Phd Degree / Doktora

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Access Right: Open AccessDepartment: search.filters.department.Thesis (Doctoral)--İzmir Institute of Technology, Chemistry

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  • Doctoral Thesis
    Molecular Modeling of Polyelectrolytes - Nucleotides / Nucleic Acids Interaction
    (01. Izmir Institute of Technology, 2022) Kıbrıs, Erman; Elmacı Irmak, Nuran
    In this thesis, poly- N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium force field parameters were generated via ffTK and CHARMM program to perform MD simulations. NBFIX parameters for the interactions of adenosine nucleotides and oligomer were also produced to improve simulations. The parameters were verified by comparing MM vs QM calculations, and simulated vs experimental UV/Vis spectra. Our results revealed that force field parameters obtained by CHARMM program can be applied successfully for the MD simulations of CPTs with different types of adenosine nucleotides (AMP, ADP, and ATP). Poly-(3-(2-((4-methylthiophen-3-yl) oxy) ethyl)-1-ethyl-4H-1λ4-imidazol-3-ium) and poly- N,N,N-trimethyl-6-((4-methylthiophen-3-yl) oxy) hexan-1-aminium are used for optical sensors, therefore parametrization and MD simulations for these compounds were performed to see the effect of nucleotides on the backbone structures of oligomers. Generally, increasing the phosphate group on nucleotides stretched out the backbone of structures, but the largest response was observed in the presence of ATP. The salt effect and temperature effect were also investigated on oligomer – nucleotide complexes. The increasing temperature shortened the backbone of the compounds, but not significant as experimentally. Addition of the monovalent or divalent cations do not affect linearity of oligomer structure in ATP medium for O3. However, O1 and O2 have a great respond to ATP with Mg2+, K+ and Ca2+ (most sensed) ions, O2 has almost no respond to ATP without these ions. Ca2+ is a key ion which regulates ATP production by mitochondria. O2 may take a part of a biosensor design to recognize ATP in the presence of Ca+2.
  • Doctoral Thesis
    Studies Toward the Synthesis of Novel 1,4-Oxazepan and Coumarin Derivatives
    (01. Izmir Institute of Technology, 2022) Akbaş, Tuğçe; Çağır, Ali
    In this study it is aimed to synthesize potential novel MDM2 inhibitor which has 1,4-oxazepan-5-one skeleton. For this purpose (R)-(4-chlorophenyl)glycine was used as a starting material. Reduction of that with LiAlH4 and the protection of amine by Trt group was performed. After oxidation to aldehyde, direct or stepwise installation of glutaconic to the structure by either Michael type addition or coupling with amine by using HATU was quite problematic and all attempts were failed toward the preparation of this skeleton. Besides, synthesis of 1,4-oxazepan-5-one was also tried starting from chiral aminoalcohol and protected 5-hydroxy-2-pentanoic acid in two steps, first coupling then oxa-Michael addition. However this did not work well too. It seems that presence of activated methylene group might be the main problem in the addition of glutaconic acid reactions. In the second part of this thesis it was aimed to synthesize the 1,2,3-triazole substituted coumarin in order to investigate the potential antiproliferative properties of these over cancer cells. Acetylsalicilic acid was used as starting material in these syntheses. That was transformed 4-acetylene substituted coumarin derivatives as key intermediates then their transformations to corresponding final products was performed by click chemistry.
  • Doctoral Thesis
    Synthesis and Characterization of Novel Organometallic-Semicondutor Nanocomposit Photoelectrodes
    (Izmir Institute of Technology, 2022) Göl, Yusuf Emre; Karabudak, Engin; Karabudak, Engin
    Studies on novel electrochemical catalyst synthesis for efficient oxygen evolution reaction (OER) attract the attention of researchers. In general, changing of synthesis method and the doping metal affect the electrochemical activities of BSCF. In this work, silver doped Ba0.5Sr0.5Co0.8Fe0.2O3-δ (BSCF-Ag) perovskite structure is shown to be a better electrocatalyst for oxygen evolution reaction (OER) due to its lower overpotential and extended durability. BSCF structure was synthesized by the EDTA-citric acid method. Appropriate amount of Ba(NO3)2 and EDTA were dissolved 0.1 M NH4OH solution. Nitrate salts of other metals were dissolved in distilled water, then mixed with prepared Ba(NO3)2 solution. The mixture was stirred at 70 °C until gelation occurred. The gelled samples obtained were baked in a drying oven at 250 °C for 24 h before being calcined at 1000 °C for 12 h. To achieve a current density of 10 mA cm−2, BSCF-Ag has required an overpotential of 0.36 V, which is very low compared to BSCF. To determine the stability of BSCF-Ag, continuous chronopotentiometry tests were carried out for 5 h and at a constant current density of 10 mA cm−2. BSCF-Ag was characterized by XRD, SEM, and XPS. Recent advances in inkjet printing technology for applications relating to heterogeneous catalysis are presented. Catalysts lie at the heart of most chemical reactions where raw materials are converted to value-added products. Therefore, synthesis and immobilization of active catalysts in the reactor are of great importance. Inkjet printing is an additive manufacturing technology introduced recently as a useful method for the fabrication and application of catalysts as a class of functional materials. Inkjet printing provides special features which can be tailored to the design of high-efficient catalytic processes. This thesis presents an overview of the technology along with developments and challenges associated with the combination of inkjet printing and heterogeneous catalysis, such as ink preparation, thin-film properties and real-life applications.
  • Doctoral Thesis
    Synthesis, Characterization and Investigation of Cytotoxic Effects of Drug Loaded Zif-8 Metal-Organic Frameworks
    (01. Izmir Institute of Technology, 2021) Mete, Derya; Şanlı Mohamed, Gülşah
    The biocompatible ZIF-8 intelligent material, a member of the metal-organic framework family, has a biodegradable property in an acidic environment due to its poor coordination bonds. Because cancerous cells are more acidic than healthy cells, our studies aim to ensure that doxorubicin, sorafenib, and apalutamide, encapsulated in ZIF-8, target cancer cells responsive to pH, thereby reducing damage to healthy cells. In addition, ZIF-8 was selected not only as a carrier system but also as a therapeutic effect. Because ZIF-8 material is biodegradable, it is divided into zinc and 2-methylimidazole components in cancer cells. Research shows that the decrease in the amount of zinc is essential in the formation of cancer cells. Zinc is reported to be in lower intracellular concentrations in HCC and prostate cell lines instead of healthy variants. It aims to create dual cytotoxic effects on cancer cells by combining the effects of zinc-drug on a single platform.
  • Doctoral Thesis
    A Comparative Study of Thin-Film Coated Silicon Wafer Surfaces for Laser-Induced Breakdown Spectroscopic Analysis of Liquids
    (01. Izmir Institute of Technology, 2021) Aras, Nadir; Yalçın, Şerife Hanım
    Laser-Induced Breakdown Spectroscopy, LIBS, is a relatively new atomic emission spectroscopic technique that shows rapid growth due to its many special peculiarities, like its ability to provide spectral signatures of all chemical species at the same time, in all environments of solid, liquid, or gas. Liquid sample analysis by LIBS is more troublesome compared to analysis of solids. Therefore, liquid analysis by LIBS requires some pretreatment steps to be applied before direct analysis of the samples. In the literature, a variety of approaches has been successfully applied and there is still plenty of room to improve methodologies used in the liquid-LIBS analysis. The main purpose of this thesis study was to perform studies for the development of a LIBS-TARGET for sampling liquids on it, after drying, by repetitive laser pulses. With this purpose, silicon wafer-based substrates with differing surface compositions; uncoated (crystalline silicon, c-Si), oxide-coated silicon, SiO2, and nitride coated silicon, Si3N4, were tested for several experimental parameters. Within the content of this study, a fast and accurate methodology for direct analysis of aqueous samples by LIBS is proposed. This methodology has two important attributes: one is the use of the non-metal substrate, silicon wafer, for the first time for direct analysis of aqueous samples dried on, and two is the use of high energy laser pulses focused outside the minimum focal point of a plano-convex lens at which relatively large laser beam spot covers the entire droplet area for plasma formation. Si-wafer-based substrates were used for both qualitative and quantitative analysis of Cd, Cr, Cu, Mn, and Pb elements, and analytical figures of merit were determined. The analytical performance of each substrate was evaluated from the experiments performed with aqueous standards and real water samples. Silicon nitride-coated substrate has shown superior properties in terms of enhancing the LIBS signal and as low as 11 pg detection limits for Pb were obtained.
  • Doctoral Thesis
    Characterization and Catalytic Applications of Hydrothermally Synthesized Poyoxotungstate Clusters Containing Organic-Inorganic Hybrid Materials
    (Izmir Institute of Technology, 2019) Ece, Özlem; Eanes, Mehtap; Çağır, Ali
    Many scientists have been interested in hydrothermal synthesis and characterization of polyoxometalate clusters containing organic-inorganic hybrid materials recently because of having different applications in lots of fields, especially, using as catalysis in chemical reactions. In this study, three novel polyoxotungstate clusters were synthesized using hydrothermal method and catalytic activities of these three novel polyoxometalates and in addition two crystals previously synthesized in our group were studied. The first compound, [(4,4’-bpyH2)3][PCuW11O39] yellow crystals, crystallize in the space group P2(1)/n of the monoclinic system with four formula units in a cell. The crystal is a Keggin polyoxometalate and includes free 4,4’-bipyridine groups between the clusters. The second compound, (4,4’-bpyH2)[H2PW12O40]2.H2O colorless crystals, crystallize in the space group Ia-3 of the cubic system with twelve formula units in a cell. The crystal is a Keggin polyoxometalate and consists of two polyoxotungstate clusters, a free 4,4’-bipyridine group and a water molecule. The third and the last novel compound, (4,4’-bpyH2)4[H2P2W18O62]2 dark yellow crystals, crystallize in the space group P-1 of the triclinic system with four formula units in a cell. The crystal is a Wells-Dawson polyoxometalate and contains two polyoxotungstate clusters and free 4,4’-bipyridine groups between clusters. The catalytic study has been carried out using starch hydrolysis reactions by using hydrothermal synthesis and five different crystals were tried and conversion results were obtained. Starch samples converted to D-glucose with glucose yields above 90 wt.%. Catalyst reusability was performed for each crystal. No appreciable loss was observed in activity after five reaction cycles for each crystal.
  • Doctoral Thesis
    Proteomic Analyses of Biological Samples by Using Different Mass Spectrometric Strategies
    (Izmir Institute of Technology, 2018) Dinç, Melilke; Yalçın, Talat
    The advent of soft ionization techniques MALDI and ESI have opened the doors of mass spectrometry to biological samples. Particularly protein research exploited this opportunity to the utmost that qualitative, quantitative, structural and distributional analyses of proteins have become achievable. Comparison of all expressed proteins belonging to two or more states is defined as differential proteomics and commonly performed either separating the proteins on a gel or separating the peptides in the mixture within a column. In this study, both of these methods were applied to a parasite that causes to the infectious disease, Leishmaniasis. Consequences of the disease become severe when parasite is multiplied in viscera rather than skin. Occurrence of different clinical manifestations is attributed to the variety in species however some species can cause to both such as L.infantum and L.tropica. The purpose of this study was to investigate this duality in L.infantum. Despite originating from two different species, cutaneous leishmaniasis isolates obtained from ten different patients exhibited considerably similar protein profiling on the gels however isolates belonging to five visceral leishmaniasis patients were discriminated from them with regards to protein abundances. Additionally, several differential proteins between cutaneous leishmaniasis and visceral leishmaniasis samples were determined by gel-free approach. Apart from that, another mass spectrometric strategy for the abovementioned distributional analysis namely mass spectrometry imaging was included in the last section. Herein, a method incorporating the application of enzyme with matrix was developed for easy sample preparation to on-tissue digestion and promising results were obtained for a start.
  • Doctoral Thesis
    Development of Colloidal Alloyed Nanocrystals for Quantum Dot Based Device Applications
    (Izmir Institute of Technology, 2018) Sevim Ünlütürk, Seçil; Özçelik, Serdar; Varlıklı, Canan
    Quantum dots (QDs) are very attractive luminescent semiconducting nanoparticles. In this study, our aim was to synthesize Cd and/or Zn based QDs with tunable optical properties by the particle size and the alloy composition. Colloidal water dispersible Mn-doped and nondoped ZnSxSe1-x QDs were synthesized by the one-pot aqueous method. Optical measurements indicate that photoluminescent properties are strongly depended on the capping agent. While MPA capped QDs showed an emission peak in the blue region, others did not show any photoluminescence at all. Mn doping up to 10% resulted in no significant effect on the optical spectra. However structural characterizations, EPR and XRD, supported that Mn ions were bounded to the 220 and 311 facets of QD. ZnxCd1-xSySe1-y quaternary nanoalloys were synthesized by using a modified two-phase approach for the first time in the literature. Optical properties of highly luminescent ZnxCd1-xSySe1-y nanoalloys were tuned from blue to yellow by the particle size, the alloy composition, and thickness of shell layer. The reactivity of the reactants, initial mole ratios, and other reaction parameters was adjusted to control alloy composition and alloy type: homogeneous and gradient. The reaction time controls the size of particles. The PL QE (up to 52%) and lifetimes (about 25 ns) were found similar regardless of core and core-shell nanoalloys. MicroPL measurements were carried out on ZnxCd1-xSySe1-y nanoalloys by fiber spectrometer integrated to confocal microscope. Photobleaching and blue-shifting, about 6 nm, were observed in the microPL spectra. Photobleaching times and rate constants obtained from single exponential decay curves showed that purification and exposure time are strongly effective. Additionally, the power the excitation light is essential that below 11 μW, photobleaching slows down, and at 2 μW there is no photobleaching. Scale-up methods with high-volume batch and flow reactor were used to synthesize CdTe and ZnxCd1-xSySe1-y QDs. LEFETs were fabricated with TUBITAK support in collaboration with Heidelberg University. PbS QDs were used as emitting material at the bottom contact top-gate unipolar LEFETs in which uniform electroluminescence was obtained.
  • Doctoral Thesis
    Synthesis, Physicochemical Characterization, and Biosensing Applications of Gold Nanoparticles
    (Izmir Institute of Technology, 2018) Üçüncü, Melek; Özçelik, Serdar
    Cancer is one of the leading diseases that cause death all around the world. In Turkey, lung cancer is the most common type of cancer type in men and it is the fifth in women. Unfortunately, the percentage of treatment of lung cancer is too low. Gold nanoparticles (AuNPs) are widely used in the biotechnology as imaging, diagnosis, and therapeutic agents because of their unique properties such as plasmon resonance, easy synthesize, biocompatibility, and facile surface modification. In this study, it is aimed to design gold nanoparticles as biosensors for lung cancer cells. For this purpose, different sizes (5-40 nm) of Au nanoparticles were synthesized and their uptake and distribution into the lung cancer cells were investigated. The results of the study revealed that cellular uptake of gold nanoparticles are high for the size of 20 and 40 nm. The optimal visibility into the cells was achieved by using DIC microscopy in which the particles uptaken into the cytoplasm and localized at around nucleus of cells. In the second part of the study, surfaces of 20 and 40 nm particles were conjugated with RGD peptides and their distribution and light scattering properties were investigated in living cells by using dark-field microscopy. Due to the receptor-mediated endocytosis, RGD-AuNPs showed different distribution within the cells. These results indicate that the RGD conjugated Au nanoparticles exhibits much higher light scattering properties than non-conjugated nanoparticles. In addition to this, synthesized Au nanoparticles were conjugated with nucleus-localized peptide (NLS) and directed to the nucleus of cancerous (A549, H358) and healthy (BEAS2B) lung cells. The nucleus targeting properties of the NLS conjugated particles were also investigated to understand if there is any cell line selectivity. The internalizations of peptide conjugated Au nanoparticles into cell lines were visualized in living cells by using DIC microscopy. NLS conjugated AuNPs internalized into nucleus of A549 and H358 cancer cells. Although NLS conjugated AuNPs present inside the cytoplasm of BEAS2B cells, they did not localize into the nucleus of normal cell lines.
  • Doctoral Thesis
    Development of Novel Solid Phase Extraction (spe) Sorbents and Solid Phase Microextraction (spme) Fiber Coatings for Determination of Endocrine Disrupting Compounds (edcs)
    (Izmir Institute of Technology, 2017) Demirkurt, Merve; Eroğlu, Ahmet Emin
    This thesis is composed of four chapters. In the first part of the study, molecularly imprinted polymer (MIP) was prepared as SPE sorbent for selective determination of BPA prior to HPLC DAD analysis. The adsorption capacity and selectivity of imprinted polymers were investigated. To improve the MISPE method, the parameters including pH of sample solution, adsorption time, amount of sorbent, desorption solvent were examined. The extraction efficiency of BPA imprinted polymer was investigated by using the spiked samples of ultrapure, drinking and tap water. The second part of the thesis was about determination of estrogen hormones. For this purpose, amino modified silica and molecular imprinted silica were prepared and their SPE performances were compared. The proposed methodology was validated through the analysis of real water samples. The preparation of MIP nanoparticles encapsulated in electrospun polystyrene fibers as the SPME fiber coating was the subject of the third part of the thesis. Developed fibers were used for selective extraction and analysis of parabens in water samples. The optimization parameters affecting the extraction and desorption of parabens were investigated. The validity of the proposed method was verified via spike recovery tests. Finally, fibers having amino functionality prepared by the sol-gel based electrospinning process were used for determination of BPA. The effect of solution pH, extraction time, agitation speed and ionic strength on the extraction performance were investigated. Validity was checked via the application of the proposed methodology on real samples.