Fizik Bölümü / Department of Physics
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Publication 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 4-Hydroxyquinolin-2(1H)-One Isolated in Cryogenic Argon and Xenon Matrices: Tautomers and Photochemistry(Elsevier, 2024) Secrieru, A.; Lopes, S.; Nikitin, T.; Cristiano, Maria L. S.; FAUSTO, RUI4-Hydroxyquinolin-2(1H)-one (4HQ2O) was synthesized, isolated in cryogenic matrices (argon and xenon), and studied by infrared spectroscopy. Quantum chemical calculations carried out at the DFT(B3LYP)/6-311++G (3df,3pd) level of theory were used to determine the conformational and tautomeric properties of the molecule. Two tautomeric forms were identified in the as-deposited matrices with the help of the theoretical data. To investigate the photochemistry of the compound, in situ broadband ultraviolet (lambda > 283 nm) irradiation of the asdeposited argon matrix was performed. This irradiation led to the generation of an additional tautomer, together with the products of fragmentation of the heterocyclic ring of the molecule, specifically isocyanic acid and carbon monoxide. Photoproducts such as 1,3-dihydro-2H-indol-2-one and cyclohepta-1,2,4,6-tetraene were also observed in the photolyzed argon matrix. A comprehensive assignment of the infrared spectra of all the species observed experimentally is presented.Publication 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 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 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 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 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 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 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 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 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 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 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 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 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 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.Publication A spectroscopic atlas of Deneb (A2 lae) lambda lambda 3826-5212(E D P SCIENCES, 7, AVE DU HOGGAR, PARC D ACTIVITES COURTABOEUF, BP 112, F-91944 LES ULIS CEDEXA, FRANCE, 2003-03) Albayrak, B.; Gulliver, A. E.; Adelman, S. J.; Aydin, C.; Koçer, DursunWe present a spectroscopic atlas of Deneb (A2 Iae) obtained with the long camera of the 1.22-m telescope of the Dominion Astrophysical Observatory using Reticon and CCD detectors. Forlambdalambda3826-5212 the inverse dispersion is 2.4 Angstrom mm(-1) with a resolution of 0.072 Angstrom. At the continuum the mean signal-to-noise ratio is 1030. The wavelengths in the laboratory frame, the equivalent widths, and the identifications of the various spectral features are given. This atlas should provide useful guidance for studies of other stars with similar spectral types. The stellar and synthetic spectra with their corresponding line identifications can be examined at ht tp://www.brandonu.ca/physics/gulliver/atlases.html.Publication A study on the generalization of Janowski functions in the unit disc(2006-01) Bolcal, Metin; Şen, A.; YAVUZ, EMEL; POLATOĞLU, YAŞAR; 199370; 111202Let › be the class of functions w(z), w(0) = 0, |w(z)| < 1 regular in the unit disc D = {z : |z| < 1}. For arbitrarily fixed numbers A 2 (¡1,1), B 2 (¡1,A), 0 • fi < 1 let P(A,B,fi) be the class of regular functions p(z) in D such that p(0) = 1, and which is p(z) 2 P(A,B,fi) if and only if p(z) = 1+((1¡fi)A+fiB)w(z) 1+Bw(z) for some function w(z) 2 › and every z 2 D. In the present paper we apply the principle of subordination ((1), (3), (4), (5)) to give new proofs for some classical results concerning the class S⁄(A,B,fi) of functions f(z) with f(0) = 0, f0(0) = 1, which are regular in D satisfying the condition: f(z) 2 S⁄(A,B,fi) if and only if z f 0 (z) f(z) = p(z) for some p(z) 2 P(A,B,fi) and for all z in D.Publication A theoretical vibrational spectroscopic investigation on free Ethyl 2- and 3-aminobenzoate molecules(Elsevier, 2007-05-27) Balcı, Kubilay; AKYÜZ, SEVİM; 54889; 10127The possible stable conformers of free Ethyl 2- and 3-aminobenzoate molecules were searched via subsequent single point energy calculations carried out at semi-empirical PM3 theory level. The final equilibrium geometrical parameters for the obtained stable conformers were defined by performing geometry optimizations with B3LYP hybrid DFT method and basis sets of different size and type. The harmonic vibrational normal modes of the two molecules and their corresponding wavenumbers and IR intensities were calculated at the obtained equilibrium geometries using the same method and basis sets used in the geometry optimizations. In the light of these calculated spectral data, a successful assignment for the fundamental bands in the IR spectra of the two molecules was given. In order to fit the calculated harmonic wavenumbers to the experimentally observed ones, two different scaling procedures, called “scaling wavenumbers in Scaled Quantum Mechanics Force Field (SQM FF) methodology” and “scaling wavenumbers with dual empirical scale factors”, were proceeded independently.Publication A theoretical vibrational spectroscopic study with density functional theory and force field refinement calculation methods on free 4-aminopyrimidine molecule(Elsevier, 2005-06-03) Balcı, Kubilay; AKYÜZ, SEVİM; 10127; 54889A detailed investigation of the geometric structure, force field, electro-optical parameters, relative IR intensities and harmonic vibrational wavenumbers of free 4-aminopyrimidine molecule (4APM) in the electronically ground state has been carried out by using both the DFT-B3LYP (with 6-31++G(d,p) double and 6-311++G(d,p) triple basis sets) and force field refinement calculation methods. The vibrational wavenumbers calculated with DFT method were scaled by using two different methods: (1) scaling with dual scaling factors, (2) deriving the scaling factors from the graph of observed versus calculated wavenumbers. In the case of force field refinement method, the force constants of the pyrimidine were slightly refined so as to fit the calculated wavenumbers to the experimental ones. In order to define the contributions of the internal coordinates of the molecule on its each normal vibrational mode, P.E.D. calculations were performed. In wavenumber and PED calculations, both methods have yield results in agreement with the experimental assignment and also with each other, particularly for ring vibrations. The relative IR intensities calculated by the force field refinement method are considerably in good agreement with experimental ones, however, the results of the IR intensities, obtained from the DFT method are found to be significantly different from the experimental values.