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    Determination of EPR Parameters of Gamma-Irradiated Powder Limettin Sample by Experimental and Theoretical Studies
    (Amer Inst Physics, 2018) 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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    DFT Study of Conformational Analysis, Molecular Structure and Properties of para-, meta- and ortho 4-Methoxyphenyl Piperazine Isomers
    (Springer, 2021) Ekincioglu, Yavuz; Kilic, Hamdi Sukur; Dereli, Omer
    In this study, conformer analysis of isomer structures of para-, meta- and ortho 4-methoxyphenyl piperazine molecules was performed using the Spartan 08 package program. The optimized geometrical parameters, energies for the highest occupied molecular orbital and the lowest unoccupied molecular orbitals, chemical reactivity descriptors, nonlinear optical properties, Mulliken population analysis, molecular electrostatic potential map, thermodynamic properties and UV-Vis spectral analysis of isomers of the N-(4-methoxyphenyl) piperazine molecule were predicted using the density functional theory (DFT) and TD-DFT/B3LYP/6-311++G(d,p) methods. The theoretical results obtained were compared with experimental results available in the literature so far, and these results were discussed for each isomer.
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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
    (Taylor & Francis Ltd, 2013) 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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    Experimental and theoretical research on -irradiated 7-methoxy-4-methylcoumarin powder through EPR and DFT methods
    (Taylor & Francis Ltd, 2018) 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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    FT-IR, micro-Raman and UV-vis spectroscopic and quantum chemical calculation studies on the 6-chloro-4-hydroxy-3-phenyl pyridazine compound
    (Elsevier Science Bv, 2017) Sarikaya, Ebru Karakas; Bahceli, Semiha; Varkal, Dondu; Dereli, Omer
    In this work, the study of the6-chloro-4-hydroxy-3-phenyl pyridazine compound, (C-10 H-7 N-2 O Cl with synonym 4-pyridazinol, 6-chloro-3-phenyl-), was verified experimentally by using the Fourier Transformed Infrared (FT-IR), micro-Raman and UV/vis (in N,N-dimethylformamide solvent) spectroscopies. Furthermore, the optimized molecular geometry, conformatinal analysis, vibrational frequencies, the simulated UV/vis spectra (in gas and in N,N-dimethylformamide solvent), H-1 and C-13 NMR chemical shift (in gas, in chloroform and N,N-dimethylformamide in solvents) values, HOMO-LUMO analysis, the molecular electrostatic potehtial (MEP) surface and thermodynamic parameters ofthe6-chloro-4-hydroxy3-phenyl pyridazine compound were calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set in ground state. The comparison of the calculated and vibrational frequencies with the experimental values provides important information about the title compound. (C) 2017 Elsevier B.V. All rights reserved.
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    Investigation of Molecular and Radical Structures of Ethylene Glycol
    (Amer Inst Physics, 2018) 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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    Molecular Structure and Spectral (FT-IR, Raman) Investigations of 3-Aminocoumarin
    (Pleiades Publishing Inc, 2016) 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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    Molecular Structure and TD-DFT Study of the Xylene Isomers
    (Gazi Univ, 2019) Kepceoglu, Abdullah; Gundogdu, Yasemin; Dereli, Omer; Kilic, Hamdi Sukur
    In this work, we have investigated the xylene isomers in concepts of vertical and adiabatic ionization energy parameters and molecular orbital (HOMO-1, HOMO/SOMO, LUMO, LUMO+1) energies of the neutrals and singly charged cation radicals. As a first step of the calculations, conformational analysis has been performed for all isomers using the semi-empirical method with PM3 core type Hamiltonian. Geometry optimization and frequency calculations were performed by using Density Functional Theory (DFT) with Becke, three-parameter, Lee-Yang-Parr (B3LYP) exchange-correlation functional and 6-311++G(d,p) basis sets. UV-Vis electronic spectra of the neutral xylene isomers were calculated by using the TD-DFT method with cam-B3LYP functional and 6-311++G(2d,2p) basis set.
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    Molecule and Radical Structures of Isobutyronitrile
    (Gazi Univ, 2017) Dereli, Omer; Erdogdu, Yusuf; Ates, Levent; Karakas Sarikaya, Ebru; Ozturan, F. Pinar
    Molecule and radical structures of Isobutyronitrile were studied by DFT computations. Results of conformational analysis performed by combination of molecular mechanic and B3LYP/6-311++G(d, p) methods showed that isobutyronitrile inelastic molecule which has only one conformer. Using this structure, radical structure was investigated. Possible radicals were modelled and the experimental Electron Paramagnetic Resonance parameters were calculated. The calculated parameters obtained from B3LYP/TZVP computations were compared with the experimental counterparts which were taken from literature. Determined Molecule and Radical structures were given in this study.
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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
    (Springer Wien, 2015) 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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    Spectroscopic and DFT study on molecular structure of 1-(o-tolyl) thiourea molecule
    (Elsevier, 2020) Bahceli, Semiha; Sarikaya, Ebru Karakas; Dereli, Omer; Ozturan, Feride Pinar
    The molecule 1-(o-Tolyl)thiourea, (C-8 H-10 N-2 S), which is biologically active, was investigated experimentally using the infrared and Raman spectroscopies and theoretically by performing at the B3LYP/6-311++G (d,p) level of theory. In this framework, the geometrical conformational analysis of the title molecule pointed out the most stable conformation with the energy of -818.732369 Hartree and the dipole moment of 5.431104 Debye. Additionally, the vibrational frequencies were calculated and compared with experimental values and a good agreement between the measured and calculated values for the molecule 1-(o-Tolyl)thiourea were obtained. Furthermore, some thermodynamic parameters of the title molecule were calculated at the mention level of the theory. (C) 2020 Elsevier B.V. All rights reserved.
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    Theoretical Calculations of Electron Paramagnetic Resonance parameters of Liquid Phase Orotic Acid Radical
    (Amer Inst Physics, 2017) 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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    Theoretical Calculations of Electron Paramagnetic Resonance Parameters of Succinimide Radical
    (Amer Inst Physics, 2018) Dereli, Omer; Ates, Levent; Erdogdu, Yusuf
    The analysis of the molecular structure and spectral properties of succinimide can be used as a reliable tool in understanding all interactions between this molecule with the other chemicals. For this reason, we first examined the conformational variety of succinimide in free state through an energy minimization calculations using the spartan 08 software. This preliminary calculation confirmed that free succinimide molecule has only one stable conformer at room temperature and the dipole moment and energy values of this conformer are 2.221 Debye and -360.779 Hartree, respectively. The optimized geometry of the conformer was then obtained at B3LYP/6-311++ G(d, p) level of theory by using the Gaussian 03 software. In the next step of the study, eleven radicals were formed from this one conformer of succinimide by removing an hydrogen atom or changing its location in the molecule. For each radical structure, the corresponding Electron Paramagnetic Resonance (EPR) parameters were calculated using the DFT/B3LYP method and TZVP basis set and then they were compared with the corresponding experimental values. The g value (EPR parameter) calculated in this study for the model radical (Rad 6) is 2.00388 and in good agreement with the corresponding experimental value (2,00339) previously reported in the literature for the radical form of succinimide.
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    Theoretical Calculations of EPR Parameters of Gas Phase Hydracrylonitrile Radical
    (Amer Inst Physics, 2017) 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.