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Li Q, Yang H, Hao N, Du M, Zhao Y, Li Y, Li X. Biodegradability analysis of Dioxins through in silico methods: Model construction and mechanism analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118898. [PMID: 37657295 DOI: 10.1016/j.jenvman.2023.118898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/18/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
The biodegradation treatment of dioxins has long been of interest due to its good ecological and economic effects. In this study, the biodegradability of polychlorinated dibenzo-p-dioxins (PCDDs) were investigated by constructing machine learning and multiple linear regression models. The maximum chlorine atomic charge (qHirshfeldCl+), which characterizes the biodegradation ability of PCDDs, was used as the response value. The random forest model was used to rank the importance on the 1471 descriptors of PCDDs, and the BCUTp-1 h, QXZ, JGI4, ATSC8c, VE3_Dt, topoShape, and maxwHBa were screened as the important descriptors by Pearson's correlation coefficient method. A quantitative structure-activity relationship (QSAR) model was constructed to predict the biodegradability of PCDDs. In addition, the extreme gradient boosting (XGBoost) and random forest model were also constructed and proved the good predictability of QSAR model. The biodegradability of polychlorinated dibenzofurans (PCDFs) can also be predicted by the constructed three models from a certain level after adjusting some model parameters, which further proved the versatility of the models. Besides, the sensitivity analysis of the QSAR model and a 3D-QSAR model was developed to investigate the biodegradability mechanisms of PCDDs. Results showed that the descriptors BCUTp-1 h, JGI4, and maxwHBa were the key descriptors in the biodegradability effect by the sensitivity analysis of the QSAR model. Coupled with the results of PCDDs biodegradability 3D-QSAR model, BCUTp-1 h, JGI4, and maxwHBa were confirmed as the main descriptors that affect the biodegradability of dioxins. This study provides a novel theoretical perspective for the research of the biodegradation of both PCDDs and PCDFs dioxins.
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Affiliation(s)
- Qing Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Hao Yang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Ning Hao
- College of New Energy and Environment, Jilin University, Changchun, 130012, China.
| | - Meijn Du
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yuanyuan Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Xixi Li
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
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V S, A S, A M, S T, Bahadur S A, S A. Structural, Vibrational and Electro-Optical Properties on Perchlorate Salt of 4-Methoxyanline Studied through Experimental and Theoretical Methods. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Siva V
- Department of Physics, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Shameem A
- Department of Physics, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Murugan A
- Department of Physics, School of Advanced Sciences, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
- Condensed Matter Physics Laboratory, International Research Centre, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Thangarasu S
- Department of Physics, School of Advanced Sciences, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
- Condensed Matter Physics Laboratory, International Research Centre, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Asath Bahadur S
- Department of Physics, School of Advanced Sciences, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
- Condensed Matter Physics Laboratory, International Research Centre, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Athimoolam S
- Department of Physics, University College of Engineering Nagercoil, Anna University, Nagercoil, Tamil Nadu, India
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Crystal structure, Hirshfeld surface analysis, and DFT calculations of methyl (Z)-4-((4-((4-bromobenzyl)selanyl)phenyl)amino)-4-oxobut-2-enoate. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Etse KS, Lamela LC, Zaragoza G, Pirotte B. Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. ACTA ACUST UNITED AC 2020. [DOI: 10.5155/eurjchem.11.2.91-99.1973] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The title compound 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione was obtained by reaction of thymine with 3-nitrobenzylbromide in the presence of cesium carbonate. Characterization of the product was achieved by NMR spectroscopy and its stability was probed in basic condition using UV-Visible analysis. Furthermore, the molecular structure was confirmed by X-ray diffraction analysis. The compound crystallizes in orthorhombic Pna21 space group with unit cell parameters a = 14.9594 (15) Å, b = 25.711 (3) Å, c = 4.5004 (4) Å, V = 1731.0 (3) Å3 and Z = 4. The crystal packing of the title compound is stabilized by intermolecular hydrogen bond, π···π and C−H···π stacking interactions. The intermolecular interactions were furthermore analyzed through the mapping of different Hirshfeld surfaces. The two-dimensional fingerprint revealed that the most important contributions to these surfaces come from O···H (37.1%), H···H (24%) and H···C/C···H (22.6%) interactions. The interaction energies stabilizing the crystal packing were calculated and were presented graphically as framework energy diagrams. Finally, the energy-framework analysis reveals that π···π and C−H···π interactions energies are mainly dispersive and are the most important forces in the crystal.
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Affiliation(s)
- Koffi Senam Etse
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
| | - Laura Comeron Lamela
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
| | - Guillermo Zaragoza
- Unidade de Difracción de Raios X, RIAIDT, Universidade de Santiago de Compostela, Campus VIDA, 15782 Santiago de Compostela, Spain
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
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Golla R, Kumar PR, Suchethan P, Foro S, Nagaraju G. Synthesis, photophysical, electrochemical properties and crystal structures and Hirschfeld surface analysis of 4′-dimethoxyphenyl-(2,6-di-2-pyrazinyl) pyridines. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Synthesis, characterisation, crystal structures, anticoagulant and antiplatelet activity studies of new 2,6-dipyrazinylpyridines with pendant trimethoxyphenyl. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Kansız S, Tolan A, İçbudak H, Dege N. Synthesis, crystallographic structure, theoretical calculations, spectral and thermal properties of trans-diaquabis(trans-4-aminoantipyrine)cobalt(II) acesulfamate. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.04.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Demircioğlu Z, Ersanli CC, Kaya kantar G, Şaşmaz S. Spectroscopic, Hirshfeld surface, X-ray diffraction methodologies and local & global chemical activity calculations of 5-(2-methoxy-4-(prop-1-en-1-yl)phenoxy)pyrazine-2,3-dicarbonitrile. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.072] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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