Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Lyotropic Liquid Crystal Templated Synthesis of Single-Crystalline Gold Microplates and Transparent Conductive Reduced Graphene Oxide Thin Films(01. Izmir Institute of Technology, 2023) Akkuş, Betül; Mert Balcı, FadimeSurfactants organize to form various mesophases of lyotropic liquid crystal (LLC) in the presence of water. In the literature, some acids, salts, and ionic liquids have also been used to form ordered LLC mesophases. In this thesis, two dimensional (2D) single-crystalline gold (Au) nano- and microplates and reduced graphene oxide (RGO) thin films have been synthesized using LLC mesophases. Stable LLC mesophases have been formed using 10-lauryl ether (C12EO10), an oligo-type surfactant, and sulfuric acid (H2SO4), a strong acid. Au plates with various anisotropic structures, such as triangular, truncated triangular, hexagonal, and gear-like, have been synthesized by a photochemical method in the presence of LLC mesophase. Most importantly, Au plates up to 39 µm in width have been obtained in the confined space of the LLC medium. The thickness of the obtained Au plates varies from 50 nm to 150 nm. The size and/or morphology of Au products synthesized in LLC medium depends on the power of the light source, the irradiation time, the amount of Au precursor added, the addition of different capping agents, and various inorganic salts. Additionally, spin-coated RGO thin films have been synthesized using the LLC mesophase for use as a transparent and conductive electrode in various electrochemical devices. The LLC mesophase has improved the sheet resistance values of RGO thin films. RGO thin films with a sheet resistance of 31 kΩ/sq and an optical transmittance of 92% at 550 nm have been achieved at the high thermal annealing temperature under an inert atmosphere.Master Thesis A Computational Chemistry Study on the Interactions Between Hydrogenated Borophene and Amino Acids(Izmir Institute of Technology, 2022) Bozkurt, Yağmur; Elmacı Irmak, NuranIn this work, the adsorption behavior of hydrogenated borophene to amino acids was examined to provide its geometric and electronic structures information and to check whether hydrogenated borophenes’ potential can be used in new biosensor devices for amino acids or not. In the aspect of this thesis adsorption of 4 amino acids from different types of amino acid classes (acidic, basic, nonpolar, and polar) on hydrogenated borophene surfaces has been studied by computational chemistry methods. Electronic and geometric structures of B36H6 and its complexes with glycine, tyrosine, aspartic acid, and histidine were obtained by DFT calculations at B3LYP-D2 / 6-311G** level of theory. In the energetically most favorable configurations of complexes, amino acids approaching from the bottom of the B36H6 surface with a horizontal orientation (exception for histidine complexes) of amino acid was observed. The most reactive parts of the B36 structure (edges) have been stabilized with hydrogenation, the whole boron cluster became more stable and adsorption ability has fallen. It was found that hydrogenated borophene has indistinguishable electronic responses for each the amino acids studied in this thesis since the complexes exhibited nearly the same band gap. Thus, hydrogenated borophene shows no sensor ability to GLY, TYR, ASP, and HIS.Master Thesis Preparation of Molecularly Imprinted Polymers for the Solid Phase Extraction of Pyridoxal 5'-phosphate Prior To Hplc Determination(Izmir Institute of Technology, 2022) Özyurt, Ömer; Eroğlu, Ahmet EminThree different sorbent materials were prepared for solid phase extraction of pyridoxal phosphate (PLP), namely, carbon sphere based molecularly imprinted chitosan polymer (MICP), magnetite based molecularly imprinted chitosan polymer (MMICP) and silica (sol-gel) based molecularly imprinted polymer (IMIP). The sorbents were characterized by FT-IR, SEM, EDX, XRD, and TGA. The characterization data have shown that, the sorbents were relatively homogeneous, had very fast sorption kinetics and quantitative sorption over a wide range of analyte concentrations (1.0-100.0 mg/L). All the sorbents were found to be selective to PLP in presence of similar compounds; namely, pyridoxamine, nicotinic acid (vitamin B3), pyridoxal and 4-pyridoxic acid. Sorption parameters for each sorbent were optimized. The optimum sorbent amount for 10.0 mL sample volume was found to be 5.0 mg for MICP and 10.0 mg for both MMICP and IMIP. A shaking duration of 30 min was employed in sorption experiments. Among the potential eluents, acetic acid solution (2%, v/v) has shown the best desorption performance for all three sorbents. Method validation was investigated via spike recovery tests on water (ultra-pure, bottled and tap) and artificial serum samples. The recoveries obtained with water samples were greater than 96%, 92%, and 91% for MICP, MMICP, and IMIP, respectively. These results show the potential application of the methodologies for samples with relatively simple matrix. High recoveries (greater than 80%) were also obtained with artificial serum samples, whereas the use of matrix-matched calibration or internal standardization is suggested together with protein precipitation for biological samples with high protein content.Master Thesis Molecular Dynamics Simulations of a Cationic Thiophene Oligomer and a Nucleotide Complex(Izmir Institute of Technology, 2022) Demirci, Fethi Can; Elmacı Irmak, Nuran; Elmacı Irmak, NuranIn this thesis, parametrization of cationic polythiophene (CPT) and molecular dynamics (MD) simulations of CPT with DNA complexes were performed to understand the behaviors of the CPT with DNA complex and CPT DNA complexes in different salt solutions (NaCl, KCl, MgCl2, CaCl2). The results of MD simulations show that the end-to-end distance of CPT is affected by both the type sequences and length of the DNA, and the addition of 20T elongates the backbone of the oligomer while 20A and MIX ssDNAs almost have no significant effect. When the complementary DNA chain is added to the duplex solutions, the backbone structure of the oligomer becomes very similar to its structure without ssDNAs since Ree values in both cases are almost the same. It was observed that the CPT-20A complex has a more random coil form than the CPT-20T complex. According to the interaction analysis of MD simulations, all the CPT-DNA duplexes except CPT-20A prefer electrostatic interaction rather than π-cation interaction. DNAs like to interact with the oligomer's side chain rather than its backbone in all systems. Thus, electrostatic interactions and the side chain of oligomer play an important role in the structure of duplexes with thymine which gets the highest response from the oligomer. The addition of 20T makes backbone of F0 more elongated and less compact. 20T has higher electrostatic and π-cation interactions. Thus, F0 is more sensitive to 20T than 20A and MIX.Master Thesis Iridium Catalyzed Boration of Dihydroisoquinoline Derivatives(Izmir Institute of Technology, 2022) Yazıcı, Ece; Artok, LeventTransition metal catalyzed borylation reactions have an important place in organometallic chemistry. In recent years, these reactions have been extensively investigated and have become a versatile tool in the synthesis of new organic materials. C-H bonds can be easily transformed into C-B bonds by borylation reactions. In particular, iridium-catalyzed borylation includes significant advances such as mild reaction conditions, additive-free, high efficiency and being in a single step. In this thesis, the borylation of dihydroisoquinolines with a wide range of biological properties was performed for the first time. Investigating the extent of the reaction has led to the development of optimization studies. Besides, the effects of steric and electronic factors on selectivity are also shown. In this new methodology, C3-borylated products with high regioselectivity and yield were formed with the directing effect of the acyl group. The use of AsPh3 as a ligand is critical to the product selectivity of the method. When the reagent scope was investigated, it was determined that the functional group tolerance of the reactions was quite high. Finally, borylated dihydroisoquinolines have been converted into various intermediates by application studies.Master Thesis First-Principles Investigation of Novel Single-Layers and Heterostructures of Group Iii-Iv Elements(01. Izmir Institute of Technology, 2022) Yayak, Yankı Öncü; Yıldız, Ümit HakanSince the discovery of graphene, two-dimensional materials have been the focus of interest in various branches in scientific community. Wide range of ultra-thin materials have been investigated both theoretically and experimentally such as metal chalcogenides, Xenes and h-BN. In addition to this, two-dimensional (2D) van der Waals heterojunctions have become one of the central research topics due to their wide range of possibilities. Since 2D van der Waals heterostructures are combinations of two or more ultra-thin materials with different properties, creating a heterostructure with desired optical, electrical and/or mechanical property is theoretically probable. Motivated by these, this thesis focus on the investigation of structural, vibrational and electronic properties of 2D materials and their heterostructures by means of density functional theory-based first-principle calculations. In chapter 3, single-layer Ge3N4 is shown to be both electronically and dynamically stable. Also, simulated Raman spectrum of single-layer Ge3N4 have characteristic vibrational properties. Another property of single-layer Ge3N4 is that it is a indirect band gap semiconductor and this property is uneffected by external strain. And lastly, the value of band gap varies with the applied external strain. In chapter 4, a dynamically stable single layer structure of AlAs is proposed and four possible stackings of AlAs/InSe heterobilayer were investigated. Electronic band dispersions revealed that all four stackings are direct band gap semiconductors and have type-II alignment. Moreover, simumlated raman spectra revelaed that identification of the 1T and 2H phase can be done with Raman spectroscopy. The band gap can be tuned based on the direction and magnitude of the electric field. Direct to indirect band gap transition as well as heterojunction type changes from type II to type I occurs under negative electric field.Master Thesis Fluorescent Gold Ion Sensors: Design, Synthesis and Imaging(01. Izmir Institute of Technology, 2021) Kaya, Beraat Umur; Emrullahoğlu, MustafaOf all transition metals, gold has long sustained attention owing to its unique chemical and physical properties. Beyond that, the ease of processing gold allows its use in science, industry, and in various chemical, biological, and medical applications. For example, gold is used in medicine to treat rheumatoid arthritis, asthma, cancer, and brain and skin lesions. However, the extensive use of gold compounds can adversely impact the natural environment and biological systems due to their potential toxicity. For those reasons, identifying trace amounts of gold species in solution and cell media is crucial. Unlike the detection methods of atomic absorption spectroscopy, atomic emission spectroscopy, and inductively coupled plasma spectrometry, fluorescence-based detection methods offer easy sample preparation, rapid response, high sensitivity, reproducibility, and efficiency, all at a low cost. Today, various types of fluorescent sensors selective to gold ions have been designed, typically with BODIPY, fluorescein, rhodamine, naphthalimide, and coumarin-based fluorophores. In the work for this thesis, for the first time an enyne-derived BODIPY-based sensor was designed and synthesised to identify Au3+ ions, after which photophysical changes in the presence and absence of the analyte were examined both in solutions and in cells.Master Thesis Design and Synthesis of a Bodipy Based Probe for Cadmium Ions(01. Izmir Institute of Technology, 2021) Cebeci, Miray; Emrullahoğlu, MustafaGiven the severely toxic effects of heavy metals on living systems and the environment in general, identifying and quantifying heavy metal ions in synthetic samples and in vivo are highly significant activities. One such heavy metal, cadmium, allows only a low level of tolerable exposure and can thus have fatal consequences or cause critical health problems such as ostial disorders, nephrotic syndromes, various types of cancer even in extremely low concentrations. Although several standard techniques for detecting cadmium have been used, including atomic absorption and emission spectroscopy and inductively coupled plasma mass spectrometry, all of them require complex instruments that are also expensive, time-consuming to use, and hardly portable. For that reason, sensitive, selective, less labour-intensive methods of detecting cadmium ions are greatly needed. In response, fluorogenic or chromogenic methods afford high analyte sensitivity and selectivity, easy sample preparation, and easy monitoring, all with affordable instrumentation. Against that background, this thesis reports the design, synthesis, and development of a fluorescent molecular sensor that can detect Cd2+ ions within spectroscopic behavior and living cells. In the design, based on the mechanism of intramolecular charge transfer (ICT), borondipyrromethene (BODIPY) dye was used as a signal reporter due to its unique properties, and di-(2-picolyl)amine (DPA) was chosen to represent the recognition unit. Altogether, the sensor offers rapid response, high selectivity, and high sensitivity in detecting Cd ions is reversible with the aid of CN- and can be used to efficiently image Cd2+ species in vitro.Master Thesis Design and Synthesis of a Bodipy Based Probe for Mercury Ions(01. Izmir Institute of Technology, 2021) Tütüncü, Büşra Buse; Emrullahoğlu, MustafaThe detection of heavy metal ions in living systems and aqueous environments has attracted significant attention in recent years, especially the detection of mercury, one of the most toxic heavy metals on Earth. To reduce mercury's lethal effects on the human body, animals, and marine life trace amounts of mercury species can be detected by using classical spectroscopic techniques for example atomic absorption and emission spectroscopy, high-performance liquid chromatography, and inductively coupled plasma mass spectrometry. However, because those techniques are time-consuming and expensive, fluorescence analysis, which offers high selectivity and sensitivity, has emerged as a suitable alternative for detecting mercury species. In the work presented here, a new BODIPY -based fluorescent probe functionalised with a phenylhydrazine unit was designed and synthesised for the selective and sensitive detection of mercury species. The probe's detection limit was determined to be 29 nM, and the probe could detect mercury species in living cells without any changes in cell morphology.Master Thesis Synthesis of Novel 6,7-Dihydro Derivatives(Izmir Institute of Technology, 2012) Kayar, Burcu; Çağır, AliIn last decades, biologically active natural compound (R)-goniothalamin and its derivatives received great attention from researchers. The reason for this interest is the wide range of biological properties of goniothalamin; including anti-microbial, antiprotozoan, anti-inflammatory, cytotoxic and anti-proliferative activities. The present study sets out the asymmetric large scale synthesis of α,β- unsaturated lactone derivative (R)-(+)-6-(2-Methylnaphthalen-1-yl)-5,6-dihydro-2Hpyran- 2-one. In recent studies, this linker modified analog of goniothalamin was shown to be cytotoxic against PC-3 (prostate cancer) and MCF-7 (human breast cancer) cell lines with half maximal inhibitory concentration values of 0.13 μM and 2.6 μM, respectively. The preparation of the target compound consists of three steps. First, asymmetric synthesis of homoallylic alcohol using (R)-Tol-BINAP AgF catalyst complex was performed with allyltrimethoysilane. After that, treating the chiral homoallylic alcohol with acryloylchloride in the presence of triethylamine followed by ring closing metathesis of acrylate ester using 1st generation Grubbs' catalyst finally yielded the lead compound. The large scale preparation of (R)-(+)-6-(2- Methylnaphthalen-1-yl)-5,6-dihydro-2H-pyran-2-one was achieved in order to evaluate its in-vivo anti-cancer activity in mice, and to study its mechanism of action in the cell. Additionally, synthesis of three new 7-membered β-ï § unsaturated lactone derivatives was carried out. Allylation reaction of corresponding aldehydes with allyltrimethoxysilane using CuCl-TBAT gave the racemic homoallylic alcohols. Coupling reactions of this homoallylic alcohol with 3-butenoic acid in the presence of DCC/DMAP yilded the esters. Ring closing metathesis of the related esters was studied by using 2nd generation Grubbs' catalyst.