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- MakaleAçık Erişim2023Scopus SJRQ4Theoretical Investigation of (E)-1-(2,4-Dichlorophenyl)-3-[4-(morpholin-4-yl)phenyl]prop-2-en-1-one Molecule As a Possible Potential COVID-19 Drug Candidate: Molecular Docking and DFT Calculations
Ekíncíoğlu, Yavuz
Abstract: In this study, a potential new drug to fight against the COVID-19 virus, (E)-1-(2,4-dichlorophen-yl)-3-[4-(morpholin-4-yl)phenyl]prop-2-en-1-one molecule has been investigated via computational assessment and molecular docking approach. From the conformer analysis and optimization, the most stable structure is determined. For this structure, geometrical parameters, Frontier molecular orbitals analysis, chemical reactivity descriptors, nonlinear optical properties, natural bond orbital, mulliken population analysis, molecular electrostatic potential map and thermodynamic properties of molecule were calculated with standard functional at the B3LYP/6-311++G(d,p) method. The geometric parameters (bond lengths and bond angles) are in good agreement with the experimental values available in the literature. The stability, structural and electronic properties obtained for the molecule can be a significant contribution to the future experimental and theoretical studies. The molecular docking mechanisms between the molecule and 7ALI protein points out that the protein-ligand systems are hydrogen bonding, π-stacking, and hydrophobic interactions.
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İncele - MakaleYalnız künye2014Scopus SJRQ2A comparative study of selected disperse azo dye derivatives based on spectroscopic (FT-IR, NMR and UV-Vis) and nonlinear optical behaviors
Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet
In the present work, a combined experimental and quantum chemical study on ground state equilibrium structure, spectroscopic and nonlinear optical properties of selected disperse azo dye molecules are reported. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state, simulated IR spectra and total energy distribution (TED) of vibrational modes. The chemical shifts were determined from the results of observed 1H and 13C NMR spectra in chloroform and dimethylsulfoxide solution. The DFT/gauge-invariant atomic orbital (GIAO) methodology was applied to predict the magnetic properties. Electronic properties were carried out by UV-Vis spectroscopy and TD-DFT/CIS approach. The nonlinear optical (NLO) features were addressed theoretically. A detailed description of spectroscopic and NLO behaviors of studied disperse azo dyes was reported with the help of comparison of experimental measurements and theoretical calculations.
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İncele - MakaleYalnız künye2013Scopus SJRQ2Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations
Sinha, Leena; Karabacak, Mehmet; Narayan, V.; Cinar, Mehmet; Prasad, Onkar
Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.
AtıfScopus53WoS53OpenAlex58İncele - MakaleYalnız künye2013Scopus SJRQ2Experimental and theoretical FTiR and FT-Raman spectroscopic analysis of 1-pyrenecarboxylic acid
Karabacak, M.; Cinar, M.; Kurt, M.; Chinna Babu, P.; Sundaraganesan, N.
The title molecule 1-pyrenecarboxylic acid (1PCA) has been characterized by FTiR, FT-Raman, NMR and UV-Vis spectral analyses. The molecular geometry, harmonic vibrational modes, the corresponding wavenumbers and iR intensities of 1PCA were calculated by DFT method with 6-311G(d, p) basis set. The assignments of the fundamentals were proposed on the basis of total energy distribution (TED) calculations. The calculated 13C and 1H NMR chemical shifts using gauge including atomic orbitals (GiAOs) approach are in good agreement with the observed chemical shifts. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. Using TD-DFT method, the electronic transitions have been compared with the experimental wavelengths. The molecular electrostatic potential map was used for prediction of possible hydrogen and oxygen bonding sites 1PCA molecule.
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