Browsing by Author "Emrullahoğlu, Mustafa"

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Adhesion of dopa functionalized gels to spin labeled surfaces
(Izmir Institute of Technology, 2017-07) Göksel, Yaman; Akdoğan, Yaşar; Emrullahoğlu, Mustafa
This 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.
Copper-catalyzed synthesis of benzo-bimane derivatives
(İzmir Institute of Technology, 2016-07) Zeybek, Hüseyin; Emrullahoğlu, Mustafa
1,5-Diazabicyclo[3.3.0]octadienediones (shortly 9,10-dioxabimanes or "bimanes") are small heterocyclic structures which have important chemical, photochemical and photophysical properties. There are two existing structural isomers for bimane compounds ("syn" and "anti"). The syn-isomers have strong UV absorption properties and high quantum yields and are highly fluorescent. Bimane compounds are widely used for fluorescent labelling in biological systems because of their high photo-stability and bio-compatibility. Despite their unique properties, there is very few examples of study in literature. Because of synthetic difficulties of literature examples and their requirements such as hazardous chemicals, new methodologies are in high demand. In this study, new methods utilising metal catalysis for the effective synthesis of bimane compounds have been developed. Bimanes, which in the literature are synthesised with extreme difficulties and low yields, were synthesised in this work through simple and efficient protocols that employ metal, ligand and base. We further investigated the photophysical properties for all newly synthesized bimane derivatives. In the course of thesis study, a new and efficient method have been developed and optimised for the facile synthesis of benzo-bimane compound via the copper(I) catalyzed intramolecular C-N bond formation reaction. Moreover, with the aid of this new methodology, various analogues of benzo-bimane compound were synthesized in moderate to good yields under mild reaction conditions . Also, photophysical properties of benzo-bimanes were investigated carefully.
Design and synthesis of a BODIPY based probe for cadmium ions
(01. Izmir Institute of Technology, 2021-12) Cebeci, Miray; Emrullahoğlu, Mustafa
Given 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.
Design and synthesis of a BODIPY based probe for mercury ions
(01. Izmir Institute of Technology, 2021-12) Tütüncü, Büşra Buse; Emrullahoğlu, Mustafa
The 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.
Design and synthesis of BODIPY based phosgene sensor
(Izmir Institute of Technology, 2018-06) Sayar, Melike; Emrullahoğlu, Mustafa
Phosgene 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.
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.
The design and synthesis of fluorescent chemosensors for the detection of gold and mercury metal species
(Izmir Institute of Technology, 2015-06) Cantürk, Ceren; Emrullahoğlu, Mustafa
This 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.
Design and synthesis of phosphine based fluorescent probes for reactive oxygen species
(Izmir Institute of Technology, 2018-12) Üçüncü, Canan; Emrullahoğlu, Mustafa
Hypochlorous 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.
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.
Desing and synthesis of BODIPY based photosensitizers for photodynamic therapy
(Izmir Institute of Technology, 2019-07) Dartar, Suay; Emrullahoğlu, Mustafa
Photodynamic 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.
Desing and synthesis of fluorescein based gold ion sensors
(Izmir Institute of Technology, 2016-07) Çetintaş, Ceyla; Emrullahoğlu, Mustafa
Gold 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.
Desing and synthesis of fluorescent chemodosimeter for the analysis of the gold ions
(Izmir Institute of Technology, 2018-12) Çevik Eren, Merve; Emrullahoğlu, Mustafa
The 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.
Fluorescent gold ion sensors: Design, synthesis and imaging
(01. Izmir Institute of Technology, 2021-12) Kaya, Beraat Umur; Emrullahoğlu, Mustafa
Of 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.
Hydrothermal treatment of biomass in hot-pressurized water
(Izmir Institute of Technology, 2015-05) Dadenov, Saken; Yüksel Özşen, Aslı; Emrullahoğlu, Mustafa
The 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.
Preparation and characterization of drug loaded cationic albumin nanoparticles
(01. Izmir Institute of Technology, 2021-06) Sözer, Sümeyra Çiğdem; Akdoğan, Yaşar; Emrullahoğlu, Mustafa
Serum albumin protein behaves as a carrier and transporter for both hydrophilic and hydrophobic drugs. Therefore, albumin could be used in the drug carrier systems. Since albumin nanoparticles have a negative charge under physiological conditions, their anionic drug loading and delivering capacities are restricted. This study aims to obtain higher anionic drug loading capacity by producing cationic bovine serum albumin nanoparticles (cBSA NPs). Firstly, the carboxyl groups of amino acids present on the surface of albumin were conjugated with ethylenediamine to change the charge of albumin from negative to positive. Then, cBSA NPs were obtained using the desolvation process. Anionic salicylic acid (SA) was used for drug loading studies of the obtained cBSA NPs. SA loading and releasing experiments were studied with UV-Vis and electron paramagnetic resonance (EPR) spectroscopy. In the UV-Vis, the drug loading capacity of cBSA NPs was found to increase ~2 fold, and drug release was slower compared to BSA NPs. For EPR studies, SA was labeled with stable radicals. Spin labels allow the simultaneous monitoring of bound and free drugs in the same sample. The drug was loaded into nanoparticles using two methods. Based on EPR results, it was found that drug was loaded to cBSA NPs with 50% and 93%, and to BSA NPs with 4% and 15% ratios, by desolvation and incubation, respectively. Thus, UV-vis and EPR measurements showed that cBSA NPs have higher SA loading potential and slower release ability compared to anionic albumin nanoparticles.
Study of drug transportation by ESR spectroscopy
(Izmir Institute of Technology, 2018-12) Tatlıdil, Duygu; Akdoğan, Yaşar; Emrullahoğlu, Mustafa
The 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.
Studying dopa adhesion on polystyrene under water
(Izmir Institute of Technology, 2021-06) Yıldız, Remziye; Akdoğan, Yaşar; Emrullahoğlu, Mustafa
Mussels 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.