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Publication Metadata only Structural and spectroscopic investigation on antioxidant dipeptide, L-Methionyl-L-Serine: A combined experimental and DFT study(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-06-05) Kecel Gündüz, Serda; Bıçak, Bilge; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 277135; 110147; 10127; 110745The focus of this study is to determine the conformational, structural and vibrational properties of Methionyl-Serine dipeptide (L-Methionyl-L-Serine, Met-Ser), a biological active molecule. To investigate their energetically preferred conformations, molecular mechanics methods were utilized to determine the optimal conformations of the 3402 different dihedral angle values of the backbone and side chains. It was found that the extended (e) backbone shape in the LB conformational range was the most stable LMethionyl-L-Serine dipeptide conformation, with 3.12 kcal/mol of energy. Density Functional Theory (DFT) was used to determine the optimized geometry, the vibrational wavenumbers and modes of the title dipeptide values, with 6-31G (d,p) and 6-311++G (d,p) basis sets. The potential energy distribution data was used to carry out the assignment of the bands. In addition, the vibrational spectra of the most stable conformer and its dimer form were determined and the obtained results were compared with the experimental IR and Raman spectra in the solid phase. To determine the presence of intramolecular charge transfer, molecular dipole moment, polarizability and hyperpolarizability, the Natural Bond Orbital (NBO), HOMO LUMO calculations, the linear polarizability (alpha) and the first order hyperpolarizability (fio) value analyses of the investigated molecule were carried out using the DFT with the B3LYP/6-31++G(d,p) basis set. This study aims to determine a relatively stable conformation of antioxidant dipeptide and to investigate the molecular geometry, molecular vibrations and hydrogen bonding interactions between monomeric and dimeric forms of Methiony-Serine dipeptide. (C) 2017 Elsevier B.V. All rights reserved.Publication Restricted Molecular Structure, Molecular Docking and Absorption, Distribution, Metabolism, Excretion and Toxicity study of Cellulose II(Wiley-VCH Verlag GmbH, 2021) Çelik, Sefa; Demirağ, Aliye Demet; Özel, E. Ayşen; AKYÜZ, SEVİMCellulose is a renewable biopolymer which is the most abundant in nature, formed by binding of glucose units with beta-1,4 glycosidic bonds. Cellulose is divided into two groups as bacterial cellulose (BC) and vegetable cellulose. This study reports the interaction mechanism of Cellulose II, which is a BC, with the cellulase enzymes, determined by molecular docking method based on key-lock theory. The most stable molecular geometry of the Cellulose II molecule was determined by density functional theory using Gaussian 09 program. The scaled vibration frequencies of optimized geometry were calculated by using Molvib program. Molecular electrostatic potential and frontier molecular orbital analyses were performed. Molecular interactions between cellulose II and endoglucanase, exogluconase and beta-glucosidase II have been determined. Moreover, the drug likeness and ADMET properties of cellulose II were analyzed for the prediction of pharmacokinetic profiles.Publication Metadata only Conformational Analysis And Vibrational Spectroscopic Investigation Of L-Proline-Tyrosine (L-Pro-Tyr) Dipeptide(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2011-05-03) Kecel, Serda; Özel, Ayşen; Çelik, Sefa; Agaeva, Gulshen; AKYÜZ, SEVİM; TR110526; TR110745; TR10127; TR110147In this study the conformational properties of the drug based dipeptide L-proline-L-tyrosine (Pro-Tyr) in its monomeric and dimeric forms, have been investigated by molecular mechanic and ab initio calculations. The energy calculations on Pro-Tyr dipeptide as a function of side chains torsion angles, enable us to determine their energetically preferred conformations. One-hundred and eight possible conformations of Pro-Tyr dipeptide have been investigated by conformational analysis and the low energy conformations of dipeptide have been determined by using the Ramachandran maps. Afterwards, the geometrical parameters of obtained stable conformations were used as starting parameters for quantum chemical calculations. The molecular structure of Pro-Tyr dipeptide, in the ground electronic state (in vacuum) was optimized by density functional theory method with B3LYP functional and using 6-31G(d,p) and 6-31++G(d,p) basis sets. The dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated using the same method and the same level of theory by using 6-31G(d,p) basic set. The fundamental vibrational wavenumbers, IR intensities and Raman activities of the global conformation of monomeric and dimeric forms of the dipeptide were calculated and compared with the experimental vibrational spectra of solid Pro-Tyr dipeptide. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Vibrational assignment was performed on the basis of calculated total energy distribution (TED) of the modes. (C) 2011 Elsevier B.V. All rights reserved.Publication Metadata only Structural and vibrational study of primidone based on monomer and dimer calculations(Taylor & Francis Inc, 530 Walnut Street, Ste 850, Philadelphia, Pa 19106 USA, 2015-04-03) Çelik, Sefa; Kecel Gündüz, Serda; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 110745; 10127Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (C12H14N2O2), has been a valuable drug in the treatment of epilepsy. In the present work, the experimental IR and Raman spectra of solid phase primidone were recorded, and the results were compared with theoretical wavenumber values of monomer and dimer forms of the title molecule. Vibrational spectral simulations in the dimer form were carried out to improve the assignment of the bands in the solid phase experimental spectra. The possible stable conformers of free molecule were searched by means of torsion potential energy surfaces scan studies through two dihedral angles. The molecular geometries of the monomer and dimer forms of title molecule were optimized using DFT method at B3LYP/6-31++G(d,p) level of theory. Using PEDs determined the contributions of internal (stretching, bending, etc.) coordinates to each normal mode of vibration. Further, HOMO-LUMO energy gap and NBO properties of the investigated molecule in monomer and dimer forms were also calculated.Publication Metadata only Vibrational Spectroscopic Investigation Of Free And Coordinated 5-Aminoquinoline: The IR, Raman And DFT Studies(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2009-04-30) Özel, Ayşen E.; Çelik, Sefa; AKYÜZ, SEVİM; TR110745; TR110147; TR10127Combined experimental and computational vibrational spectra of 5-aminoquinoline (5-AQ) and its zinc chloride complex {Zn(5-AQ)(2)Cl-2}, together with the computational results of 5-AQ interacting with H2O through the ring nitrogen {5-AQ center dot H2O} have been reported. The geometry of the free 5-AQ were optimized using DFT method at B3LYP/6-31G(d,p) and 6-31++G(d,p) levels of theory. Coordinated 5-AQ molecules: {5-AQ center dot H2O} and {Zn(5-AQ)(2)Cl-2} were optimized using DFT/B3LYP/6-31G(d,p) level of theory. Harmonic and anharmonic vibrational frequencies and infrared intensities were calculated at the same level of theory. The fundamental vibrational modes were characterised depending on their total energy distribution (TED%). Coordination effects on 5-AQ vibrational frequencies were investigated. (C) 2009 Elsevier B.V. All rights reserved.