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Elangovan N, Thirumavalavan M, Sankar Ganesan T, Sowrirajan S, Chandrasekar S, Arumugam N. Comparison study (experimental and theoretical), hydrogen bond interaction through water, donor acceptor investigation and molecular docking study of 3,3-((1,2-phenylenebis (azaneylylidene)) bis (methaneylylidene)) diphenol. J Biomol Struct Dyn 2024:1-16. [PMID: 38656235 DOI: 10.1080/07391102.2024.2333465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024]
Abstract
The novel Schiff's base (CS6) was synthesized and confirmed by various studies. The B3LYP/cc-pVDZ basis set was used for theoretical study and the results indicated that both the theoretical and experimental studies correlated well. The interaction energy of CS6-water complex calculated by using the local energy decomposition analysis was found to be -7.28 kcal/mol. The TD-TFT method was used for the calculation of electronic absorption spectrum. This study confirmed that the observed wavelength and the simulated wavelength in the electronic spectra were almost similar. The electrophilic and nucleophilic attacking sites of the titled compound were identified by using FMO and MEP studies. The highest stabilization energy (30.19 kcal/mol) formed by LP (2) O24 to anti-bonding σ*(C18-C19) was confirmed by the NBO study. The localized and delocalized electrons were confirmed by ELF and LOL studies. The hydrogen bond interaction as well as the physical and chemical properties of CS6 indicated that it showed a moderate similarity to the drugs. The docking study confirmed that the dehydro-L-gulonate decarboxylase inhibitor (1Q6O) could interact with CS6 compound with the binding energy of -5.26 kcal/mol.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Musiri, Tiruchirappalli, Tamilnadu, India
| | - Munusamy Thirumavalavan
- Department of Chemistry, Saveetha Engineering College, Thandalam, Chennai, Tamil Nadu, India
| | - T Sankar Ganesan
- Department of Chemistry, Arignar Anna Government Arts College, Musiri-621211, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Musiri, Tiruchirappalli, Tamilnadu, India
| | - S Chandrasekar
- Department of Chemistry, Arignar Anna Government Arts College, Musiri-621211, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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Sankar Ganesan T, Elangovan N, Thirumavalavan M, Seenan S, Sowrirajan S, Chandrasekar S, Arumugam N, Almansour AI, Mahalingam SM, V M DD, Kanchi S, Sivaramakrishnan V. Synthesis, topology, molecular docking and dynamics studies of o-phenylenediamine derivative. J Biomol Struct Dyn 2024:1-20. [PMID: 38577881 DOI: 10.1080/07391102.2024.2317981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/07/2024] [Indexed: 04/06/2024]
Abstract
The N, N'-(1,2-phenylene) bis (1- (4- chlorophenyl) methanimine) (CS4) was synthesized and characterized by infrared (IR), absorption (UV-vis) and NMR (1H and 13C) spectral analyses. The structural parameters, vibrational frequencies, potential energy and the distribution analysis (PED) were calculated by using DFT with the basis set of B3LYP/cc-pVDZ and these spectral values were compared to the experimental values. HOMO and LUMO studied were performed in order to understand the stability and biological activity of the compound. The most reactive sites on the compound were investigated by utilizing MEP energy surface and Fukui function descriptor with the natural population analysis (NPA) of the charges. The study of the natural bond orbitals (NBO) reveals the delocalization of the intramolecular interaction of the charges in the compound. Additionally, topological investigations (ELF, LOL), determination of thermodynamic parameters and noncovalent interaction (NCI) study by using topology (RDG) analysis were also carried out. Finally, the molecular docking and molecular dynamics simulations was carried out by examining against glycosylphosphatidylinositol phospholipase D inhibitor receptor for distinct protein targets (3MZG).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Sankar Ganesan
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | | | - Shanthi Seenan
- Department of Chemistry, Saveetha Engineering College, Chennai, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | - S Chandrasekar
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
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Philip BM, John JS, George M, Kumar KM, M V, HS HK, Devarajegowda H, Kotresh O, Paulose TAP, Sajan D. Synthesis, comprehensive spectroscopic investigation and molecular docking studies of (6-Fluoro-2-oxo-2H-chromen-4-yl) methyl morpholine-4-carbodithioate. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Philip BM, John JS, V S, Kuruvilla TK, Paulose TAP, Sajan D. Vibrational spectra and molecular docking studies of bergapten isolated from Melicopedenhamii leaves as anti-breast cancer agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Arulaabaranam K, Muthu S, Mani G, Irfan A. Conformational study, FT-IR, FT-Raman, solvent effect on UV–Vis, charge transfer and protein–ligand interactions of Methyl-2-pyrazinecarboxylate. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116934] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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6
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Chaudhary D, Pramanik T, Santra S. Thiocoumarins and Dithiocoumarins: Advances in Synthesis and Pharmacological Activity. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200812132707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Thiocoumarins and dithiocoumarins are two important classes of sulphurcontaining
heterocyclic compounds, which are bioisosteres of coumarins. Herein, various
synthetic strategies for these two classes of heterocyclic compounds reported in the literature
have been discussed. Different solvents, catalysts, reagents and reaction conditions,
which were employed successfully for synthesizing thiocoumarins and dithiocoumarins
have also been described concisely in this review. Mechanistic overview has been given
wherever it was necessary. In addition, a comparative view of various solvents, catalysts
and reagents focusing on their efficiency for synthesizing thiocoumarins and dithiocoumarins,
has been discussed as well. Furthermore, pharmacological activities of these two
classes of compounds have also been discussed.
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Affiliation(s)
- Diksha Chaudhary
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Tanay Pramanik
- Department of Chemistry, University of Engineering and Management, University Area, Action Area III, B/5, Newtown, Kolkata, West Bengal - 700160, India
| | - Soumava Santra
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
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Celikezen F, Orek C, Parlak A, Sarac K, Turkez H, Tozlu ÖÖ. Synthesis, structure, cytotoxic and antioxidant properties of 6-ethoxy-4-methylcoumarin. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127577] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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DFT, spectroscopic, DSC/TGA, electronic, biological and molecular docking investigation of 2,5-thiophenedicarboxylic acid: A promising anticancer agent. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Prediction of structural, vibrational and nonlinear optical properties of small organic conjugated molecules derived from pyridine. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Computational study of new 1,2,3-triazole derivative of lithocholic acid: Structural aspects, non-linear optical properties and molecular docking studies as potential PTP 1B enzyme inhibitor. Comput Biol Chem 2019; 78:144-152. [DOI: 10.1016/j.compbiolchem.2018.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/09/2018] [Accepted: 11/18/2018] [Indexed: 01/14/2023]
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11
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Molecular docking and spectral analysis of (5,7-Dimethyl-2-oxo-2H-chromen-4-yl)-methyl diethyldithiocarbamate : A potential bioactive agent. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Molecular docking, Hirshfeld surface, structural, spectroscopic, electronic, NLO and thermodynamic analyses on novel hybrid compounds containing pyrazole and coumarin cores. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.06.069] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Pegu D, Deb J, Saha SK, Paul MK, Sarkar U. Molecular structure, chemical reactivity, nonlinear optical activity and vibrational spectroscopic studies on 6-(4-n-heptyloxybenzyoloxy)-2-hydroxybenzylidene)amino)-2H-chromen-2-one: A combined density functional theory and experimental approach. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Mohamed Asath R, Premkumar S, Mathavan T, Milton Franklin Benial A. Vibrational spectroscopic, molecular docking and quantum chemical studies on 6-aminonicotinamide. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Shukla A, Khan E, Tandon P, Sinha K. Study of vibrational spectra and hydrogen bonding network in dimeric and tetrameric model of ampicillin using DFT and AIM approach. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Issaoui N, Ghalla H, Bardak F, Karabacak M, Aouled Dlala N, Flakus H, Oujia B. Combined experimental and theoretical studies on the molecular structures, spectroscopy, and inhibitor activity of 3-(2-thienyl)acrylic acid through AIM, NBO,FT-IR, FT-Raman, UV and HOMO-LUMO analyses, and molecular docking. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Prajapati P, Pandey J, Shimpi MR, Srivastava A, Tandon P, Velaga SP, Sinha K. Combined spectroscopic and quantum chemical studies of ezetimibe. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Tanak H, Pawlus K, Marchewka M. Molecular structure, vibrational spectra and DFT computational studies of melaminium N-acetylglycinate dihydrate. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Arockia Doss M, Savithiri S, Rajarajan G, Thanikachalam V, Anbuselvan C. Synthesis, electronic structure investigation of 3-pentyl-2,6-di(furan-2-yl)piperidin-4-one by FT-IR, FT-Raman and UV-Visible spectral studies and ab initio/DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:773-784. [PMID: 26172464 DOI: 10.1016/j.saa.2015.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 06/04/2023]
Abstract
FT-IR and FT-Raman spectra of 3-pentyl-2,6-di(furan-2-yl) piperidin-4-one (3-PFPO) were recorded in the solid phase. The structural and spectroscopic analyses of 3-PFPO were made by using B3LYP/HF level with 6-311++G(d, p) basis set. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3-PFPO with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The electronic properties such as excitation energies, oscillator strength, wavelengths and HOMO-LUMO energies were obtained by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E((2))) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen, oxygen and hydrogen were calculated using B3LYP/6-311++G(d, p) level theory. Moreover, thermodynamic properties (heat capacities, entropy and enthalpy) of the title compound at different temperatures were calculated in gas phase.
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Affiliation(s)
- M Arockia Doss
- Department of chemistry, Annamalai University, Annamalainagar 608 002, India
| | - S Savithiri
- Department of chemistry, Annamalai University, Annamalainagar 608 002, India
| | - G Rajarajan
- Department of chemistry, Annamalai University, Annamalainagar 608 002, India.
| | - V Thanikachalam
- Department of chemistry, Annamalai University, Annamalainagar 608 002, India
| | - C Anbuselvan
- Department of chemistry, Annamalai University, Annamalainagar 608 002, India
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Deval V, Kumar A, Gupta V, Sharma A, Gupta A, Tandon P, Kunimoto KK. Molecular structure (monomeric and dimeric) and hydrogen bonds in 5-benzyl 2-thiohydantoin studied by FT-IR and FT-Raman spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:15-26. [PMID: 24845873 DOI: 10.1016/j.saa.2014.04.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/12/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
In the present work the structural and spectral characteristics of 5-benzyl-2-thiohydantoin (5-BTH) have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G++(d,p) basis set. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-vis spectrum of the compound was recorded in methanol solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using PCM and 6-311++G(d,p) basis set. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied.
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Affiliation(s)
- Vipin Deval
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India
| | - Amit Kumar
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India; Department of Physics, Lucknow University, Lucknow, India
| | - Vineet Gupta
- Department of Physics, Lucknow University, Lucknow, India
| | - Anamika Sharma
- Department of Physics, Lucknow University, Lucknow, India
| | - Archana Gupta
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India.
| | - Poonam Tandon
- Department of Physics, Lucknow University, Lucknow, India
| | - Ko-Ki Kunimoto
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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Moghanian H, Mobinikhaledi A, Monjezi R. Synthesis, spectroscopy (vibrational, NMR and UV–vis) studies, HOMO–LUMO and NBO analysis of 8-formyl-7-hydroxy-4-methylcoumarin by ab initio calculations. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.08.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Arjunan V, Kalaivani M, Senthilkumari S, Mohan S. Vibrational, NMR and quantum chemical investigations of acetoacetanilde, 2-chloroacetoacetanilide and 2-methylacetoacetanilide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:154-174. [PMID: 23832223 DOI: 10.1016/j.saa.2013.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/27/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
The vibrational assignment and analysis of the fundamental modes of the compounds acetoacetanilide (AAA), 2-chloroacetoacetanilide (2CAAA) and 2-methylacetoacetanilide (2MAAA) have been performed. Density functional theory studies have been carried out with B3LYP method utilising 6-311++G(**) and cc-pVTZ basis sets to determine structural, thermodynamic and vibrational characteristics of the compounds and also to understand the influence of chloro and methyl groups on the characteristic frequencies of amide (CONH) group. Intramolecular hydrogen bond exists in acetoacetanilide and o-substituted acetoacetanilide molecules and the N⋯O distance is found to be around 2.7Å. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecules were determined and the same have been calculated using the gauge independent atomic orbital (GIAO) method. The energies of the frontier molecular orbitals have been determined. In AAA, 2CAAA and 2MAAA molecules, the nN→πCO(∗) interaction between the nitrogen lone pair and the amide CO antibonding orbital gives strong stabilization of 64.75, 62.84 and 64.18kJmol(-1), respectively. The blue shift in amide-II band of 2MAAA is observed by 45-50cm(-1) than that of AAA. The steric effect of ortho methyl group significantly operating on the NH bond properties. The amide-III, the CN stretching mode of methyl and chloro substituted acetoacetanilide compounds are not affected by the substitution while the amide-V band, the NH out of plane bending mode of 2-chloroacetoacetanilide compound is shifted to a higher frequency than that of AAA. The substituent chlorine plays significantly and the blue shift in o-substituted compounds than the parent in the amide-V vibration is observed. The amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA are significantly raised than that of AAA. A blue shift of amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA than AAA is observed.
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Affiliation(s)
- V Arjunan
- Department of Chemistry, Kanchi Mamunivar Centre for Post-Graduate Studies, Puducherry 605 008, India.
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Wandas M, Talik Z. Theoretical and experimental NMR data of 3,5-dinitro-2-(2-phenylhydrazinyl)pyridine and of its 4- and 6-methyl derivatives. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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