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Publication Embargo Multivalued Sakaguchi functions(2007)Let A be the class of functions f(z) of the form f(z) = z +a2z2 + ··· which are analytic in the open unit disc U = {z ∈ C||z| < 1}. In 1959 [5], K. Sakaguchi has considered the subclass of A consisting of those f(z) which satisfy Re zf (z) f(z)−f(−z) > 0, where z ∈ U. We call such a functions “Sakaguchi Functions”. Various authors have investigated this class ([4], [5], [6]). Now we consider the class of functions of the form f(z) = zα(z +a2z2 +···+anzn +···) (0 <α< 1), that are analytic and multivalued in U, we denote the class of these functions by Aα, and we consider the subclass of Aα consisting of those f(z) which satisfy Re zDα z f(z) Dα z f(z)−Dα z f(−z) > 0 (z ∈ U), where Dα z f(z) is the fractional derivative of order α of f(z). We call such a functions “Multivalued Sakaguchi Functions” and denote the class of those functions by Sα s . The aim of this paper is to investigate some properties of the class Sα s . 2000 Mathematical Subject Classification: Primary 30C45.Publication Restricted Auxiliary Differential Diagnosis of Schizophrenia and Phases of Bipolar Disorder Based on the Blood Serum Raman Spectra(Wiley, 2020) ILDIZ, GÜLCE ÖĞRÜÇ; Bayari, Sevgi; Aksoy, Umut M.; Yorguner, Neşe; Bulut, Hüseyin; Yılmaz, Sultan S.; Halimoğlu, Gökhan; Kabuk, Hayrunnisa Nur; YAVUZ, GİZEM; Fausto, RuiSchizophrenia (SZ) and bipolar disorder (BP) are severe psychiatric disorders that are characterized by an extensive spectrum of symptoms and affect approximately 2% of the world population. BP exhibits three well-distinct phases, which are classified as manic and depressive episodes and euthymic phase. These disorders are of difficult differential clinical diagnosis due to the similarity of their symptoms. Diagnostic approaches for SZ and BP are based on constructed patient interviews and subjective evaluations of clinical symptoms, and there are still no molecular-based auxiliary diagnostic tools to support the clinical diagnosis. In this study, an analytical model for auxiliary differential diagnosis of SZ and BP, based on the analysis of patients' blood serum Raman spectra, is developed, which is able to account for the different BP phases and can also differentiate SZ and BP patients from healthy individuals. The model is based on a hierarchical sequence of four two-class PLS-DA steps where the Raman spectra are theX-predictor variables. It is concluded that the full 400-3,100 cm(-1)Raman spectroscopic range is a sensitive probe for the disorders, thus working as a general spectroscopic biomarker for the illnesses. The proposed methodology is reliable, fast, cheap, essentially minimal-invasive, and might be implemented easily in the clinical environment.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 Restricted Molecular Modeling, DFT Quantum Chemical Analysis, and Molecular Docking on Edotecarin, an Indolocarbazole Anticancer Agent(Taylor & Francis Ltd., 2022) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Edotecarin is an indolocarbazole class antitumor agent that has significant anticancer effects against various types of cancer, especially lung, breast, and stomach cancer.The conformation analysis of the edotecarin was performed using the PM3 method and six stable conformations were obtained.Afterwards the obtained lowest energy conformation was optimized at the DFT/B3LYP/6-31++G(d,p) level of theory. The vibrational wavenumbers, the highest occupied molecular orbital, the lowest unoccupied molecular orbital and molecular electrostatic potential of the most stable conformer of edotecarin were calculated at the DFT/B3LYP/6-31++G(d,p) level of theory.The molecular docking of the edotecarin molecule against DNA, Topoisomerase I, DNA-Topoisomerase I complex,alpha(5)beta(1) and alpha(IIb)beta(3) integrins were performed to reveal its binding modes and binding affinities.Publication Open Access Micro-Raman Spectroscopy and X-ray Diffraction Analyses of the Core and Shell Compartments of an Iron-Rich Fulgurite(MDPI, 2022) KARADAĞ, AHMET; Kaygısız, Ersin; Nikitin, Timur; Öngen, Sinan; ILDIZ, GÜLCE ÖĞRÜÇ; Aysal, Namık; Yılmaz, Ayberk; Fausto, RuiFulgurites are naturally occurring structures that are formed when lightning discharges reach the ground. In this investigation, the mineralogical compositions of core and shell compartments of a rare, iron-rich fulgurite from the Mongolian Gobi Desert were investigated by X-ray diffraction and micro-Raman spectroscopy. The interpretation of the Raman data was helped by chemometric analysis, using both multivariate curve resolution (MCR) and principal component analysis (PCA), which allowed for the fast identification of the minerals present in each region of the fulgurite. In the core of the fulgurite, quartz, microcline, albite, hematite, and barite were first identified based on the Raman spectroscopy and chemometrics analyses. In contrast, in the shell compartment of the fulgurite, the detected minerals were quartz, a mixture of the K-feldspars orthoclase and microcline, albite, hematite, and goethite. The Raman spectroscopy results were confirmed by X-ray diffraction analysis of powdered samples of the two fulgurite regions, and are consistent with infrared spectroscopy data, being also in agreement with the petrographic analysis of the fulgurite, including scanning electron microscopy with backscattering electrons (SEM-BSE) and scanning electron microscopy with energy dispersive X-ray (SEM-EDX) data. The observed differences in the mineralogical composition of the core and shell regions of the studied fulgurite can be explained by taking into account the effects of both the diffusion of the melted material to the periphery of the fulgurite following the lightning and the faster cooling at the external shell region, together with the differential properties of the various minerals. The heavier materials diffused slower, leading to the concentration in the core of the fulgurite of the iron and barium containing minerals, hematite, and barite. They first underwent subsequent partial transformation into goethite due to meteoric water within the shell of the fulgurite. The faster cooling of the shell region kinetically trapped orthoclase, while the slower cooling in the core area allowed for the extensive formation of microcline, a lower temperature polymorph of orthoclase, thus justifying the prevalence of microcline in the core and a mixture of the two polymorphs in the shell. The total amount of the K-feldspars decreases only slightly in the shell, while quartz and albite appeared in somewhat larger amounts in this compartment of the fulgurite. On the other hand, at the surface of the fulgurite, barite could not be stabilized due to sulfate lost (in the form of SO2 plus O-2 gaseous products). The conjugation of the performed Raman spectroscopy experiments with the chemometrics analysis (PCA and, in particular, MCR analyses) was shown to allow for the fast identification of the minerals present in the two compartments (shell and core) of the sample. This way, the XRD experiments could be done while knowing in advance the minerals that were present in the samples, strongly facilitating the data analysis, which for compositionally complex samples, such as that studied in the present investigation, would have been very much challenging, if possible.Publication Open Access Thiabendazole and Thiabendazole-Formic Acid Solvate: A Computational, Crystallographic, Spectroscopic and Thermal Study(2020-07) Tabanez, A.M.; Nogueira, B.A.; Milani, A.; S. Eusébio, M.E.; Paixão, J.A.; Kabuk, H.N.; Jajuga, M.; Fausto, Rui; ILDIZ, GÜLCE ÖĞRÜÇThiabendazole (TBZ) is a substance which has been receiving multiple important applications in several domains, from medicine and pharmaceutical sciences, to agriculture and food industry. Here, a comprehensive multi-technique investigation on the molecular and crystal properties of TBZ is reported. In addition, a new solvate of the compound is described and characterized structurally, vibrationally and thermochemically for the first time. Density functional theory (DFT) calculations were used to investigate the conformational space of thiabendazole (TBZ), revealing the existence of two conformers, the most stable planar trans form and a double-degenerated-by-symmetry gauche form, which is ~30 kJ mol−1 higher in energy than the trans conformer. The intramolecular interactions playing the major roles in determining the structure of the TBZ molecule and its conformational preferences were characterized. The UV-visible and infrared spectra of the isolated molecule (most stable trans conformer) were also calculated, and their assignment undertaken. The information obtained for the isolated molecule provided a strong basis for the understanding of the intermolecular interactions and properties of the crystalline compound. In particular, the infrared spectrum for the isolated molecule was compared with that of crystalline TBZ and the differences between the two spectra were interpreted in terms of the major intermolecular interactions existing in the solid state. The analysis of the infrared spectral data was complemented with vibrational results of up-to-date fully-periodic DFT calculations and Raman spectroscopic studies. The thermal behavior of TBZ was also investigated using differential scanning calorimetry (DSC) and thermogravimetry. Furthermore, a new TBZ–formic acid solvate [2-(1,3-thiazol-4-yl)benzimidazolium formate formic acid solvate] was synthesized and its crystal structure determined by X-ray diffraction. The Hirshfeld method was used to explore the intermolecular interactions in the crystal of the new TBZ solvate, comparing them with those present in the neat TBZ crystal. Raman spectroscopy and DSC studies were also carried out on the solvate to further characterize this species and investigate its temperature-induced desolvation.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 Open Access Crystallization Kinetics: Relationship Between Crystal Morphology and the Cooling Rate-Applications for Different Geological Materials(MDPI, 2023-01-24) Aysal, Namık; Kurt, Yiğit; ILDIZ, GÜLCE ÖĞRÜÇ; Öztürk, Hüseyin; Yeşiltaş, Mehmet; Laçin, Davut; Öngen, Sinan; Nikitin, Timur; FAUSTO, RUICrystal morphology is controlled by several physicochemical parameters such as the temperature, pressure, cooling rate, nucleation, diffusion, volatile composition, and viscosity. The development of different crystal morphologies is observed as a function of the cooling rate in many different rock types (i.e., glassy volcanic rocks, and archeometallurgical slags). Crystallization is a two-stage kinetic process that begins with the formation of a nucleus and then continues with the accumulation of ions on it. The shapes of the crystals depend on the degree of undercooling (& UDelta;T), and euhedral crystals, having characteristic forms that reflect their crystallographic internal structure, that grow just below their liquidus temperature. In this study, crystal morphologies in different minerals (e.g., quartz, sanidine, olivine, pyroxene, magnetite, etc.) that had developed in silicic volcanic rocks (spherulites) and slags from ancient mining were investigated and characterized using optical microscopy, X-ray diffraction, and Fourier-transform infrared (FTIR), Raman, and scanning electron microscope-energy dispersive X-ray fluorescence (SEM-EDX) spectroscopic techniques. Depending on the increase in the cooling rate, quartz, feldspar, olivine, pyroxene, and magnetite minerals were found to crystallize in subhedral, skeletal, dendritic, spherical, bow-tie and fibrous forms in glassy volcanic rocks and archeometallurgical slags.Publication Open Access Interactions Mechanism of Commonly Used Drugs for the Treatment of COVID-19(Bulletin of the Chemical Society of Ethiopia, 2020) Çelik, Sefa; Demirağ, A. Demet; Özel, Ayşen E.; AKYÜZ, SEVİMIn this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (M-P(ro)) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 M-P(ro) and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of MP' system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 M-P(ro) and spike glycoprotein can play an important role for the treatment of COVID-19.Publication Embargo Excitation energy-dependent nature of Raman scattering spectrum in GaInNAs/GaAs quantum well structures(Springer, 233 Spring St, New York, Ny 10013 Usa, 2012-11-28) Erol, Ayşe; Akalın, Elif; Sarcan, Fahrettin; Dönmez, Ömer; Arıkan, Mehmet Çetin; Puustinen, Janne; Guina, Mircea; AKYÜZ, SEVİM; TR54563; TR1362; TR108291; TR46357; TR150431; TR10127The excitation energy-dependent nature of Raman scattering spectrum, vibration, electronic or both, has been studied using different excitation sources on as-grown and annealed n- and p-type modulation-doped Ga1 -aEuro parts per thousand x In (x) N (y) As1 -aEuro parts per thousand y /GaAs quantum well structures. The samples were grown by molecular beam technique with different N concentrations (y = 0%, 0.9%, 1.2%, 1.7%) at the same In concentration of 32%. Micro-Raman measurements have been carried out using 532 and 758 nm lines of diode lasers, and the 1064 nm line of the Nd-YAG laser has been used for Fourier transform-Raman scattering measurements. Raman scattering measurements with different excitation sources have revealed that the excitation energy is the decisive mechanism on the nature of the Raman scattering spectrum. When the excitation energy is close to the electronic band gap energy of any constituent semiconductor materials in the sample, electronic transition dominates the spectrum, leading to a very broad peak. In the condition that the excitation energy is much higher than the band gap energy, only vibrational modes contribute to the Raman scattering spectrum of the samples. Line shapes of the Raman scattering spectrum with the 785 and 1064 nm lines of lasers have been observed to be very broad peaks, whose absolute peak energy values are in good agreement with the ones obtained from photoluminescence measurements. On the other hand, Raman scattering spectrum with the 532 nm line has exhibited only vibrational modes. As a complementary tool of Raman scattering measurements with the excitation source of 532 nm, which shows weak vibrational transitions, attenuated total reflectance infrared spectroscopy has been also carried out. The results exhibited that the nature of the Raman scattering spectrum is strongly excitation energy-dependent, and with suitable excitation energy, electronic and/or vibrational transitions can be investigated.