Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis The Rational Design of a Novel Biocatalyst Using the Heme-Nitric Oxide/Oxygen Binding Protein(Izmir Institute of Technology, 2017) Aggrey-Fynn, Joana Efua; Meşe Özçivici, GülistanRecent advances in recombinant DNA technology and protein design have led to the application of biocatalysis as an alternative to chemical catalysis in the synthesis of enantiopure products due to high regio- and enantioselectivity. Hemeproteins are proteins with a heme prosthetic group that play diverse roles in biological systems, making them good candidates for biocatalysis. The Heme-nitric oxide/oxygen binding (H-NOX) protein was identified by homology to the soluble guanylate cyclases. Here, the H-NOX domain from the methyl-accepting chemotaxis protein, Thermoanaerobacter tencogenesis (TtH-NOX), was tuned into a biocatalyst using rational design. Four variants of TtH-NOX were cloned, purified and characterized. Each variant was then tested for their catalase and peroxidase activities. The wild type TtH-NOX inefficiently catalyzed the hydrogen peroxide decomposition (catalase activity) and 2,2’-azino-bis(3- ethylbenzthiazoline-6-sulfonic acid (ABTS) oxidation (peroxidase activity). However, the Y140H mutant exhibited an efficient five-fold increase in catalase and peroxidase activities as compared to the wild type. The other mutants, H102Y, H102C and Y140A TtH-NOX, were not good catalysts for both reactions. Therefore, the mutations resulted in changes in reaction rates and electronic properties of the heme group. The mutations affected the molecular mechanism of the hemeprotein, showing that both the proximal and distal pocket residues are vital for catalysis. However, the mutation of the distal tyrosine to histidine of TtH-NOX has significantly improved its catalytic activities. These observations contribute to the understanding of the physiological roles of hemeproteins. This project could also lead to discovery of novel biocatalysts and aid in the design of future biocatalysts.Master Thesis Electrical Surface Modification and Characterization of Metallic Thin Films Using Scanning Probe Microscope (spm) Nanolithography Method(Izmir Institute of Technology, 2009) Büyükköse, Serkan; Okur, SalihThis thesis focuses on local oxidation of metallic thin films using atomic force microscopy (AFM). The primary aim of this thesis is to investigate the growth kinetics of oxide forms of these metallic materials and characterize the resulted oxide structures. In this study, tantalum, hafnium and zirconium thin films were used to be oxidized via AFM. During this work, metallic thin films were grown on Si and SiOx substrates with DC magnetron sputtering method. Thin films were characterized via x-ray diffraction, scanning electron microscopy and atomic force microscopy. Oxidation experiments were performed under different environmental conditions to explore the effect of influential parameters; such as bias voltage, oxidation time and relative humidity, and line shape oxide structures were created on metallic films. Dimensional analysis of created oxide structures was carried out measuring height and line-width of oxide lines as a function of applied voltage, oxidation time and relative humidity. In addition to the dimensional analysis, electrical characterization of metal-oxides was performed via AFM electrical characterization methods which are two terminal I-V measurements, electric force microscopy and spreading resistance measurements. At the end of the thesis, the capability of this method to create lateral metal-oxide-metal junction was shown oxidizing a tantalum stripe and performing in-situ resistance measurement. Patterning of tantalum stripes was accomplished by standard photolithography process and lift-off technique.Master Thesis Physiological and Biochemical Characterization of Drought Tolerance in Chickpea(Izmir Institute of Technology, 2012) Keskin, Hilal; Frary, AnneChickpea (Cicer arietinum cv. Gokce.) is an agronomically and economically significant plant for Turkey. It is successfully grown under severe drought conditions which limit the growth of other plants. It is generally affected by terminal drought which causes retardation of flowering and decreases yield in Mediterranean and subtropical climates. The aim of this study was to determine significant factors which can be used to identify chickpea plant tolerance to drought stress. With this objective we assessed physiological (fresh and dry weight, relative and real water content) and biochemical (enzymatic and non-enzymatic antioxidants, malondialdehyde, total protein and phytohormone contents) parameters which were used to measure the impact of drought on chickpea. To determine drought's effects, we collected stressed (drought treated) and control (non drought treated) samples from the chickpea cultivar Gokce. Results showed that both fresh and dry weights of plants increased while real and relative water contents of plants decreased under drought stress. There was an increase in both malondialdehyde (MDA) and total protein contents under drought stress. Furthermore, glutathione reductase (GR) and catalese (CAT) enzyme activity increased in drought treated plants whereas guaiacol peroxidase (POD) and superoxide dismutase (SOD) enzyme activity decreased. Moreover, contents of indole acetic acid (IAA) and abscisic acid (ABA) increased in all tissue parts while contents of salicylic acid (SA), gibberellic acid (GA) and jasmonic acid (JA) increased in specific plant tissue parts during drought treatment. In conclusion it is obvious that all of these characters play essential roles in the drought tolerance of plants.Master Thesis The Production of Thymoquinone From Thymol and Carvacrol by Using Zeolite Catalysts(Izmir Institute of Technology, 2005) Güneş, Alev; Bayraktar, OğuzIn this thesis study, by using general flexible ligand method, Cr(III), Fe(III),Bi(III), Ni(II) and Zn(II) complexes of N,Nbis(salicylidene)propane-1,3-diamine (H2salpn) encapsulated in NaY-zeolite were prepared. All catalyst were characterized by Fourier transform infrared (FT-IR), X-ray diffraction (XRD) and Scanning electron microscopy (SEM) analyses to confirm the complex encapsulation. Activities of all prepared catalysts for the decomposition of hydrogen peroxide and oxidation of carvacrol were tested. Leaching test or heterogeneity test was also performed. The performances of all catalysts were compared based on the leaching test results and carvacrol conversion. Thymohydroquinone and benzoquinones were observed as by-products at high conversions of carvacrol. No product was formed in the absence of a catalyst. Fe(salpn)-NaY catalyst has shown the highest carvacrol conversion of 27.6% with a yield of 22.0% which was followed by Cr(salpn)-NaY catalyst with 23.5% carvacrol conversion with a yield of 17.6%. Other catalysts have shown relatively lower performances in terms of carvacrol conversion and leaching. The Cr(salpn)-NaY catalyst was found to be a more efficient catalyst than others based on leaching and activity tests. Selected catalyst was extra characterized by Brunauer Emmett and Teller (BET) and Thermal gravimetric (TGA) analyses. With selected catalyst Cr (salpn)-NaY, temperature, catalyst amount, reactant carvacrol to hydrogen peroxide molar ratio effects were investigated in carvacrol oxidation reactions. Increasing the temperature from 40 to 60C caused the increment of thymoquinone yield from 6.2 to 16.0%. In addition to that the yield of thymoquinone was increased from 7.4 to 20.7% by increasing catalyst amount from 0.05 to 0.2 g. And also thymoquione yield was increased from 3.7 to 23.0% by decreasing carvacrol to hydrogen peroxide molar ratio from 1 to 3. Moreover, Cr (salpn)-Y catalyst was also tested in thymol and essential oil oxidation reactions.Master Thesis Oxidation of Ethanol and Carbon Monoxide on Alumina-Supported Metal/Metal Oxide Xerogel Catalysts(Izmir Institute of Technology, 2011) Ateş, Selcan; Şeker, ErolThe main goal of the study is to investigate the effect of metal type, metal oxide type and metal/oxide loading on the conversion as a function of temperature for the complete combustion of ethanol and CO in air over single step sol-gel made Al2O3 supported metal and mixed metal oxides. Two types of catalysts, Pt/Al2O3 (1, 2, and 3 % Pt loaded) and CuO-Mn2O3/Al2O3, with Cu/Mn molar ratio of 1:1, 5:1 and 12:1, and 50, 70, and 90% metal loading, were synthesized by impregnation and single step sol-gel methods, respectively. In addition, by synthesizing CuO/Al2O3, Mn2O3/Al2O3 and Pd-Mn2O3/Al2O3, the catalytic activity relationship between metal and metal oxides were clarified. Characterization of the samples was performed by XRD, BET, and FT-IR techniques and it was observed that among the metal oxide catalysts, CuO-Mn2O3/Al2O3 (70 wt%; (Cu/Mn)molar=1) showed the highest activity due to the formation of Cu1.5Mn1.5O4 phase while 3% Pt loaded alumina was the catalyst demonstrated the highest catalytic activity among the noble metal catalysts. Also, Pd addition enhanced the activity of metal oxide catalyst by lowering the temperature at which ~99% ethanol conversion was obtained. Moreover, deactivation of CuO-Mn2O3/Al2O3 mixed oxides was observed due to the irreversible adsorption of CO2 on catalyst surface at low temperatures. Except for Pt containing catalysts, the catalysts that showed high catalytic activity in ethanol oxidation was also tested for CO oxidation and CO2 formation was detected qualitatively at varying operating temperatures.Master Thesis Effects of Dimethyl Ether on N-Butane Oxidation(Izmir Institute of Technology, 2011) Bekat, Tuğçe; İnal, FikretEffects of dimethyl ether on the oxidation of n-butane were investigated using Detailed Chemical Kinetic Modeling approach. Oxidation process was carried out in a tubular reactor under laminar flow conditions. The formations of various oxidation products, especially toxic species were investigated for the addition of dimethyl ether in different mole fractions to n-butane. Pure dimethyl ether oxidation was also investigated for comparison. Pure dimethyl ether oxidation resulted in lower mole fractions of carbon monoxide, methane, acetaldehyde and aromatic species, but higher mole fractions of formaldehyde when compared to pure n-butane oxidation. The addition of dimethyl ether to n-butane in different mole fractions was observed to decrease mole fractions of acetaldehyde and aromatic species and increase the mole fraction of formaldehyde, while other toxic species investigated were not affected significantly. The effects of three important process parameters on the formations of oxidation products were also investigated. Inlet temperatures between 500 and 1700 K, pressures of 1 and 5 atm, and equivalence ratios of 2.6 and 3.0 were studied. Increasing pressure and equivalence ratio were observed to increase the mole fractions of toxic species in general. The effect of temperature was more complicated depending on the species and the temperature interval. Reaction path analysis indicated that the most important precursors playing role in the formation of the first ring benzene were acetylene, ethylene, propargyl, allene, allyl, propene and fulvene during n-butane/dimethyl ether oxidation. Finally, a skeletal chemical kinetic mechanism was developed and validated for the oxidation of n-butane/dimethyl ether mixture.