Phd Degree / Doktora
Permanent URI for this collectionhttps://hdl.handle.net/11147/2869
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Doctoral Thesis Synthesis and Characterization of Near-Infrared (nir) Emissive Conjugated Polymer Dots for Tumoroid Imaging(01. Izmir Institute of Technology, 2024) Karabacak, Soner; Yıldız, Ümit HakanThis thesis describes the synthesis and characterization of near-infrared (NIR) emissive conjugated polymers and their polymer dots (Pdots). The Pdots were exploited to image the tumor cells and tumor spheroids. The penetration behavior of NIR emissive Pdots was characterized in five different tumor spheroid models. Three different polymerization techniques were tried to synthesize the NIR emissive polymers, namely oxidative, direct arylation, and Stille polymerization. The obtained NIR emissive polymers underwent structural and optical characterization. P1 was chosen as a model polymer to obtain Pdots from NIR emissive polymers for imaging tumoroids. Pdot preparation includes using ultrasonic emulsification to modify nonionic D-A-D type alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (P1) with amphiphilic cetyltrimethylammonium bromide (CTAB). The technique yields Pdots with a significant positive surface charge of +56.5 mV ± 9.5 and an average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots were found as emissive in the NIR region, with a maximum wavelength of 860 nm. These Pdots possess colloidal and optical properties that make them appropriate for use as fluorescence emissive probes in bioimaging applications. The advantageous use of positively charged Pdots has been proven in diffusion-limited settings such as tissues, specifically in certain tumor spheroid models produced from the tumoroid cell lines. After the fluorescence imaging analysis, the Pdots' emission intensity profile indicates that they have high penetration capability into the tumoroid models' center parts. The results show that Pdots with a single-chain donor-acceptor polymer structure that has been cationized with CTAB can penetrate through dense materials over about 1 μm. This provides valuable insights into the progression of targeted theranostic strategies in cancer therapy.Doctoral Thesis Molecular Modeling of Polyelectrolytes - Nucleotides / Nucleic Acids Interaction(01. Izmir Institute of Technology, 2022) Kıbrıs, Erman; Elmacı Irmak, NuranIn 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 Development of New Chemometrics Approaches To Determine Physical and Chemical Properties of Crude Distillation Unit Products Based on Molecular Spectroscopy(01. Izmir Institute of Technology, 2022) Meşe Sezen, Ayten Ekin; Özdemir, DurmuşCrude distillation units are the first processing units of crude oils based on fractional distillation. The properties of the petroleum products obtained from refinery units are frequently analyzed to ensure that the off-spec product cannot be obtained and that the process is working under the desired conditions. This study aims to develop a method based on multivariate data analysis to determine physical and chemical properties of petroleum samples as an alternative to time-consuming and conventional analytical methods. Four different petroleum products obtained from CDU for years were selected and used in this study, which are heavy and light diesel, heavy and light straight run naphtha. Four different spectroscopic methods which are UV-Vis, Fluorescence, FT-NIR and FTIR-ATR spectroscopy, were performed and compared. Multivariate calibration models were developed using Partial least Squares (PLS) and Genetic Inverse Least Squares (GILS) algorithms. For heavy and light diesel, predictive performance of three different spectroscopic methods were compared and for heavy diesel UV-Vis spectroscopy, for light diesel FT-NIR spectroscopy was selected for most of the parameters. Developed models by fluorescence analysis of light diesel samples conducted with two different measurement modes and synchronized fluorescence spectral data has resulted in better models compared to total fluorescence spectra. Studies with straight run naphtha samples were obtained from three different refineries and prediction performances were compared. All obtained model results indicates that developed methodology can be used in routine operations instead of conventional analytical methods.Doctoral Thesis Studies Toward the Synthesis of Novel 1,4-Oxazepan and Coumarin Derivatives(01. Izmir Institute of Technology, 2022) Akbaş, Tuğçe; Çağır, AliIn 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, Characterization and Investigation of Cytotoxic Effects of Drug Loaded Zif-8 Metal-Organic Frameworks(01. Izmir Institute of Technology, 2021) Mete, Derya; Şanlı Mohamed, GülşahThe 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 Preparation of Nanostructured Interface by Polymer Grafting on Various Solid Substrates for Biosensor Applications(Izmir Institute of Technology, 2021) Özenler, Sezer; Yıldız, Ümit HakanThis thesis presents the utilization, various applications, and characterization of the soft material-based coating formed on the gold surface with varying thickness and chemical properties resulting from the isocyanate-gold interaction. Theoretical calculations regarding the interaction of isocyanate with the gold surface revealed the character of the bond formed and the orientation of the functional groups on the surface. Results by X-ray photoelectron spectroscopy showed the tendency to shift to the high energy at N 1s and C 1s binding energies in the gold-interacting isocyanate group. In the next steps, the isocyanate-activated gold substrate was subjected to sequential incubation of 1,4-butanediol/hexamethylene diisocyanate, and thin-film formation was achieved by surface assisted (SurfAst) urethane polymerization. It was revealed with three different applications that a nano-porous polyurethane (PU) structure was formed on the gold substrate and could be postmodified by using SurfAst polymerization method. In the first application, modification with polyethylene glycol (PEG) was provided to obtain antifouling properties. The PEG-terminated PU structure on the gold surface was shown to reduce protein adhesion by approximately ten-fold. In the second application, SurfAst was applied on the 11-mercaptodecanoic acid incubated surface and grafting onto the poly (N-allyl-N-methyl-N-(3-((4-methylthiophen-3-yl)oxy)propyl) prop-2-en-1-aminium surface was characterized. As a result of PT grafting, PT nanowires with an average height of 100 nm, a width of 250 nm, and a length of 7 μm were obtained on the gold surface. In the last application, a soft nanogel was obtained by a reactive layer-layer (rLBL) coating method using the aza-Michael addition reaction of branched polyethyleneimine and polyester on the isocyanate functional surface. The mechanical and electrical permeability and coating properties of the nanogel layer were assessed. In conclusion, the high potential of isocyanate in surface activation has been demonstrated theoretically and experimentally. Effective modification of gold surfaces by polymer grafting with the SurfAst method and rLBL coating techniques has been achieved.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 HanımLaser-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, AliMany 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, TalatThe 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, CananQuantum 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.