Fizik Bölümü / Department of Physics
Permanent URI for this collectionhttps://hdl.handle.net/11413/6785
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Browsing Fizik Bölümü / Department of Physics by Author "Akkaya, Yasemin"
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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 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 vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations(Pergamon-Elsevier Science Ltd, The Boulevard, Langford Lane, Kidlington, Oxford Ox5 1Gb, England, 2015-08-05) Akkaya, Yasemin; Balcı, Kubilay; Gören, Yeliz; AKYÜZ, SEVİM; 175409; 54889; 263178; 10127In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their ipossible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretatiori of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted. (C) 2015 Elsevier B.V. All rights reserved.Publication Metadata only A Vibrational Spectroscopy Study on Anserine and Its Aqueous Solutions(Pergamon-Elsevier Science Ltd, The Boulevard, Langford Lane, Kidlington, Oxford Ox5 1Gb, England, 2015-10-05) Akkaya, Yasemin; Balcı, Kubilay; Gören, Yeliz; Stricker, Moogega C.; Ritzhaupt, G.; Stover, D. D.; Collier, W. B.; AKYÜZ, SEVİM; 175409; 54889; 10127In this study based on vibrational spectroscopic measurements and Density Functional Theory (OFF), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule. (C) 2015 Elsevier B.V. All rights reserved.Publication Metadata only A vibrational spectroscopy study on the chemotheraphy drug flutamide by DFT calculations(2017) Arman, Cansu; Avcı, Kubilay; Akkaya, Yasemin; Collier, William Bridgman; AKYÜZ, SEVİM; 54889; 175409; 10127Publication Metadata only An Experimental And Theoretical Vibrational Spectroscopic Study On Niflumic Acid, A Non-Steroidal Anti-İnflammatory Drug(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2010-07-20) Balcı, Kubilay; Akkaya, Yasemin; AKYÜZ, SEVİM; TR10127; TR54889; TR175409The theoretically possible stable conformers of niflumic acid (NFA) molecule in electronic ground state were investigated by means of potential energy surface scan and thermochemistry calculations carried out at room temperature using DFT-B3LYP method and different Pople-style basis sets. The data obtained from these calculations confirmed that the two planar conformers in which the carboxyl and fluoromethyl functional groups are located either in "trans" or in "cis" position to each other are the most favorable ones in energy among all the stable conformers of the free molecule. This conclusion was also confirmed by the energy values obtained from the higher-accuracy thermochemistry calculations carried out using G3MP2B3 composite method. For both conformers and also for their most favorable dimer forms in energy, the equilibrium geometry, force field and vibrational spectral data were calculated first at B3LYP/6-31G(d) and then at B3LYP/6-311++G(d,p) levels of theory. On the basis of these theoretical data, the effects of the conformation and dimerization on the corresponding experimental data of NFA molecule were discussed in detail. The overestimations of the calculated harmonic wavenumbers were corrected by the aid of two different empirical scaling procedures referred to as "scaled quantum mechanical force field (SQM FF) methodology" and "dual scale factors". In the light of the improved theoretical data obtained in these two approaches applied independently from each other, a successful assignment of the fundamental bands observed in the room-temperature IR and Raman spectra of the molecule was given. (C) 2010 Elsevier B.V. All rights reserved.Publication Metadata only An experimental and theoretical vibrational spectroscopic study on Zn(II) halide complexes of 4-aminopyrimidine(2017) Akkaya, Yasemin; Balcı, Kubilay; AKYÜZ, SEVİM; 175409; 54889; 10127Publication Metadata only An Experimental and Theoretical Vibrational Spectroscopic Study on Zn(II) Halide Complexes of 4-Aminopyrimidine(2017) Akkaya, Yasemin; Balcı, Kubilay; AKYÜZ, SEVİM; 175409; 54889; 10127Publication Metadata only DFT And MP2 Based Quantum Mechanical Calculations And A Theoretical Vibrational Spectroscopic Investigation On Roscovitine, A Potential Drug To Treat Cancers(Wiley-Blackwell, 111 River St, Hoboken 07030-5774, NJ USA, 2011-04) Balcı, Kubilay; Akkaya, Yasemin; Palavan-Ünsal, Narçin; AKYÜZ, SEVİM; TR54889; TR175409; TR10127; TR6125Theoretically possible stable conformers of free roscovitine molecule in its electronic ground state were searched by means of molecular dynamics and energy minimization calculations performed using the MM2 force field. Afterwards, geometry optimization and thermochemistry calculations were carried out at room temperature for each of the found minimum-energy conformers using the MP2 and DFT based electronic structure methods and different Pople-style basis sets. The results obtained from these calculations confirmed that the strong intramolecular hydrogen bonding between the purine-nitrogen and hydroxyl-hydrogen atoms plays an important role on the rigidity of roscovitine molecule and causes a dramatic reduction in the number of the possible stable conformers of this molecule at room temperature. Furthermore, the same calculation results also revealed that two of the found seven stable conformers are considerably more favorable in energy than the others and thus dominate the experimental room-temperature spectra of the molecule. In the light of the theoretical vibrational spectral data obtained for these two conformers, a successful assignment of the fundamental bands observed in the experimental IR and Raman spectra recorded at room temperature for solid roscovitine and for its ethanol solution is given, and the effects of the substitution and intramolecular hydrogen bonding on the fundamental bands associated with purine and phenyl group vibrations are discussed in detail. In the fitting of the calculated harmonic wavenumbers to the corresponding experimental wavenumbers, two different scaling procedures, called 'dual scale factors' and `Scaled Quantum Mechanical Force Field(SQMFF) methodology', were applied independently. Both procedures yielded results generally in good agreement with the experiment; however, the SQM FF methodology proved its superiority over the other. Copyright (C) 2010 John Wiley & Sons, Ltd.Publication Metadata only Infrared and Raman Spectra, Ab Initio Calculations Vibrational Assignment of 4-Aminosalicylic Acid(Elsevier, 2006-11-24) Akkaya, Yasemin; AKYÜZ, SEVİM; 175409; 10127The experimental and theoretical study on the structures and vibrations of 4-aminosalicylic acid are presented. The infrared spectra (4000–400 cm−1) and the Raman spectra (4000–50 cm−1) of the molecule in solid phase have been measured. There are seven stable conformers, C1,C2, C3, C4, C5, C6, and C7 for this molecule. The computational results identify the most stable conformer of 4-aminosalicylic acid as the C1 form. The geometrical parameters and energies have been obtained for all seven conformers from ab-initio calculations. The vibrations of the five more stable conformers of 4-aminosalicylic acid are investigated with the aid of quantum chemical calculations. The spectroscopic and theoretical results are compared to the corresponding properties for 4-aminosalicylic dimer of C1 conformers.Publication Metadata only Infrared and Raman spectroscopic study of 4-aminopyrimidine tetracyanonickelate complexes(ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS, 2007-05-27) Akkaya, Yasemin; Akalın, Elif; AKYÜZ, ZEKİ TANIL; AKYÜZ, SEVİM; TR111424; TR10127; TR175409; TR463574-Aminopyrimidine tetracyanonickelate, M(4APM)(2)Ni(CN)(4) {where M = Mn, Co, Ni, Zn or Cd; 4APM = 4-aminopyrimidine}, coordination polymer compounds have been prepared for the first time and their FT-IR (400-4000 cm(-1)) and FT-Raman (704000 cm(-1)) spectra are reported. 4APM is coordinated to M(II) through one of the pyrimidine ring nitrogen atoms as a monodentate ligand; the amino group is not involved in the complex formation. Vibrational bands arising from both 4APM and the Ni(CN)(4) group, were assigned. The effect of coordination on 4APM vibrational wavenumbers is analysed by comparison with isostructural compounds. (C) 2006 Elsevier B.V. All rights reserved.Publication Metadata only The effects of conformation and zwitterionic tautomerism on the structural and vibrational spectral data of anserine(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2016-09) Balcı, Kubilay; Akkaya, Yasemin; Collier, W. B.; Stricker, Moogega C.; Stover, D. D.; Ritzhaupt, G.; Koch, Andreas; Kleinpeter, Erich; AKYÜZ, SEVİM; 54889; 175409; 10127In this study, the stable conformers of neutral anserine were searched by molecular dynamics simulations and energy minimization calculations using the MM2 force field. Thermochemical calculations at B3LYP/6-31G(d) level of theory followed these preliminary calculations. The results confirmed that neutral anserine has quite a flexible structure and many stable gauche and trans conformers at room temperature. Nevertheless, two are considerably more favourable in energy than the others and expected to dominate the gas-phase and matrix IR spectra of the molecule. The corresponding structural and vibrational spectral data for these two conformers of neutral anserine, whose relative stabilities were also examined by high-accuracy energy calculations carried out using G3MP2B3 method, and for the most stable conformer of anserine in zwitterion form were calculated at B3LYP/6-311++G(d,p) level of theory. The calculated harmonic force constants were refined using the Scaled Quantum Mechanical Force Field (SQM-FF) method and then used to produce the refined wavenumbers, potential energy distributions (PEDs) and IR and Raman intensities. These refined data together with the scaled harmonic wavenumbers obtained using another method, Dual Scale factors (DS), enabled us to correctly analyse the observed IR and Raman spectra of anserine and revealed the effects of conformation and zwitterionic tautomerism on its structural and vibrational spectral data. (C) 2016 Elsevier B.V. All rights reserved.Publication Metadata only Vibrational Spectroscopic Investigation of Tetracyanopalladate Bridged Two Dimensional Coordination Polymer Compounds of Pyrimidine(Asian Journal Of Chemistry, 11/100 Rajendra Nagar, Sector 3,, Sahibabad 201 005, Ghaziabad, India, 2013-11) Akkaya, Yasemin; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 175409; 10127; 111424The two dimensional layered polymer compounds, M(PM)(2)Pd(CN)(4) {where M = Mn, Zn or Cd; PM = pyrimidine} have been prepared for the first time and their FT-IR (4000-400 cm(-1)) and Raman (4000-50 cm(-1)) spectra are reported. The compounds built up of [M(PM)(2)](2+) cations and square-planar [Pd(CN)(4)](2-) anions, which are linked by the bridging mu(2)-CN- groups. Pyrimidine was coordinated to M(II) through one of the nitrogen atom of its heterocyclic ring, as monodentate ligand. Vibrational assignments are given for the bands arising from the tetracyanopalladate layers and coordinated pyrimidine. The main bands of the vibrational spectra in the low frequency region were assigned to the stretching and deformational vibrations {nu(Pd-C), delta(PdCN), pi(PdCN), delta(CPdC)} originating from the host lattices.