Fizik Bölümü / Department of Physics
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Publication Metadata only 4 4 Bipyridyl Vibrational Assignments and Force Field(Elsevier, 1995-04) Topaçlı, Arzu; AKYÜZ, SEVİM; 170067; 10127A normal coordinate analysis of 4,4′-bipyridyl (4,4′-bipy) is carried out to establish consistent vibrational assignment and to determine a Urey-Bradley force field. The potential energy distribution of 4,4′-bipy is calculated which has provided certainty for the assignments. Additional information is obtained from the vibrational spectra of M (4,4′-bipy)Cl2 complexes (where M = Zn, Cu or Cd) and calculated wave numbers of complexed 4,4′-bipy. Several vibrational modes of 4,4′-bipy in the IR and Raman spectra of the complexes are found to have upward shifts in frequency compared to those in the free molecule and the shifts are metal dependent. An explanation supported by the normal coordinate analysis is provided in terms of coupling with low frequency vibrations, particularly the M-N stretching frequencies.Publication Metadata only 5-Methylhydantoin: From isolated molecules in a low-temperature Aaon matrix to solid state polymorphs characterization(2017-12) Nogueira, Bernardo.A.; Canotilho J.; Eusébio MES; Henriques MSC; Paixão JA; Fausto R.; ILDIZ, GÜLCE ÖĞRÜÇThe molecular structure, vibrational spectra and photochemistry of 5-methylhydantoin (C4H6N2O2; 5-MH) were studied by matrix isolation infrared spectroscopy and theoretical calculations at the DFT(B3LYP)/6-311++G(d,p) theory level. The natural bond orbital (NBO) analysis approach was used to study in detail the electronic structure of the minimum energy structure of 5-MH, namely the specific characteristics of the σ and π electronic systems of the molecule and the stabilizing orbital interactions. UV irradiation of 5-MH isolated in argon matrix resulted in its photofragmentation through a single photochemical pathway, yielding isocyanic acid, ethanimine, and carbon monoxide, thus following a pattern already observed before for the parent hydantoin and 1-methylhydantoin molecules. The investigation of the thermal properties of 5-MH was undertaken by differential scanning calorimetry (DSC), polarized light thermal microscopy (PLTM) and Raman spectroscopy. Four different polymorphs of 5-MH were identified. The crystal structure of one of the polymorphs, for which it was possible to grow up suitable crystals, was determined by X-ray diffraction (XRD). Two of the additional polymorphs were characterized by powder XRD, which confirmed the molecules pack in different crystallographic arrangements.Publication Metadata only 5-Methylhydantoin: from isolated molecules in a low-temperature argon matrix to solid state polymorphs characterization(Amer Chemical Soc, 1155 16th St, Nw, Washington, Dc 20036 USA, 2017-07-20) Nogueira, Bernardo A.; Canotilho, J.; Eusebio, M. E. S.; Henriques, M. S. C.; Paixao, J. A.; Fausto, Rui; ILDIZ, GÜLCE ÖĞRÜÇ; 107326The molecular structure, vibrational spectra and photochemistry of 5-methylhydantoin (C4H6N2O2; 5-MH) were studied by matrix isolation infrared spectroscopy and theoretical calculations at the DFT(B3LYP)/6-311++G(d,p) theory level. The natural bond orbital (NBO) analysis approach was used to study in detail the electronic structure of the minimum energy structure of 5-MH, namely the specific characteristics of the sigma and pi electronic systems of the molecule and the stabilizing orbital interactions. UV irradiation of 5-MH isolated in argon matrix resulted in its photofragmentation through a single photochemical pathway, yielding isocyanic acid, ethanimine, and carbon monoxide, thus following a pattern already observed before for the parent hydantoin and 1-methylhydantoin molecules. The investigation of the thermal properties of 5-MH was undertaken by differential scanning calorimetry (DSC), polarized light thermal microscopy (PLTM) and Raman spectroscopy. Four different polymorphs of 5-MH were identified. The crystal structure of one of the polymorphs, for which it was possible to grow up suitable crystals, was determined by X-ray diffraction (XRD). Two of the additional polymorphs were characterized by powder XRD, which confirmed the molecules pack in different crystallographic arrangements.Publication Metadata only 5-Methylhydantoin: Structure, Spectroscopy, Photochemistry and Polymorphism(2017) Nogueira, Bernardo, A.; Canotilho, Joa; Eusebio, M. E. S.; Henriques, M. S. C.; Paixao, Antonia; Rui, Fausto; ILDIZ, GÜLCE ÖĞRÜÇ; 107326Publication Metadata only A comparative study of auditory and visual event related coherences(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2012-09) Tülay, Elif; Turp Gölbaşı, Bilge; Güntekin, Bahar; BAŞAR, EROL; 142226; 204666Publication Metadata only A comparative study of the yellow dent and purple flint maize kernel components by Raman spectroscopy and chemometrics(2019-05-15) Kabuk, Hayrunnisa Nur; Kaplan, Ekin Su; Halimoğlu, Gökhan; Fausto, Rui; ILDIZ, GÜLCE ÖĞRÜÇIn this investigation the potential of micro-Raman spectroscopy, coupled to a simple, standard chemometric method (principal component analysis, PCA), as a fast, cheap, field method to investigate maize kernel components (endosperm, germ and peel) is demonstrated. Particular emphasis was given to the determination of the relative protein and amylose/amylopectin contents in maize endosperm of yellow dent and purple flint corn species, the two major maize varieties produced in Turkey. It is shown that the studied yellow dent corn type has a comparatively larger content of protein (3.4%) and a higher amylopectin/amylose ratio in the endosperm than the studied purple flint variety (a 11% decrease of amylopectin was found in going from the studied yellow dent to the purple flint corn), while the germs of the two species differ mostly by the presence of a slightly larger amount of starch in the case of the yellow dent corn, the oil composition of both species being identical within the resolution of the used method of analysis. The spectra of the maize peels reveal essentially the presence of cellulose and lignin in similar amounts in the two types of corn. (C) 2019 Elsevier B.V. All rights reserved.Publication Metadata only A Conformational Analysis and Vibrational Spectroscopic Investigation on 1,2-bis(o-carboxyphenoxy) Ethane Molecule(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2012-01) Balcı, Kubilay; Yapar, Gönül; Akkaya, Yasemin; Koch, A.; Kleinpeter, E.; AKYÜZ, SEVİM; 54889; 119404; 175409; 10127The minima on the potential energy surface of 1,2-bis(o-carboxyphenoxy)ethane (CPE) molecule in its electronic ground state were searched by a molecular dynamics simulation performed with MM2 force field. For each of the found minimum-energy conformers, the corresponding equilibrium geometry, charge distribution, HOMO-LUMO energy gap, force field, vibrational normal modes and associated IR and Raman spectral data were determined by means of the density functional theory (DFT) based electronic structure calculations carried out by using B3LYP method and various Pople-style basis sets. The obtained theoretical data confirmed the significant effects of the intra- and inter-molecular hydrogen bonding interactions on the conformational structure, force field, and group vibrations of the molecule. The same data have also revealed that two of the determined stable conformers, both of which exhibit pseudo-crown structure, are considerably more favorable in energy to the others and accordingly provide the major contribution to the experimental spectra of CPE. In the light of the improved vibrational spectral data obtained within the "SQM FF" methodology and "Dual Scale Factors" approach for the monomer and dimer forms of these two conformers, a reliable assignment of the fundamental bands observed in the experimental room-temperature IR and Raman spectra of the molecule was given, and the sensitivities of its group vibrations to conformation, substitution and dimerization were discussed. (C) 2011 Elsevier B.V. All rightsPublication Metadata only A Density Functional Theory based study of the solvent effects on the experimental vibrational spectra of 4-aminopyrimidine(2017) Akkaya, Yasemin; Balcı, Kubilay; AKYÜZ, SEVİM; 175409; 54889; 10127Publication Metadata only A Fourier-transform infrared and laser-Raman spectroscopic investigation of 4,4′-bipyridyl-transition metal(II) tetracyanonickelate clathrates(1996-03) Davies, J. Eric D.; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127The FT-IR and Raman spectra are reported of M(4,4-bipyridyl)Ni(CN)4nG (where M = Mn, Fe, Co, Cu or Zn and G = benzene or aniline;n = 0–2) clathrates. The host structure consists of a three-dimensional rigid lattice formed by infinite polymeric layers of {M-Ni(CN)4} and 4,4-bipyridyl bridges between the metal (M) atoms of the adjacent polymeric layers. Bidentate 4,4-bipyridyl molecules are found to be centrosymmetric in the structure.Publication Embargo A mechanism for the dependence of sunspot group tilt angles on cycle strength(Iop Publıshıng Ltd, Temple Circus, Temple Way, Bristol Bs1 6Be, England, 2015-11-01) Işık, EmreThe average tilt angle of sunspot groups emerging throughout the solar cycle determines the net magnetic flux crossing the equator, which is correlated with the strength of the subsequent cycle. I suggest that a deep-seated, non-local process can account for the observed cycle-dependent changes in the average tilt angle. Motivated by helioseismic observations indicating cycle-scale variations in the sound speed near the base of the convection zone, I determined the effect of a thermally perturbed overshoot region on the stability of flux tubes and on the tilt angles of emerging flux loops. I found that 5-20 K of cooling is sufficient for emerging flux loops to reproduce the reported amplitude of cycle-averaged tilt angle variations, suggesting that it is a plausible effect responsible for the nonlinearity of the solar activity cycle.Publication Metadata only A Microsoft Visual Basic software for B spline solution of the one dimensional heat equation(2009) Çağlar, Hikmet; Çağlar, Nazan; Özer, Mehmet; CUHACI, LEVENT; 114368; 112369; 110809; 2509Publication Metadata only A Molecular Mechanics Conformational Study of Peptide T(Elsevier, 1997-01-20) Godjayev, Niftali M.; Akverdieva, G.; AKYÜZ, SEVİM; 10127Conformational behaviour of peptide T, a competitor of the human immuno-deficiency virus in the binding to human T cells, was investigated by theoretical conformational analysis. Two types of conformations are found to be the most stable: quasi cyclic conformation, which is favourable for intensive electrostatic interaction between the charged terminal groups, and spiral conformation, which provides optimal nonvalent interaction of atoms of the polypeptide skeleton. A β-turn of the polypeptide chain was revealed on the section Thr4-Tyr7.Publication Metadata only A molecular modeling study on the structure and vibrational properties of the chemotherapy drug letrozole(2017) Balcı, Kubilay; Akkaya, Yasemin; Collier, William Bridgman; King, Hannah M.; Knight, Emily A.; Coates, Joel T.; Ritzhaupt, Gary; AKYÜZ, SEVİM; 54889; 175409; 10127Publication Metadata only A Multi-Technique Approach to the Study of Hydantoins(2017) ILDIZ, GÜLCE ÖĞRÜÇ; 107326Publication Metadata only A Multi-Technique Approach to The Study of Hydantoins: From Isolated Molecules to Polymorphs(2019-07-22) ILDIZ, GÜLCE ÖĞRÜÇ; 107326Hydantoins have remarkable interest from the chemical and biological perspectives, and they have also been shown to receive widespread applications in medicine, agriculture and chemical industry. They have been clinically used as antiepileptic and antibacterial drugsand for cancer and AIDS treatments, and are also used currently as herbicides and fungicides. In this talk, 1 will present recent data on a series of simple hydantoins, obtained using a multi-technique approach that allowed characterizing the single molecules of these compounds in relation to their structure, vibrational spectra and photochemistry, and also to determine the spectroscopic and thermal properties oftheir neat condensed phases (with emphasis given to polymorphism). The main technique used for the investigation of the isolated molecules was matrix isolation infrared spectroscopy, complemented by up-to-date quantum chemical calculations. For the investigation of the condensed phases, differential scanning calorimetry (DSC), polarized-light thermomicroscopy, X-ray diffraction, and infrared and Raman spectroscopies were used. The used multidisciplinary methodology allowed to attain a considerably broad understanding of the structural, vibrational, photochemical and thermal properties of the hydantoin moiety, which may be seen as a gateway for assessing the reactivity and biological activity of this type of compounds.Publication Metadata only A Natural Limit on the Observable Periods of Anomalous X-ray Pulsars and Soft Gamma-ray Repeaters(Amer Inst Physics, 2 Huntington Quadrangle, Ste 1No1, Melville, Ny 11747-4501 USA, 2011) Ertan, Ünal; Çalışkan, Şirin; Ekşi, Kazım Yavuz; Erkut, M. Hakan; Alpar, M. Ali; 179806; 273308; 26028We investigate the dependence of the evolution of neutron stars with fallback disks on the strength of the magnetic dipole field of the star. Using the same model as employed by Ertan et al. (2009), we obtain model curves for different dipole fields showing that the neutron stars with magnetic dipole fields greater than similar to 10(13) G on the surface of the star are not likely to become anomalous X-ray pulsars (AXPs) and soft gamma-ray repeaters (SGRs). Other sources with conventional dipole fields evolve into the AXP phase if their disk can penetrate the light cylinder. The upper limits to the observed periods of AXP and SGRs could be understood if the disk becomes inactive below a low temperature around 100 K. We summarize our present and earlier results indicated by the evolutionary model curves of these sources with an emphasis on the importance of the minimum disk temperature and the X-ray irradiation in the long-term evolution of AXPs and SGRs with fallback disks.Publication Metadata only A new correlation with lower kilohertz quasi-periodic oscillation frequency in the ensemble of low-mass x-ray binaries(Iop Publishing Ltd, Temple Circus, Temple Way, Bristol Bs1 6Be, England, 2016-11-01) Erkurt, M. Hakan; Duran, Sivan; Çatmabacak, Önder; Çatmabacak, OnurWe study the dependence of kilohertz quasi-periodic oscillation (kHz QPO) frequency on accretion-related parameters in the ensemble of neutron-star low-mass X-ray binaries. Based on the mass accretion rate, M, and the magnetic field strength, B, on the surface of the neutron star, we find a correlation between the lower kHz. QPO frequency and M/B-2. The correlation holds in the current ensemble of Z and atoll sources and therefore can explain the lack of correlation between the kHz. QPO frequency and X-ray luminosity in the same ensemble. The average run of lower kHz. QPO frequencies throughout the correlation can be described by a power-law fit to source data. The simple power. law, however, cannot describe the frequency distribution in an individual source. The model function fit to frequency data, on the other hand, can account for the observed distribution of lower kHz. QPO frequencies in the case of individual sources as well as the ensemble of sources. The model function depends on the basic length scales, such as the magnetospheric radius and the radial width of the boundary region, both of which are expected to vary with M to determine the QPO frequencies. In addition to modifying the length scales, and hence the QPO frequencies, the variation in M, being sufficiently large, may also lead to distinct accretion regimes, which would be characterized by Z and atoll phases.Publication Metadata only A possible link between kHz quasi-periodic oscillations and the magnetospheric boundary(E D P Sciences, 17 Ave Du Hoggar Parc D Activites Coutaboeuf Bp 112, F-91944 Cedex A, France, 2014) Erkut, Mehmet HakanThe quasi-periodic oscillations (QPOs) observed with a 200-1300 Hz frequency range in the X-ray power spectra of low mass X-ray binaries (LMXBs) might be considered as one of the observational clues to the physics at the innermost regions of accretion disks around neutron stars. In a neutron star LMXB, the magnetospheric boundary is likely to be close to the surface of the neutron star because of its presumably weak magnetic dipole field. The kHz QPOs can therefore be interpreted as the modulation of X-ray emission with smallest timescales associated with the dynamics of accreting disk matter at the magnetospheric boundary. As a result of magnetosphere-disk interaction we expect the rotational dynamics of the disk matter in the boundary region to be characterized by either sub-Keplerian or super-Keplerian flow depending on the fastness of the neutron star. We summarize our current understanding of the kHz QPO frequency correlations in terms of the oscillatory modes amplified in the magnetic boundary region and discuss the future prospects related to the possible link between kHz QPOs and the rotational dynamics at the magnetospheric boundary.Publication Metadata only A Proposal to Extend Brodmann's Areas Concept to a New Model(Anka Publisher, 116-11 Sok No.10 K 2 D 2, Bornova, Izmir 35050, Turkey, 2014) Düzgün, Aysel; Güntekin, Bahar; BAŞAR, EROL; 142226; 204666Since the beginning of the last century, the localization of brain function is presented by Brodmann areas, or maps that are a result of anatomic organization. They are used in order to give a global idea of cortical structures for given sensory cognitive functions. In the last decades, the analysis of brain oscillations gained high importance for the correlation of brain functions. Moreover, the use of the spectral connectivity provides information on dynamic connectivity between various structures. Beside this, according to (Luria, 1966), brain responses have dynamic features and structural localization is almost impossible. According to these uses, brain functions are very difficult to localize and need joint analysis of oscillation and event related coherences. In the present report, a model called "CLAIR" is described to extend and possibly to replace the concept of the Brodmann areas. To design a perfect functioning CLAIR model requires years; however, the beginning step is provided in the present report.Publication Metadata only A Remark on multivalently convex and starlike functions(2007-01) Nunokawa, Mamoru; Owa, Shigeyoshi; Yavuz Duman, Emel; POLATOĞLU, YAŞAR; 199370; 111202Applying the result for certain analytic functions due to M. Nunokawa [Proc. Japan Acad. 68A, 152–153 (1992; Zbl 0773.30020)], some properties for multivalently convex and starlike functions ar discussed.