Doktora Tezleri

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Applications of electrospun nanofibers in filtration processe
(Izmir Institute of Technology, 2013) Horzum Polat, Nesrin; Elçi, Latif
Electrospinning is a simple and versatile method to fabricate ultrathin fibrous mats from a wide variety of organic and/or inorganic materials. Since it allows fabricating fiber diameter and surface/internal structures by solution and instrumental parameters, electrospun fibers provide much enhanced functionalities, which can not be obtained by bulk materials. This thesis examines the filtration, sensing and catalytical applications associated with the remarkable features of electrospun nanofibers. The systems studied are reported herein; (i) The first part of this dissertation deals with the filtration applications of electrospun nanofibrous membranes.  Nano-sized chitosan fibers were utilized for sorption of Fe(III), Cu(II), Ag(I), and Cd(II) ions from aqueous solutions.  The surface of chitosan fibers were further functionalized by monodisperse nano zero-valent iron (nZVI) particles for the removal of inorganic arsenic species.  Sorption of radioactive U(VI) ions from aqueous systems via column sorption under continuous flow was performed using amidoximated polyacrylonitrile fibers. (ii) The second part of this dissertation presents sensing applications of ceramic fibers.  Humidity sensing properties of electrospun ZnO fiber mats were investigated by quartz crystal microbalance (QCM) method and electrical measurements.  Electrospinning technique was used as coating process for deposition of CeO2/ZnO and ZnO based nanofibers on the electrode of QCM. The fiber-coated QCM sensors were used for the detection of volatile organic compounds (VOCs). (iii) The last part of this dissertation describes an approach to fabricate hierarchically structured composite nanofibers. The nanostructured materials prepared by the simultaneous electrospinning of CeO2 and LiCoO2 precursors and SiO2 nanoparticles were used for the photocatalytic degradation of Rhodamine B.
Asymmetric synthesis of 5,6-dihydro-2H-pyran-2-one derivatives
(Izmir Institute of Technology, 2014-09) Akçok, İsmail; Çağır, Ali
α,β-unsaturated lactone derivatives are very important structural core which are isolated from nature and shown as source for several biological activities. Biologically active styryl δ-lactones are well known α,β-unsaturated-δ-lactones. Up to date, many α,β- unsaturated-δ-lactones and their analogues have been isolated and synthesized, exhibiting promising anti-proliferative properties against different cancer cell lines. In this thesis, large scale asymmetric syntheses of (R)-4’-methylklavuzon and (R)- 2’-methylklavuzon were completed successfully. Also, syntheses of heteroatom functionalized naphthyl substituted novel α,β-unsaturated-δ-lactone (5,6-dihydro-2Hpyran- 2-one) derivatives, α,β-unsaturated-γ-lactone (furan-2(5H)-one) derivatives and 7- membered α,β-unsaturated lactone (6,7-dihydro-5H-oxepin-2-one) derivatives were accomplished. Development of a method for one-pot synthesis of 6-membered α,β-unsaturated- δ-lactone was also studied, and a new vinylogous aldol addition method was developed. By this method, new α,β-unsaturated methyl esters were prepared via dienolate formation starting with methyl buten-3-oate.
Characterization and catalytic applications of hydrothermally synthesized poyoxotungstate clusters containing organic-inorganic hybrid materials
(Izmir Institute of Technology, 2019-07) Ece, Özlem; Eanes, Mehtap; Çağır, Ali
Many 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.
A comparative study of thin-film coated silicon wafer surfaces for laser-induced breakdown spectroscopic analysis of liquids
(Izmir Institute of Technology, 2021-07) Aras, Nadir; Yalçın, Şerife Hanım; Izmir Institute of Technology
Laser-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.
A computational study on the structures of protonated peptides
(Izmir Institute of Technology, 2014-07) Karaca, Sıla; Elmaci Irmak, Nuran
The reliable protein identification can be achieved by the knowledge of the structures and fragmentation mechanisms of gas-phase peptide fragment ions. Depending on the size and variety of amino acids in the peptide sequence, the probable structures of b-type fragments have been proposed as an acylium, a diketopiperazine, and an oxazolone structures. Recently, a macrocyclic structure has also been reported in the literature for larger b ions (b4 and greater). The macrocyclic structure is one of the problems for determining the correct sequence of peptides because original primary peptide structure is lost. Another problem is the unclear structure of the fragment ions depending on the peptide size and type. In such cases, the databases which are used with the MS/MS results will be insufficient to identify peptide/protein. In this thesis, the structures of peptide bn + ions having different size and type with a sequence of XAAAA, AAXAA and AAAAX (where A is Ala and X is Asn, Asp, Leu, Phe, Tyr or Cys) have been analyzed by using computational methods. The results showed that, the macrocyclic structure is more favorable than linear oxazolone structure for all b5 + ions studied in this work. The proton prefers to be on the oxygen atoms in the macrocycle while it likes to be on the nitrogen atom for the corresponding linear isomer. However, histidine containing b5 + ions do not obey this observation, for those, proton always is found on the nitrogen on the side chain of histidine. There is no significant position effect of amino acid residue for those b5 + ions, the energies of the most of the linear isomers with different position are very similar. Additionally, the proton affinity calculations have also been carried out to explain intensities of PX (where P is Pro and X is Ala, Phe, Asp, Trp or His) and AAAA fragment ions in the mass spectra. The results demonstrated that the mass spectrum consist of both PX and AAAA fragments were in competition with each other, this is explained by the proton affinity calculations.
Design and synthesis of boron-dipyrromethene (BODIPY) based fluorescent and colorimetric sensors for the detection of gold and mercury ions
(İzmir Institute of Technology, 2016-05) Üçüncü, Muhammed; Emrullahoğlu, Mustafa
The identification and quantification of heavy metal ions such as gold and mercury species in synthetic samples and living cells have crucial importance for scientific research. Even at very low concentrations, heavy metal ions can cause mortal consequences. Hence, there is a huge need for the development of new, sensitive, and selective methods to detect biologically active molecules, heavy metal ions, and anions that have significant effects on humans or animals. Up to now, trace metal analyses have been performed by classical spectroscopic methods such as atomic absorption and emission spectroscopy and inductively coupled plasma mass spectrometry. However, these methodologies require sophisticated devices and must be preceded by complicated sample preparation steps. In contrast to these time-consuming and expensive methods, fluorogenic and chromogenic methods that have high analyte sensitivity and selectivity and easy sample preparation steps and that use cheaper instrumentation have become important alternatives in recent years. There are many organic dye molecules that act as signaling units for fluorogenic-sensing strategies such as rhodamine derivatives, fluorescein, coumarin, and BODIPY. For this thesis, we chose the BODIPY core as a signal reporter unit because of such unique properties as long excitation/emission wavelengths, high molar absorption coefficients and fluorescence quantum yields, and wide pH range for the sensing event. Also, BODIPY dyes can be easily derivatized from their various positions so that they produce an important advantage over other florophore molecules. The main purpose of this thesis is to design and synthesize new BODIPY derivatives that bear highly selective and sensitive receptor units towards gold and mercury ions. In addition, to investigate the photophysical properties of designed molecules in the absence and presence of targeted metal ions in both synthetic samples and living cells.
Design and synthesis of rhodamine based fluorescent and colorimetric sensors for the detection of gold ions
(Izmir Institute of Technology, 2017-07) Karakuş, Erman; Emrullahoğlu, Mustafa
The usage of chemosensors for the detection of heavy and transition metal ions is prevalent. Because these metal ions play crucial roles in living systems and have extremely toxic effects on the environment. Among these metal ions, gold species have interesting biological properties and uses. They play important roles in biological systems and often have significant impacts on human health. For instance, gold based drugs have long been used in the treatment of rheumatoid arthritis and other autoimmune diseases. In addition, gold nanoparticles function as carriers for drugs and gene delivery systems. Gold ions, on the other hand, are potentially toxic to humans. Because of their reactive nature, ionic gold species can interact with proteins, DNA and other biomolecules and disturb a series of cellular processes, leading to serious health problems. Detection of gold ions can be performed by spectroscopic methods such as atomic absorption and atomic emission spectroscopy and inductively-coupled plasma spectrometry that required complicated sample preparation steps, and sophisticated instrumentation. In contrast to these highly expensive and time consuming methods, fluorogenic or chromogenic methods can be good alternatives for the detection of these species that provides high analyte sensitivity and selectivity, visual simplicity, instantaneous response, as well as real time monitoring. The rhodamine scaffold is an ideal template for the construction of metal ion chemosensors because they have large molar extinction coefficient, long excitation and emission wavelengths, high fluorescence quantum yields, good water solubility, and the potential for colorimetric and turn-on fluorescent detection. In this thesis work, we focus on design and synthesis of novel rhodamine based molecules for the detection of gold ions. Moreover, we investigate the photophysical properties of synthesized molecules in the absence and presence of gold ions in both synthetic samples and living cells.
Design, construction and optimization studies of a hydride generation laser-induced breakdown spectrometric system, (hg-libes), for the determination of toxic elements in aqueous samples
(Izmir Institute of Technology, 2013-05) Ünal Yeşiller, Semira; Yalçın, Şerife Hanım
In this thesis study, design, construction and optimization of a continuous flow hydride generation laser-induced breakdown spectroscopic system, HG-LIBS, for the determination toxic and environmentally important elements: arsenic, selenium, lead, antimony, tin, bismuth, germanium and tellurium, has been performed. The HG-LIBS system, which has been constructed from its commercially available components, consisted of four main parts: a laser source, a hydride generation unit, a sample/plasma cell and a detection unit. In order to maximize LIBS emission signal, some instrumental parameters such as laser energy and detector gating parameters were investigated. Some chemical parameters such as acid/reductant concentration and flow rate, carrier gas type and flow rate, presence of pre-reducing/oxidizing agent that effect hydride generation efficiency and transportation of hydrides were also studied. Under optimized conditions detection limits of 0.2 mg L-1, 1.1 mg L-1, 1.0 mg L-1, 1.3 mg L-1 and 0.2 mg L-1 were obtained for Sn, As, Sb, Pb and Ge, respectively. No analytical signal could be detected from Se and Te elements with the system developed. The applicability of the HG-LIBS system for the determination of As, Sb, Pb and Ge in aqueous environments has been tested on several real water samples including tap water, drinking water and reference river water standard. Temporal variation of electron temperature and electron density values for tin and germanium hydride plasma was determined under argon and nitrogen environment. Electron temperatures were calculated by making use of neutral atomic lines in Boltzmann equation. Plasma electron density was evaluated from the Stark-broadened line shapes of Hα line at 656.3 nm. In order to investigate the main cause of increase in germanium signal under argon environment, physical plasma parameters were evaluated in argon and nitrogen gas mixtures. With this thesis study, the applicability of the HG-LIBS system for on-line monitoring of environmental pollutants has been shown.
Development of clustering and classification strategies for the determination of geographical origin of honey by using atomic and molecular spectrometry
(Izmir Institute of Technology, 2011) Yersel, Müşerref; Özdemir, Durmuş
Honey is a natural, nutritious and healthy food produced by honeybees from the nectar of plants. The classification of honey based on geographical origin is of great interest since the quality of honey depends on its chemical composition and geographical origin. In this study, it is aimed to develop classification models using elemental and molecular composition of honey samples via atomic and molecular spectrometry. For this purpose, honey samples from different regions of Turkey were collected from producers and they were scanned with Fourier Transform infrared spectrometer equipped with attenuated total reflectance (FTIR-ATR) accessory, and fluorescence spectrophotometer (synchronous fluorescence mode and 3D excitation emission mode). Afterwards, any clustering of the samples based on their regions was investigated using principal component analysis (PCA) and hierarchical cluster analysis (HCA) and soft independent modeling of class analogies (SIMCA). Finally, inductively coupled plasma mass spectrometry was applied to determine the metal concentrations (Mg, Al, Mn, Fe, Co, Ni, Cu, Zn, Sr, Ba) in honey samples and then the same classification methods were performed to compare the results. In conclusion, molecular spectrometry gave better classification results based on geographical origin compared to the results obtained with atomic spectrometry. Molecular spectrometry is more advantageous for the classification of honey samples in the case of saving time, saving chemicals and ease of usage.
Development of colloidal alloyed nanocrystals for quantum dot based device applications
(Izmir Institute of Technology, 2018-06) Sevim Ünlütürk, Seçil; Özçelik, Serdar; Varlıklı, Canan
Quantum 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.
Development of genetic algorithm based classification and cluster analysis methods for analytical data
(Izmir Institute of Technology, 2009) Öztürk, Betül; Özdemir, Durmuş
In this study genetic algorithm based classification and clustering methods were aimed to develop for the spectral data. The developed methods were completely achieved hybridization of nature inspired algorithm (genetic algorithms, GAs) to other classification or clustering methods. The first method was genetic algorithm based principal component analysis (GAPCAD), and the second was genetic algorithm based discriminant analysis (GADA). Both methods were performed to achieve the best discrimination between the olive oil and vegetable oil samples. The classifications of samples were examined directly from their spectral data obtained from using near infrared spectrometry, Fourier transform infrared (FTIR) spectrometry, and spectrofluorometry. The GA was used to optimize the performance of classification or clustering techniques. on training set in order to maximize the correct classification of acceptable and unacceptable samples or samples of dissimilar properties and to reduce the spectral data by wavelength selection. After GA optimization the classification results of training set were controlled by validation set. Lastly, the success of both algorithms was compared to the results of PCA and SIMCA.
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, 2022-12) Meşe Sezen, Ayten Ekin; Özdemir, Durmuş
Crude 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.
Development of novel functionalized solid phase extraction (SPE) sorbents and solid phase microextraction (SPME) fiber coatings for analytical applications
(Izmir Institute of Technology, 2011) Boyacı, Ezel; Eroğlu, Ahmet Emin
In the first part of the study, amino-, mercapto- and bifunctional silica-based solid phase extraction (SPE) sorbents were developed, characterized and utilized for sorption and speciation of inorganic As(III)/As(V). Critical parameters on sorption and desorption of species were investigated. The proposed methodology was validated through the analysis of a standard reference material. The subsequent studies were concentrated on the transfer of the experience gained during the modification of silicate surface for preparation of SPE sorbents to the preparation of SPME coatings. The second part of the thesis includes the development, characterization and use of solid phase microextraction (SPME) fibers for the speciation of inorganic and organometallic arsenic compounds. SPME fiber coatings have been prepared by two routes, namely, sol-gel synthesis and nanoparticle immobilization. Fibers having amino functionality synthesized through the sol-gel process were used in the speciation of As(III), As(V), monomethyl arsonic acid (MMA) and dimethyl arsinic acid (DMA). HPLC-HGAAS or HPLC-ICPMS was used in the measurements. Speciation of arsenic compounds was also realized using SPME fibers modified with zero valent iron nanoparticles embedded into an agarose matrix. The detection of the solid phase microextracted analytes was realized by HPLC-ICPMS. Prepared fibers have shown superior extraction for arsenicals. The effect of several parameters on the extent of extraction of arsenic species; namely, solution pH, extraction time, agitation speed and ionic strength were investigated. Validity was checked via the application of the proposed methodology on real samples (tap water, bottled water and geothermal water, urine samples) and standard reference materials.
Development of novel solid phase extraction (SPE) sorbents and solid phase microextraction (SPME) fiber coatings for determination of endocrine disrupting compounds (EDCs)
(Izmir Institute of Technology, 2017-12) Demirkurt, Merve; Eroğlu, Ahmet Emin
This thesis is composed of four chapters. In the first part of the study, molecularly imprinted polymer (MIP) was prepared as SPE sorbent for selective determination of BPA prior to HPLC DAD analysis. The adsorption capacity and selectivity of imprinted polymers were investigated. To improve the MISPE method, the parameters including pH of sample solution, adsorption time, amount of sorbent, desorption solvent were examined. The extraction efficiency of BPA imprinted polymer was investigated by using the spiked samples of ultrapure, drinking and tap water. The second part of the thesis was about determination of estrogen hormones. For this purpose, amino modified silica and molecular imprinted silica were prepared and their SPE performances were compared. The proposed methodology was validated through the analysis of real water samples. The preparation of MIP nanoparticles encapsulated in electrospun polystyrene fibers as the SPME fiber coating was the subject of the third part of the thesis. Developed fibers were used for selective extraction and analysis of parabens in water samples. The optimization parameters affecting the extraction and desorption of parabens were investigated. The validity of the proposed method was verified via spike recovery tests. Finally, fibers having amino functionality prepared by the sol-gel based electrospinning process were used for determination of BPA. The effect of solution pH, extraction time, agitation speed and ionic strength on the extraction performance were investigated. Validity was checked via the application of the proposed methodology on real samples.
Development of novel sorbents for the determination of mercury in waters by cold vaporatomic absorption spectrometry
(Izmir Institute of Technology, 2011) Erdem, Arzu; Eroğlu, Ahmet Emin
Mercury is one of the most toxic heavy metal ions to all living organisms. A novel solid support with selective functional groups was developed for mercury sorption from waters prior to its determination by cold vapor atomic absorption spectrometry. The support was prepared by immobilization of several functional groups (amino, mercapto, etc.) on silica. Among the sorbents developed, 3-MPTMS-silica has been shown to be an efficient material for the sorption of mercury species due to its selectivity. Sorption experiments were performed to optimize the necessary parameters and conclusively, sorption pH of 7.0, reaction temperature of 25 oC, sorbent amount of 10.0 mg and shaking time of 30 min were applied throughout the study. Various mineral acids, organic acids, oxidizing agents and sulfur- or nitrogen-containing ligands were tried for the elution of mercury species and 2.0 M TGA was found to offer the maximum desorption. The validity of the method was checked via spike sorption experiments with four different types of water; namely, ultra pure, bottled drinking, tap and sea water. The method worked efficiently (>95%) for all types of water. Permeable reactive barriers, such as zero-valent iron and zero-valent copper were also applied for the removal of mercury species. Similar optimization parameters with 3-MPTMS-silica were also obtained for both sorbents. The method validation was also performed and although sea water is a heavy matrix, high uptake results were achieved for both sorbents.
Development of solid phase microextraction (SPME) fibers for various analytical applications: (I) Selenium speciation in waters. (II) Separation and determination of triclosan and triclocarban in waters
(İzmir Institute of Technology, 2016-07) Ziyanak, Esen; Eroğlu, Ahmet Emin
In the first part of this study, four selenium species namely selenite, selenate, selenomethionine and selenocystine in water samples were tried to be separated using single solid phase microextraction (SPME) fiber on the same chromatographic run. Bare silica fibers were immersed into agarose matrix containing nano zerovalent iron (nZVI), ceria (CeO2) or zirconia (ZrO2). After characterization of fibers sorption/desorption parameters were optimized and standard reference materials were used to validate the proposed method. Direct mode of SPME method was used to extract the analytes prior to their separation with HPLC and detection with ICPMS. The optimum conditions for the extraction of selenium species with nZVI-agarose fibers are obtained as extraction pH: 4.0, agitation speed: 700 rpm, extraction time: 60 min, desorption matrix: 10.0 mM citrate solution, desorption time: 30 min, solution temperature: 25 °C, ionic strength: no NaCl addition. In the second part of this study, same fibers were used to separate triclosan (TCS) and triclocarban (TCC) using HPLC-DAD. Among all fibers prepared, nZVI-agarose modified fibers demonstrated the best extraction performance. The optimum conditions for the extraction of TCS and TCC with nZVI-agarose fibers are obtained as extraction pH: 5.0 and 7.0, agitation speed: 400 rpm, extraction time 60 min, desorption matrix: % 90 methanol - %10 water (adjusted to pH 3.0 with acetic acid), desorption time: 30 min, ionic strength: no NaCl addition.
Gas-phase fragmentation mechanisms of protonated peptides via tandem mass spectrometry
(Izmir Institute of Technology, 2013) Taşoğlu, Çağdaş; Yalçın, Talat
Protein identification based on enzymatic digestion of proteins and tandem mass spectrometric (MS/MS) analysis of peptide fragments has become a more popular method than classical approaches like Edman degradation. However, today’s protein sequencing tools have been constructed on a limited basis of peptide fragmentation chemistry such that some peptides can fragment in unusual ways that may not be predicted by the current bioinformatics software. Thus, erroneous assignments can be done in protein identification, which can lead to vital problems. Herein, it was aimed to reveal the rich chemistry lying behind the gas-phase fragmentation of peptides containing specific residues using MS/MS and collision induced dissociation (CID) analysis. As a result, the implementation of more detailed peptide fragmentation mechanisms into bioinformatics algorithms will no doubt help to improve database search tools. Results clearly indicate that b6 and b7 ions have higher tendency towards macrocyclization when compared to b5 ions. Besides it was observed that neighboring amino acid influences the selective opening of the macrocyclic structure and no preferential cleavage order can be specified depending on the amino acid residue. Next study showed that proline-containing peptides have high tendency to place the proline residue in the N-terminal position during the ring opening of macrocyclic structure. This is then followed by dipeptide elimination of proline with its adjacent C-terminal residue. Moreover, we demonstrated that sequence-scrambling exists for all histidine-containing peptides whatever the residue position and neighbor residue is. Additionally, we suggest that α-amino-ε-caprolactam formation at the side chain of lysine prevents macrocyclization reaction of b7 when K is positioned at the C-terminus. Finally, it was observed that macrocyclization reaction proceeds for peptides containing arginine when arginine gets closer to the C-terminus. Besides arginine was found to behave like lysine and forms ornithine when located at the C-terminus.
Investigation of carotenoid contents of various microalgae by chromatographis/spectroscopic methods
(Izmir Institute of Technology, 2013) Erdoğan, Ayşegül; Eroğlu, Ahmet Emin
Microalgae are the most important energy sources among microorganisms. Carotenoids, as important pigments and antioxidants, are produced by microalgae and are used both for health purposes and as natural colorants. There has been considerable research for the development, identification and determination of new strains of organisms to produce a variety of carotenoids. New methods for the isolation of carotenoids should be developed also for analytical purposes. This study aimed the biosynthesis of carotenoids from microalgae, (Prochlorococcus sp., Scenedesmus protuberans and Nitzschia sp.) their identification and quantification. It is known that some types of microalgae can produce high amount of carotenoids under different stress conditions while some others can produce carotenoids only under stress. For this purpose, cultivation conditions were optimized for the production of new or high value of carotenoids in the selected microalgal strains. Freeze-dried microalgae were extracted using different organic solvents and their carotenoid contents were investigated by high performance liquid chromatography (HPLC) and other chromatographic techniques such as liquid chromatography-mass spectrometry (LC-MS); in addition to (UV-VIS) spectroscopy. In green microalgae lutein (2.54 mg/g for Prochlorococcus sp. and 2.45 mg/g for Scenedesmus protuberans) is the most abundant carotenoid. On the other hand, in brown microalga fucoxanthin (6.58 mg/g for Nitzschia sp.) is the highly accumulated carotenoid. Under stress conditions, many microalgae alter their biosynthetic pathways for the formation and accumulation of carotenoids. Therefore, the effect of different nitrogen sources, oxidative stress conditions and different light sources on lutein content in green microalgae and on fucoxanthin content in brown microalga were investigated.
Metal-catalyzed coupling reactions of conjugated enyne alcohol derivatives with organometallics: An effective method in synthesis of functionalized vinylallenes
(Izmir Institute of Technology, 2016-11) Taç, Doğan; Artok, Levent
Transformations of organic compounds using transition metals are common methods in the toolbox of a synthetic chemist. Metal catalyzed C-C couplings are one of the most useful technique in this toolbox. Conjugate addition of soft/hard carbon nucleophiles to form allenes which are synthetically and pharmaceutically key precursors has been of great interest. Within the scope of this thesis functionalized vinylallene derivatives were prepared in two different types of new methods. The first method is Pd/Cu-catalyzed conjugate addition of terminal alkynes on enyne carbonates. The other method is iron-catalyzed conjugate addition of Grignard reagents on enyne acetates. In the case of the former method, alkynyl-substituted vinylallenes (1,3,4-trien-6-yne) were prepared with optimized conditions up to 91% yield in relatively short reaction periods. The optimized conditions of the cross coupling were successfully applied with various types of terminal alkynes and enyne substrates. The latter method involves the synthesis of alkylated vinylallenes with up to 90% yield with proper conditions.
Molecular modeling of polyelectrolytes - nucleotides / nucleic acids interaction
(01. Izmir Institute of Technology, 2022-12) Kıbrıs, Erman; Elmacı Irmak, Nuran
In 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.

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