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Publication Metadata only Molecular Mechanics Studies of Antihypertensive Val-Tyr Dipeptide(Asian Journal Of Chemistry, 11/100 Rajendra Nagar, Sector 3,, Sahibabad 201 005, Ghaziabad, India, 2010-01) Akverdieva, G. A.; Godjayev, N. M.; Doğan, N. E.; AKYÜZ, ZEKİ TANIL; AKYÜZ, SEVİM; TR10127; TR111424The spatial structure of anti hypertensive dipeptide,Valine-Tyrosine was investigated within molecular mechanics framework. It ha, been shown that the molecule has such a structural organization which does not exclude the realization of two types of conformation: folded and extended. The energy and geometrical parameters for the optimal conformations of dipeptide are obtained. The electronic characteristics for these structures were analyzed by quantum chemical calculations.Publication Restricted Molecular Structure, Vibrational Spectra, Molecular Docking, and ADMET Study of Cellulose Triacetate II(Pleiades Publishing Inc., 2020) Çelik, Sefa; Demirağ, A. Demet; Özel, Ayşen E.; AKYÜZ, SEVİMPeople have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental problems that remain intact in nature for years. In this study, molecular structure analysis of cellulose triacetate II (CTA II) molecule, obtained from cellulose II and acetate, was carried out. There is an important relationship between the structure and activity of molecules, so it is very important to determine the geometric structure of a molecule. Therefore, using density functional theory (DFT) the most stable molecular geometries of the cellulose triacetate II monomer (C12H18O9) as well as dimer (C24H36O18), which included intermolecular H-bonding, were calculated. The analogous calculations were carried out for the (CTA-II)(2)nano-cluster (C24H34O17), which represents the local structure of CTA-II crystal, and created by binding the two most stable CTA II molecules by covalent bond. Scaled wavenumbers and potential energy distribution of the vibrational modes of CTA monomer and (CTA-II)(2)nano-cluster were computed. In order to evaluate the interaction of CTA II with theAspergillus nigercellulase enzyme,which is an important that is active in cellulose digestion and CTA II, molecular docking studies were carried out. H-binding interactions between CTA II (in monomeric, dimeric, and cluster forms) and the active site of theAspergillus nigercellulase enzyme were shown. Moreover, in silico ADMET prediction study was calculated for CTA-II monomer to predict its druglikeness properties.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 Structure and Vibrational Spectra of Benzidine(Elsevier, 2003-06-01) Akalın, Elif; AKYÜZ, SEVİM; 46357; 10127The geometry and vibrational spectrum of benzidine have been computed by ab initio calculations using the DFT/B3LYP method with 6-31+G(d,p) basis set. In the most stable geometry, the dihedral angle between the two phenyl rings was found to be around 38°. Calculated wavenumbers were scaled by a single factor 0.965 to approximately correct for vibrational anharmonicity as well as for overestimation of the force constants. Normal coordinate analysis of benzidine and some of its deuterated derivatives have also been performed in valance force field approximation in order to demonstrate the transferability of the force field of aniline. Good agreements between the two different calculation results (ab initio and force field refinement methods) and between the calculated and observed values are found.Publication Metadata only Radioisotope Excited X Ray Fluorescence Analysis of Ashes From Coal Power Plants of Turkey(Kluwer Academic Publishers, 1998-01) Başsarı, A.; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127Fifteen ash samples taken from filters and bottom products of boilers or chimneys of seven coal fired power plants in Turkey have been analysed quantitatively for some minor elements using radioisotope energy dispersive X-ray fluorescence (EDXRF). It is found that samples contain Cu, Zn, Rb, Sr, Zr, Mo, Cs, Sb, Ba, Pb, Y, La, Ce, Nd and Sm in different amounts. An ash sample taken from the electro-filter of the Ambarli, fuel oil fired-power plant was also analysed for comparison and found that it contained the smallest amount of potentially toxic elements.Publication Metadata only Conformational Analysis And Vibrational Spectroscopic Studies On Dapsone(Maik Nauka/Interperiodica/Springer, 233 Spring St, New York, Ny 10013-1578 Usa, 2012-11) AKYÜZ, SEVİM; ILDIZ, GÜLCE ÖĞRÜÇ; TR107326; TR10127In this study, the theoretical conformation analysis of free dapsone has been performed by single point energy calculations at both semi-empirical PM3 and DFT/B3LYP-3-21G theory levels and three stable conformers were determined. Both the IR and Raman spectra of the molecule in solid phase have been recorded. The IR intensities and harmonic vibrational wavenumbers of each conformer were calculated by DFT method at B3LYP/6-31++G(d,p) theory level. For the fundamental characterization, the total energy distribution (TED) calculations of the vibrational modes were done using parallel quantum mechanic solution program (SQM) and the fundamental modes were assigned. The theoretical results are in agreement with the experimental ones.Publication Metadata only Ft-Ir And Edxrf Analysis Of Wall Paintings Of Ancient Ainos Hagia Sophia Church(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2009-04-30) Başaran, Sait; Kocabaş, I.; Güleç, A.; Çeşmeli, H.; Uçar, B.; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; TR10127; TR111424The wall paintings of ancient Ainos Hagia (Saint) Sophia Church were investigated by FT-IR and EDXRF spectroscopy. Calcite, aragonite, gypsum, and quartz were detected in all the samples. Feldspar phases and pigments were inferred from both band component analysis and the second derivative profiles of the IR spectra. The black, dark brown, and red colouration was due to different concentrations of MnO2, Mn2O3, magnetite, and haematite. (C) 2009 Elsevier B.V. All rights reserved.Publication Metadata only Fluorescence Spectra of Salt Solutions of Coumarin Crown Ethers(Taylor and Francis Online, 1995) Bulut, Mustafa; Göçmen, Ayten; Erk, Clakil; AKYÜZ, SEVİM; 10127; 205874The fluorescence spectra of the coumarin derivatives of crown ethers obtained from 7,8-dihydroxycoumarins were studied in the presence of some alkali and alkaline earth cations in acetonitrile. The altered fluorescence spectra were examined qualitatively from the point of enhancement of fluorescent quantum yields as well as a resonance. Heavy metal effects were eliminated since there is no influence of the metal salts on the spectra of the initial coumarin derivatives. However, both the complexation-enhanced fluorescence and complexation-enhanced quenching spectra is observed in the fluorescence emission and excitation spectra of macrocyclic ether-coumarin / metal salt systems. The origin of results are briefly discussed in terms of crown ether complexation. In water solutions almost no such effects were observed.Publication Metadata only Investigation of adsorption of 5-Chlorouracil onto montmorillonite: An IR and Raman spectroscopic study(Elsevier, 2018-11) AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127In this study, the adsorption of 5-Chlorouracil (5-ClU) on natural montmorillonite from Anatolia was investigated using FT-IR and Raman spectroscopy. The 5-ClU is a thymine antagonist and has some antitumor properties. The comparison of the vibrational spectra of the adsorbed 5-ClU with those of the free molecule provided data on the nature and characteristics of the clay organic complexes. The intercalation of 5-ClU within montmorillonite has been shown by X-ray diffraction to increase the interlayer spacing. Vibrational spectroscopy indicates that adsorbed 5-ClU molecules on montmorillonite are coordinated to exchangeable cations, directly or indirectly through water bridges.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.