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Öğe 1,3-Disubstituted urea derivatives: Synthesis, antimicrobial activity evaluation and in silico studies(Academic Press Inc Elsevier Science, 2020) Gunduz, Miyase Gozde; Ugur, Sumeyye Buran; Guney, Funda; Ozkul, Ceren; Krishna, Vagolu Siva; Kaya, Serdal; Sriram, DharmarajanThe development of new antimicrobial compounds is in high demand to overcome the emerging drug resistance against infectious microbial pathogens. In the present study, we carried out the extensive antimicrobial screening of disubstituted urea derivatives. In addition to the classical synthesis of urea compounds by the reaction of amines and isocyanates, we also applied a new route including bromination, oxidation and azidination reactions, respectively, to convert 2-amino-3-methylpyridine to 1,3-disubstituted urea derivatives using various amines. The evaluation of antimicrobial activities against various bacterial strains, Candida albicans as well as Mycobacterium tuberculosis resulted in the discovery of new active molecules. Among them, two compounds, which have the lowest MIC values on Pseudomonas aeruginosa, were further evaluated for their inhibition capacities of biofilm formation. In order to evaluate their potential mechanism of biofilm inhibition, these two compounds were docked into the active site of LasR, which is the transcriptional regulator of bacterial signaling mechanism known as quorum sensing. Finally, the theoretical parameters of the bioactive molecules were calculated to establish their drug-likeness properties.Öğe Core-shell magnetic nanoparticles deliver singlet oxygen for mild oxidations: rechargeable, removable, reusable(Royal Soc Chemistry, 2022) Yildiz, Deniz; Kaya, Serdal; Turksoy, Abdurrahman; Akkaya, Engin U.Singlet oxygen is a useful reactive species. In addition to its role in photodynamic therapy, a variety of synthetically useful reactions can be carried out using singlet oxygen generated by photosensitization. In this work, we present a novel approach for synthetic applications, where singlet oxygen can be generated both via photosensitization and by thermal cycloreversion reaction of a singlet oxygen storage/photo-sensitizer compound on nanoparticles. With this goal in mind, a BODIPY photosensitizer-pyridone conjugate was covalently tethered to silica-iron oxide core-shell nanoparticles. The modified nanoparticles serve as singlet oxygen sources through photosensitization of the BODIPY core, or alternatively, once the pyridone module is transformed into an endoperoxide, they can be used as a chemical source of singlet oxygen under mild conditions in the dark. The nanoparticle-based agent can easily be recovered with a magnet and can be reused repeatedly. We expect ready and convenient availability of singlet oxygen to broaden the scope of reactions for this reactive oxygen species.Öğe Exploring of indole derivatives for ESIPT emission: A new ESIPT-based fluorescence skeleton and TD-DFT calculations(Elsevier Science Sa, 2021) Kaya, Serdal; Aydin, Hatice Gulten; Keskin, Selbi; Ekmekci, Zeynep; Menges, NurettinABS T R A C T Appropriate synthesis methods gave six different indole derivatives substituted at the C-2 or C-3 position. ESIPT emission capacities of these derivatives were investigated. It was concluded that the indole derivative containing the 1,2-dicarbonyl group at the C-2 position has ESIPT emission. Although adding water to the DMSO solution of the ESIPT-based molecule (9:1) resulted in ESIPT quenching, steady-state measurements in MeOH did not occur ESIPT quenching. TD-DFT calculation for uncovering the ESIPT mechanism emerged that the ESIPT mechanism occurred as a barrierless process. The X-ray analysis and DFT conformational analysis revealed that NH and CO groups involving proton transfer mechanisms are in the cis position. A mono-exponential decay was observed in DMSO and MeOH solutions, in which lifetimes were measured as 6.1 and 5.5 ns, respectively. pH studies revealed that acidic and basic solutions of molecule 7 did not influence ESIPT emission.Öğe Imaging of intracellular singlet oxygen with bright BODIPY dyes(Elsevier Sci Ltd, 2021) Kaya, Serdal; Ismaiel, Yahya A.; Kwon, Nahyun; Kim, Gyoungmi; Bila, Jose L.; Yoon, Juyoung; Seven, OzlemSinglet oxygen is a cytotoxic reactive species which is involved in the photodynamic therapy of cancer. It is also known to be produced endogenously in most eukaryotic cells and implicated in many biochemical processes, including apoptotic response. We now report that Bodipy based fluorescent dyes with singlet oxygen reactive modules, signal the intracellular generation of singlet oxygen through photosensitization. We believe long wavelength probes of singlet oxygen, based on this approach will be highly valuable.Öğe Magnetically separable nickel ferrite supported palladium nanoparticles: Highly reusable catalyst in Sonogashira cross-coupling reaction(Academic Press Inc Elsevier Science, 2022) Keskin, Selbi; Citlakoglu, Meryem; Akbayrak, Serdar; Kaya, SerdalThere is an increasing attention in developing highly efficient and reusable palladium-based catalysts used for the coupling reactions due to the high cost of palladium metal salts. Magnetically separable palladium nanoparticles have a high potential to be used as catalysts in numerous organic reactions due to their facile separation from the reaction medium by an external magnet. Herein, NiFe2O4 supported palladium nanoparticles (Pd/NiFe2O4) were successfully prepared by impregnation and reduction method in water and used as catalysts for Sonogashira cross-coupling reactions. Magnetically separable Pd/NiFe2O4 catalysts were found to be highly active and reusable in this reaction. Pd/NiFe2O4 provided an outstanding turnover frequency value (106.4 h(-1)) in the reaction between phenylacetylene and iodobenzene in ethanol at 70 degrees C and it was also found to be highly active in the water. Magnetically separable Pd/ NiFe2O4 exhibited high catalytic performance even after the tenth use in this reaction. (C) 2022 Elsevier Inc. All rights reserved.Öğe Rapid and Highly Selective BODIPY Based Turn-Off Colorimetric Cyanide Sensor**(Wiley-V C H Verlag Gmbh, 2021) Kaya, SerdalCyanide ion (CN- ion) is one of the most harmful inorganic pollutants wasted by various industrial processes. Although some spectroscopic methods are being used, these methods need advanced instrumentation and have high detection limits. Because of this, rapid, low-cost and sensitive methods are highly required to detect CN- ion. Chemosensor application is one of the most useful methods for selective detection of the target analyte. BODIPY (boradiazaindacene) dyes are one of the promising candidates for these types of applications because of the unique optical and photophysical properties. Here, we report the first application of the meso-formyl-BODIPY dye-based, rapid and naked-eye CN- ion sensor application depending on the reaction of CN- ion and aldehyde functionality of the meso-formylated BODIPY derivative (BODIPY-BAL). Absorption and emission experiments were successfully conducted. Additionally, colorimetric tests were performed in solution and on test strips. The limit of detection of the chemosensor was calculated as 10.4 mu M. Real sample experiments in seawater were also performed and CN- ion was detected at 50 mu M concentration, which is the limit level of CN- ion concentration causes acute effects determined by the U.S. Environmental Protection Agency (EPA).Öğe Seasonal distribution and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in surface sediments from the Giresun coast of southeastern Black Sea(Pergamon-Elsevier Science Ltd, 2022) Tepe, Yalcin; Aydin, Handan; Ustaoglu, Fikret; Kaya, SerdalSeasonal sediment samples were collected along the Giresun coastline of southeastern Black Sea and analyzed to detect the levels of 16 polycyclic aromatic hydrocarbons (PAHs). The PAH levels, ranging from 28.47 to 444.36 ng g(-1) with the mean of 102.57 ng g(-1) remained lower than those detected in most of the other sediment studies conducted worldwide. The percentage of three-ring PAHs (38.9%) was rather high, followed by that of 5-ring PAHs (21.8%). Detection rates revealed that PAHs in surface sediments along the Giresun coastline are mainly associated with coal combustion and local emissions. The evaluation with sediment quality guidelines (SQGs) showed that the level of PAHs was comparable to that at which the risk of adverse biological effects cannot be ruled out (>= TEL and < PEL) in some stations. The risk posed by PAHs in Giresun coastal sediments appears to be low to moderate ecological risk according to the risk quotient.Öğe Structural, Bioactivity, Molecular Docking, Spectroscopic and Electronic Properties of a Synthesized Meldrum's Acid Derivative(Wiley-V C H Verlag Gmbh, 2021) Gokce, Halil; Alpaslan, Gokhan; Kaya, Serdal; cakir, NezaketThe molecular structure, tautomeric forms (enol and keto), spectroscopic and electronic properties of a synthesized Meldrum's acid derivative were studied by using the experimental (SCXRD, FT-IR, NMR and UV) and computational (DFT/B3LYP/6-311++G(d,p) level) methods. Hirshfeld surface analysis were used to investigate the presence of inter-molecular interactions within crystal packing. The biological activity, drug-likeness and interactions between the target protein and the ligand compound were studied by in silico ADME and molecular docking methods. The non-linear optical (NLO) activity of the compound was determined with static computations of dipole moment, polarizability and first-order hyperpolarizability values. Thermo-chemical features were theoretically analyzed for both enol forms. Comparatively with the experimental vibrational frequencies, detailed assignments and interpretations of the computed harmonic vibrational wavenumbers were carried out in PED. The certain structural form at the room temperature of the compound was analyzed by H-1- and C-13-NMR chemical shift studies. The UV, HOMO and LUMO analyses were studied to research electronic properties of the compound. The nature, structure and existence of the hyper-conjugative interaction for the O-H...O intra-molecular hydrogen bonding in two enolic forms were investigated with Natural Bond Orbital (NBO) analysis. The reactive sites were obtained from atomic charges and Molecular Electrostatic Potential (MEP) map.Öğe Structural, spectroscopic, and theoretical investigations of (E)-methyl-3-(3,5-di-tert-butyl-2-hydroxybenzylideneamino)-4-methylbenzoate(Wiley-V C H Verlag Gmbh, 2021) Bingol Alpaslan, Yelda; Gokce, Halil; Macit, Mustafa; Kaya, Serdal; Alpaslan, GokhanA novel Schiff base ((E)-methyl-3-(3,5-di-tert-butyl-2-hydroxybenzylideneamino)-4-methylbenzoate (MDM), C24H31NO3) at phenol-imine form with the O-HMIDLINE HORIZONTAL ELLIPSISN intra-molecular hydrogen bond was synthesized. Its structural and spectroscopic characterizations were performed by using experimental (single crystal X-ray diffraction, Fourier transform infrared [FT-IR], NMR chemical shift, and UV-vis spectroscopies) and theoretical (DFT/B3LYP/6-311+G[2d,p] computational level) methods. X-ray diffraction investigation shows that the MDM crystallized in phenol-imine form with O-HMIDLINE HORIZONTAL ELLIPSISN intra-molecular hydrogen bond. Detailed investigations of the presence and nature of the inter-molecular contacts within solid state crystal packing form of MDM were examined by Hirshfeld surface analysis. The intra-molecular electronic transitions in the compound were investigated and determined by UV-vis electronic absorption wavelengths and FMOs analyses. The structural, vibrational, and NMR chemical shift analyses of azomethine (-CH(sic)N-) and phenolic hydroxyl (-OH) groups in MDM supported its phenol-imine structural formation.Öğe Synthesis of Carbazole-Substituted thiosemicarbazone and its Cu(II) Complex, DNA/Protein Binding, Cytotoxic, antiproliferative activities and molecular docking studies(Elsevier, 2023) Findik, Mukerrem; Kuzu, Burak; Pehlivanoglu, Suray; Kaya, Serdal; Sayin, Ulku; Akgemci, Emine Guler; Saf, Ahmet OzgurIn this study, 9-ethyl-3-carbazolecarboxaldehyde-4-ethyl-thiosemicarbazone (ECCAET) and its copper(II) com-plex (Cu(ECCAET)2) were firstly synthesized and characterized. DFT and EPR studies confirmed that the complex is mononuclear and has square planar geometry. The interaction of all synthesized compounds with calf thymus DNA (CT-DNA) was examined by absorption and fluorescent spectroscopy. The experimental results showed that Cu(ECCAET)2 interacts with DNA via an intercalative binding mode. The binding interactions of the complex with CT-DNA have been confirmed through viscosity measurements revealing that the complex interacts with DNA via intercalation. Furthermore, the protein binding ability of ECCAET and Cu(ECCAET)2 was investigated using BSA via electronic absorption spectral titration, fluorescence quenching, and synchronous fluorescence spectrum studies, which revealed that the Cu(ECCAET)2 strongly bound to BSA over the ligand. Molecular docking studies were also performed to support the bonding mechanism of ECCAET and Cu(ECCAET)2 with DNA and BSA. The biological activity studies of ECCAET and Cu(ECCAET)2 against cancer cells were also investigated. A panel of cancer cell lines, including A2780 human ovarian adenocarcinoma, MDA-MB-231 human triple-negative breast adenocarcinoma, and as a control non-cancerous L929 fibroblast cell lines were also used to test the compounds' anticancer activities. Cytotoxic and antiproliferative properties of Cu(ECCAET)2 were visibly higher than its ligand (ECCAET) for all tested cell lines. The Cu(ECCAET)2 had a distinctive biological effects on A2780, and MDA-MB-231 cells compared to non-cancerous cells. Within these results, Cu(ECCAET)2 was found a promising drug candidate against gynecologic cancer diseases.
