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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 Metadata only Experimental, Ab İnitio And Density Functional Theory Studies On Sulfadiazine(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2009-04-30) Özel, Ayşen E.; AKYÜZ, SEVİM; ILDIZ, GÜLCE ÖĞRÜÇ; TR10127; TR107326; TR110745In the present study, combined experimental and computational study on molecular vibrations of free sulfadiazine has been reported. The theoretically possible stable conformers of free sulfadiazine molecule in electronically ground state were searched by means of torsion potential energy surfaces scan studies through C1-C7-S8-N9, C7-S8-N9-C10 and S8-N9-C10-N11 dihedral angles, at both semi-empirical PM3 and B3LYP/3-21G levels of theory. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization carried out at ab initio HF/6-31G++(d,p) and DFT/B3LYP/6-31G++(d,p) theory levels. The harmonic and anharmonic vibrational wavenumbers and IR intensities were calculated at the same theory levels used in geometry optimization. The modes of the fundamental vibrations were characterized depending on their the total energy distribution (TED%). In order to fit the calculated harmonic wavenumbers to experimental ones, dual scale factors were used. The experimental infrared and Raman spectra of sulfadiazine in solid phase have been measured and compared with the calculated vibrational spectra of each conformer. (C) 2009 Elsevier B.V. All rights reserved.Publication Metadata only Vibrational Analysis and Quantum Chemical Calculations of 2,2′-Bipyridine Zinc(II) Halide Complexes(Elsevier, 2007-05-27) Özel, Ayşen E.; Kecel Gündüz, Serda; AKYÜZ, SEVİM; 110745; 110526; 10127In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (X = Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2′-bipyridine were carried out with the Gaussian03 program package by using Hartree–Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2′-bipyridine were determined.Publication Metadata only Molecular Structure and Vibrational Assignment of 2-,4-,6-Methylquinoline by Density Functional Theory (DFT) and Ab Initio Hartree-Fock (HF) Calculations(Elsevier, 2006-11-24) Özel, Ayşen E.; Kecel Gündüz, Serda; AKYÜZ, SEVİM; 110745; 110526; 10127The molecular geometry, the normal mode frequencies and corresponding vibrational assignments of 2-,4-,6-methylquinoline (2-,4-,6-mq) in the ground state were performed by HF and DFT/B3LYP levels of theory using the 6-31++G(d,p) basis set. Harmonic and anharmonic vibrational frequencies were calculated. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method by using parallel quantum mechanic solutions program. The general agreements between the observed and calculated frequencies are shown.Publication Metadata only FT-IR and Raman Spectroscopic and Quantum Chemical Studies of Zinc Halide Complexes with 2,2 '-Biquinoline(ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS, 2008-11-20) Özel, Ayşen E.; Keçel, Serdal; AKYÜZ, SEVİM; TR10127; TR110745The molecular structure, vibrational frequencies and the corresponding vibrational assignment of Zn(biq)X-2 (X = CI and Br; biq = 2,2'-biquinoline) have been studied by employing the hybrid density functional theory (B3LYP) method and the complete basis set (DFT) method together with the 6-31G(d,p) basis set for X = Cl and Br. The FT-IR (400-4000 cm(-1)) and Raman (100-3200 cm(-1)) spectra of compounds were recorded and compared with that of the calculated spectra, which allowed authors to assign most of the observed bands. It was demonstrated that cis conformer is suitable for the Zn(biq)X2 Compounds. The fundamental vibrational modes were characterized by their total energy distribution. The coordination effects on vibrational wavenumbers of biq were discussed in detail. (C) 2008 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.