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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 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.
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İncele - MakaleAçık Erişim2013Scopus SJRQ2An experimental and theoretical investigation of Acenaphthene-5-boronic acid: Conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra
Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M.; Cinar, Mehmet
The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400 cm1 and 4000-10 cm 1, respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H·O hydrogen bonding have been discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability (β), its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.
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