M.S. Theses
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Item Synthesis and characterization of Zn (Zinc), Co (Cobalt), Fe (Iron) containing metal organic frameworks (MOFs) for microbial fuel cells (MFCs)(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Eryılmaz, Müşerref.; Demircan, Oktay.Metal organic Frameworks (MOFs) with their unique characteristics such as high surface area, variable functionalities and structural diversity, stability, and porous structure can be used as Microbial Fuel Cell (MFC) cathode catalysts. In this study, MOFs are synthesized from metal salts of zinc (Zn), cobalt (Co) and iron (Fe) and organic linkers as fumaric acid, terephthalic acid, 2-aminoterephthalic acid and 2- methlyimidazole via room temperature and sonochemical synthesis methods which are easy and energy-efficient. Effect of metal doping, reactant molar ratios and concentrations and metal ion precursors on synthesis of MOFs were investigated and formed frameworks are characterized by Scanning Electron Microscopy/ Energy Dispersive X-Ray Analysis and X-Ray Diffraction Analysis. Obtained MOFs’ applicability as Microbial Fuel Cell (MFC) cathode catalysts are studied by preparing slurries with carbon black (CB) and polyvinyl alcohol (PVA) as binder, coating them on stainless-steel mesh (SSM) current collectors for the first time. Electrochemical characterization of coated SSMs were performed via Chronopotentiometry and Cyclic Voltammetry (CV) and morphology of the coatings were established via SEM. SSM coated with 80% ZIF-L/10% CB/10% PVA slurry demonstrated the best oxygen reduction reaction (ORR) performance via CV. SSMs with ZIF-8/CB/PVA, ZIF-L/CB/PVA, Zn- doped ZIF-67/CB/PVA, and MIL-88A/CB/PVA composites that had demonstrated catalytic activity towards ORR utilized in MFCs for further performance analysis by Open Circuit Voltage (OCV), Linear Sweep Voltammetry (LSV) and Electrochemical Impedance Spectroscopy (EIS) in a two-chamber MFC inoculated with E.Coli K-12. Among the MFCs with novel cathodes, MFC with SSM cathode containing 80% ZIF-L/10% CB/10% PVA coating demonstrated the lowest charge transfer resistance and highest current density.Item Synthesis and evaluations of cyclopolymerizable and cyclopolymeric Type I photoinitiators(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Balaban, Burcu.; Semiz, Duygu Avcı.The aim of this thesis is to synthesize novel cyclopolymerizable and cyclic photoinitiators with high reactivity, water solubility, low migration and high thermal stability. In the first part of this work, two novel cyclopolymerizable Type I photoinitiators (DAA-I2959 and DAA-I184) were synthesized from reaction of diallyl amine (DAA) with tosyl ester of 2-hydroxy -4’-(2-hydroxyethoxy)-2-methylpropiophenone (Irgacure 2959, I2959) in the presence of sodium hydroxide as catalyst or with acrylate ester of 1- hydroxycyclohexyl phenyl ketone (Irgacure 184, I184). A water soluble, linear polymeric photoinitiator (p-DADMAC-co-DAA-I2959-QS) was synthesized by thermal copolymerization of DAA-I2959 with diallyldimethylammonium chloride (DADMAC) in the presence of hydrochloric acid. This photoinitiator has five-membered cyclic units on the backbone and its Mn value was in the range of 40,000-60,000 D. DAA -I2959, its copolymer and DAA-I184 have strong absorbances at 272, 266 and 244 nm (ε ~ 14705, 8000 and 11625), respectively, in methanol. In the second part of this work, reaction of DAA with tosylate ester of Irgacure 2959 was performed in the absence of a catalyst to give a mixture of two quaternary ammonium monomers, DAA-I2959-QS and DAA-Ts (tosylate salt of DAA). This photoinitiator has a strong absorbance at 269 nm (ε ~ 15731) in methanol. The photoinitiating capabilities of the synthesized photoinitiators for the photopolymerization of poly(ethylene glycol) diacrylate (PEGDA, Mn = 575 D) or 2- hydroxyethyl methacrylate (HEMA) were investigated by differential scanning photo calorimetry (Photo-DSC) and compared with I2959 and I184. DAA-I2959, p-DADMAC-co-DAA-I2959- QS and DAAI2959- QS/DAA-Ts exhibited fairly good migration stabilities (~ 3.5, 6.8 and 15.6 times higher) than that of I2959.Item Investigating the photophysical properties of novel chlorin derivatives as photosensitizer molecules for photodynamic therapy(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Bozoflu, Mert.; Çatak, Şaron.Photodynamic therapy (PDT) is a non-invasive cancer treatment that offers several advantages over traditional methods. This successful therapy has been effectively applied in the treatment of various cancer types, especially tumors located near the body surface. However, the limitations of photosensitizer (PS) molecules, particularly for deep-seated tumors, impede the widespread clinical adoption of PDT. Consequently, there is a need for novel photosensitizer molecules to improve treatment efficacy and advance the field of cancer therapy. This study presents a comprehensive investigation into the photophysical properties of substituted chlorin derivatives as potential PS molecules to enhance PDT. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT), along with hybrid quantum mechanical/molecular mechanical methods (hybrid QM/MM), were applied to examine their photophysical properties. Moreover, the molecules are thoroughly investigated in various physiological environments, including vacuum and water phase, encapsulated with drug carriers, and on lipid membranes with molecular dynamics (MD) simulations. The results provide insights into the absorption and emission spectra, natural transition orbitals, spinorbit coupling values, singlet-triplet energy gaps, and intersystem crossing channels of these molecules. By demonstrating the photophysical properties of these customized chlorins and their dependence on environmental factors, this research offers valuable information for the design and optimization of such molecules.Item Novel irgacure 2959-based salts as photoinitiators for low migration products(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Karıksız, Neslihan.; Avcı, Duygu.The aim of this thesis is to improve the "green" aspects of photopolymerization processes. So novel photoinitiators with high reactivity, low migration, water solubility and biocompatibility are designed, synthesized and evaluated. In the first part of this work, a new cyclopolymerizable, doubly I2959 functionalized allyl-acrylate quaternary ammonium salt (2xI2959-QS) and its copolymer with diallyldimethylammonium chloride (DADMAC) were synthesized and their characterizations were done. Also, their photochemical properties, migration stabilities and photopolymerization behaviours were examined. The water soluble polymer, p-DADMAC-co-2xI2959-QS has five- membered pyrrolidine rings in the backbone and shows excellent thermal stability. These photoinitiators (PIs) have similar maximum UV absorption wavelength (271 and 272 nm in ethanol) to I2959, the molar absorption coefficient value of 2xI2959-QS is twice that of I2959. The photochemical mechanisms studied by electron spin resonance (ESR) and photolysis indicate formation of isopropyl ketyl radicals. Photopolymerization of 2- hydroxyethylmethacrylate (HEMA) initiated by both PIs shows higher efficiency than via I2959. The synthesized photoinitiators show higher migration stability compared to I2959 as reference. In the second part of this work, a new facile route to prepare highly water-soluble and migration stable photoinitiator was reported. A doubly Irgacure 2959 (I2959) functionalized meso-2,3-dimercaptosuccinic acid (DMSA) salt (DMSA-I2959-DBU) with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) counterion was synthesized in one-pot thiol-Michael addition reaction. It has excellent water solubility (33 g/L), about 16 times higher than that of I2959. DMSA-I2959-DBU has similar maximum UV absorption wavelength value (272 nm in ethanol) but slightly lower molar absorption coefficient value (~11000) compared to I2959. Its decomposition mechanism was investigated by steady state photolysis. It shows reasonable photoinitiating reactivity towards (meth)acrylic double bonds.Item Design of temoporfin molecules functionalized with two-photon absorbing antennas and their potential use in photodynamic therapy(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Uyar, Ege Su.; Çatak, Şaron.Since its approval in 2003 by the European Agency of Medicine (EAM), temoporfin has been clinically used as a photosensitizer for photodynamic therapy. However, Temoporfin’s significant limitations such as low solubility in water and high aggregation probability in biological environments have created a window of opportunity for increasing its efficacy through modifications. In this thesis, three new drug molecules are proposed and obtained by modifying the temoporfin molecule with the addition of three different two-photon absorbing (TPA) dye molecules. To explore the newly proposed molecules’ suitability to photodynamic therapy, various theoretical chemistry tools are utilized such as Density Functional Theory (DFT), and Time- Dependent Density Functional (TD-DFT) on various levels of theory for quantum mechanical (QM) calculations. The results shed light on the electronic spectra of candidate drug molecules. Later, molecular dynamic techniques are exploited for further analysis of the novel drug molecules’ behavior in settings similar to biological environments.Item Green synthesis and characterization of metal oxide nanoparticles : Fe (Iron), Cu (Copper), and Zn (Zinc)(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Şengönül, Hüseyin.; Demircan, Oktay.The interest in the green synthesis of nanoparticles has significantly increased in the last decade as an alternative approach to chemical nanoparticle synthesis. Green synthesis is a technique that produces highly valuable materials by minimizing hazardous chemicals and using environmentally friendly, low-cost, and energy and time-saving materials, such as plant-based, industrial wastes, and recycled substances. This study presents the isolation and characterization of quercetin from Prunus serrulata (cherry blossom) and aims to control and understand the synthesis of nanoparticles (iron oxide, copper oxide, and zinc oxide) utilizing Prunus serrulata leaf extract as both reducing and capping agents. The effects of the mixing ratio of the volume of metal ions solution to Prunus serrulata leaf extract, the concentration of metal ions solutions, the pH, and the temperature of the reaction on the synthesis of nanoparticles are examined individually. The characterization of the plantmediated extract is completed through Ultraviolet-Visible Spectroscopy (UV-Vis), Fourier Transform-Infrared Spectroscopy (FT-IR), Liquid Chromatography- Mass Spectrometry (LC-MS), and Nuclear Magnetic Resonance Spectroscopy (NMR). The synthesized nanoparticles were characterized by several instrumental analyses including FT-IR, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The optimum conditions for all of the synthesized nanoparticles were determined separately. For Fe3O4 nanoparticles, it follows as: 3:1 (Fe+3 solution:Prunus serrulata leaf extract) mixing ratio, 10 mM Fe+ 3 solution, pH 6, and 25 °C reaction temperature. For CuO nanoparticles, it follows as: 2:1 (Cu+2 solution:Prunus serrulata leaf extract) mixing ratio, 25 mM Cu+2 solution, pH 5, and 25 °C reaction temperature. Finally, for ZnO nanoparticles, it follows as: 2:1 (Zn+2 solution:Prunus serrulata leaf extract) mixing ratio, 25 mM Zn+2 solution, pH 5, and 25 °C reaction temperature.Item A comparative study on selective biosorption in aqueous mixtures of dyes with different ionic characters by chlorella sp. biomass(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Yılmaz, Beyza.; İlker, Mehmet Fırat.In this study, the adsorption percentages of Chlorella Sp. biomass towards five ionic dyes and their relevant combinations in aqueous media were studied as a model system for wastewater remediation compared to a proper type of activated carbon. Since wastewater effluents often contain a large variety of ionic micropollutants, there are an ongoing need to determine biosorption potential against various structures of single chemical contaminants. To have a more realistic model and understanding of biosorption to remove aqueous chemical contamination, combinations of aqueous contaminants are herein proposed to be monitored. Five molecules with distinct ionic and structural characteristics, namely a cationic dye Methylene Blue, anionic dyes Isolan Dark Blue and Eriochrome Black T, a zwitterionic dye Methyl Orange, and a larger molecular weight zwitterionic dye Congo Red constituted the targeted set of model adsorbates. Cationic molecules demonstrate a higher tendency to be adsorbed onto Chlorella Sp. than anionic and zwitterionic dyes. Therefore, the cationic dye was selected to investigate its potential to facilitate better biosorption of the selected anionic and zwitterionic dyes, through the possible generation of additional positive charges on the adsorbent surface of microalgae biomass. Single dyes and selected mixtures of them were employed to determine the removal percentages of Chlorella Sp., by monitoring dye removal through observation of decreasing concentrations using UV absorption spectroscopy, under different aqueous conditions. Reliable measurements of concentration changes in the case of dye mixtures based on light absorption from multiple wavelengths were established.Item Optical properties of novel photosensitizers for photodynamic therapy(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Aslanoğlu, Busenur.; Çatak, Şaron.Computational chemistry plays an important role in interpreting various phenomena regarding properties of complex molecular and biological systems via several computational approaches. In this thesis, the full characterization of the photophysical properties of the temoporfin chromophore(mTHPC) and newly designed metal coordinated photosensitizer candidate (Zn-Ar) will be investigated in the light of molecular modeling and simulation techniques presently used in photodynamic therapy. Notably, the photosensitizers follows different photophysical pathways which lead to intersystemcrossing and thus, the triplet state population occurs. This is essential for producing the singlet oxygen, which leads to cell death. In this thesis, molecular dynamics (MD) and quantum mechanics simulations, we employed to shed light on the formation of stable interactions between the temoporfin and the membrane; particularly, the penetration of temoporfin into its hydrophobic center. These processes will allow us to determine the specific interactions between temoporfin and the lipid oxidizable double bond pointing towards the production of singlet oxygen. In addition to temoporfin, a novel photosensitizer candidate was investigated with the same protocol. This novel photosensitizer candidate will expose the effects of the metal coordinated chromophores and their photodynamic therapy abilities.Item Effect of Hofmeister ions on thermodynamics of complex coacervation of hyaluronic acid and chitosan(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Kantarcı, Gökçe.; Kayıtmazer, A. Başak.The Hofmeister series is an ion series that was discovered to have significant effects on the behavior of aqueous protein solutions as a result of Franz Hofmeister's studies in 1888, and its effects on other biomacromolecules have also been investigated. This study aims to examine the effect of this series on the complexation and coacervation of hyaluronic acid (HA) with chitosan (CHI) polyelectrolytes in three different pH values (3.25, 5.25, and 6.25) and two different molecular weights (HA, 1200 kDa & 199 kDa) in terms of thermodynamics. While turbidimetric titration experiments were used to optimize conditions affecting coacervation such as salt type, pH and concentration of buffering agent and polyelectrolyte, images were taken by light microscopy to ensure that the HA/CHI system produces coacervates that could be used in areas such as encapsulation, tissue engineering, and not just precipitate particles. Isothermal titration calorimetry has been found suitable to understand the thermodynamics of coacervation. The results majorly agree with the direct Hofmeister effect for the cations and the reverse Hofmeister effect for the anions. In addition, the salt screening effect can be clearly observed as the interaction between the two polyelectrolytes are most intense in the absence of salt. It was also observed that the interaction between the two macromolecules was greater as the pH increases.Item Protein encapsulation within oppositely charged polyelectrolyte complexes(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Akbulut, İlayda.; Kayıtmazer, A. Başak.In this study, it is aimed to perform enzyme immobilization with the coacervation, which is used as a physicochemical encapsulation method. By using this encapsulation technology, active agents like drugs and enzymes can be protected from several non desirable conditions of the environment such as high pH, organic solvents, and chaotic agents. In this research, one of the objectives is to form complex coacervate droplets with poly (diallyldimethylammonium chloride) (PDADMAC) which is a synthetic homopolymer, and pectin which is a carbohydrate found in the cell walls of plants. The biggest driving force in the formation of coacervation is the electrostatic interactions of the positive charges in PDADMAC with the negative charges in pectin. To learn more about protein encapsulation within complex coacervates, encapsulation of trypsin enzyme within complex coacervates comprised of a cationic polyelectrolyte, PDADMAC, and an anionic polyelectrolyte, pectin, was investigated as a function of mixing order of macromolecules and at different salt concentrations. Three different mixing orders was performed. Additionally, turbidimetric titrations of pectin – PDADMAC mixtures were done at six different salt concentrations. Formation of coacervate microdroplets was observed by light microscopy at these salt concentrations. Potentiometric titration experiments were performed for pectin to find the degree of ionization of pectin at the optimum pH of trypsin, which is 7.5. For further experiments, the most appropriate mixing order is selected, and the remaining experiments are performed with that addition sequence. Then trypsin and polyelectrolyte concentrations were changed and its effect on encapsulation was examined. After determining the most effective encapsulation method, enzyme activity was measured. Finally, it was investigated whether the secondary structure of trypsin changed with encapsulation by circular dichroism experiments.Item Synthesis and characterization of Fe (iron), Co (cobalt), Ni (nickel) containing metal organic frameworks (MOFs)(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Galın, Çağla.; Demircan, Oktay.In recent years, scientists and industries have been interested in metal organic frameworks (MOFs), a class of porous materials. Metal organic frameworks are formed by connecting metal clusters or ions with organic linkers. In addition to porous structures of MOFs, they have high surface areas, structural diversity, adjustable chemical functionality, high thermal stability, and easy synthesis. MOF can be used in many applications such as gas storage (e.g., hydrogen, methane, acetylene, and carbon dioxide), catalysts, and energy applications (e.g., batteries and supercapacitors). In this study, cheaper starting materials (metal salts of iron (Fe), cobalt (Co), and nickel (Ni)) based MOFs were synthesized via sonochemical synthesis method due to its fast, energy -efficient, and environment friendly method, and fumaric acid and terephthalic acid were used as organic linkers. The effects of temperature, pH, concentration, and solvent on MOF material were investigated. X-Ray Diffraction Analysis (XRD), Scanning Electron Microscope/Energy Dispersive X-Ray Analysis (SEM /EDX), and Infrared (IR) Spectroscopy, were used for characterization of synthesized compounds. In this thesis, the synthesis conditions for Fe (iron) with fumaric acid-based MOFs are optimized for the first time by using 1 mmol starting materials at 75 ⁰C and pH=natural (2.57) in 90 minutes sonication. Fe, Co, and Ni containing MOFs are synthesized for the first time by using terephthalic acid as organic linker and DMF as solvent, successfully by exploiting 90 minutes sonication. When pH of organic ligands solutions increased for faster deprotonation of organic ligands, iron oxide nanoparticles, cobalt (II) hydroxide and nickel (II) hydroxide were obtained instead of MOF structures.Item A computational approach to evaluate the pKa's of quinazoline derivatives(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Kıran, Melisa.; Akın, Fatma Ahu.; Aviyente, Viktorya.One of the most important constants in chemistry is the ionization (dissociation) constant (pKa). Estimating the pKa value(s) for a potential drug is critical, especially since computations are considerably less expensive than obtaining pKa values experi mentally. Nearly 68 % of ionized medicines are said to have weak bases [1]. As a first step in developing an efficient estimation methodology for the pKa of quinazoline and derivatives we studied three protocols. First one is based on the linear relationship between computed atomic charges of quinazoline and derivatives and the experimental pKa. Based on our observations, the optimum method for reproducing observed pKa’s is to compute NPA (Natural Population Analysis) atomic charge using the CPCM (Conductor Like Polarizable Continuum Model) at the M06L/6-311++G** level (R2 = 0.93). The experimental pKa of a collection of quinazoline and derivatives were compared to several Conceptual Density Functional Theory descriptors computed. The highest approximations were observed when employing the M06L/6-311++G** with the CPCM solvation model using water as a solvent. In the final part of our study, M06L/6-311++G** have been used, in combination with CPCM continuum solvent model, to calculate the aqueous pKa values of quinazoline derivatives by using an isodesmic reaction. Possible improvements to current methodology are suggested.Item Synthesis and application of thiol-reactive zwitterionic copolymers(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Taylan, Nazlı.; Sanyal, Amitav.In recent years, zwitterionic polymeric materials have gained attention thanks to their ultra-hydrophilicity due to the equimolar number of evenly distributed anionic and cationic moieties that they contain along their polymer chains while still preserving their overall charge neutrality. Moreover, zwitterionic polymers are typically regarded as an alternative to the popular poly(ethylene glycol) (PEG) polymers for anti- biofouling applications to prevent nonspecific protein adsorption and to reduce bacterial or mammalian cell adhesion. Due to its potential uses in interdisciplinary fields, including biomaterials, material science, and targeted delivery, the synthesis of zwitterionic polymers with reactive functional groups is a popular area of research. Polymers with reactive maleimide units as functional groups at the side chains can be obtained by a copolymerization technique using zwitterionic monomers and maleimide-containing monomers. In the thesis, the functionalization of zwitterionic structures was done by copolymerization with an acrylate-based 'latent- reactive' monomer in which maleimide is masked with furan by the Diels-Alder reaction to protect the double bond of the maleimide moiety. By using the advantage of the thermo- responsive behavior of the cycloadduct, the thiol-reactive maleimide unit was activated by the retro DA reaction. To show the effectiveness of the maleimide unit, the thiol-containing hydrophobic dye was conjugated to the linear polymeric structure by the 'click' reaction. Since the hydrophobic dye can become soluble in water when attached to the designed zwitterionic polymer, the methodology serves as a model of drug conjugation.Item Selectivity of zeolite supported rhodium and iridium catalysts for the hydrogenation of alkenes and alkynes(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Saltuk, Aylin.; Demircan, Oktay.; Aviyente, Viktorya.Alkene and alkyne hydrogenation reactions are currently one of the most common industrial procedures for reducing unsaturated organic compounds to a variety of useful chemicals. In the catalytic hydrogenation of alkenes and alkynes under both homogeneous and heterogeneous conditions, several metal-based catalysts have been used. Metals in supported catalysts are usually cationic and chemically bonded to the supports when they are atomically distributed. The study of noble metals in this class is continually expanding, resulting in the discovery of novel catalysts with unique features. In this study, the selectivity of zeolite supported Rh and Ir catalysts for the hydrogenation of alkenes and alkynes is investigated by using Density Functional Theory (DFT). The reaction pathways for the hydrogenation have been modeled to monitor which pathway is energetically more favorable by comparing the activation barriers between the states. The results have shown that ethylene production is selective with zeolite supported Rh(C2H2)2 catalyst. Moreover, the ethylene selectivity for the hydrogenation is more favorable when the metal is Ir. However, the regeneration of the catalyst is facile with Rh metal. This outcome is elucidated by analyzing geometric parameters, ligand bond dissociation energies and potential energy surfaces. This study contributes to a better understanding of ethylene selectivity along the hydrogenation of acetylene. This study is expected to shed light on the synthesis and usage of single atom catalysts for the hydrogenation of acetylene and ethylene.Item Benchmarking TADF activity of sulfone based compounds(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Hepgüler, Aslıhan.; Çatak, Şaron.Thermally activated delayed fluorescence (TADF) mechanism can be explained as transfer of excitons from the first triplet excited state (T1) to the first singlet ex cited state (S1) by reverse intersystem crossing (RISC). In this study, the activity of sulfone-based TADF compounds was examined with descriptors by using density func tional theory (DFT). Besides structural properties, photophysical properties of studied compounds were investigated. Dihedral angles obtained from optimized geometries are shown to change with respect to donor units. The nature of excited states was exam ined because of its impact on TADF efficiency. As seen in results, we can say that M062X functional is the only functional that gives locally excited (LE) character at triplet excitations. The energy difference between S1 and T1 excited states (∆EST ) is one of the analyzed descriptors and generated with three different functionals. The cal culated ∆EST values are consistent with experimental values. To evaluate efficiency of functionals, the relationship of experimental kRISC with calculated 1/∆EST and spin orbit coupling (SOC) that is required for reverse intersystem crossing (RISC) process is examined. As a result, B3LYP accidentally generates the best ∆EST values while M062X is the only functional that gives correct relationship between kRISC-SOC. Ac cording to comparison based on the effect of ∆EST and SOC values on the (R)ISC possibility (χ), M062X is the most reliable functional. The obtained visualization of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) and Φs indices are consistent with other descriptors. Finally, absorp tion and emission spectra are generated and compared with experimental spectra. The obtained results will have contributions to the selection of the most reliable functional and design strategies for TADF compounds.Item Modelling the enantiomerization and atroposelectivity in thiohydantoin derivatives(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Azizoğlu, İpek.; Doğan, İlknur.; Aviyente, Viktorya.Thiohydantoins have a wide range of pharmacological and biological properties. In the previous studies, nonracemic axially chiral thiohydantoins were synthesized and computational investigations have rationalized the synthesis mechanism of the prod ucts. Two kinds of isomerism are studied; atropisomerism due to hindered rotation around a chiral axis and central chirality. Selective synthesis of one enantiomeric form is important during drug synthesis because of the different pharmacological properties of enantiomers and diastereomers. Enantiopure products have less complex and more selective pharmacodynamic profile compared to racemic mixtures. In order to shed light on the factors determining the selectivity on the reactions of thiohydantoin molecules, DFT methods have been used to investigate the substituent and solvent effect on the kinetics of the reactions and the thermal stabilities of thiohydantoin stereoisomers SP, SM, RP and RM. This study consists of four parts, with different reaction conditions and mechanisms. In the first part, the substituent effect on the rotational barriers has been investigated and the results have been compared with the experimental data. In the second part, the solvent assisted racemization and rotation reactions have been modelled and their activation energies were calculated to establish the most plausable mechanism. After determination of the racemization mechanism in ethanol, the sub stituent effect on racemization has been modelled and the results have been compared with the experimental data. In the third part, we proposed an approach to calculate the product distributions of thiohydantoin stereoisomers by the Boltzmann distribu tion. In the last part, we have modeled the aldol formation reactions and explored the face selectivity of the enolate due to the bulky ortho-aryl substituent.Item Dual reactive polymer brush coated magnetic nanoparticles(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Tunca, Tuba Ayça.; Sanyal, Amitav.In recent years, iron oxide nanoparticle based systems have attracted attention for biomedical applications due to their nanoscale size and unique magnetic properties. For many applications they are coated with polymers, which provide them desired dispersibility, as well impart desired properties for enabling biomedical applications. In this study, we synthesized dual reactive polymer brush coated iron oxide nanoparticles. Nanoparticles were synthesized via the thermal decomposition method to obtain near monodisperse size distribution. Dopamine terminated polymers were synthesized for use in grafting-to method. Also, nanoparticles with chain transfer agent (CTA) anchored to their surface using dopamine were synthesized to obtain polymer brushes using the graft- from approach. Reversible addition fragmentation chain transfer (RAFT) polymerization was utilized to obtain polymers using both grafting-to and grafting from approach. Polymers containing the thiolactone unit could be synthesized with good control over composition and molecular weight using the dopamine-containing CTAs. For the grafting-from approach, CTA was anchored onto nanoparticles, and surface-initiated RAFT polymerization was used. The thiolactone unit was used as a reactive group to impart the system with dual reactivity. The thiolactone ring reacts with amine-containing molecules, and in the process releases a free thiol as a second reactive unit. In our work, we used an azide-containing amine for the thiolactone ring-opening, followed by trapping of the newly formed thiol group as a pyridyl disulfide unit which is known to undergo exchange reactions with thiolated molecules. As a model cargo, thiolated hydrophobic fluorescent dye, BODIPY thiol, was conjugated to the system via thiol-disulfide exchange reaction. As a result, we obtained magnetic nanoparticles bearing a clickable azide and a thiol- exchangeable PDS group to attach any desired cargo for intended applications.Item Reduced graphene oxide embedded polymeric nanofibers for thermo- responsive drug delivery systems(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Sancar, Tugay.; Sanyal, Amitav.In recent years, nanofibers have become popular in biomedical applications because of their distinctive qualities, such as the large surface area to volume ratio, porosity, and appreciable mechanical strength. Electrospinning is the most widely utilized method to manufacture nanofibers due to its straightforward setup and cost-effective production. Fabricated nanofibers can be modified with different functional groups to impart characteristic properties and enable their application. In recent years, ‘click’ chemistry transformations have been preferred to functionalize nanofibers. In this thesis, clickable copolymers were synthesized to generate furan functionalized polymeric nanofibers with the help of electrospinning. Morphological features of the produced nanofibers were characterized with SEM. Reduced graphene oxide (r-GO) was embedded into the nanofiber during electrospinning to provide a photothermal property to the fibrous material. Irradiation of r-GO- containing materials with near-infrared (NIR) light results in the conversion of the light into heat and increases the temperature of the surface of the fibrous substrate. Doxorubicin (DOX) was modified with a maleimide functional group to enable Diels-Alder (DA) cycloaddition between furan- functionalized nanofibers and maleimide-modified drug molecules. After successfully conjugating the drug molecule, exposing drug conjugated nanofiber to NIR light leads to retro Diels-Alder (rDA) reaction resulting in drug release thanks to rapid light-to-heat conversion.Item Modeling the solvent effect in free radical polymerization and deamidation of peptides(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Doğan, Berna.; Aviyente, Viktorya.In the first part of this study, the kinetics free radical polymerization of ethyl methacrylate (EMA) and ethyl α-hydroxy methacrylate (EHMA) in solution is investigated; in the second part the deamidation in three different dipeptides is modeled in solution by using Density Functional Theory (DFT). In the first part of this study, the propagation kinetics of EMA and EHMA has been subjected to a computational study in order to understand their free radical polymerization (FRP) behavior in bulk and in solution. Methacylates are among the most commonly used monomers in FRP and can be used as dental materials, biomaterials, adhesives, optical adhesives, coatings, fiber-optic coatings and in many other areas. The hydroxy-functional methacrylate monomers have drawn attention due to their hydrophilicity, crosslinking sites and functionality for subsequent reactions. The correlation between the calculated propagation rate constants and the experimental results has been reproduced with the MPWB1K/6-311+G(3df,2p) methodology. In the second part of this study, the deamidation reaction mechanism in peptides is investigated. Out of the twenty naturally occurring amino acid residues, two of them, namely Asparagine (Asn) and Glutamine (Gln) are known to be unstable under physiological solvent conditions. The amide group from the backbone of the amino acid residue of Asn and Gln cleaves to form Aspartly (Asp) and Glutamyl (Glu) residues. Peptides and proteins that contain Asn and/or Gln with different primary sequence are known to have very different half-life times for deamidation. Therefore, the effect of the primary sequence on deamidation is studied by choosing three different peptides as models.Item Modeling stereoselective reactions in solution(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Yıldırım, Aslı.; Aviyente, Viktorya.In this study, ring-chain-ring tautomerization and asymmetric desymmetrization reactions are investigated by taking the solvent effect into account. In the first part, ring-chain-ring tautomerization mechanism is investigated by taking the effect of solvation into account in order to explain the enantiomeric interconversion of heterocyclic 2-oxazolidinone derivatives which are isolated as single enantiomers and have potential to be used as axially chiral catalysts. Density functional calculations reveal that there are two possible pathways with two different intermediary species which are amido and imino intermediates. This part of the study sheds light on the mechanistic details of both possible pathways to be able to understand and predict the ring-chain-ring tautomerization mechanism of similar heterocyclic systems. In the second part, the asymmetric desymmetrization mechanism is subjected to a computational analysis in an effort to investigate the alcoholysis of cyclic meso anhydrides in the presence of cinchona alkaloids. In the first step of this part of the study, the conformational analysis of cinchona alkaloids is carried out since the conformation plays a crucial role in enantioselectivity. Then, the mechanism of methanolysis of cyclic meso anhydrides catalyzed by cinchona alkaloids is considered by studying both stepwise and concerted pathways.