Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Studying Dopa Adhesion on Polystyrene Under Water(Izmir Institute of Technology, 2021) Yıldız, Remziye; Akdoğan, Yaşar; Emrullahoğlu, MustafaMussels wet adhesive performance has been arousing curiosity for a long time. It is found that 3,4-dihydroxyphenylalanine (DOPA) is responsible for adhesive properties of mussels. Despite a large body of research characterizing the interactions DOPA with hydrophilic surfaces, relatively few works have addressed the mechanism of interactions with hydrophobic surfaces. The benzene ring of DOPA is the main attributor to the adhesion on hydrophobic polystyrene (PS) surface. However, here we showed that two hydroxyl groups of catechol have also effects on wet adhesion. We studied wet adhesive properties of DOPA, tyrosine and phenylalanine functionalized PEG polymers, PEG-(N-Boc-L-DOPA)4, PEG-(N-Boc-L-Tyrosine)4, PEG-(N-Boc-L-Phenylalanine)4, on spin labeled PS nanobeads (SL-PS) by electron paramagnetic resonance (EPR) spectroscopy. Surface coverage ratio of SL-PS upon additions of PEG-(N-Boc-L-DOPA)4, PEG-(N-Boc-L-Tyrosine)4 and PEG-(N-Boc-L-Phenylalanine)4 showed that SL-PS was covered with 70%, 50% and 0%, respectively. This showed that spontaneous wet adhesion on PS increases with the number of amino acids hydroxyl groups. This is also supported with the density functional theory (DFT) energy calculations and ab-initio molecular dynamics (AIMD) simulations. In water, interactions between water molecules and hydroxyl groups on the catechol induce catechol adhesion via π-π stacking between the catechol and double styrene rings which were already tilted out with water.Master Thesis Desing and Synthesis of Bodipy Based Photosensitizers for Photodynamic Therapy(Izmir Institute of Technology, 2019) Dartar, Suay; Emrullahoğlu, Mustafa; Emrullahoğlu, MustafaPhotodynamic therapy is a promising modality for the non-invasive treatment of several cancerous and non-cancerous diseases. PDT is more preferable than other therapies due to its low damage to non-targeted tissues and its controllable characteristics. The therapy involves the activation of a photosensitizer under light illumination to generate singlet oxygen which is the cytotoxic agent employed against the cancerous tissues. Thus, there is currently a great effort to develop various photosensitizers. Among these, BODIPY based photosensitizers are distinguished due to certain characteristics, including excellent photostability, high extinction coefficients and high resistance to photobleaching. In this study, we aimed to synthesize and develop new BODIPY based photosensitizers for the use of photodynamic therapy agents. BODIPY skeleton was devised using the dibromoethylene unit from the 2,6-positions in order to enhance the π-conjugation system for red shift to longer wavelengths resulting in a deep penetration of tissue. Heavy atoms such as bromine were introduced to the BODIPY core to ensure the transition from singlet states to triplet states via intersystem crossing for the generation of singlet oxygen. Photophysical properties and spectroscopic measurements of photosensitizers were performed successfully. Finally the photodynamic activities of photosensitizers in cancerous cells were also investigated.Master Thesis Desing and Synthesis of Fluorescent Chemodosimeter for the Analysis of the Gold Ions(Izmir Institute of Technology, 2018) Çevik Eren, Merve; Emrullahoğlu, MustafaThe gold element has been used in many different areas throughout history. This includes the treatment of various diseases with drugs containing gold. In contrast to gold metal, gold ions are known to be extremely harmful to the human body. Therefore, the determination of the gold ions in the human body is very important. Gold ion determination can be made by using expensive spectroscopic methods. In contrast to highly expensive spectroscopic methods, chemosensors with high sensitivity and selectivity are a good option to make the gold determination. The bodipy fluorophore is a good example for the metal ion chemosensor. In this study, a bodipybased fluorescence sensor derived from a unique motif that has a triple bond was designed and synthesized. By activating the triple bond of the gold ions, it becomes selective to the gold ions as a result of ırreversible intramolecular cycling.Master Thesis Study of Drug Transportation by Esr Spectroscopy(Izmir Institute of Technology, 2018) Tatlıdil, Duygu; Akdoğan, Yaşar; Emrullahoğlu, MustafaThe ability to track drug binding and release makes electron spin resonance (ESR) spectroscopy well suited for drug delivery studies. Using the continuous wave cw ESR technique to extract information about the dynamics of the spin labeled drugs we can simultaneously determine the bound and unbound drugs. In this study, ESR technique was used to detect the binding and release of spinlabeled salicylic acid (SLSA) to and from bovine serum albumin (BSA), and to detect different binding interactions between them. We have labeled salicylic acid with stable nitroxide-based tempo radicals to monitor the BSA bound and unbound conditions of the drug. Studying with the different concentrations of SLSA-BSA binding showed that the drug-protein stoichiometry increases significantly in the physiological range of BSA concentration. Also, during the release of SLSA from BSA, there is an unchanging balance between the bound and unbound SLSA. In order to study various drug binding interactions, SL-benzoic acid, SL-phenol, SL-benzene, SL-cyclohexane, SL-hexane and SL-methyl were prepared. We showed that the main conjugation in the binding of these drugs to BSA is hydrophobic interaction. In addition, cationic BSA (cBSA) was prepared to investigate the effect of electrostatic interaction on drug binding. The SLSA loading capacity of cBSA is significantly higher than that of BSA, this result indicates the importance of electrostatic interactions for the drug binding. Finally, we examined the competitive binding behaviors of salicylic acid, ibuprofen and aspirin to BSA. Binding sites of SL-salicylic acid and SL-ibuprofen in BSA show 96% of similarities. In addition, our results showed that binding sites of SL-salicylic acid and SL-aspirin in BSA have 73% of similarities.These results demonstrate that cw ESR spectroscopy with the spin labeling technique is an effective technique for the determination of drug-protein interactions and stoichiometric analysis of drug binding.Master Thesis Design and Synthesis of Phosphine Based Fluorescent Probes for Reactive Oxygen Species(Izmir Institute of Technology, 2018) Üçüncü, Canan; Emrullahoğlu, Mustafa; Emrullahoğlu, MustafaHypochlorous acid is a cleansing agent known as bleach in daily life. Apart from the household chemicals feature, HOCl plays an active role in the defence system of living cells. It is an important reactive oxygen species that exhibits anti-microbial properties against invaders. However, the increase in the amount of cells in the cell due to oxidative stress causes serious damage to the structure and function of the organism and can cause fatal diseases. Determination of reactive oxygen species in the cell is of great importance. Although different detection methods are used for this purpose, fluorescent sensors are preferred for their precision, easy preparation, high resolution, and quick response. In this study, a "turn on" probe has been designed to detect HOCl based on these reasons. Anthracene dye has been found to be non-fluorescent due to PET when derivatized with phosphorus. In the presence of HOCl, it was determined that the phosphorus was oxidized, inhibiting PET and causing fluorescent radiation. The aim of this thesis is to examine the spectroscopic analysis of the probe which is developed as sensitive to HOCl in various ways and to display the presence of HOCl in the living cell.Master Thesis Design and Synthesis of Bodipy Based Phosgene Sensor(Izmir Institute of Technology, 2018) Sayar, Melike; Emrullahoğlu, MustafaPhosgene was used in World War I as a chemical warfare agent and now, it is used as only a chemical intermediate in the industrial field according to laws. Because of the result of exposure to phosgene, its detection plays a significant role to protect civilians against terrorist attacks, and also to warn people if there would be any leakage in industrial facilities. To determine the phosgene, there are several methods like gas chromatography, which has several disadvantages such as poor portability and sensitivity and high cost or requiring of sophisticated procedures. However, fluorescence analysis has high sensitivity, resolution, and simplicity which provides real-time visual detection of analytes. For this thesis, boron-dipyrromethene (BODIPY) dye was used as the signal reporter by synthesizing the new BODIPY derivative, to benefit from its outstanding photophysical properties. In addition to that, as the main purpose of this thesis, this is the first time an o-aminobenzyl amine group was used due to be the phosgene-specific reactive motif for research in phosgene sensing which is an investigation of photophysical properties of designed BODIPY derivative in the absence and presence of phosgene.Master Thesis Adhesion of Dopa Functionalized Gels To Spin Labeled Surfaces(Izmir Institute of Technology, 2017) Göksel, Yaman; Akdoğan, Yaşar; Emrullahoğlu, MustafaThis study investigates the force free adhesive properties of synthetic polymer in aqueous media using electron paramagnetic resonance (EPR) spectroscopy. Due to poor performance of commercial adhesives in wet environments, scientists are interested in different types of adhesives to overcome this difficulty. On this context, mussels attract attention because of their versatile properties to adhere different types of surfaces from rocks to ship hulls underwater. Adhesion occurs when mussel secretes mussel foot proteins (MFPs) in order to form threads and plaques. Seven types of MFPs are unique in plaque contains high amount of L-3,4-dihydroxyphenylalanine (DOPA) amino acid which is reputed to be responsible for adhesion. In this research, branched polyethylene glycol (PEG) based polymers functionalized with DOPA were synthesized and their force-free adhesive properties to hydrophobic polystyrene and hydrophilic silica nanobeads were investigated in solution. These nanobead surfaces were conjugated with spin label molecules to probe adhesion dynamics using EPR spectroscopy. In addition, gel forms of polymers obtained using NaIO4, FeCl3 and Cr2O7 were used as adhesive materials for EPR measurements. All of these adhesive materials showed adhesion to spin labeled polystyrene (SL-PS) surface. However, non-DOPA containing PEG showed no indication of adhesion thus, demonstrating the importance of DOPA in wet adhesion. In addition, EPR results showed that DOPA based PEG polymers were unable to adhere to spin labeled silica (SL-SiO2) surface. This behavior was attributed to hydration layers around silica nanobeads. These layers formed around hydrophilic SiO2 surface prevent interaction between nanobead surface and polymeric material.Master Thesis Desing and Synthesis of Fluorescein Based Gold Ion Sensors(Izmir Institute of Technology, 2016) Çetintaş, Ceyla; Emrullahoğlu, MustafaGold has been a part of people’s lives for ages and is used as money, goods and jewellery. In recent years, gold has played a key role in chemistry, medicine and biology. Since the 1970s, gold has been extensively used as a catalyst in several chemical transformations. Due to its high biocompatibility, functionalized gold nanoparticles have been extensively employed as drug and gene delivery systems, biosensors and bio-imaging materials. However, gold complexes can become toxic to the human body by interacting with biomolecules such as DNA and enzymes. Therefore, detection of trace amounts of gold species is an important issue and can be achieved via spectroscopic methods such as atomic absorption spectroscopy, atomic emission spectroscopy and inductively coupled plasma spectrometry. However, these analytical methods require complicated sample preparation steps and sophisticated instrumentation. In contrast to these extremely expensive and time-consuming methods, fluorogenic or chromogenic methods, which provide high analyte sensitivity and selectivity, can serve as good alternatives for detecting gold species. To develop new probes for the detection of Au3+ ions, we focused on the design of new fluorescein-based probes that are soluble in aqueous media. We aimed to investigate the in vivo activity of these fluorescent probes. In the proposed detection system, gold ions are expected to mediate a chemical reaction through coordination to an alkyne moiety that results in a ring opening reaction to yield a highly fluorescent derivative.Master Thesis Hydrothermal Treatment of Biomass in Hot-Pressurized Water(Izmir Institute of Technology, 2015) Dadenov, Saken; Yüksel Özşen, Aslı; Emrullahoğlu, MustafaThe aim of this study is to observe conversion of cellulose, which is the main compound of biomass, into its building-block chemicals in hot-pressured water as reaction medium with no addition of organic solvents. Water in liquid state under temperature and pressure above boiling point and below the critical point (374. 15 ºC and 22.1 MPa) is called as hot-pressurized water (or sub-critical water). Nowadays the biomass has great attention across the World as renewable source of energy, at the background of the quickly growing energy demand, since it is widely available and cheap. This technology is totally environmentally friendly and uses water as a reaction medium. As well known, since plant biomass contains up to 50% cellulose, it was decided to use it as a model compound in this study. Decomposition of cellulose leads to formation of various compounds. Among them levulinic acid is the most attractive chemical. Moreover, this acid marked as “Top 12 Building Blocks” of most perspective chemicals and obtaining from biomass by hydrothermal treatment is not widely studied. During this study, different reaction parameters such as temperature, pressure, reaction time and external oxidizer addition were studied to clarify their effects on cellulose decomposition and product yields to achieve the highest selectivity of the desired product. Addition of H2SO4 led to increase cellulose conversion up to 73% at 200 oC with a H2SO4 concentration of 125 mM at 60 min reaction time. Under same conditions, the yield of levulinic acid was successfully achieved to 38% after 60 min.Master Thesis The Design and Synthesis of Fluorescent Chemosensors for the Detection of Gold and Mercury Metal Species(Izmir Institute of Technology, 2015) Cantürk, Ceren; Emrullahoğlu, MustafaThis study describes the design, synthesis and spectral behaviour of a fluorescent molecular sensor which is able to recognize Hg2+ and Au3+ ions via different emission modes. Determination of identity and amount of heavy metal ions has crucial importance for scientific researches. Detection of trace metal ions can be achieved by classical spectroscopic methods such as atomic absorption and atomic emission spectroscopy and inductively-coupled plasma spectrometry. In contrast to these highly expensive and time consuming methods, fluorogenic or chromogenic methods provide an alternative way for the detection of these species. There are many organic molecules that act as signaling unit for fluorogenic sensing strategy such as rhodamine, fluorescein, coumarin and BODIPY derivatives. Among these, BODIPY fluorophore was chosen for this work as a signal reporter due to its unique properties. In this research, the detection of Hg(II) and Au(III) ions was recognized in two distinct fluorescence changes: one resulting from a reversible Hg2+/sensor complex formation, the other an irreversible Au3+-mediated hydrolysis reaction. The minimum amount of Au(III) and Hg(II) ions detectable in aqueous solution was determined to be 128 nM and 160 nM, respectively. The capacity of the developed probe for imaging was studied in living cells. The investigation showed that the probe can be used efficiently for in vitro imaging of Au3+ and Hg2+ species.