Browsing by Author "Karaca, C"

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    Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine
    Atac, A; Karaca, C; Gunnaz, S; Karabacak, M
    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, H-1 and C-13 NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 4000-10 cm(-1), respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for H-1 and C-13 NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, H-1 and C-13 chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results. (C) 2014 Elsevier B.V. All rights reserved.
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    THE RELATION BETWEEN EPICARDIAL ADIPOSE TISSUE WITH VOLUME MARKERS AND INFLAMMATION MARKERS, WITHIN DIALYSIS AND TRANSPLANT PATIENTS
    Colak, H; Kylyçaslan, B; Sert, I; Tanrysev, M; Ekmekci, C; Karaca, C; Kursat, S; Töz, H
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    Synthesis, analysis of spectroscopic and nonlinear optical properties of the novel compound: (S)-N-benzyl-1-phenyl-5-(thiophen-3-yl)-4-pentyn-2-amine
    Karabacak, M; Karaca, C; Atac, A; Eskici, M; Karanfil, A; Kose, E
    In this study, a novel compound (S)-N-benzyl-1-phenyl-5-(thiophen-3-yl)-4-pentyn-2-amine (abbreviated as BPTPA) was synthesized and structurally characterized by FT-IR, NMR and UV spectroscopy. The molecular geometry and vibrational frequencies of BPTPA in the ground state have been calculated by using the density functional method (B3LYP) invoking 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated. The fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were given. The energy and oscillator strength of each excitation were calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The NMR chemical shifts (H-1 and C-13) were recorded and calculated using the gauge invariant atomic orbital (CIAO) method. The dipole moment, linear polarizability and first hyperpolarizability values were also computed. The linear polarizability and first hyper polarizability of the studied molecule indicate that the compound is a good candidate of nonlinear optical materials. Finally, vibrational wavenumbers, absorption wavelengths and chemical shifts were compared with calculated values, and found to be in good agreement with experimental results. (C) 2012 Elsevier B.V. All rights reserved.
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    NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of nicotinic acid N-oxide: A combined experimental and theoretical study
    Atac, A; Karabacak, M; Karaca, C; Kose, E
    In this work, the experimental and theoretical UV, NMR, and vibrational features of nicotinic acid N-oxide (abbreviated as NANO. C6H5NO3) were studied. The ultraviolet (UV) absorption spectrum of studied compound that dissolved in water was examined in the range of 200-800 nm. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The H-1 and C-13 NMR spectra in DMSO were recorded. The geometrical parameters, energies and the spectroscopic properties of NANO were obtained for all four conformers from density functional theory (DFT) B3LYP/6-311++G(d,p) basis set calculations. There are four conformers, C-n, n = 1-4 for this molecule. The computational results identified the most stable conformer of title molecule as the Cl form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. C-13 and H-1 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (CIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by CIS approach. Finally the calculation results were applied to simulate infrared, Raman, and UV spectra of the title compound which show good agreement with observed spectra. (C) 2011 Elsevier B.V. All rights reserved.
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    Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT
    Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, AM; Karabacak, M; Kose, E
    Isophthalic acid (C6H4(CO2H)(2)) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, H-1 and C-13 NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts CH and C-13) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm(-1) and 3500-50 cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311 ++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The C-13 and H-1 nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. (C) 2016 Elsevier B.V. All rights reserved.
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    Spectroscopic (NMR, UV, FT-IR and FT-Raman) analysis and theoretical investigation of nicotinamide N-oxide with density functional theory
    Atac, A; Karabacak, M; Kose, E; Karaca, C
    The spectroscopic properties of the nicotinamide N-oxide (abbreviated as NANO, C6H6N2O2) were examined by FT-IR, FT-Raman, NMR and UV techniques. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The H-1 and C-13 NMR spectra were recorded in DMSO. The UV absorption spectrum of the compound that dissolved in water was recorded in the range of 200-800 nm. The structural and spectroscopic data of the molecule in the ground state were calculated by using Density Functional Theory (DFT) employing B3LYP methods with the 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The optimized structure of compound was interpreted and compared with the reported experimental values. The observed vibrational wavenumbers, absorption wavelengths and chemical shifts were compared with calculated values. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results. (C) 2011 Elsevier B.V. All rights reserved.
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    Synthesis, spectroscopic characterization and quantum chemical computational studies of (S)-N-benzyl-1-phenyl-5-(pyridin-2-yl)-pent-4-yn-2-amine
    Kose, E; Atac, A; Karabacak, M; Karaca, C; Eskici, M; Karanfil, A
    The synthesis and characterization of a novel compound (S)-N-benzyl-1-phenyl-5-(pyridin-2-yl)-pent-4-yn-2-amine (abbreviated as BPPPYA) was presented in this study. The spectroscopic properties of the compound were investigated by FT-IR. NMR and UV spectroscopy experimentally and theoretically. The molecular geometry and vibrational frequencies of the BPPPYA in the ground state were calculated by using density functional theory (OFT) B3LYP method invoking 6-311++G(d,p) basis set. The geometry of the BPPPYA was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The results of the energy and oscillator strength calculated by time-dependent density functional theory (TD-OFT) and CIS approach complement with the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis were presented. The theoretical NMR chemical shifts (H-1 and C-13) complement with experimentally measured ones. The dipole moment, linear polarizability and first hyperpolarizability values were also computed. The linear polarizabilities and first hyper polarizabilities of the studied molecule indicate that the compound is a good candidate of nonlinear optical materials. The calculated vibrational wavenumbers, absorption wavelengths and chemical shifts showed the best agreement with the experimental results. (C) 2012 Elsevier B.V. All rights reserved.
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    A comprehensive study on the effect of substitution position and solvent effect on absorption and emission characteristics of n-methylindoles via linear response and State-Specific formalisms
    Karaca, C; Bardak, F; Kose, E; Atac, A
    The light absorption emission characteristics of n-methylindoles (n = 1-7) have been explored thoroughly by taking solvatochromic, substitution position, and solvation model effects into account. Experimental UV-Vis and Fluorescence spectra were recorded between 200 and 400 nm, and 250-800 nm, respectively, in cyclohexane, dichloromethane, and acetonitrile. Molecular geometry optimizations and excited state calculations were conducted using DFT and TD-DFT methods with a long-range corrected hybrid exchange-correlation functional CAM-B3LYP. Absorption emission characteristics were determined based on the polarizable continuum model accompanied with Linear-Response and State-Specific formalisms. Absorption spectra were resolved using Franck-Condon analysis for a more accurate representation of experimental data and underlying vibronic transitions were determined. Overall, although the Linear-Response and State-Specific approaches provide a quantitative explanation of experimental spectra, the approach used for the calculations can affect the solvent polarity-dependent shifts by nearly an order of magnitude. Besides, the State-Specific model provides slightly better results in the determination of Stokes shifts. The shouldered fluorescence peak observed in weakly polar solvents diminishes at higher polarities indicating the elimination of solute-solute interactions and domination of solute-solvent interactions with increasing solvent polarity.
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    Anionic dependency of electronic and nonlinear optical properties of ionic liquids
    Bardak, F; Bardak, C; Karaca, C; Kose, E; Bilgili, S; Atac, A
    Nonlinear optical phenomena play significant roles in the bulk properties and responsive characteristics of ionic liquids, especially when used under strong electric fields. The variability of the anion-cation pair in ionic liquids makes them designer solvents; thus, the anion or cation dependency of the physicochemical properties should be understood in depth. Accordingly, the electric field-induced characteristics of eight ionic liquids with [Br] , [BE4] , [PF6] , [Ac] , [TFAc] , [MS] , [NTf2] , and [Tos] anions paired with the 1-butyl-3-methyl imidazolium cation were investigated using density functional theory modeling at four theoretical levels: B3LYP-6-31G(d), M06-2X 6-31G(d), M06-2X 6-311++G(d,p), and M06-2X aug-ccPVTZ. The frontier molecular orbitals, electrostatic potential surface, and electron density difference maps were obtained to visualize the electrostatic characteristics. The permanent electric dipole moment, linear electric polarizability, and first-order and second-order hyperpolarizabilities were also determined. While the static dipole moment and dipole polarizabilities could be obtained using low-level quantum chemistry at a satisfactory level, the functionalization of more intensive methods was required to accurately obtain the nonlinear optical properties. (C) 2021 Elsevier B.V. All rights reserved.
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    Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide
    Karaca, C; Atac, A; Karabacak, M
    In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results. (C) 2014 Elsevier B.V. All rights reserved.
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    Experimental and computational insights into the electronic structures and absorption-emission characteristics of coumarin, C-6H, C-153, and C-343 dyes
    Karaca, C; Bardak, F; Köse, E; Ataç, A
    This paper explores the electronic structure and spectral characteristics of coumarin (C), C-6H, C-153, and C-343 in the protic polar solvent acetonitrile, combining computational methods via Density Functional Theory (DFT) and time-dependent Density Functional Theory (TD-DFT) with experimental analysis of UV-Vis and fluorescence spectra. The optoelectronic features of C, C-6H, C-153, and C-343 are primarily utilized in the solution phase for various applications, such as lasers and dye-sensitized solar cells. Computational studies were conducted using four different Modal Chemistry methods [MC1: CAM-B3LYP/6-311++G(d.p), MC2: CAM-B3LYP/6-31 + G(d.p), MC3: B3LYP/6-311++G(d.p), and MC4: B3LYP/6-31 + G(d.p)]. The excited state features were investigated based on TD-DFT/Polarizable Continuum Model-Linear Response and TD-DFT/Polarizable Continuum ModelState Specific formalisms. Molecular orbital configurations, molecular electrostatic potentials, and electron density difference isosurface of the dyes were analyzed to uncover the factors influencing the absorption and emission properties. The decomposed UV-Vis and fluorescence spectra of compounds indicate that emission characteristics are complex and contribute to low-lying energy transitions. The state-specific solutions provide more reliable estimates for smaller molecular structures with less intramolecular charge transfer, whereas the linear response approach excels when more electron-donating functional groups are present. The effect of the basis set in determining both absorption and emission features is almost negligible compared to Hartree-Fock exchange contributions in DFT functionals. B3LYP appears to provide satisfactory results for systems where long-range HF exchange is not as crucial.
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    Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid
    Karaca, C; Atac, A; Karabacak, M
    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the Cl form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for Cl conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (H-1 and C-13) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results. (C) 2014 Elsevier B.V. All rights reserved.
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    The Relation between Serum Testosterone Levels and Cardiovascular Risk Factors in Patients with Kidney Transplantation and Chronic Kidney Disease
    Colak, H; Sert, I; Kurtulmus, Y; Karaca, C; Toz, H; Kursat, S
    The objective of the study is to evaluate the relationship between serum testos-terone levels and cardiovascular risk factors (CVRF) in patients after kidney transplantation and with chronic kidney disease (CKD). Seventy-five male patients, aged between 18 and 68 years, who had kidney transplantation at least six months earlier, were enrolled into the study. Only renal transplant recipients and CKD patients with a creatinine level of <2.5 mg/dL were included in this study. Patients were divided into three groups as patients receiving calcineurine inhibitors (CNIs) and Mammalian target of rapamycin inhibitors (m-TORi) and CKD. Serum ceatinine, testosterone, follicle stimulating hormone (FSH), luteinizing hormone (LH), prolactin, high-sensitivity C-reactive protein (hs-CRP), total cholesterol (TC), triglyceride (TG) as well as left ventricle mass (LVM), left ventricle mass index (LVMI), left atrium (LA), inferior vena cava (IVC) inspiratory and expiratory diameters and collapse index (CI) and blood pressure (BP) were evaluated. Serum testosterone levels were significantly higher in the m-TORi and CNIs groups when compared with the CKD cases (P < 0.05). When kidney recipients (both groups) were compared with CKD patients, we observed positive outcomes in serum testosterone levels and CVRF at significant levels. There was no significant difference in terms of age, serum creatinine, serum testosterone, FSH, LH, prolactin, hs-CRP, LVMI, TC and TG and between the CNIs and mTORi groups (P > 0.05). Serum testosterone levels were independent risk factors affecting IVC collapse index, systolic BP and LA. m-TORi and CNIs drugs might have no negative effect on serum testosterone levels, and improvement of the serum testosterone levels after transplantation might have a positive contribution on cardiac risk factors.