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Öğe Combined spectroscopic, XRD crystal structure and DFT studies on 2-(ethylthio)pyrimidine-4,6-diamine(Elsevier, 2017) Aktan, Ebru; Babur, Banu; Seferoglu, Nurgul; Catikkas, Berna; Kaynak, F. Betul; Seferoglu, ZeynelIn this study, the compound 2-(ethylthio)pyrimidine-4,6-diamine (ETPD) was re-synthesized and its single crystals were obtained by slow evaporation of ethanol solution. The characterization of the molecule was done experimentally and theoretically. The single-crystal X-ray diffraction analysis shows that ETPD crystallizes in the orthorhombic space group P2(1)2(1)2(1). The ground state geometry, vibrational spectra, NMR spectra, frontier molecular orbitals and also the map of molecular electrostatic potential (MEP) of ETPD obtained using DFT calculations were evaluated in detail. In addition, the global reactivity descriptors were obtained within the frontier molecular orbitals calculations. The comparison of the DFT results obtained by different methods and basis sets with X-ray diffraction analysis display the DFT can well reproduce the structure of the compound. (C) 2017 Elsevier B.V. All rights reserved.Öğe Density functional studies of antimony complexes derived from carboxamide ligands(Iop Publishing Ltd, 2023) Catikkas, BernaThe anti-leishmanial activity of antimony (III) complexes [1a-3a] bearing carboxamide ligands has been reported in the literature. In this study, a complete assignment of the vibrational spectra of these complexes was performed using the Scaled Quantum Mechanics Force Field (SQMFF) methodology in the solid phase at the DFT/ B3LYP/ LanL2DZ level. Quantum chemical descriptors (FMO, hardness, softness, etc) of these complexes were calculated to investigate the relationship between the calculated descriptors and their anti-leishmanial activities. As the softness of the complexes increased, the anti-leishmanial activity also increased. No correlation was found between the vibrational frequencies of the complexes and anti-leishmania activity.Öğe DFT, FT-Raman, FTIR, NMR, and UV-Vis studies of a hetarylazo indole dye(Wiley, 2013) Catikkas, Berna; Aktan, Ebru; Seferoglu, ZeynelIn this study, computational calculations of 1,2-dimethyl-3-[(5-methylsulfanyl-1,3,4-thiadiazol-2-yl)diazenyl]-1H-indole have been carried out using the Becke-3-LeeYangParr density functional methods with 6-311+G(d,p) basis set. The geometry optimization and fundamental frequencies of the most stable configuration have been calculated. The FTIR and FT-Raman spectra of the compound have been recorded and compared to the calculated frequency values. The total energy distribution of the fundamental modes has been obtained using scaled quantum mechanical program. The 1H NMR chemical shifts have been calculated using the gauge-independent atomic orbital approach. The theoretical electronic absorption spectra have been calculated using time-dependent density functional theory. The conductor-like screening solvation model has been applied to calculate the chemical shifts and maximum absorption wavelength values. The calculated values have been compared with the corresponding experimental results. (C) 2012 Wiley Periodicals, Inc.Öğe Infrared and Raman spectra, DFT investigation of the tautomerism, conformational equilibrium, structure and vibrational assignment of 1-(2-benzothiazolyl)-3-methyl pyrazol-5-one(Elsevier, 2013) Aktan, Ebru; Catikkas, BernaThe low energy conformations of the three tautomers, imine-enol, enamine-keto and imine-keto forms of the title compound have been determined at the B3LYP/6-31 + G(d) level of theory using the relaxed PES scan method and their geometries have been refined at B3LYP/6-311 + G(d,p) and PBE0/6-311 + G(d,p) levels. The results show that the title compound exists in the imine-enol tautomeric form, in contrast to the enamine-keto form which exists in the solid crystalline state, followed by enamine-keto and imine-keto forms with extremely low abundances. The geometry parameters of all tautomeric forms calculated at PBE0/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) levels have been compared with those from the experimental X-ray diffraction. The vibrational (FT-IR and Raman) spectroscopic studies of the most stable tautomer, enamine-keto form have been carried out. The assignment of the fundamental bands observed in the IR and Raman spectra have been facilitated by the SQM force field procedure. The frequencies from SQM procedure have a very good fit to the experimental ones. The total root-mean-square error is only ca. 11 cm(-1). (C) 2013 Elsevier B.V. All rights reserved.Öğe Microwave-assisted synthesis of new sulfonyl hydrazones, screening of biological activities and investigation of structure-activity relationship(Springer Birkhauser, 2016) Karaman, Nurcan; Oruc-Emre, Emine Elcin; Sicak, Yusuf; Catikkas, Berna; Karakucuk-Iyidogan, Aysegul; Ozturk, MehmetSulfonyl hydrazone scaffold and the piperidine rings have important role in medicinal chemistry. This study shows the synthesis of two novel series of sulfonyl hydrazone having piperidine derivatives by condensing benzene sulfonyl hydrazides with ethyl 4-oxopiperidine-1-carboxylate and 2,6-diphenylpiperidin-4-one. Physical and chemical properties of compounds have been characterized and reported by utilizing their melting point, elemental analysis, IR, H-1-NMR, C-13 NMR, 2D NMR and mass spectra results. Synthesized compounds were evaluated for antioxidant capacity and anticholinesterase activity. The antioxidant capacity of the compounds were screened through four complementary test, i.e., beta-carotene-linoleic acid for lipid peroxidation, DPPH free radical (DPPH center dot), ABTS cation radical (ABTS(+center dot)) and CUPRAC assays. Assay results showed that N'-(2,6-diphenylpiperidin-4-ylidene)-4-bromobenzenesulfonohydrazide (11) has the highest lipid peroxidation inhibitory activity. Within the assay series, N'-(2,6-diphenylpiperidin-4-ylidene)-4-bromobenzenesulfonohydrazide (11) exhibited better activity than standard BHT in DPPH center dot scavenging, while N'-(2,6-diphenylpiperidin-4-ylidene)benzenesulfonohydrazide (10) showed the best ABTS(+center dot) scavenging assay. The CUPRAC assay revealed that ethyl 4-(2-(4-methoxyphenylsulfonyl)hydrazono)piperidine-1-carboxylate (5) indicated the best activity with A (0.50) value among the tested compounds than the antioxidant standard alpha-tocopherol. According to AChE assay, N'-(2,6-diphenylpiperidin-4-ylidene)-4-chlorobenzenesulfonohydrazide (12) had the best activity, while in BChE assay the highest activity was found for compound N'-(2,6-diphenylpiperidin-4-ylidene)-4-methylbenzenesulfonohydrazide (16). Electronic and structural characteristics and density functional studies of the all newly synthesized compounds have been reported for better understanding in molecular-level. NMR, molecular electrostatic potential (MEP), Delta E (HOMO-LUMO) band gap and the dipole moments of the molecules have been also analyzed and reported.Öğe Molecular Docking and Dynamics Simulations of Ammi visnaga L. Constituents as Antimelanogenic, Anti-Inflammatory and Anticoagulant Agents(Wiley-V C H Verlag Gmbh, 2023) Catikkas, Berna; Karacan, NurcanIn this study, anti-melanogenic, anti-inflammatory and anti-coagulant potentials of eighteen selected constituents of Ammi visnaga L. were investigated by Induced Fit Docking (IFD) and molecular dynamic simulation with Schrodinger software. The binding free energies of the selected natural compounds were computed by means of Delta G MM-GBSA studies. Anti-melanogetic activity of the constituent against agaricus bisporus tyrosinase, Priestia megaterium tyrosinase and Homo sapiens tyrosinase were evaluated. The result showed that apiumetin had more negative binding free energy against three tyrosinase enzymes than cognate ligands, tropolone and kojic acid. Docking analysis was also performed to predict the constituents with anti-inflammatory activity against human Tumor necrosis factor, Cyclooxygenase-2, Prostaglandin D-2 11-ketoreductase AKR1C3 and Prostaglandin reductase PTGR2. The results showed that pyranocoumarins (visnadin, dihydrosamidin, samidin) have more negative binding free energy against Cyclooxygenase-2 and Prostaglandin D-2 11-ketoreductase receptors than cognate drugs, rofecoxib and indomethacin. In addition, docking analysis shows that pyranocoumarins, apiumetin and cimifugin have more negative binding free energy against Vitamin K epoxide reductase than S-warfarin drug, predicting that they have anticoagulant activity. Furthermore, the constituents and their cognate drugs were subjected to 100 ns MD Simulation to predict their stability at the active sites of the enzymes.Öğe Pressure effects on the structural, electronic, elastic, optical, and vibrational properties of YMg intermetallic compounds: a first-principles study(Iop Publishing Ltd, 2024) Ciftci, Yasemin O.; Catikkas, BernaThe properties of YMg in B2 structure have been comprehensively analysed using the first-principles plane-wave pseudopotential method. Specifically, the structural, electronic, elastic, vibrational, and optical properties were investigated using the generalized gradient approximation (GGA) method in the context of density functional theory. The Vienna ab initio simulation package (VASP) was utilized for these calculations. The computed lattice parameter (3.803 & Aring;) and bulk modulus (41.33 GPa) are consistent with the earlier data on ambient pressure. The electronic band structure and energy-dependent density of states reveal the metallic nature of the titled compounds. The Born stability requirements confirmed the mechanical stability. The analysis of Pugh's and Poisson's ratios and Cauchy's pressure reveals that YMg is ductile under the pressures in consideration. According to several anisotropy indices, the compound is noticeably anisotropic both in ambient and under pressure. Our investigation includes an analysis of several fundamental mechanical parameters of the material, including the bulk modulus, the pressure derivative of the Zener anisotropy factor, Poisson's ratio, isotropic shear modulus and Young's modulus with a particular focus on their dependence on pressure. We have determined that the elastic constants obtained remain mechanically stable, satisfying the Born Stability conditions even at high pressures of up to 60 GPa. To explore the dynamic stability of YMg, we analysed the material's phonon dispersion curves. The examined compound displays stability under dynamic conditions from 0 GPa to 30 GPa, as evidenced by its positive vibration frequencies. However, this stability is not sustained under higher pressure, as the compound becomes unstable after 30 GPa to 70 GPa. The electronic band structure and density of states diagrams demonstrate YMg's metallic properties. At atmospheric pressure (0 GPa), the total density of states (TDOS) near the Fermi level is approximately 1.63 states/eV, with pressure application reducing DOS. The dielectric function, refractive index, and energy loss spectra are examined within the 0-20 eV energy range. YMg exhibits its highest absorption between 4 and 11 eV. The peak optical conductivity is observed around 0.78 eV (equivalent to 1589.5409 nm), while the most significant energy loss occurs at 11.90 eV, roughly corresponding to 2.8 Hz in the ultraviolet spectrum. Moreover, we extensively analyzed the material's phonon thermodynamic and optical properties, providing insights into its behavior under various conditions. The outcomes acquired at zero pressure are generally coherent with the current theoretical values.Öğe Structure, conformational landscape and UV-induced selective rotamerization of 2-aminoacetanilide(Elsevier Science Sa, 2023) Brito, Anna Luiza B.; Justino, Licinia L. G.; Catikkas, Berna; Lopes, Susy; Ildiz, Gulce O.; Fausto, RuiThe molecular structure, conformational space and UV-induced rotamerization and decarbonylation of 2-aminoacetanilide (2AA) were investigated by matrix isolation infrared spectroscopy and quantum chemical electronic structure calculations. The compound was isolated in a cryogenic (15 K) argon matrix, and four conformers were spectroscopically identified: two trans-amide (O--C-N-H dihedral - 180 degrees) conformers (trans-I and trans-II), and two higher-energy cis-amide (O--C-N-H dihedral - 0 degrees) conformers (cis-I and cis-II). These four conformers were found to be present in the as-deposited matrix of 2AA in a population ratio matching well that predicted by the calculations for the gas-phase equilibrium at the temperature of the vapor of the compound before deposition (60 degrees C = 333.15 K). The calculations predicted also the existence of an additional higherenergy trans-amide conformer (trans-III) which was not observed experimentally. In situ broadband UV irradiation (lambda > 235 nm) of the matrix-isolated compound was found to induce selective conversion of conformer trans-I into conformer trans-II, in a few minutes (55 % after 2 min. of irradiation; 70 % after 10 min.), while the populations of the cis-amide conformers did not change. Prolonged UV irradiation was found to result in decomposition of the compound, leading to generation of carbon monoxide and 2-amine-N-methylaniline. The infrared spectra of the experimentally relevant conformers of 2AA were interpreted and assigned with help of normal coordinate analysis, and the different behavior of the conformers of 2AA upon UV-irradiation of the argon matrix was explained with help of time-dependent DFT (TD-DFT) calculations.Öğe Synthesis, characterization and catecholase-like activity of new Schiff base metal complexes derived from visnagin: Theoretical and experimental study(Elsevier, 2016) Beyazit, Neslihan; Catikkas, Berna; Bayraktar, Sahin; Demetgul, CahitA new tetradentate, unsymmetrical Schiff base ligand (H2L) containing a donor set of N2O2 and its mononuclear Cu(II) and Fe(II) complexes ([CuL] and [FeL]), were synthesized and characterized on the basis of their elemental analysis, FT-IR, Raman, H-1 and C-13 NMR spectra, electronic and mass spectra, molar conductivity and magnetic susceptibility measurements. Density functional theory (DFT) calculations were performed in order to clarify molecular structures, 1H NMR and 13C NMR chemical shift values, frontier molecular orbitals (FMOs), nonlinear optical properties and map of molecular electrostatic potential (MEP) of the title molecules. In agreement with trials, the results provide a full explanation of the highest efficiency observed for the compounds in relation to the electronic and the structural characteristics. The catecholase-like activity of the complexes toward the oxidation of 3,5-ditert-butylcatechol (3,5-DTBC) to the corresponding quinone showed that both complexes have moderate catalytic activity. [FeL] shows higher activity (k(cat) = 26.4 h(-1)) than that of [CuL] (k(cat) = 23.4 h(-1)). (c) 2016 Elsevier B.V. All rights reserved.Öğe Vibrational and electronic investigations, NLO, FMO analysis on a hetarylazoindole disperse dye by density functional theory(Elsevier, 2016) Catikkas, Berna; Aktan, Ebru; Yalcin, ErginThis work deals with the optimized molecular structure, vibrational spectra, nonlinear optic (NLO) and frontier molecule orbital (FMO) properties of 1-Methy1-2-pheny1-3-(1,3,4-thiadiazol-2-yldiazeny1)-1Hindole (MPI) by quantum chemical calculations. The Fourier transform infrared (Fr-MIR and Fr-FIR) and Raman spectra of 1-Methyl-2-phenyl-3-(1,3,4-thiadiazol-2-yldiazenyl)-1H-indole (MPI) were recorded in the region (4000-400 cm(-1) and 400-30 cm(-1)) and (3200-92 cm(-1)), respectively. The analysis and complete vibrational assignments of the fundamental modes of the MPI molecule were carried out by using the observed Fr-IR and Fr-Raman data and calculated Total Energy Distribution (TED) according to Scaled Quantum Mechanics procedure. The calculated geometrical parameters of the MPI molecule are in agreement with the obtained values from XRD studies. On the other hand, the difference between the scaled and observed wavenumber values of the most of the fundamentals are very sma11.1H NMR and 13C NMR chemical shift values, and energy gap between LUMO-HOMO and molecular electrostatic potential (MEP) were investigated by using density functional theory (B3LYP) methods. UV/Visible spectra and X maximum absorption values, the oscillator strengths in the chloroform, methanol and DMSO solvation in combination with different basis sets were calculated by using the time-dependent density functional theory (1D-DFT). Additionally, the predicted nonlinear optical (NLO) properties of the MPI are quite greater than that of urea at the B3LYP/6-31++G(d,p) level. (C) 2016 Elsevier B.V. All rights reserved.
