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Palafox MA, Belskaya NP, Kostova IP. Study of the Molecular Architectures of 2-(4-Chlorophenyl)-5-(pyrrolidin-1-yl)-2 H-1,2,3-triazole-4-carboxylic Acid Using Their Vibrational Spectra, Quantum Chemical Calculations and Molecular Docking with MMP-2 Receptor. Pharmaceutics 2023; 15:2686. [PMID: 38140027 PMCID: PMC10747663 DOI: 10.3390/pharmaceutics15122686] [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: 10/16/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
1,2,3-triazole skeleton is a valuable building block for the discovery of new promising anticancer agents. In the present work, the molecular structure of the synthesized anticancer drug 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid (1b) and its anionic form (2b) was characterized by means of the B3LYP, M06-2X and MP2 quantum chemical methods, optimizing their monomer, cyclic dimer and stacking forms using the Gaussian16 program package. The molecular structure was found to be slightly out of plane. The good agreement between the IR and Raman bands experimentally observed in the solid state with those calculated theoretically confirms the synthesized structures. All of the bands were accurately assigned according to functional calculations (DFT) in the monomer and dimer forms, together with the polynomic scaling equation procedure (PSE). Therefore, the effect of the substituents on the triazole ring and the effect of the chlorine atom on the molecular structure and on the vibrational spectra were evaluated through comparison with its non-substituted form. Through molecular docking calculations, it was evaluated as to how molecule 1b interacts with few amino acids of the MMP-2 metalloproteinase receptor, using Sybyl-X 2.0 software. Thus, the relevance of triazole scaffolds in established hydrogen bond-type interactions was demonstrated.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Nataliya P. Belskaya
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., 620012 Yekaterinburg, Russia;
| | - Irena P. Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
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Experimental and computational investigation on spectroscopic characterization, molecular modeling and biological evaluation of 3, 3′, 4′7-tetrahydroxyflavone, 3, 3′, 4′7-tetrahydroxyflavone-6-methoxymethane against in A549 cells. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sathya A, Prabhu T, Ramalingam S. Structural, biological and pharmaceutical importance of antibiotic agent chloramphenicol. Heliyon 2020; 6:e03433. [PMID: 32154407 PMCID: PMC7057209 DOI: 10.1016/j.heliyon.2020.e03433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 10/26/2022] Open
Abstract
The vibrational, magnetic resonance and electronic spectral techniques are used to evaluate structural activity associated physico-chemical properties. The biological affinity and drug importance was validated by calculating biological parameters using HyperChem. Mulliken charge assignment for restoring chemical potential for generating drug potential in the molecular site was mapped and analyzed. The vibrational spectral pattern was estimated by identifying active and inactive bands and hindrance of vibrational activity of Acetamide group was monitored and thereby drug malfunction was tested. The chemical reaction pathway around the core carbons of chain and ring was keenly noted and the cause of chemical potential for the inducement of drug mechanism was reported. The stimulation of chemical mechanism for antibiotic activity was addressed by suitable evidence and further improvement for enhancing activity was made. The electronic HOMO and LUMO interaction over different molecular entities are discussed to expose accompany of drug mechanical transitions. The CT complex was recognized to be C=N and C=C bonds and operating drug mechanism was monitored. The unwanted drug property induced by perplexes of charge depletion on α-hydroxyl group was assessed from MEP map. The hyperactive polarization energy of 266.18 X10-33 esu and 327 X10-33 esu of present compound is causing biological activity in good order. The uncontrolled breathing region of Acetamide group was clarified in VCD profile and this is main cause to produce toxicity in drug process.
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Affiliation(s)
- A. Sathya
- Department of Physics, A.V.C. College, Mayiladuthurai, Tamilnadu, India
- Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - T. Prabhu
- Department of Physics, A.V.C. College, Mayiladuthurai, Tamilnadu, India
- Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - S. Ramalingam
- Department of Physics, A.V.C. College, Mayiladuthurai, Tamilnadu, India
- Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
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Pandey SK, Pratap S, Tiwari MK, Marverti G, Jasinski JP. Experimental and theoretical exploration of molecular structure and anticancer properties of two N, N′–disubstituted thiocarbamide derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vibrational spectra and molecular structure of isomeric 1-(adamantan-1-ylcarbonyl)-3-(dichlorophenyl)thioureas. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.09.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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John Xavier R, Dinesh P. A study of the molecular, vibrational, electronic and quantum chemical investigation of 2-methyl-1-vinylimidazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1569-1581. [PMID: 25459718 DOI: 10.1016/j.saa.2014.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/01/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
The spectroscopic properties of 2-methyl-1-vinylimidazole (abbreviated as 2M1VIM) were examined by FT-IR, FT-Raman and NMR techniques. FT-IR and FT-Raman spectra were recorded in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. The (1)H and (13)C NMR spectra were recorded in CDCl3. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP and LSDA methods with 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibration were assigned on the basis of potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanical (SQM) method. The optimized structure of the compound was interpreted and compared with the reported experimental values. The observed vibrational ware numbers, absorption wavelengths and chemical shifts were compared with calculated values. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. As a result, the optimized geometry, and calculated spectroscopic data show a good agreement with the experimental results.
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Affiliation(s)
- R John Xavier
- Department of Physics, Periyar EVR College (Autonomous), Tiruchirappalli 620 023, India.
| | - P Dinesh
- Department of Physics, Periyar EVR College (Autonomous), Tiruchirappalli 620 023, India
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Govindasamy P, Gunasekaran S. Spectroscopic (FT-IR, FT-Raman and UV) investigation, NLO, NBO, molecular orbital and MESP analysis of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1543-1556. [PMID: 25459716 DOI: 10.1016/j.saa.2014.10.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/27/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
In this work, FT-IR and FT-Raman spectra of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid (abbreviated as 2DCPAPAA) have been reported in the regions 4000-450cm(-1) and 4000-50cm(-1), respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (ΔH). The important non-linear optical properties such as electric dipole momentum, polarizability and first hyperpolarizability of 2DCPAPAA have been computed using B3LYP/6-311++G(d,p) quantum chemical calculations. The Natural charges, HOMO, LUMO, chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported. The oscillator's strength, wave length, and energy calculated by TD-DFT and 2DCPAPAA is approach complement with the experimental findings. The molecular electrostatic potential (MESP) surfaces of the molecule were constructed.
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Affiliation(s)
- P Govindasamy
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India.
| | - S Gunasekaran
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India; Research and Development St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India
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Govindasamy P, Gunasekaran S, Ramkumaar GR. Natural bond orbital analysis, electronic structure and vibrational spectral analysis of N-(4-hydroxyl phenyl) acetamide: a density functional theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:621-633. [PMID: 24813292 DOI: 10.1016/j.saa.2014.03.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/14/2014] [Accepted: 03/21/2014] [Indexed: 06/03/2023]
Abstract
The Fourier transform infrared (FT-IR) and FT-Raman spectra of N-(4-hydroxy phenyl) acetamide (N4HPA) of painkiller agent were recorded in the region 4000-450 cm(-1) and 4000-50 cm(-1) respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using Vibrational energy distribution analysis (VEDA 4) program. The oscillator's strength calculated by TD-DFT and N4HPA is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The molecular electrostatic potential (MESP) and electron density surfaces of the molecule were constructed. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated.
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Affiliation(s)
- P Govindasamy
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India
| | - S Gunasekaran
- Research and Development St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India.
| | - G R Ramkumaar
- PG and Research Department of Physics, Pachaiyappa's College, Chennai 600030, TN, India
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Xavier RJ, Dinesh P. Spectroscopic (FTIR, FT-Raman, 13C and 1H NMR) investigation, molecular electrostatic potential, polarizability and first-order hyperpolarizability, FMO and NBO analysis of 1-methyl-2-imidazolethiol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:999-1011. [PMID: 24184581 DOI: 10.1016/j.saa.2013.09.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 09/06/2013] [Accepted: 09/26/2013] [Indexed: 06/02/2023]
Abstract
In this work, experimental and theoretical study on the molecular structure and vibrational spectra of 1-methyl-2-imidazolethiol (MIME) were presented. The vibrational frequencies of the title compound were obtained theoretically by ab initio HF and DFT (B3LYP/LSDA) employing 6-311G (d,p) and 6-311++G(d,p) basis sets and compared with experimental spectral bands (FTIR and FT-Raman). The thermodynamic properties of the studied compound have been computed at different temperatures. The atomic charges and charge delocalization of the molecule have been analyzed by natural bond orbital (NBO) analysis. The reactivity sites are identified by mapping the molecular electrostatic potential (MESP) surface. Electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. Besides, (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule in chloroform solvent calculated using the Gauge-Independent Atomic Orbital (GIAO) method are found to be in good agreement with experimental values.
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Affiliation(s)
- R John Xavier
- Department of Physics, Periyar EVR College (Autonomous), Tiruchirappalli 620 023, India.
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Arivazhagan M, Rexalin DA, Ilango G. DFT analysis of P-nitrobenzotrifluoride--a combined study of experimental (FT-IR and FT-Raman) and theoretical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 121:641-649. [PMID: 24366159 DOI: 10.1016/j.saa.2013.09.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/04/2013] [Accepted: 09/07/2013] [Indexed: 06/03/2023]
Abstract
In this, a combined experimental and theoretical study on molecular structure and vibrational analysis of P-nitrobenzotrifluoride (PNBTF) is reported. The Fourier transform infrared and FT-Raman was recorded in the solid phase. The molecular geometry and vibrational frequencies of PNBTF in the ground state have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as basis set. Comparison of the observed fundamental vibrational frequencies with calculated results by density functional methods indicates that B3LYP/6-311++G(d,p) is superior to other methods for molecular vibrational problems. The bioactivity of the compound is analyzed by the HOMO-LUMO analysis. The reactivity sites are identified by mapping of electron density into electrostatic potential surface (MEP). Besides, (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts are calculated by using the gauge-invariant atomic orbital (GIAO) method. Furthermore, the compound can be used as a good nonlinear optical material due to the higher value of first hyperpolarizability. Solventation effect of NMR spectra by CPCM model of P-nitrobenzotrifluoride has been analyzed.
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Affiliation(s)
- M Arivazhagan
- P.G & Research Department of Physics, A.A. Government Arts College, Musiri 621 211, Tamil Nadu, India.
| | - D Anitha Rexalin
- P.G & Research Department of Physics, A.A. Government Arts College, Musiri 621 211, Tamil Nadu, India
| | - G Ilango
- Department of Physics, M.I.E.T Engineering College, Tiruchirappalli 620 007, Tamil Nadu, India
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Arivazhagan M, Muniappan P, Meenakshi R, Rajavel G. PCM/TD-DFT analysis of 1-bromo-2,3-dichlorobenzene--a combined study of experimental (FT-IR and FT-Raman) and theoretical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 105:497-508. [PMID: 23352918 DOI: 10.1016/j.saa.2012.11.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/03/2012] [Accepted: 11/06/2012] [Indexed: 06/01/2023]
Abstract
This study represents an integral approach towards understanding the electronic and structural aspects of 1-bromo-2,3-dichlorobenzene (BDCB). The experimental spectral bands were structurally assigned with the theoretical calculation, and the thermodynamic properties of the studied compound were obtained from the theoretically calculated frequencies. The relationship between the structure and absorption spectrum and effects of solvents have been discussed. It turns that the hybrid PBE1PBE functional with 6-311+G(d,p) basis provide reliable λ(max) when solvent effects are included in the model. The NBO analysis reveals that the studied compound presents a structural characteristic of electron-transfer within the compound. The frontier molecular orbitals (HOMO-LUMO) are responsible for the electron polarization and electron-transfer properties. The reactivity sites are identified by mapping the electron density into electrostatic potential surface (MESP). Besides, (13)C and (1)H have been calculated using the gauge-invariant atomic orbital (GIAO) method. The thermodynamic properties at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. Furthermore, the studied compound can be used as a good nonlinear optical material due to the higher value of first hyper polarizability (5.7 times greater than that of urea (0.37289×10(-30) esu)). Finally, it is worth to mentioning that solvent induces a considerable red shift of the absorption maximum going from the gas phase, and a slight blue shift of the transition S(0)→S(1) going from less polar to more polar solvents.
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Affiliation(s)
- M Arivazhagan
- Department of Physics, A.A. Govt. Arts College, Musiri 621 201, Tamil Nadu, India.
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