179.71 kJ mol-1 and meet the requirement for HEDCs. Detonation velocity and detonation pressure were found to be 5.77-9.65 km s-1 and 12.30-43.64 GPa, respectively. After comprehensive consideration of thermal stability, impact sensitivity and detonation properties, A7, A8, B8, C8, D7, E7, F7 and G6 may be considered as potential HEDCs. Especially, A8, B8, C8, and D7 have better detonation properties than the famous caged nitramine CL-20 (D = 9.40 km/s, P = 42.00GPa). Besides, all the designed potential HEDCs have reasonable impact sensitivity. Graphical abstract New high-energy density compounds (HEDCs) with low impact sensitivity (A8, B8, C8 and D7 have better detonation properties than CL-20).
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Prana V, Rotureau P, André D, Fayet G, Adamo C. Development of Simple QSPR Models for the Prediction of the Heat of Decomposition of Organic Peroxides. Mol Inform 2017; 36. [PMID: 28402598 DOI: 10.1002/minf.201700024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/30/2017] [Indexed: 12/22/2022]
Abstract
Quantitative structure-property relationships represent alternative method to experiments to access the estimation of physico-chemical properties of chemicals for screening purpose at R&D level but also to gather missing data in regulatory context. In particular, such predictions were encouraged by the REACH regulation for the collection of data, provided that they are developed respecting the rigorous principles of validation proposed by OECD. In this context, a series of organic peroxides, unstable chemicals which can easily decompose and may lead to explosion, were investigated to develop simple QSPR models that can be used in a regulatory framework. Only constitutional and topological descriptors were employed to achieve QSPR models predicting the heat of decomposition, which could be used without any time consuming preliminary structure calculations at quantum chemical level. To validate the models, the original experimental dataset was divided into a training and a validation set according to two methods of partitioning, one based on the property value and the other based on the structure of the molecules by the mean of PCA. Four QSPR models were developed upon the type of descriptors and the methods of partitioning. The 2 models issuing from the PCA based method were highlighted as they presented good predictive power and they are easier to apply than our previous quantum chemical based model, since they do not need any preliminary calculations.
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Affiliation(s)
- Vinca Prana
- Institut National de l'Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France.,Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005, Paris, France
| | - Patricia Rotureau
- Institut National de l'Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France
| | - David André
- ARKEMA, rue Henri Moissan, BP63, 69493, Pierre Benite, France
| | - Guillaume Fayet
- Institut National de l'Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005, Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005, Paris, France
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Yosipof A, Shimanovich K, Senderowitz H. Materials Informatics: Statistical Modeling in Material Science. Mol Inform 2016; 35:568-579. [DOI: 10.1002/minf.201600047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/11/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Abraham Yosipof
- Department of Business Administration; Peres Academic Center; Rehovot 76102 Israel
- College of Law & Business; Ramat-Gan 26 Ben Gurion Street Israel
| | - Klimentiy Shimanovich
- Department of Chemistry; Bar Ilan University; Ramat-Gan 5290002 Israel
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering; Tel Aviv University; Ramat Aviv 69978 Israel
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Mathieu D. Physics-Based Modeling of Chemical Hazards in a Regulatory Framework: Comparison with Quantitative Structure–Property Relationship (QSPR) Methods for Impact Sensitivities. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b01536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Keshavarz MH, Keshavarz Z. Relation between Electric Spark Sensitivity and Impact Sensitivity of Nitroaromatic Energetic Compounds. Z Anorg Allg Chem 2016. [DOI: 10.1002/zaac.201600015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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