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Ipek C, Gümüş H, Şimşek M, Tosun M. DFT and Molecular Docking Study of 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) (TTCP) Molecule as Antiviral to Covid-19 Main Protease. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2023; 48:1031-1040. [PMID: 36321067 PMCID: PMC9612599 DOI: 10.1007/s13369-022-07293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Thiophene-containing compounds have antiviral properties and may be among the drugs tested for the treatment of COVID-19 diseases. In order to better understand the molecular definition of the 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) molecule from thiophene-containing compounds, the physico-chemical (molecular structure analysis, spectroscopic properties, boundary orbital analysis) mechanisms underlying the protein-ligand interaction should be examined in detail. For this reason, geometric parameters, IR and UV-vis spectra, conformational analysis, electronic, NBO and NLO properties, molecular electrostatic potential map and Mulliken charge distributions of the TTCP molecule were investigated theoretically using DFT theory in the Gaussian program. Accordingly, molecular docking calculations with COVID-19 main protease (PDB 5R7Y) were performed to determine the pharmaceutical activities of the TTCP molecule against coronavirus diseases.
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Affiliation(s)
- Cengiz Ipek
- Department of Civil Engineering, Istanbul Medeniyet University, Unalan Campus, Uskudar, 34700 Istanbul, Turkey
| | - Hacer Gümüş
- Kocaeli University, Golcuk Vocational School, Automotive Technology Program , Kocaeli University, Kocaeli, Turkey
| | - Merve Şimşek
- Department of Physics, Faculty of Arts and Sciences, Sakarya University, 54187 Serdivan, Sakarya Turkey
| | - Murat Tosun
- Mechanical Engineering Department, Faculty of Mechanical Engineering, Istanbul Technical University, 34437 Gumussuyu, Istanbul, Turkey
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Abbas Manthiri A, Ramalingam S, George G, Aarthi R. Molecular structure analysis and biological properties investigation on antiseptic drug; 2-amino-1-phenyl-1-propanol using spectroscopic and computational research analysis. Heliyon 2021; 7:e06699. [PMID: 33898825 PMCID: PMC8056422 DOI: 10.1016/j.heliyon.2021.e06699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/17/2020] [Accepted: 04/01/2021] [Indexed: 11/28/2022] Open
Abstract
The inducement of physical, chemical, structural and biological properties to entice of pharmaceutical property was analyzed by Vibrational spectroscopic, biological and theoretical tools. The structural arrangement for describing structure activity was investigated by injecting ligand groups in internal coordinate system by molecular tools (FT adopted IR, Raman, and NMR). Bond length and bond angle strain was pronounced much due to the chemical equivalent forces extension due to the injection of substitutional groups on base compound and thus non-Centro symmetry was processed. The molecular charge depletion profile was thoroughly studied to persuade protonic and electronic delocalization setup for arranging the drug potential. The chemi-equivalent potential exchange was monitored among different parts of the molecule for obtaining drug mechanism. The biological profile was keenly observed to look at the biological ambiance of the present molecule to fabricate advanced drug. The Lipinski five rule parameters; MV = 137.18, LogP = 0.27, HBD = 2, HBA = 2 and TPSA = 46.2 A2 showed the enhancement of additive drug quality. The exchange of oscillating chemical energy in the core and allied carbons of the base skeleton was keenly noted to find the prearranged chemical environment for successful drug mechanism. The non bonded transitions between Lewis acid and base of bonded molecular system were observed to determine the restoring potential to customize drug potential. The drug assistance for enantiomer characteristics of chirality sequence was displayed to expose the toxicity effect of the molecule. The active molecular bondings on different sites of molecule were measured by estimating polarizability and associated biological inhibition was validated.
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Affiliation(s)
- A. Abbas Manthiri
- Department of Physics, Jamal Mohamed College, Tiruchirappalli, Tamilnadu, India
| | - S. Ramalingam
- Department of Physics, A.V.C. College, Mayiladuthurai, Tamilnadu, India
| | - Gene George
- Department of Physics, T.B.M.L. College, Porayar, Tamilnadu, India
| | - R. Aarthi
- Department of Physics, ST. Theresa's Arts and Science College, Tharangambadi, Tamilnadu, India
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Yabalak E, Dal H, Arslan H. The molecular structure and vibrational spectra of 4-bromo-2-(((5-methylpyridin-2-yl)imino)methyl)phenol by density functional method. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Nageswari G, George G, Ramalingam S, Govindarajan M. Electronic and vibrational spectroscopic (FT-IR and FT-Raman) investigation using ab initio (HF) and DFT (B3LYP and B3PW91) and HOMO/LUMO/MEP analysis on the structure of l -serine methyl ester hydrogen chloride. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Ramalingam S, Periandy S, Sugunakala S, Prabhu T, Bououdina M. Insilico molecular modeling, docking and spectroscopic [FT-IR/FT-Raman/UV/NMR] analysis of Chlorfenson using computational calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:118-135. [PMID: 23832220 DOI: 10.1016/j.saa.2013.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/23/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
In the present work, the recorded FT-IR/FT-Raman spectra of the Chlorfenson (4-Chorophenyl-4-chlorobenzenesulfonate) are analysed. The observed vibrational frequencies are assigned and the computational calculations are carried out by DFT (LSDA, B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are investigated with the UV/NMR data. The fluctuation of structure of Chlorobenzenesulfonate due to the substitution of C6H4Cl is investigated. The vibrational sequence pattern of the molecule related to the substitutions is intensely analysed. Moreover, (13)C NMR and (1)H NMR chemical shifts are calculated by using the gage independent atomic orbital (GIAO) technique with HF/B3LYP/B3PW91 methods on same basis set. A study on the electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, are performed by HF and DFT methods. The calculated energy of Kubo gap (HOMO and LUMO) ensures that the charge transfer occurs within the molecule. Besides frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) is executed. NLO properties and Mulliken charges of the Chlorfenson is also calculated and interpreted. Biological properties like the target receptor identification, and Identification of interacting residues, of this compound is identified and analysed by using SWISSMODEL, Castp, Hex and Pdb Sum. By using these properties, the mechanism of action of this compound on ATP Synthase of Tetranychus urticae is found and it is very much useful to develop efficient pesticides having less toxic to the environment.
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Affiliation(s)
- S Ramalingam
- Department of Physics, AVC College, Mayiladuthurai, Tamilnadu, India.
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Imene D, Leila N, Haiahem Sakina MF, Abdelaziz B, DjamelEddine K. Inclusion complexes of ortho-anisidine and β-cyclodextrin: A quantum mechanical calculation. CR CHIM 2013. [DOI: 10.1016/j.crci.2013.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yabalak E, Günay F, Kasumov VT, Arslan H. The molecular structure and vibrational spectra of N-(3-tert-butyl-2-hydroxybenzylidene)-2,6-diphenyl-4-hydroxyaniline. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 110:291-303. [PMID: 23583846 DOI: 10.1016/j.saa.2013.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 02/18/2013] [Accepted: 03/03/2013] [Indexed: 06/02/2023]
Abstract
The molecular structure, vibrational frequencies and intensities of N-(3-tert-butyl-2-hydroxybenzylidene)-2,6-diphenyl-4-hydroxyaniline were calculated by the Density Functional Theory methods (BLYP, B3PW91 and B3LYP) using the 6-31G(d,p) basis set. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of optimized by B3LYP method (r=0.9825). The harmonic vibrations computed for this compound by the B3LYP/6-31G(d,p) method are in good agreement with the observed IR and Raman spectral data. The root mean square values error of the observed and calculated IR bands are found to be 9.80, 9.40 and 8.42 for B3LYP, B3PW91 and BLYP/6-31G(d,p) methods, respectively. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using the SQM 2.0 program. A general better performance of the investigated methods was calculated by PAVF 1.0 program.
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Affiliation(s)
- Erdal Yabalak
- Mersin University, Faculty of Arts and Science, Department of Chemistry, Mersin TR-33343, Turkey
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Benghodbane S, Khatmi D. Quantum chemical calculations based on ONIOM and the DFT methods in the inclusion complex: doxycycline/2-O-Me-β-cyclodextrin. J INCL PHENOM MACRO 2012. [DOI: 10.1007/s10847-012-0237-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ramalingam S, Jayaprakash A, Mohan S, Karabacak M. Vibrational investigation on FT-IR and FT-Raman spectra, IR intensity, Raman activity, peak resemblance, ideal estimation, standard deviation of computed frequencies analyses and electronic structure on 3-methyl-1,2-butadiene using HF and DFT (LSDA/B3LYP/B3PW91) calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 82:79-90. [PMID: 21813316 DOI: 10.1016/j.saa.2011.06.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/29/2011] [Accepted: 06/30/2011] [Indexed: 05/31/2023]
Abstract
FT-IR and FT-Raman (4000-100 cm(-1)) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H).
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Affiliation(s)
- S Ramalingam
- Department of Physics, A.V.C. College, Mayiladuthurai, Tamilnadu, India.
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