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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 Temperature Dependent FT IR Spectroscopic Study of The Interaction of alfa Tocopherol and alfa Tocopheryl Acetate with Phospholipid bilayers(Elsevier, 1997-08-11) Davies, J. Eric D.; AKYÜZ, SEVİM; 10127FTIR spectroscopy has been employed in order to investigate α-tocopherol (α-T) and α-tocopheryl acetate (α-TA) induced effects on the molecular organization of dimyristoyl-l-α-phosphatidylcholine (DMPC) bilayers, at various temperatures and concentrations. It was concluded that α-T interacts much more strongly than α-TA, indicating that α-T has a more polar location in the membrane than α-TA. The observed changes in the carbonyl and phosphate group vibrational modes of DMPC on addition of α-T or α-TA are discussedPublication Restricted Shedding Light Into the Biological Activity of Aminopterin, Via Molecular Structural, Docking, and Molecular Dynamics Analyses(Taylor & Francis Inc., 2023) Çelik, Sefa; YILMAZ, GÖZDE; AKYÜZ, SEVİM; Özel, Ayşen E.In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1)integrins, human dihydrofolate reductase, main protease (M-pro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1) integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), M-pro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.Publication Metadata only Vibrational spectroscopic and structural investigations of bioactive molecule Glycyl-Tyrosine (Gly-Tyr)(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-09) Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110147; 10127; 110745This study investigated the conformational behavior of biological active molecule Glycyl-Tyrosine (Gly-Tyr) dipeptide and its dimers, by Boltzmann jump and DET calculations. The energy calculations on Gly-Tyr dipeptide as a function of side chain torsion angles enabled us to determine the preferred conformations. The most stable conformations obtained from the above process were further optimized by the DFT calculations. The geometry optimization and vibrational wavenumbers calculations of Gly-Tyr dipeptide were carried out with the Gaussian03 program by using density functional theory (DFF) with B3LYP functional and 6-31++G (d,p) basis set. The dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated using the same method and the same basis set. The results provided a good account of the role of the number and type of inter- or/and intramolecular H-bond interactions existing in the dialer and monomer forms of the dipeptides. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of monomeric and dimeric forms of the dipeptide were calculated and compared with the experimental vibrational spectra of solid Gly-Tyr dipeptide. Vibrational assignment of the molecule was done using the potential energy distribution analysis. HOMO-LUMO energy has been used to elucidate the reasons for intra molecular charge transfer. (C) 2017 Elsevier B.V. All rights reserved.Publication Metadata only Elemental and spectroscopic characterization of plasters from Fatih Mosque-Istanbul (Turkey) by combined micro-Raman, FTIR and EDXRF techniques(Pergamon-Elsevier Science Ltd, The Boulevard, Langford Lane, Kidlington, Oxford Ox5 1Gb, England, 2015-10-05) Güleç, Ahmet; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127The characterization of the plasters and coloring agents of the wall paintings of Fatih Mosque have been performed using combined micro-Raman, FTIR and EDXRF techniques. The investigations show that the plaster used on the walls has mixed gypsum lime binders. Cinnabar {HgS}, lead red {Pb3O4} and hematite {alpha-Fe2O3} were identified in the red surfaces. Blue color is attributed to ultramarine blue {Na8-10Al6Si6O24S2-4}. Green color is assigned to mixtures of green earth, copper phthalocyanine {Cu(C32Cl16N8)} and brochantite {CuSO4 center dot 3Cu(OH)(2)}. Strontium yellow {SrCrO4} and zinc white {ZnO} were also used to ensure the color tone. The results provide a basis for future restoration of wall paints. (C) 2015 Elsevier B.V. All rights reserved.Publication Metadata only FTIR and EDXRF ınvestigations of the second generations of salt tolerant soybean mutants(2012-08) AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; ATAK, ÇİMEN; ÇELİK, ÖZGE; 10127; 113987; 6653Publication Open Access Evaluation of Anti-Cancer and Anti-Covid-19 Properties of Cationic Pentapeptide Glu-Gln-Arg-Pro-Arg, From Rice Bran Protein and Its D-Isomer Analogs Through Molecular Docking Simulations(Elsevier Science Inc., 2021) Gasymov, Oktay K.; Çelik, Sefa; Ağaeva, Gülşen; AKYÜZ, SEVİM; Keçel-Gündüz, Serda; Qocayev, Niftali M.; Özel, Ayşen E.; Ağaeva, Ülker; Bakhishova, Matanat; Aliyev, Jamil A.Bioactive peptides derived from food proteins are becoming increasingly popular due to the growing awareness of their health-promoting properties. The structure and mechanism of anti-cancer action of pentapeptide GluGln-Arg-Pro-Arg (EQRPR) derived from a rice bran protein are not known. Theoretical and experimental methods were employed to fill this gap. The conformation analysis of the EQRPR pentapeptide was performed first and the obtained lowest energy conformer was optimized. The experimental structural data obtained by FTIR and CD spectroscopies agree well with the theoretical results. D-isomer introduced one-by-one to each position and all D-isomers of the peptide were also examined for its possible anti-proteolytic and activity enhancement properties. The molecular docking revealed avid binding of the pentapeptide to the integrins alpha(5)beta(1) and alpha(IIb)beta(3), with K-d values of 90 nM and 180 nM, respectively. Moreover, the EQRPR and its D-isomers showed strong binding affinities to apo-and holo-forms of M-pro, spike glycoprotein, ACE2, and dACE2. The predicted results indicate that the pentapeptide may significantly inhibit SARS-CoV-2 infection. Thus, the peptide has the potential to be the leading molecule in the drug discovery process as having multifunctional with diverse biological activities.Publication Restricted Vibrational Spectroscopic Characterization and Structural Investigations of Cepharanthine, a Natural Alkaloid(Elsevier, 2022) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Cepharanthine, a natural alkaloid obtained from the Stephania cepharantha Hayata plant, that has anti-tumor, anti-inflammatory, antioxidative, antiparasitic, and antiviral properties, has been widely used for many years to treat a wide variety of diseases in Japan. However, to elucidate its mechanism of action needs further study. This study aimed to enlighten the molecular structure, and the anticancer and antiviral action mechanisms of Cepharanthine. To evaluate the molecular structure of Cepharanthine, conforma-tional analysis was performed using the DFT/B3LYP with 6-31G(d,p) basis set. The obtained most stable molecular geometry was then optimized at the DFT/B3LYP/6-311 ++ G(d,p) level of theory. The observed IR and Raman bands were compared with harmonic vibrational frequencies of the optimized structure of cepharanthine, calculated using the same level of theory, and assigned on the base of potential energy distribution (PED). The experimental UV-Vis absorption spectrum was recorded and compared with the simulated Time Dependent (TD-DFT/B3LYP/6-311 ++ G(d,p)) method. Moreover, (1) H and C-13 NMR spectra has been calculated and compared by the experimental spectra. To reveal pharmacological importance of Cepharanthine, a molecular docking study was performed with NF-kappa B (nuclear factor kappa-light-chain-enhancer of activated B cells) receptor which controls transcription of DNA, cytokine production and cell survival. Molecular docking simulations revealed that Cepharanthine showed strong binding affinity to NF-kappa B receptor ( Delta G = -8.9 kcal/mol). In addition, to enlight the antiviral properties of cepharantine and to explore the possibility of its use in the treatment of COVID-19, the interactions of cepharanthine with ACE2, apo and holo forms of COVID-19 main protease enzyme (M-pro) and spike glycoprotein of SARSCoV-2 receptors were investigated. (c) 2022 Elsevier B.V. All rights reserved.Publication Metadata only FT-IR, EDXRF analysis of the Mardin-Mazidag phosphate deposit of Turkey and relations between phosphate, uranium and fluorine(ASIAN JOURNAL OF CHEMISTRY, 11/100 RAJENDRA NAGAR, SECTOR 3,, SAHIBABAD 201 005, GHAZIABAD, INDIA, 2008-06) Çağlar, Hikmet; Çağlar, Nazan; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; TR111424; TR10127; TR114368; TR110809EDXRF and FT-IR spectral analyses of the composite sample of Mardin-Mazidag phosphate deposit, in which the main phosphate mineral has been known to be collophane and dahllite, were reported. Uranium, phosphate and fluorine contents of the 25 individual phosphate samples were analyzed by EDXRF (U and P) and wet chemical methods (F). Quadratic regression model were applied on the U, P and F analyses results, in order to show the interrelation between phosphate, uranium and fluorine contents.Publication Metadata only Investigations on Empire series postage stamps of Ottomans (printed 1880-1890) by vibrational spectroscopic and energy dispersive X-ray fluorescence techniques(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-03) AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127In this study Empire series of stamps, the first postage stamps of Ottomans (printed in 1880-1890) after the Ottoman Empire became a member of Universal Postal Union, have been analyzed for the first time, non-destructively, using Fourier-transform infrared (FTIR), Raman and energy dispersive X-ray fluorescence (EDXRF) spectrometry methods Lead chromate, Prussian blue, vermillion, calcium carbonate, gypsum, cellulose, and oil were identified. The merging of data coming from vibrational spectroscopy and EDXRF techniques has allowed the characterization of the pigments used on the surface of each stamp and dispersed between the paper fibers. Additionally, the paper of the stamps was also analyzed. (C) 2017 Elsevier B.V. All rights reserved.