Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis A Computational Chemistry Study on the Interactions Between Hydrogenated Borophene and Amino Acids(Izmir Institute of Technology, 2022) Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn 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) Eroğlu, Ahmet Emin; Eroğlu, Ahmet Emin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyThree 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 Investigation of the Proteins of Leishmania Tropica Causing Viscerotropism in Humans Using Mass Spectrometry(Izmir Institute of Technology, 2022) Yalçın, Talat; Yalçın, Talat; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyLeishmaniasis is a neglected tropical disease in 98 countries and five continents worldwide. The most prevalent forms of this parasitic disease are Cutaneous, Mucocutaneous, and Visceral Leishmaniasis. While Cutaneous Leishmaniasis causes disfiguring skin conditions and lesions, Mucocutaneous Leishmaniasis damages the mucosal tissues of the mouth, nose, and throat. The visceral form of Leishmaniasis causes weight loss, fever, diarrhea, lymph nodes, and spleen or liver enlargement. Today, Leishmania tropica, one of the strains of the Leishmania parasite, no longer causes only Cutaneous Leishmaniasis (CL) but also Visceral Leishmaniasis (VL). The reason for this visceralism in L. tropica is not fully understood. Mass spectrometry has a vital place in proteomic analyses; it provides information about expression levels and the identification of proteins. In this study, the proteins of L. tropica causing CL and CL are analyzed using the mass spectrometric shotgun method. Off-line HPLC separation followed by LC-MS/MS analyses are performed, and differential proteins between CL and VL isolates of L. tropica are determined. Results indicate that among the differentially abundant proteins between two sample groups, paraflagellar rod proteins, elongation factor 1-alpha protein, and surface antigen proteins might play a role in avoiding immune recognition. Also, proteins with peroxidoxin function, cytochrome b5, and endoribonuclease might help parasite survival in macrophages. And finally, thiol-specific antioxidant protein may have a role in viscerotropism in L. tropica.Master Thesis Synthesis and Characterization of High Nickel Content Cathode Materials for High Performance and Capacity Reach in Li-Ion Batteries(Izmir Institute of Technology, 2022) Karabudak, Engin; Karabudak, Engin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyDue to their high energy density, low self-discharge properties, nearly negligible memory effect, high open-circuit voltage, and extended service life, lithium-ion batteries continue to gain interest as a promising energy storage technology. In the automotive industry, high-energy lithium-ion batteries have become the preferred power source for electric vehicles and hybrid electric vehicles in recent years. With the development of lithium-ion battery technology, several materials have been used into the cathodes and anodes in order to improve performance. LiNiCoAlO4, LiMn2O4, LiNiMnCoO4, Li4Ti5O12 and LiFePO4are five lithium-ion batteries that are commonly utilized in commercial EVs today. NMC cathode material is one of the most effective lithium-ion battery materials for balancing specific qualities. The battery cathode of NMC is strengthened with a specific ratio of three synthetic components (Nickel, Manganese and Cobalt). Depending on the proportions of these three chemical constituents, battery performance can vary. Synthesis, characterisation, and electrochemical studies of cathode materials with a high Nickel content were performed in this project in an effort to boost the specific capacity and durability of Li-ion batteries. In these preliminary studies, the synthesis and characterization of Ni(OH)2 structures, which serve as a starting material for the synthesis of cathode materials with a high Nickel content, was also a goal. In the research, the spherical Ni(OH)2 structure was effectively synthesized, and excellent electrochemical results were achieved. SEM and XRD analyses were performed on the resulting products.Master Thesis Molecular Dynamics Simulations of a Cationic Thiophene Oligomer and a Nucleotide Complex(Izmir Institute of Technology, 2022) Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn 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 Studies Toward the Synthesis of Novel Mdm2 Inhibitor Candidates(Izmir Institute of Technology, 2018) Dilek, Fikrican; Çağır, Ali; Çağır, Ali; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyProtein protein interactions are valuable targets to discover novel anticancer agents. One of these is the p53-MDM2 interaction. In one of these interaction MDM2 protein inhibits p53 protein and may cause cancer. New drugs that inhibit this interaction are important for the treatment of cancer. One class of these anticancer agents are morpholinone derivative. In this study, it is aimed to synthesize new morpholinone derivatives. (R)-2-amino-2-(4-chlorophenyl)acetic acid was used as starting material for the synthesis. The first step was a trityl protection of amine with trityl chloride. Trityl protected amino acid was first reduced to N-Trt amino alcohol with LiAlH4 then oxidized to aldehyde by using Dess-Martin periodinane. The resulting aldehyde was reacted with 3-chlorophenylmagnesium bromide. This part of the synthesis was performed successfully. Then addition of methyl fumarate to this Grignard product was studied by a coupling reagents such as HATU. All attempts were failed. Then trityl group was removed by TFA and successfully coupled with methyl fumarate by using HATU. All cyclization reactions in the presence of a base like hydroxide, alkoxide or NaH to form morpholinone skeleton was failed. The cyclization reaction with the potassim carbonate in alcohol was successful and the morpholinone skeleton was formed.Master Thesis Colloidal Plexcitonic Nanocrystals(Izmir Institute of Technology, 2022) Yalçın, Şerife; Yalçın, Şerife Hanım; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyNoble metal nanocrystals, especially gold and silver, which have attracted a great deal of attention due to the supporting of surface plasmon polaritons (SPPs), have been extensively investigated and studied. With recent developments in colloid chemistry, synthesis of noble metal nanocrystals with tunable optical properties in the visible region of the electromagnetic spectrum has become easier. Until now, noble metal nanocrystals (NPs) synthesized by using various synthetic methods, have a variety of shapes, such as bipyramid, rod, disk, prism, and ring, etc. In the strong coupling regime, SPPs supported by metal nanocrystals interact strongly with excitons of organic dyes, semiconducting quantum dots (carbon or perovskite quantum dots) to generate a new hybrid optical mode called plexciton (plasmon-exciton). Plexcitonic nanocrystals have received interest owing to their ease of synthesis, scalability, and ability to provide sub-wavelength confinement of incident light and offer promising applications. Plasmon–exciton interaction at nanoscale dimension can be improved by generating new plexcitonic nanoparticles with tunable optical properties, which may be utilized in critical applications such as nanolasers, sensors, nano-optics, solar cells, and light emitting diodes. Therefore, there has been a tremendous amount of interest in the synthesis of new plexcitonic nanocrystals having excellent optical and chemical properties. The main goal of this thesis is to synthesize new plexcitonic nanoparticles with tunable optical properties in the visible spectrum: (i) synthesis of different shaped colloidal monometallic and bimetallic nanocrystals, (ii) synthesis of new colloidal plexcitonic nanocrystals, (iii) synthesis of carbon quantum dots (CDs), (iv) coupling of excitons of CDs and SPPs on the silver thin film.Master Thesis Iridium Catalyzed Boration of Dihydroisoquinoline Derivatives(Izmir Institute of Technology, 2022) Artok, Levent; Artok, Levent; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyTransition 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 Development of Multi Metal Oxide Photo-Electrodes for Energy Applications(Izmir Institute of Technology, 2020) Karabudak, Engin; Karabudak, Engin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyWater splitting via artificial photosynthesis uses only sunlight and water to produce hydrogen and oxygen. Hydrogen can be used as a green energy source. To be able this reaction to occur there is a catalyst needed as reaction center. Platinum and Iridium are the state-of-art catalyst used for water splitting reactions. The goal of this study is to develop an earth abundant, highly stable and efficient catalyst as an alternative to noble metal catalysts. For this purpose, ABO3 type perovskites was chosen to study for their abundancy and proven electrochemical efficiencies. BSCF was chosen as the starting point of this study because it is known for its great catalytic activity compared to state-of-art catalysts such as Iridium Oxide. To enhance the stability and catalytic activity of synthesized perovskite oxides, several foreign atoms (dopants) were introduced to their structure from B-site. Each perovskite was synthesized by the EDTA-Citrate complexing Sol-Gel method. Also, for dopants, cost-efficient and electron conductive elements was chosen in each study. As HER catalysts, manganese, zinc, and copper were introduced to BSCF structure as dopant, while for OER, silver was used as a dopant. In this study, catalytic activities and stabilities were tested by electrochemical methods. All electrochemical measurements were performed in alkaline media by three-electrode configurations. Perovskite oxides were prepared by the coating of their inks on Ni foam substrates by drop coating for HER and OER activity measurements by electrochemical methods. For the bulk and surface characterization of synthesized perovskite oxide powders, SEM, XRD, XPS, and BET analysis was performed.Master Thesis Synthesis of Polythiophene-Polyurethane Soft Nanoparticles for Bioimaging Applications(Izmir Institute of Technology, 2020) Karabacak, Soner; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, synthesis of fluorescent polythiophene and polyurethane soft nanoparticles carrying them was carried out for bioimaging applications. Conjugated polythiophenes and polyurethane derivatives were obtained by changing their structural properties such as size, charge, and group, and were characterized by nuclear magnetic resonance, infrared spectroscopy, dynamic functional light scattering, fluorescent microscopy, methods. In the study, changing characteristics of polyurethane nanoparticle materials were investigated depending on the synthesis conditions. Synthesis of polyurethane nanoparticles was carried out by miniemulsion polymerization technique and synthesized as nanosphere to be more controllable on nanoparticle size, morphology and stability. The sizes of the polyurethane nanospheres varied in the range from 10 to 500 nm. Polyelectrolyte-polyelectrolyte complexation was investigated using cationic polythiophene-anionic polythiophene for use in bioimaging applications. Synthesized conjugated polythiophenes are divided into two groups as anionic and cationic polythiophenes. In this thesis, three kinds of cationic polythiophene synthesis are included, but poly (1,4-dimethyl-1- (3- ((4-methylthiophene-3-yl) oxy) propyl) piperazine-1-ium bromide) (PT4) was used as cationic conjugated polythiophene in the studies. Anionic polythiophene acetic acid (PTAA) was used as a counter-charged polythiophene. In addition to these studies, dual-mode imaging agents were prepared, consisting of PTAA as fluorescent agent and gadolinium metals as magnetic agent. The bioimaging studies continued under conditions imitating biological systems, and the potential of the proposed bioimaging agents was investigated.