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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 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 Vibrational study on Zn(Pyrimidine)(2)Cl-2, Pyrimidine-Al(OH)(3) and Pyrimidine-(Al(OH)(3))(2) complexes(ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS, 2008-11-20) Akalın, Elif; AKYÜZ, SEVİM; TR10127; TR46357A molecular modeling analysis was performed via density functional theory (DFT), using B3LYP/6-31++G(d,p) basis set on Zn(PM)(2)Cl-2, PMAI(OH)(3) and PM-(AI(OH)(3))(2) complexes (PM: Pyrimidine) in order to investigate monodentate and bidentate coordination effects on pyrimidine vibrational wavenumbers. The Zn(PM)(2)Cl-2. Complex was synthesized and the FT-IR and FT-Ra spectra were recorded which, when compared to the calculated wavenumbcrs of the model mono- and bidentate Al(OH)(3) Complexes, showed that pyrimidine behaved as a rnonodentate ligand. Anharmonic corrections to the calculated wavenumbers of the Zn(PM)(2)Cl-2 complex were done and the results led to a good overall agreement with the observed wavenurnbers. A complete assignment of the fundamentals was proposed based on the internal mode analysis done by Gaussian03 programme. (C) 2007 Elsevier B.V. All rights reserved.Publication Metadata only Ab Initio and Raman Study of Medium Range Ordering in GeSe2 Glass(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2013-08-01) Akalın, Elif; Holomb, R.; Mitsa, V.; Sichka, M.; AKYÜZ, SEVİM; 10127; 46357High resolution Raman spectra of GeSe2 glass were measured and fitted using individual Gaussian components. The structural origin of the components were interpreted using the results of ab initio density functional theory calculations performed on GenSem nanoclusters (n = 2-6, 12; m = 6-9, 12, 14-16, 30) which represent the local structure of GeSe2 glass and on some "defect" GenSem clusters that are thought to be related to the inhomogeneity of the structure at the nanoscale. The calculated vibrational properties of GenSem nanoclusters and their couplings with the short- and medium-range order structure formations in GeSe2 glass are analyzed and discussed. (c) 2013 Elsevier B.V. All rights reserved.Publication Metadata only New Ring-Like Models and ab Initio DFT Study of the Medium-Range Structures, Energy and Electronic Properties of GeSe2 Glass(Taylor & Francis Ltd, 4 Park Square, Milton Park, Abingdon Ox14 4Rn, Oxon, England, 2013-07-01) Akalın, Elif; Holomb, R.; Mitsa, V.; AKYÜZ, SEVİM; 46357; 10127Ab initio DFT calculations were performed on GenSem nanoclusters (n=2, 3, 5, 6, 12; m=6-9, 14, 16, 30) that represent the local structure of GeSe2 glass and on some defect' GenSem clusters that are thought to be related to the inhomogeneity of the structure at the nanoscale. The optimal geometries, total energies and their derivatives as well as the electronic properties of GenSem nanoclusters were calculated using traditional DFT method. In addition, the TD-DFT method has been applied to calculate the electronic band gaps of the clusters. The calculated physico-chemical properties of GenSem nanoclusters and their couplings with the local-and medium-range order structure formations in GeSe2 glass are analysed and discussed.Publication Metadata only Vibrational Analysis of Free and Hydrogen Bonded Complexes of Nicotinamide and Picolinamide(Elsevier, 2006-11-24) Akalın, Elif; AKYÜZ, SEVİM; 46357; 10127Harmonic and anharmonic vibrations of free nicotinamide (NIA) and picolinamide (PIA) molecules together with their hydrogen bonded complexes H2O–NIA and H2O–PIA have been studied by means of density functional method. The calculation results of the vibrational spectra of free molecules have been investigated and are compared to the available experimental spectra. The vibrational wavenumbers of both molecules have also been calculated by polarizable continuum model (PCM) that represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent (water is chosen as the solvent in this study). The results of PCM calculations and the H2O–NIA, H2O–PIA complexes, are used to investigate the H-bonding interactions of both molecules with the water molecule. The harmonic wavenumbers have been scaled by proper factors obtained by comparing the observed versus calculated wavenumbers and it is shown that anharmonic corrections on the vibrational spectra provided a better agreement between the observed and calculated wavenumbers compared to the results obtained by scaling factor method.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.