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Now showing items 1 - 11 of 11

  • Effects of gamma irradiation on the single crystal ergosterol: An EPR study

    Sayin, Ulku   Dereli, Omer   Turkkan, Ercan  

    Single crystals of ergosterol were investigated by Electron Paramagnetic Resonance (EPR) technique, with gamma irradiation of the crystals at different orientations in the magnetic field between temperatures of 120 and 380 K, and the spectra were found to be slightly dependent on temperature. Because of the importance of ergosterol it is important to determine the irradiation effects on this molecule. Taking into consideration the chemical structure and the experimental spectra of the irradiated single crystal ergosterol, we found that two paramagnetic species which were labeled as radical A. (center dot)CH2(alpha)H(beta), and radical B-1 (CH alpha H beta H gamma H sigma)-C-center dot, were produced in the host crystal. The EPR parameters; spectroscopic splitting factor, g, and hyperfine coupling constant, a, were determined for each radical. (C) 2011 Elsevier B.V. All rights reserved.
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  • Experimental and theoretical research on -irradiated 7-methoxy-4-methylcoumarin powder through EPR and DFT methods

    Sarikaya, Ebru Karakas   Ates, Levent   Sayin, Ulku   Ozmen, Ayhan   Dereli, Omer  

    In this paper, the effects of gamma irradiation on 7-Methoxy-4-methylcoumarin (7M4MC) molecule, an essential coumarin derivative, which has an inherent variety of biological activities, therapeutic properties and industrial usage were examined. For this purpose, the sample was irradiated with Co-60-gamma ray source for about 100kGy total doses. Theoretical calculations were performed using GAUSSIAN03 program for the possible radicals that were modeled from two stable conformations with lowest energies. In order to get well-resolved spectra and to determine the radical identity experimentally, EPR spectra of the irradiated 7M4MC sample were recorded at several spectrometer conditions. By considering the molecular structure and EPR spectra, alkyl-type radical was assumed to be formed by gamma irradiation. To support the estimations, simulations were done using theoretical EPR parameters as an initial value. The experimental spectra were well matched with the sum of simulated spectra obtained from two same type modeled radicals of two different conformations. As a result of experimental estimations and theoretical calculations, radiation-induced radicals were identified as two neutral alkyl radicals, originated from two stable conformations.
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  • Investigation of Molecular and Radical Structures of Ethylene Glycol

    Dereli, Omer   Karakas Sarikaya, Ebru   Erdogdu, Yusuf  

    In this study, the conformational variety of ethylene glycol molecule was theoretically searched via energy minimization calculations carried out by using the Merck Molecular Force Field (MMFF) and eight stable conformers were determined for the free molecule. For each of the found conformers, a geometry optimization calculation was performed by using the DFT/B3LYP method and 6-311++G(d, p) basis set. From these calculations some structural data of the conformers, such as optimized geometry, relative energy and dipol moment, were obtained and then they were used in evaluation of the stabilities of the investigated conformers. In the next step of the study, theoretically possible forteen radicals were derived from the most stable conformer of free ethylene glycol and geometry optimization was also performed for each of them. Afterwards, the "Electron Paramagnetic Resonance (EPR)" parameters of these radicals were calculated using DFT/B3LYP method and TZVP basis set and then the obtained values were compared to the corresponding experimental data reported in the literature. The results have demonstrated that the experimentally observed EPR parameters match the theoretical EPR values obtained for the model radical called here "Rad 5" (COHCH2OH). The model "Rad 5" is an anion radical formed by abstraction of an hydrogen atom from the neutral free molecule.
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  • An electron paramagnetic resonance and density-functional theory study on the methyl isotropic hyperfine coupling constants in gamma-irradiated 2,6-di-tert-butyl-4-methylphenol

    Turkkan, Ercan   Dereli, Omer   Sayin, Ulku   Tapramaz, Recep  

    Single crystal of gammairradiated 2,6-di-tert-butyl-4-methylphenol (BHT) was investigated using an electron paramagnetic resonance (EPR) technique at different orientations in the magnetic field at room temperatures. Taking into consideration the chemical structure and the experimental spectra of the irradiated single crystal of BHT, we assumed that one phenoxyltype paramagnetic species was produced having an unpaired electron localized at the methyl fragment side of the phenyl ring. Depending on this assumption, one possible radical was modeled using the B3LYP/6-311+G(d) level of density-functional theory. EPR parameters were calculated for these modeled radical using the B3LYP/TZVP and B3LYP/EPR-III level. The averaged value of isotropic hydrogen hyperfine coupling constants of rotating methyl functional group of phenoxyl radical is calculated for the first time. Theoretically calculated values of the modeled radical are in reasonably good agreement with the experimental data determined from the spectra (differences in averaged coupling constant values smaller than 5%, and differences in isotropic g values fall into 1ppt).
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  • Molecular Structure and Spectral (FT-IR,Raman) Investigations of 3-Aminocoumarin

    Dereli, Omer  

    The molecular structure of 3-Aminocoumarin was determined by conformational analysis. Conformational space was scanned by conformer distribution option of Spartan 08 program package using Merck Molecular Force Field (MMFF) method. Then obtained conformers were optimized by B3LYP/6-311++G(d, p) and B3LYP/6-311G(d, p) levels of Density Functional Theory. As a result of these calculations, only one conformer was determined. Vibrational frequencies of this conformer were calculated by Gaussian 03 program package using the same levels of geometry optimizations. The FT-IR and Raman spectra of 3-Aminocoumarin were recorded and compared with the calculated values. Consequently, a good agreement between experimental and the calculated values were founded. Molecular electrostatic potentials (MEPs), HOMO-LUMO energies, thermodynamic properties and Mulliken atomic charges were also covered in this study.
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  • Magnetic properties of single crystal alpha-benzoin oxime: An EPR study

    Sayin, Ulku   Dereli, Omer   Turkkan, Ercan   Ozmen, Ayhan  

    The electron paramagnetic resonance (EPR) spectra of gamma irradiated single crystals of alpha-benzoinoxime (ABO) have been examined between 120 and 440 K. Considering the dependence on temperature and the orientation of the spectra of single crystals in the magnetic field, we identified two different radicals formed in irradiated ABO single crystals. To theoretically determine the types of radicals, the most stable structure of ABO was obtained by molecular mechanic and B3LYP/6-31G(d,p) calculations. Four possible radicals were modeled and EPR parameters were calculated for the modeled radicals using the B3LYP method and the TZVP basis set. Calculated values of two modeled radicals were in strong agreement with experimental EPR parameters determined from the spectra. Additional simulated spectra of the modeled radicals, where calculated hyperfine coupling constants were used as starting points for simulations, were well matched with experimental spectra. (C) 2011 Elsevier Ltd. All rights reserved.
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  • Determination of EPR Parameters of Gamma-Irradiated Powder Limettin Sample by Experimental and Theoretical Studies

    Karakas Sarikaya, Ebru   Erdogdu, Yusuf   Dereli, Omer  

    Limettiit. also known as "c traptene", is a dimethoxycoumar n (DMC),(CIIH,004), easily obtained from the sediment which is deposited from the expressed oil of limes'. In this study, the Limettin sample was irradiated for about 100 kGy total dose at room temperature by a 'Co-7 ray source. As a result of this irradiation, a stable radical has been obtained. In order to determine the produced radical experimentally, the spectra were taken at 0.1-20 mW microwave power and 123-393 K spectrometer temperature intervals. And experimental g values and hfccs of radical were determined. So we have modeled eight possible radical forms from two different stable conformations with approximately the same conformation energies. g values and hfccs of the model radicals were calculated with DFT/B3LYP using the TZVP basis set. As a result we compared the experimental and theoretically calculated values. Thus, we deduced that (:1-12(C902H4)0CH3, alkyl radicals (carbon centered) which are produced by abstraction of a single hydrogen atom were formed 41 the irradiated sample.
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  • Quantum chemical investigations of a co-crystal of 1,3,5-tris(4-hydroxyphenyl)benzene and 2,4,6-trimethoxy-1,3,5-triazine

    Dereli, Omer   Bahceli, Semiha   Abbas, Asghar   Naseer, Muhammad Moazzam  

    In the present study, quantum chemical investigations were carried out on our previously reported co-crystal based on 1,3,5-tris(4-hydroxyphenyl)benzene and 2,4,6-trimethoxy-1,3,5-triazine, which showed CH center dot center dot center dot pi and pi center dot center dot center dot pi interactions driven layer-by-layer self-assembly of hydrogen-bonded hexagonal blocks in the solid state. Using the DFT/B3LYP calculation method with 6-311++G(d,p) basis set in the ground state, the optimized molecular geometric parameters, conformational analysis, vibrational wavenumbers and their assignments, the HOMO-LUMO analysis, molecular electrostatic potential, thermodynamic properties, and atomic charges were calculated to understand various structural features that are playing an important role in its packing. Furthermore, the simulated infrared and Raman spectra of the co-crystal are plotted using the calculated results. The calculated results are in a good agreement with experimental data. The study with constructive propositions may be helpful in understanding complex self-assembled systems and in the construction of similar molecular self-assemblies.
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  • Theoretical Calculations of EPR Parameters of Gas Phase Hydracrylonitrile Radical

    Karakas Sarikaya, Ebru   Dereli, Omer  

    As a result of detailed conformational search of the hydracrylonitrile, four different conformers of molecule have been obtained. For these conformations, eleven possible radicals were modelled by using density functional theory (DFT) computations vial respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were calculated by B3LYP method using 6-311++G(d,p) basis sets in gas phase.
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  • (2-Hydroxyethyl)triphenylphosphonium chloride

    Ceylan, Umit   Tanak, Hasan   Turkkan, Ercan   Dereli, Omer   Buyukgungor, Orhan  

    In the crystal structure of the title compound, C(20)H(20)OP(+)center dot Cl(-), the cations and anions are linked by intermolecular CH center dot center dot center dot Cl and O-H center dot center dot center dot Cl hydrogen bonds into chains running parallel to the b axis. In the cation, the hydroxyethyl group is disordered over two orientations with site-occupancy factors of 0.554 (4) and 0.446 (4).
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  • Theoretical Calculations of Electron Paramagnetic Resonance parameters of Liquid Phase Orotic Acid Radical

    Karakas Sarikaya, Ebru   Dereli, Omer  

    To obtain liquid phase molecular structure, conformational analysis of Orotic acid was performed and six conformers were determined. For these conformations, eight possible radicals were modelled by using Density Functional Theory computations with respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were performed using Becke's three-parameter hybrid-exchange functional combined with the Lee-Yang-Parr correlation functional of Density Functional Theory and 6-311++G(d,p) basis sets in p-dioxane solution. Because Orotic acid can be mutagenic in mammalian somatic cells and it is also mutagenic for bacteria and yeast; it has been studied.
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