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Oliveira RSS, Oliveira MAS, Borges I. The effect of the electronic structure method and basis set on the accuracy of the electric multipoles computed with the distributed multipole analysis (DMA). J Mol Model 2023; 29:357. [PMID: 37917318 DOI: 10.1007/s00894-023-05758-3] [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: 09/02/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
CONTEXT An accurate description of the molecular charge density is crucial for investigating intra- and inter-molecular properties. Among the different ways of describing and analyzing it, the widely used distributed multipole analysis (DMA) is an accurate method for decomposing the molecular charge density into atom-centered electric multipoles (monopole, dipole, quadrupole, and so on) that have a direct chemical interpretation. In this work, DMA was employed to decompose the molecular charge density of six chemically distinct molecules, namely, (2R)-2-amino-3-[(S)-prop-2-enylsulfinyl] propanoic acid (AAP), 4-amine-2-nitro-1,3,5 triazole (ANTA), (RS)-Propan-2-yl methylphosphonofluoridate (SARIN), chloromethane (CLMET), and 2-aminoacetic acid (GLY) into monopole, dipole, and quadrupole values. A hypothetical variation of ANTA built by exchanging all the nitrogen atoms with phosphorus that we named 4-phosphine-2-phosphite-1,3,5-phosphorine (ANTAP) was also studied. These molecules have different chemical structures bearing distinct carbon skeletons, electronegative atoms, and electron-withdrawing/donating groups. We found that although DFT multipole values can depend considerably on the exchange-correlation functional for specific atomic sites, the associated root-mean-square errors (RMSEs) compared to benchmark MP4 mainly were about [Formula: see text] The most significant variations were for monopoles and dipoles of sites highly polarized by adjacent atoms, and to a lesser degree, for the quadrupoles. The double hybrid B2PLYP and the hybrid meta M06-2X functionals, as expected in the framework of Jacob's ladder, overall give the most accurate results among the DFT methods. The MP2 DMA multipole values have an RMSE in relation to the MP4 benchmark mainly in the range [Formula: see text], thus representing a lower computational cost to obtain results with similar good accuracy without the ambiguity of choosing a DFT functional. The deviations of the HF multipoles from the benchmark in most cases were less than 20%, in agreement with the well-known fact that non-correlated charge densities have a slight dependence on the electronic correlation. We also confirmed that DMA values have a small dependence on the size of the basis set: deviations did not exceed 5% in most cases. However, the dependence of the DMA values on the size of the basis set increases with the rank of the electric multipole. To compute accurate values of DMA multipoles of an atom bonded to very electronegative atoms, especially dipoles and quadrupoles, a large basis set including diffuse functions is necessary. Despite that, for a given polarized basis set, the choice of the basis set to compute accurate DMA multipole values is not critical. METHODS The molecular charge densities were computed using the electronic structure methods Hartree-Fock (HF), MP2, MP4, DFT/PBE, DFT/B3LYP, DFT/B3PW91, DFT/M06-2X, and DFT/B2PLYP implemented in the Gaussian 09 package. MP4 was the benchmark method. The DMA multipoles were obtained with the GDMA program of Stone. The 6-311G + + (d,p) basis set was used for the production calculations, and the augmented correlation-consistent Dunning's hierarchy of basis sets was employed to evaluate the dependence of the DMA multipoles on the basis set size.
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Affiliation(s)
| | - Marco Aurélio Souza Oliveira
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Rio de Janeiro, RJ, 22290-270, Brazil
| | - Itamar Borges
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Rio de Janeiro, RJ, 22290-270, Brazil.
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Duarte JC, da Rocha RD, Borges I. Which molecular properties determine the impact sensitivity of an explosive? A machine learning quantitative investigation of nitroaromatic explosives. Phys Chem Chem Phys 2023; 25:6877-6890. [PMID: 36799468 DOI: 10.1039/d2cp05339j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We decomposed density functional theory charge densities of 53 nitroaromatic molecules into atom-centered electric multipoles using the distributed multipole analysis that provides a detailed picture of the molecular electronic structure. Three electric multipoles, (the charge of the nitro groups), (the total dipole, i.e., polarization, of the nitro groups), (the total electron delocalization of the C ring atoms), and the number of explosophore groups (#NO2) were selected as features for a comprehensive machine learning (ML) investigation. The target property was the impact sensitivity h50 (cm) values quantified by drop-weight measurements, with a large h50 (e.g., 150 cm) indicating that an explosive is insensitive and vice versa. After a preliminary screening of 42 ML algorithms, four were selected based on the lowest root mean square errors: Extra Trees, Random Forests, Gradient Boosting, and AdaBoost. Compared to experimental data, the predicted h50 values of molecules having very different sensitivities for the four algorithms have differences in the range 19-28%. The most important properties for predicting h50 are the electron delocalization in the ring atoms and the polarization of the nitro groups with averaged weights of 39% and 35%, followed by the charge (16%) and number (10%) of nitro groups. A significant result is how the contribution of these properties to h50 depends on their actual sensitivities: for the most sensitive explosives (h50 up to ∼50 cm), the four properties contribute to reducing h50, and for intermediate ones (∼50 cm ≲ h50 ≲ 100 cm) #NO2 and contribute to increasing it and the other two properties to reducing it. For highly insensitive explosives (h50 ≳ 200 cm), all four properties essentially contribute to increasing it. These results furnish a consistent molecular basis of the sensitivities of known explosives that also can be used for developing safer new ones.
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Affiliation(s)
- Julio Cesar Duarte
- Departamento de Engenharia de Computação, Instituto Militar de Engenharia, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Urca, Rio de Janeiro (RJ), 22290-270, Brazil. .,Programa de Pós-Graduação em Engenharia de Defesa, Militar de Engenharia, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Urca, Rio de Janeiro (RJ), 22290-270, Brazil
| | - Romulo Dias da Rocha
- Programa de Pós-Graduação em Engenharia de Defesa, Militar de Engenharia, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Urca, Rio de Janeiro (RJ), 22290-270, Brazil
| | - Itamar Borges
- Departamento de Engenharia de Computação, Instituto Militar de Engenharia, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Urca, Rio de Janeiro (RJ), 22290-270, Brazil. .,Departamento de Química, Militar de Engenharia, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Urca, Rio de Janeiro (RJ), 22290-270, Brazil
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Salam HAAE, Mohamed GG, Zayed EM. Synthesis, spectroscopic characterization, biological application and molecular docking studies of some transition metal complexes of isophthalamide ligand. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Klapec DJ, Czarnopys G, Pannuto J. Interpol review of the analysis and detection of explosives and explosives residues. Forensic Sci Int Synerg 2023; 6:100298. [PMID: 36685733 PMCID: PMC9845958 DOI: 10.1016/j.fsisyn.2022.100298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Douglas J. Klapec
- Arson and Explosives Section I, United States Department of Justice, Bureau of Alcohol, Tobacco, Firearms and Explosives, Forensic Science Laboratory, 6000 Ammendale Road, Ammendale, MD, 20705, USA
| | - Greg Czarnopys
- Forensic Services, United States Department of Justice, Bureau of Alcohol, Tobacco, Firearms and Explosives, Forensic Science Laboratory, 6000 Ammendale Road, Ammendale, MD, 20705, USA
| | - Julie Pannuto
- United States Department of Justice, Bureau of Alcohol, Tobacco, Firearms and Explosives, Forensic Science Laboratory, 6000 Ammendale Road, Ammendale, MD, 20705, USA
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Zayed EM, Mohamed GG, Abd El Salam HA. Ni(II), Co(II), Fe(III), and Zn(II) mixed ligand complexes of indoline-dione and naphthalene-dione: Synthesis, characterization, thermal, antimicrobial, and molecular modeling studies. INORG CHEM COMMUN 2023. [DOI: 10.1016/j.inoche.2022.110276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abd El Salam HA, Moustafa G, Zayed EM, Mohamed GG. Isophthaloylbis (Azanediyl) Dipeptide Ligand and Its Complexes: Structural Study, Spectroscopic, Molecular Orbital, Molecular Docking, and Biological Activity Properties. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | - Gaber Moustafa
- Peptides Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Ehab M. Zayed
- Green Chemistry Department, National, Research Centre, Dokki, Giza, Egypt
| | - Gehad G. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
- Nanoscience Department, Basic and Applied Sciences Institute, Egypt-Japan University of Science and Technology, Alexandria, Egypt
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Zengel ER, Garcia JR, Goodrich DA, Bayse CA. Trigger bond analysis of azo‐based energetic materials. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elizabeth R. Zengel
- Department of Chemistry and Biochemistry Old Dominion University Norfolk VA USA
| | - Jenna R. Garcia
- Department of Chemistry and Biochemistry Old Dominion University Norfolk VA USA
| | - Daja A. Goodrich
- Department of Chemistry and Biochemistry Old Dominion University Norfolk VA USA
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry Old Dominion University Norfolk VA USA
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Oliveira MAS, Oliveira RSS, Borges I. Quantifying bond strengths via a Coulombic force model: application to the impact sensitivity of nitrobenzene, nitrogen-rich nitroazole, and non-aromatic nitramine molecules. J Mol Model 2021; 27:69. [PMID: 33543327 DOI: 10.1007/s00894-021-04669-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/12/2021] [Indexed: 11/28/2022]
Abstract
The quantification of bond strengths is a useful and general concept in chemistry. In this work, a Coulombic force model based on atomic electric charges computed using the accurate distributed multipole analysis (DMA) partition of the molecular charge density was employed to quantify the weakest N-NO2 and C-NO2 bond strengths of 19 nitrobenzene, 11 nitroazole, and 10 nitramine molecules. These bonds are known as trigger linkages because they are usually related to the initiation of an explosive. The three families of explosives combine different types of molecular properties and structures ranging from essentially aromatic molecules (nitrobenzenes) to others with moderate aromaticity (nitroazoles) and non-aromatic molecules with cyclic and acyclic skeletons (nitramines). We used the results to investigate the impact sensitivity of the corresponding explosives employing the trigger linkage concept. For this purpose, the computed Coulombic bond strength of the trigger linkages was used to build four sensitivity models that lead to an overall good agreement between the predicted values and available experimental sensitivity values even when the model included the three chemical families simultaneously. We discussed the role of the trigger linkages for determining the sensitivity of the explosives and rationalized eventual discrepancies in the models by examining alternative decomposition mechanisms and features of the molecular structures.
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Affiliation(s)
- Marco Aurélio Souza Oliveira
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Rio de Janeiro, RJ, 22290-270, Brazil
| | | | - Itamar Borges
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, Rio de Janeiro, RJ, 22290-270, Brazil.
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Siqueira Soldaini Oliveira R, Borges I. Correlation Between Molecular Charge Properties and Impact Sensitivity of Explosives: Nitrobenzene Derivatives. PROPELLANTS EXPLOSIVES PYROTECHNICS 2021. [DOI: 10.1002/prep.202000233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Itamar Borges
- Departamento de Química Instituto Militar de Engenharia (IME) Praça General Tibúrcio, 80 Rio de Janeiro RJ 22290-270 Brazil
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