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Hydrolysis Mechanism of Carbamate Methomyl by a Novel Esterase PestE: A QM/MM Approach. Int J Mol Sci 2022; 24:ijms24010433. [PMID: 36613879 PMCID: PMC9820155 DOI: 10.3390/ijms24010433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Methomyl is one of the most important carbamates that has caused potential hazardous effects on both human beings and the environment. Here, we systematically investigated the hydrolysis mechanism of methomyl catalyzed by esterase PestE using molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The hydrolysis mechanism involves two elementary steps: (Ⅰ) serine-initiated nucleophilic attack and (Ⅱ) C-O bond cleavage. Our work elicits the atomic level details of the hydrolysis mechanism and free energy profiles along the reaction pathway. The Boltzmann-weighted average potential barriers are 19.1 kcal/mol and 7.5 kcal/mol for steps Ⅰ and Ⅱ, respectively. We identified serine-initiated nucleophilic attack as the rate determining-step. The deep learning-based kcat prediction model indicated that the barrier of the rate-determining step is 15.4 kcal/mol, which is in good agreement with the calculated results using Boltzmann-weighted average method. We have elucidated the importance of the protein-substrate interactions and the roles of the key active site residues during the hydrolysis process through noncovalent interactions analysis and electrostatic potential (ESP) analysis. The results provide practical value for achieving efficient degradation of carbamates by hydrolases.
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Ermiş E, Ermiş T, Şahiner A. Synthesis, characterization of (E)-3-((2‑hydroxy-5-(thiophen-2-yl)benzylidene)amino)benzonitrile and optimization of its energy by Fuzzy Logic Modelling. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133056] [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]
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3
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Kowsalya P, Neelakantan M, Bhuvanesh NS. Tetranuclear Cu(II) complex with [2+4] Cu4O4 cubane based core framework derived from 2-[{2-(1-hydroxy-ethyl)-phenylimino}-methyl]-6-methoxy-phenol: Quantifying conventional and unconventional interactions and QTAIM analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132396] [Citation(s) in RCA: 2] [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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Salih KSM. Solvent Influence on Absorption Spectra and Tautomeric Equilibria of Symmetric Azomethine-Functionalized Derivatives: Structural Elucidation and Computational Studies. ChemistryOpen 2022; 11:e202100237. [PMID: 35191603 PMCID: PMC8862155 DOI: 10.1002/open.202100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
A new series of azomethine-functionalized compounds was synthesized from the condensation of 2-hydroxy-1,3-propanediamine and 2-thienylcarboxaldehydes in the presence of a drying agent. The derivatives were spectroscopically characterized by NMR, LC-MS, UV/Vis, IR and elemental analysis. Variable temperature 1 H-NMR (-60 to +60 °C) was performed to investigate the effect of solvent polarity; the capability of solvent to form H-bond was found to dramatically influencing the tautomerization process of the desired structures. The calculated thermochemical parameters (ΔH298 , ΔG298 and ΔS298 ) at DFT and MP2 levels of theory explained that 3 b exists in equilibrium with two tautomers. The basis of the electronic absorptions was pursued through Time-Dependent Density-Functional Theory (TD-DFT). Analysis of the structural surfaces was inspected and the molecular electrostatic potential (MEP) demonstrated that the three functionalized compounds were relatively analogous in the electronic distributions. Furthermore, the electrophilic and nucleophilic centers lying on the molecular surfaces were probably playing a key-role in stabilizing the compounds through the nonclassical C-H⋅⋅⋅π interactions and hydrogen bonding. The impact of solvent polarity on absorption spectra were investigated via solvatochromic shifts. For instance, compound 3 c displayed a gradual shift of the maximum absorption to the red area when the solvent polarity was increased, recording a 21 nm of bathochromic shift. In contrast, no significant solvent-effect on 3 a and 3 b was observed. The solvation relation was pursued between Gutmann's donicity numbers the experimental λmax ; exhibited almost positive linear performance with a minor oscillation, that ascribe to the possible weak interface between the molecules of solute and designated solvents. The bandgap energy of all products were assessed experimentally using optical absorption spectra following Tauc approach, giving -4.050 (3 a), -3.900 (3 b) and -3.210 (3 c) eV. However, the ΔE were computationally figured out from TD-DFT simulation to be -4.258 (3 a), -4.022 (3 b) and -3.390 (3 c) eV.
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Affiliation(s)
- Kifah S. M. Salih
- Department of Chemistry and Earth SciencesCollege of Arts and SciencesQatar UniversityP. O. Box 2713DohaState of Qatar
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Prasad HSN, Ananda A, Lohith T, Prabhuprasad P, Jayanth H, Krishnamurthy N, Sridhar M, Mallesha L, Mallu P. Design, synthesis, molecular docking and DFT computational insight on the structure of Piperazine sulfynol derivatives as a new antibacterial contender against superbugs MRSA. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Synthesis, characterization, surface analysis, optical activity and solvent effects on the electronic absorptions of Schiff base-functionalized amino thiophene derivatives: Experimental and TD-DFT investigations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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7
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Boshaala A, Salih KS, Bader N, Almughery AA, Zarrouk A, Warad I. XRD/HSA, noncovalent interactions and influence of solvent polarity on spectral properties of dithiocarbazate schiff base and its cis-Cu(II) complex: Experimental and theoretical studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115551] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Ermiş E, Aydın A, Ünver H, Sezen S, Mutlu MB. Microwave assisted synthesis, experimental and theoretical characterization and antibacterial activity screening of novel azomethine compounds containing thiophene and aminophenol functionality. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 243:118761. [PMID: 32854082 DOI: 10.1016/j.saa.2020.118761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Eight new azomethine compounds (3a-3h) containing thiophene and aminophenol functionality were synthesized in excellent yields by using conventional heating and microwave assisted synthesis methods. The structures of newly synthesized compounds were characterized by spectroscopic techniques such as UV-Vis, FTIR, 1H and 13C NMR and elemental analysis. UV-Vis and 1H NMR results show that all compounds prefer the phenol-imine tautomer form in solvent media. The chemical structure of 3a, 3b and 3g was also confirmed by single crystal X-ray diffraction method. The molecular conformations of 3a, 3b and 3g are stabilized by an N+-H⋯O- type intramolecular hydrogen bond in zwitterionic form in the crystalline solid state. The optimized molecular structures, 1H and 13C NMR chemical shift values, UV-Vis spectroscopic parameters, HOMO-LUMO energies, Mulliken (MPA) and natural (NBO) atomic charges, Natural bond orbitals (NBO), molecular electrostatic potential (MEP) maps and solvent accessible surfaces (SASs) for 3a-3h were calculated by using DFT/B3LYP/6-311G(2d,p) approach. The theoretical spectroscopic features obtained by DFT calculations show a very good agreement with the experimental data. In addition, the synthesized compounds (3a-3h) were screened for their antibacterial activities against Bacillus cereus (NRRL-B3711), Bacillus subtilis (NRRL-B4378), Escherichia coli (NRRL B-3008), Staphylococcus aureus (ATCC-6538) and Salmonella typhimurium (ATCC-13311). The results show that investigated compounds have either moderately active, slightly active or inactive among the tested microorganisms. 3a exhibited the stronger antibacterial activity against all test bacteria than other compounds. It also has been observed that compounds with relatively low HOMO-LUMO energy gaps exhibit better antibacterial effects.
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Affiliation(s)
- Emel Ermiş
- Eskisehir Technical University, Faculty of Science, Department of Chemistry, Yunus Emre Campus, 26470 Tepebasi, Eskisehir, Turkey.
| | - Atakan Aydın
- Eskisehir Technical University, Faculty of Science, Department of Chemistry, Yunus Emre Campus, 26470 Tepebasi, Eskisehir, Turkey
| | - Hakan Ünver
- Eskisehir Technical University, Faculty of Science, Department of Chemistry, Yunus Emre Campus, 26470 Tepebasi, Eskisehir, Turkey
| | - Suat Sezen
- Eskisehir Technical University, Faculty of Science, Department of Biology, Yunus Emre Campus, 26470 Tepebasi, Eskisehir, Turkey
| | - Mehmet Burçin Mutlu
- Eskisehir Technical University, Faculty of Science, Department of Biology, Yunus Emre Campus, 26470 Tepebasi, Eskisehir, Turkey
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Novel thiophene-benzothiazole derivative azomethine and amine compounds: Microwave assisted synthesis, spectroscopic characterization, solvent effects on UV–Vis absorption and DFT studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Joshi R, Kumari A, Singh K, Mishra H, Pokharia S. Triorganotin(IV) complexes of Schiff base derived from 1,2,4-triazole moiety: Synthesis, spectroscopic investigation, DFT studies, antifungal activity and molecular docking studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127639] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Saini V, Krishnan R, Khungar B. Exploration of fluorescence behavior of an imidazolium-based chemosensor in solution and in the solid state and its turn-on response to Al3+ in pure aqueous medium. Photochem Photobiol Sci 2020; 19:931-942. [DOI: 10.1039/c9pp00477g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An imidazolium-based quinoline framework is constructed, and its fluorescence behaviour studies with fluorescence turn-on chemosensory response to the selective detection of Al3+ in aqueous medium are discussed in detail.
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Affiliation(s)
- Vaishali Saini
- Department of Chemistry
- Birla Institute of Technology and Science Pilani
- Pilani
- India
| | - Rangan Krishnan
- Department of Chemistry
- Birla Institute of Technology and Science Pilani
- Secunderabad
- India
| | - Bharti Khungar
- Department of Chemistry
- Birla Institute of Technology and Science Pilani
- Pilani
- India
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Synthesis, structural characterization, and theoretical studies of new pyrazole (E)-2-{[(5-(tert-butyl)-1H-pyrazol-3-yl)imino]methyl}phenol and (E)-2-{[(1-(4-bromophenyl)-3-(tert-butyl)-1H-pyrazol-5-yl]imino]methyl}phenol. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Sandoval-Lira J, Solano-Altamirano JM, Cortezano-Arellano O, Cruz-Gregorio S, Meza-León RL, Hernández-Pérez JM, Sartillo-Piscil F. Can an n (O) → π* Interaction Provide Thermodynamic Stability to Naturally Occurring Cephalosporolides? J Org Chem 2019; 84:2126-2132. [PMID: 30649874 DOI: 10.1021/acs.joc.8b03116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stereocontrolled synthesis of naturally occurring products containing a 5,5-spiroketal molecular structure represents a major synthetic problem. Moreover, in a previous work, the stereocontrolled synthesis of cephalosporolide E (ceph E), which presumably was obtained from its epimer congener (ceph F) through an acid-mediated equilibration process, was reported. Consequently, we performed a theoretical investigation to provide relevant information regarding the title question, and it was found that the higher thermodynamic stability of ceph E, relative to ceph F, is caused by an n → π* interaction between a lone electron pair of the oxygen atom of the spiroketal ring (nO) and the antibonding orbital of the carbonyl group (π*C=O). Although similar stereoelectronic interactions have been disclosed in other molecular structures, its presence in ceph E, and very likely in other related naturally occurring products, represents a novel nonanomeric stabilizing effect that should be introduced into the chemical literature.
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Affiliation(s)
- Jacinto Sandoval-Lira
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México.,Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM , Personal de la UNAM , Carretera Km. 14.5, Unidad San Cayetano, Toluca - Atlacomulco , 50200 Toluca de Lerdo , México
| | - Juan M Solano-Altamirano
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Omar Cortezano-Arellano
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Silvano Cruz-Gregorio
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | | | - Julio M Hernández-Pérez
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Fernando Sartillo-Piscil
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
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Yilmaz E. Theoretical and experimental studies of newly synthesized (Z)-4-(2-(3,5-dibromo-2-hydroxy-4-methoxybenzylidene)hydrazinyl)benzonitrile compound. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Joshi R, Pandey N, Yadav SK, Tilak R, Mishra H, Pokharia S. Synthesis, spectroscopic characterization, DFT studies and antifungal activity of (E)-4-amino-5-[N'-(2-nitro-benzylidene)-hydrazino]-2,4-dihydro-[1,2,4]triazole-3-thione. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.081] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Romanova A, Lyssenko K, Ananyev I. Estimations of energy of noncovalent bonding from integrals over interatomic zero-flux surfaces: Correlation trends and beyond. J Comput Chem 2018; 39:1607-1616. [PMID: 29701303 DOI: 10.1002/jcc.25235] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/24/2022]
Abstract
Bonding energies of 50 associates composed by neutral molecules (atoms) and bounded by various weak noncovalent interactions are calculated within the DFT framework using the PBE0/aug-cc-pVTZ combination. The electronic virial and electron density values at bond critical points together with their integrals over interatomic surfaces are tested to check their ability to estimate bonding energies. Two correlations schemes dealing with integrals over interatomic surface are suggested to estimate bonding energy of any noncovalent interaction. The physical meaning of explored and several known correlations is discussed. Methods to estimate interatomic surface integrals of electronic virial and electron density are proposed. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Anna Romanova
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova 28, Moscow, 119991, Russia.,D.I. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, Moscow, 125047, Russia
| | - Konstantin Lyssenko
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova 28, Moscow, 119991, Russia
| | - Ivan Ananyev
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova 28, Moscow, 119991, Russia.,D.I. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, Moscow, 125047, Russia
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Kowsalya PS, Bhuvanesh NSP, Neelakantan MA. Chemical Reactivity and Quantifying the Intra- and Intermolecular Interactions in Zwitterionic Compounds. ChemistrySelect 2018. [DOI: 10.1002/slct.201702730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Perumal samy Kowsalya
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
| | | | - Mallanpillai A. Neelakantan
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
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Physicochemical properties of novel methyl 2-{(E)-[(2-hydroxynaphthalen-1-yl)methylidene] amino}-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylate as turn-off fluorometric chemosensor for detection Fe3+ ion. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.07.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Pokharia M, Yadav SK, Mishra H, Pandey N, Tilak R, Pokharia S. Synthesis, spectroscopic characterization, biological activity and theoretical studies of (E)-N3-(2-chlorobenzylidene)-H-1,2,4-triazole-3,5-diamine. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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