Item Open AccessElectrocatalytic water splitting with Prussian blue analogues under external stimuli(Bilkent University, 2023-09) Ahmad, Waqar; Karadaş, FerdiThe development of long-lasting and efficient catalysts for water splitting is crucial for the advancement of a carbon emission-free world. A well-known class of compounds called Prussian blue analogues (PBAs) offers several advantages such as high stability, diversity, and simple synthesis for the development of sustainable water-splitting devices. This thesis investigates the construction of PBA-based overall water-splitting electrolytic cells assisted with external stimuli. Alsac et al. investigated the oxygen evolution reaction (OER) efficiency of various PBAs and concluded that Co-Co exhibits the best performance as an OER catalyst among the Co-M PBAs. Ahmad et al. studied the hydrogen evolution reaction (HER) performance of various PBAs and observed that Co-Ni stands out in performance. Furthermore, Chalil Oglou et al. elucidated the effect of the magnetic field on the OER catalytic activity of Co-Fe PBA electrodeposited on the surface of the FTO. His findings unveiled an enhanced catalytic activity under the influence of a magnetic field. To further explore these concepts, we aim to move one step ahead and combine all these studies to investigate overall water splitting (OWS) under the influence of magnetic field and solar light irradiation. In this thesis, [Co-Co] was used for the OER reaction, while [Co-Ni] was utilized for the HER reaction. Both electrodes were prepared involving a two-step electrodeposition method and comprehensively characterized with SEM, EDAX, P-XRD, XPS, and ATR-FTIR. SEM images unveiled threat-like and needle-like grown particles with uniform sizes of 1-2 µm for [Co-Co] and [Co-Ni] formed on the fluorine-doped tin oxide (FTO) electrode respectively. The oxidation states of the pristine and post-catalytic electrodes and the stability during the electrocatalytic process were confirmed with XPS and FTIR studies. The electrochemical characterization of these catalysts was thoroughly investigated with linear sweep voltammetry (LSV), chronoamperometry (CA), and cyclic voltammetry (CV) profiles. The electrochemical performance was investigated in three chapters; OER, HER, and overall water splitting under magnetic and solar light irradiation. (i) OER performance of FTO/[Co-Co] was evaluated with LSV, which shows prominent enhancement peaks under the influence of external stimuli. Under the influence of the magnetic field, it illustrated an enhancement of 11.9% with an overpotential of 949 mV, while in the presence of solar light, it showed an augmentation of 10.7% with an overpotential of 949 mV. CA profiles, recorded under magnetic field showed that there is a direct relation between magnetic field strength and the enhancement in the current density. On the contrary, an opposite trend is observed with the CA profiles under solar light irradiation, which suggests that the origin of the enhancement under the magnetic field is different from the one under solar light irradiation. (ii) Similar to OER studies, HER activity of FTO/[Co-Ni] was investigated under the effect of solar light irradiation and magnetic field. The LSV profile showed enhancement only in the case of solar light, while no significant enhancement was observed under the magnetic field, contrary to the previous studies. Similar to OER, the CA profiles of FTO/[Co-Ni] illustrated the opposite trend with respect to overpotential applied. In the case of HER, CA under a magnetic field showed a small enhancement (1.4%) with an overpotential of 300 mV, which was attributed to the magnetohydrodynamic effect. (iii) Two and three-electrode systems were used to conduct the investigation into overall water splitting. To achieve a current density of 1 mA/cm2 in the two-electrode having FTO/[Co-Co] on the working/working sense electrode (W/WS) and FTO/[Co-Ni] on the counter/reference electrode R/C configuration, the system required an overpotential of roughly 1013 mV. The subsequent analysis of each electrode's unique voltage contributions helped explain this observation. OER takes around 1.3 V while it is 0.6 V for the HER side. On the other hand, in the three-electrode configuration, the working electrode was FTO/[Co-Co], the counter electrode was FTO/[Co-Ni], and the reference electrode was Ag/AgCl. The observed profile notably showed significant improvement seen when solar light and magnetic fields were present. Overall, this study indicates that there is still plenty of room for enhancement in catalysis, with slight modification in reaction conditions from another perspective i.e., external stimulus. This thesis takes a progressive step by raising the bar and adding a new dimension to the challenge of using PBAs in catalytic applications, building on earlier efforts. Item Open AccessTowards understanding the catalytic bond-breaking sequences of polyol oxidation on PD(111) single crystal model catalysts(Bilkent University, 2023-09) Sadak, Ömer Faruk; Özensoy, EmrahUnderstanding the bond-breaking sequences of catalytic polyol oxidation on transition metal catalysts is critical for the chemical transformation of biomass derived chemical feedstock into value-added products which may also offer new alternatives to fossil fuel-based commodity chemicals. In the current work, oxidation of ethylene glycol on an atomically well-defined Pd(111) single crystal planar model catalysts was investigated via temperature programmed desorption (TPD) technique under ultra-high vacuum (UHV) conditions. Presence of surface oxygen atoms was found to promote the formation of formaldehyde (H2CO) and carbon dioxide as the most prominent catalytic oxidation products. Enhancement in formaldehyde generation was observed upon increasing the ethylene glycol-to-oxygen ratio. Our results indicate that the activation of C-C bonds was primarily facilitated by atomic oxygen, preceding the complete dehydrogenation of the C2HxOz surface species. The formation of H2CO was mainly attributed to the most unstable surface species in terms of C-C bond scission, namely -OCH2CO- and -OCH2CHO-. Other surface species such as -OCHCHO- and -OCHCO- led to additional decomposition products such as CO rather than formaldehyde. Item EmbargoIntramolecular through-space charge-transfer in naphthalene-based compounds and development of an efficient heterogeneous catalytic method for the aerobic C-H oxidation of alkylarenes(2023-09) Çalıkyılmaz, Eylül; Türkmen, Yunus EmreThe transfer of electrons between two molecules or between different groups attached to a molecule is known as charge transfer. Electronic communication can take place either through chemical bonds or through space. Intramolecular through-space charge transfer occurs between donor and acceptor parts of a molecule depending on the electron density difference, the distance between them, and their relative positions. The main objective of the project is to study the phenomenon of intramolecular through-space charge transfer in naphthalene-based organic materials. We investigated the charge transfer in 1,8-substituted naphthalene derivatives and the effect of different electron-donating and electron-withdrawing groups. To investigate the role of these groups, a variety of control substrates which have different electronic structures were synthesized. Subsequently, it was determined which substances possess a charge transfer band by examining the UV-Vis spectra of these substances. Additionally, it was found that substances with charge transfer bands in UV-Vis absorption spectroscopy had multiple emission values when fluorescence spectra were analyzed. In addition, to observe the effect of different solvents on charge transfer, the substance with observed charge transfer was dissolved in different solvents and examined in terms of color, absorption, and emission values. A key objective of the second part is to develop an environmentally friendly and efficient earth-abundant metal hydroxide catalyst that can be used in aerobic C-H activation reactions for a variety of organic compounds. Metal hydroxides are used for this purpose because of their ability to operate at relatively low temperatures and it allows metal hydroxides to act as highly effective catalysts for oxidation reactions. As an earth-abundant metal-containing catalyst, FexMn(1-x)(OH)y has been prepared by the Özensoy research group with different elemental ratios. In addition, the concentration of NaOH was systematically investigated during the synthesis of the catalyst. The catalytic activities of all catalysts were studied in the aerobic oxidation of fluorene to fluorenone as a model reaction. The optimized conditions were used for the oxidation of diphenylmethane to benzophenone. Subsequently, diphenylmethanes functionalized with electron-donating and electron-withdrawing groups were synthesized, and the yields of oxidation reactions were determined. Finally, the results of the kinetic isotope effect experiment were combined with the yields of the previous experiments to shed light on the mechanism of oxidation. Item Open AccessBrønsted acid-catalyzed inverse electron-demand diels-alder reactions of 1,2-diazines(Bilkent University, 2023-09) Korkmaz, Hatice Seher; Türkmen, Yunus EmreThe discovery of Diels-Alder reaction by Otto Diels and Kurt Alder in 1928 marked an important development in synthetic organic chemistry. This [4+2] cycloaddition reaction has been used in a variety of ways over the years, from natural product synthesis to medicinal chemistry. The process produces derivatives of cyclohexane by the coordinated addition of a conjugated diene and a dienophile. As a subclass of Diels-Alder reactions, inverse electron-demand Diels-Alder (IEDDA) reactions are covered in this thesis, along with their intricate mechanisms and applications. IEDDA cycloaddition reactions have become more well-known recently, especially in the fields of chemical biology, bio-orthogonal reactions and the synthesis of complex molecules. These reactions generally have excellent regio- and stereoselectivity and they occur between electron-poor dienes and electron-rich dienophiles. They have been crucial in the synthesis of bioactive substances with potential use for the cancer treatment, such as halenaquinone and rhodexin A. Catalysts have become an effective means of promoting IEDDA reactions in the search for milder reaction conditions and higher yield. To modify the energy levels of dienes and increase reactivity, Brønsted acid catalyst has been used in this project. This study involves the investigation of pyridinium salts as Brønsted acid catalyst intended to reduce the LUMO energy levels of 1,2-diazines. The goal is to make diazines more reactive in IEDDA reactions, creating new pathways for the synthesis of a variety of complex molecules. By bridging the gap between difficult reaction conditions and effective IEDDA reactions, this project aims to increase the usefulness of this potent synthetic method in contemporary organic chemistry. Item EmbargoEvolution of Liesegang patterns through gel concentration borders and thermal changes(Bilkent University, 2023-08) Akbulut, Elif Sıla; Baytekin, BilgeLiesegang Patterns (LPs) are under the umbrella of periodic precipitation patterns that are formed through reaction- diffusion (RD). Liesegang Patterns can be used to track down the changes in the physical environment, because different physical environments produce different environments. Since their discovery effects of various parameters such as temperature, magnetic ,and electric fields, concentrations of electrolytes and gels have been studied to understand the formation mechanisms of these patterns. In this study an LP system (CuSO4 (outer electrolyte)/ K2CrO4 (inner electrolyte) in agarose hydrogel) that responds to changes in the gel environments was generated. The medium uniformity with different gel concentration regions designed in various geometries (circle, square, triangle, and pentagon) were used to break the symmetry ,and homogeneity in the medium. The propagation of LP waves across the boundaries between the regions was visually inspected. The LP band spacings, the size ,and morphology of the product within the bands were altered in comparison to those observed in with LPs in homogenous media. The first part of the work is the first display of LP waves travelling through concentration boundaries. The visual patterns obtained in spatially heterogeneous media provide complex patterning of matter, which is not only fundamentally interesting for the study of artificial patterning but also can be useful in fields such as catalysis, and soft functional materials. Second, the propagation of the “bio” waves of bacteria colony Bacillus Subtilis growth through different concentration gel media was monitored. Different concentrations of agar ,and tryptone across a boundary in the growing medium led to changes in the growth patterns of bacteria upon passing to the “other side”. These changes growing bacterial patterns can be used to analyse how the spatial changes in the environment affect the growing colonies ,and give a more realistic view on the bacterial growth on complex terrain. Finally, we explore the effect of temperature ,and the hydrogel chemistry (gelatin, agarose, and PVA) on the formation of Mg(OH)2 LPs. Previously, temperature was used only to change the LP spacings and particle size. This work shows that it can also be used to alter the morphology of the formed particles. The results of this part of the project imply that a temperature gradient can be used to produce patterns with diverse morphologies of the same species in the same spatial environment. All these parts in the thesis work point out that simple symmetry breaking in the medium can make significant changes in the ‘developing’ systems in the macro, and micro scales. This information can be used in analysis ,and utilization of natural ,and synthetic patterns systems. Item EmbargoMolecular interactions and binding mechanisms of hydrophobic hofmeister cations to macromolecules(Bilkent University, 2023-08) Ertekin, Umay Eren; Okur, Halil İbrahimIt’s been known for over a century that ions specifically affect the bulk properties of solutions, behavior of macromolecules and a myriad of interfacial phenomena occurring in solution. Yet, the molecular mechanisms underlying these so-called Hofmeister effects are only recently being realized within the last few decades. In the resurgence in specific ion effects studies, the role attributed to cations has been relatively understated in comparison to the effects of anions. Whereas various molecular mechanisms have been elucidated for a diverse spectrum of anions, cationic effects have largely remained limited to common metal ions. Within the cationic Hofmeister series for cations, strongly-hydrated cations exhibit very weak binding to polar, electronegative groups, but weakly-hydrated cations in particular are classified as non-interacting. This thesis brings a much-needed expansion to specific cation effects by investigating the interactions between the weakly-hydrated tetraalkylammonium cations and model neutral thermoresponsive polymers, principally poly(N-isopropylacrylamide) (PNIPAM). The hydrophobicity of the cations is incrementally tuned by increasing the length of their alkyl chains, thus forming the series of salts investigated herein: NR4Cl where R = H, Me, Et, n-Pr, n-Bu, and the anion is kept constant as Cl-. By using a multi-instrumental approach, it is demonstrated that the largest of these cations exhibit a significant binding to the polymers and that the resulting salting-in effects are comparable in magnitude to those observed for sodium salts of weakly-hydrated anions. Thermodynamic phase transition measurements of the polymers are complemented by ATR-FTIR and quantitative 1H-NMR spectroscopic studies to systematically investigate the nature and molecular-level mechanism of the interaction. In stark contrast to the known behavior of the strongly-hydrated cations, through the temperature-controlled ATR-FTIR investigations it is found that carbonyl moieties are not the primary sites of interaction. Instead, it is found that these weakly-hydrated, ‘greasy’ cations preferentially interact with the most hydrophobic groups on the polymer: the isopropyl group on the PNIPAM side-chain, as revealed by a quantitative externally-referenced 1H-NMR methodology developed to elucidate ion-macromolecule interactions. The binding generally follows a Langmuir-type saturation behavior and exhibits site-specific dissociation constants as low as KD ≈ 0.2 M. This unprecedented, hydrophobically-mediated interaction between weakly-hydrated tetraalkylammonium cations and neutral macromolecules is then demonstrated to be a general mechanism and is shown to extend to polymers of vastly different molecular architectures. The results presented, thus, signify a new, more expansive view of cationic Hofmeister effects, where the far weakly-hydrated region of the series interacts with a novel mechanism entirely unlike that of other cations. Item Open AccessRole of silica in the self-assembly of salt-surfactant mesophases and synthesis of mesoporous metal oxides(Bilkent University, 2023-07) Ullah, Najeeb; Dağ, ÖmerIn recent years, mesoporous metal oxides have attracted great attraction due to their unique optical, electrochemical, and catalytic properties. Mesoporous nickel oxide (m-NiO) is a p-type semiconductor, versatile in its application due to its high surface area, and has been investigated towards electrochromic devices, electrodes, supercapacitors, and catalysts. The electrochemical properties of NiO depend on its morphology, surface area, and particle size. In this thesis, mesoporous nickel oxide has been synthesized by combining soft templating (molten salt-assisted self-assembly method) and hard templating methods to attain a high surface area. Homogeneous aqueous solutions of nickel(II) nitrate hexahydrate ([Ni(H2O)6](NO3)2), TMOS (as silica source), and two surfactants, CTAB (charged surfactant) and C12E10 (nonionic surfactant) are stable only if a concentrated nitric acid is added before the TMOS addition. In the absence of nitric acid, TMOS hydrolyzes and condenses quickly, resulting in silica precipitation. The silica precipitation also occurs by using other salts, such as nickel(II) chloride hexahydrate, nickel(II) sulfate hexahydrate, cobalt(II) nitrate hexahydrate, and manganese(II) nitrate tetrahydrate. The silica precipitate is characterized by ATR-FTIR, small-angle, and wide-angle XRD and N2 adsorption-desorption measurements. The diffraction lines at 1.7 and 23o, 2θ, indicate the formation of mesostructured amorphous silica, in which the surfactant species fill the pores. . The silica precipitate is calcined at 450 oC for two hours to remove the surfactant completely, and characterized by ATR-FTIR, small-angle and wide-angle XRD measurements, N2- adsorption-desorption analysis and SEM-EDX techniques. The maximum surface area (1395 m2/g) is obtained from the cobalt(II) nitrate hexahydrate salt, and the EDX analysis confirms that there is no element other than silicon and oxygen in its elemental detection limit. The homogeneous, stable aqueous solutions of the nickel(II) nitrate hexahydrate ([Ni(H2O)6](NO3)2), HNO3, TMOS (as silica source), and two surfactants, CTAB (charged surfactant) and C12E10 (nonionic surfactant) solution is drop-casted on a glass slide to form a mesophase and analyzed by small-angle XRD, ATR-FTIR and POM techniques. The diffraction lines at 1.5 and 1.6o, 2θ, show the formation of ordered lyotropic liquid crystalline mesophases. The mesophases are then calcined at different temperatures (from 250 to 500 °C), to obtain m-NiO/SiO2 powders and characterized by ATR-FTIR, XRD measurements, N2- adsorption-desorption analysis, and SEM-EDX techniques. The XRD patterns show broad lines at small- and wide-angles, indicating the formation of m-NiO/SiO2 at 300 °C, where the pore-walls are made up 2.6 nm crystalline NiO coated amorphous silica . The NiO particle size (on the pore wall) grows with increasing annealing temperature, and at 500 °C, the particle size reaches 7.9 nm. This is also supported by the BET surface area that decreases at higher temperatures. At 300 °C, the BET surface area is 305 m2/g, which drops to 174 m2/g at 500 °C. However, the pore size of m-NiO/SiO2 does not responds to annealing temperature. It means that the pore walls grow in 2D space rather than 3D due to the presence of silica as a hard template. Therefore, combining the hard- and soft-templating methods can efficiently synthesize the crystalline materials with a high surface area. The m-NiO/SiO2 films can be coated over the FTO glass and calcined at different temperatures to fabricate the electrodes for oxygen evolution reaction (OER). During CV measurement, the NiO pore-walls get oxidized to NiOOH and reduced to Ni(OH)2 in the back cycle. Moreover, overpotential that is determined for the OER improves with the usage of the electrode, independent of the electrode thickness. Item Open AccessUtilization of ethanol to enhance photocatalytic NOx oxidation and storage on TiO2(Bilkent University, 2023-06) Türk, Ahmet Arda; Özensoy, EmrahNitrogen oxides (NOx), especially nitric oxide (NO) and nitrogen dioxide (NO2) severely affect human health. In this regard, semiconductor photocatalysis present an appealing approach, since the only requirements for this procedure are sunlight, water and oxygen which are naturally abundant. Despite its favorable properties like chemical inertness, long-term stability and low cost, titania (TiO2) has a lower NOx abatement performance due to its low selectivity towards nitrites/nitrates as final product. In this work, we report a simple monohydric alcohol impregnation protocol at mild temperature range to synthesize colored TiO2 nanoparticles for efficient photocatalytic NOx oxidation and storage (PHONOS) application under UVA illumination. The ethanol induced coloration of commercial benchmark TiO2 (P25) and photocatalytic activity for NOx abatement were observed to be dependent on heat-treatment temperature; the highest activity was obtained at 150 °C. Comprehensive analyses of the optimized photocatalyst suggest the presence of surface functionalities of adsorbed formic acid and acetate. The doping of TiO2 with these in situ generated impurities results in the generation of Ti3+ and oxygen vacancies (Vos) (intrinsic defects) which are aimed to be observed using X-Ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy and Diffuse Reflectance UV Visible Spectroscopy (DR-UV-Vis). These fine-tuned materials demonstrated superior photocatalytic performance surpassing conventional P25 benchmark in short (1 h) and long term (15 h) evaluation studies. Special attention has been paid to the selectivity of the designed photocatalyst toward nitrate/nitrite formation and CaO was introduced as NOx storage domains to further improve the stability of best performing photocatalysts for extended time period. Item EmbargoFabricaiton, characterization, and electrolysis of mesoporous CaFe2O4 thin film electrodes(Bilkent University, 2023-06) Raza, Hamid Ali; Dağ, ÖmerTransition metal ferrites have attracted the attention of many scientists because of their low cost, high earth abundance, low band gap, and biocompatibility. They can be prepared in different morphologies, and because of this, they may have a high surface area and excellent electrochemical and photoelectrochemical properties. In this thesis, we have prepared mesoporous calcium iron oxide (CFO) thin films using the molten-salt assisted self assembly (MASA) method and analyzed its electrochemical applications for oxygen evolution reaction (OER). The clear and homogeneous aqueous solution of metal salts (Calcium nitrate tetrahydrate, iron (III) nitrate nonahydrate) and surfactants (cethyltrimethyl ammonium bromid, CTAB, and C12H25(OCH2CH2)10OH, C12EO10) were coated on microscope glass slides by various coating techniques to obtain mesophases. Later on, the mesophases and their aging process were analyzed by the small-angle XRD measurements, ATR-FTIR and POM. Diffraction lines between 1 and 5°, 2θ, indicate the formation of ordered lyotropic liquid crystalline mesophases. These mesophases were subjected to calcination at various temperatures, and the powders obtained were further characterized by wide-angle XRD measurements, SEM, EDX, TEM, XPS, ATR-FTIR, and N2-adsorption and desorption techniques. The calcium iron oxide in highly crystalline form are prepared at 800 °C, having thin film morphology. Interestingly, we are able to retain the porous structure even at such a high temperature. The amorphous phase contains calcium carbonate as a side product that was confirmed by ATR-FTIR, XRD and XPS data. The maximum surface area of mesoporous material is 145 m2/g, while water being used as a solvent. Similarly, we prepared the same materials using different precursors (chlorides) and solvent (ethanol) to see the effect of counter anion and solvent on the porosity, self-assembly, morphology, and electrocatalytic performance of the material in the OER. We observed that while using chloride precursors, the material was quite crystalline even at low calcination temperature, i.e., 300 °C. Iron oxide forms at low temperatures and with the increase in temperature, it finally transforms to calcium iron oxide. But in this case, the materials are not as porous and display a surface area of only 5 m2/g at 300 °C. Similarly, we also characterized these materials using the above-mentioned techniques. While using ethanol as a solvent, keeping nitrate precursors the same, and using two different mole ratios of calcium and iron (2:4, 3:6), we also tried to elucidate the effect of solvent on morphology and catalytic properties of materials. In this case, we observed that the surface area did not drop immediately (as in the case of water) but gradually. The maximum surface area, obtained are almost similar to the material prepared by water as a solvent. All the solutions mentioned above (prepared by using different precursors, solvent, and mole ratios) are coated (by dip-coating) on the graphite rod to determine the catalytic activities by various electrochemical experiments (cyclic Voltammetry (CV), chronopotentiometry (CP), and chronoamperometry (CA)). Electrodes are quite stable in all cases, even in harsh conditions (CP at 100 mA for 2 h). Also, enhanced activity may be because of reduced resistance and increased conductivity with the usage. In all cases, the minimum Tafel slopes are almost similar, and vary between 47 and 83 mV/dec. The overpotentials at various current densities are 260 mV for 1 mA/cm2, about 450 mV for 10 mA/cm2, and about 700 mV for 100 mA/cm2. Additionally, effect of the coated material's thickness on the electrocatalyst's activity is also investigated. It has been found that by decreasing the amount of coated material (by diluting up to 100 times), there is no change in the activity of the material. Finally, our results indicate that these types of energy material's (CFO) performance depends on the surface's characteristics rather than the coating material's thickness or the pores' size. Also, we found it unnecessary to waste a large amount of metal salts to fabricate these materials; OER performance is similar regardless of coating thickness. Therefore, the surface reaction is the primary factor in electrode activity, with pore shape being the critical characteristic. Item Open AccessSpongy polydimethylsiloxane preparation and its applications for soft robotics(Bilkent University, 2022-09) Ilyas, Muhammad; Baytekin, BilgeSoft Robotics has come to the fore in the last decade as a new way of conceptualizing, designing, and fabricating robots. Soft materials empower robots with locomotion, manipulation, and adaptability capabilities beyond those possible with conventional rigid robots. The field of soft robotics utilizes compliant architects to minimize machine complexity and approach biological systems' mechanical and sensing capabilities. Recently, soft (i.e., compliant, and extensible) materials and structures have enabled machines capable of versatile locomotion as well as analogs for caterpillars, fish, jellyfish, and octopus tentacles. With reduced control complexity, these soft machines allow natural motion through continuous deformation and interact gently with fragile objects. The porous, elastic polymers are attracting the attention of researchers in this regard. Here, we demonstrate a facile method for fabricating the lightweight, low-density, elastic PDMS spongy material using sugar as a porogen for different soft robotics applications. The poroelastic material can hold the weight of the robot’s body as legs. This PDMS sponge also successfully demonstrates the application of oil-water separation material for swimming robots. The recyclability of absorption and ability to separate oil from water at different pH levels demonstrate that this material can be effectively used in various conditions. A solvent-light responsive biomimetic soft gripper engineering was investigated by changing the degree of crosslinking and successfully manipulating the swelling of PDMS porous material in different organic media. This soft gripper can lift and release objects in response to NIR light. Item Open AccessElucidation of the denaturation mechanism of urea on macromolecules in aqueous medium(Bilkent University, 2022-09) Mutlu, Ferhat; Okur, Halil İbrahimThe urea molecule is a well-known denaturant for a wide range of macromolecules. To date, there is no unified molecular-level explanation for urea-induced denaturation of all macromolecules. As a result, considerable effort has been directed toward this subject in recent years, because osmolyte protein interactions are of central interest and have implications ranging from polymer physics to cell biology. Detailed urea denaturation mechanisms, focusing on the entropically driven formation of urea clouds, urea induced cross-linking mechanism, and osmolyte clouding around macromolecules, have been proposed in the literature. However, no agreement has been reached on the molecular machinery of urea denaturation. In this thesis, the urea-induced solubility changes of macromolecules in aqueous solutions were investigated by utilizing the lower critical solution temperature (LCST) of poly (N - isopropylacrylamide) (PNIPAM) and poly (N,N-diethylacrylamide) (PDEA) as a function of urea concentration up to 6.0 M. Due to the lack of suitable probing methods for the collapsed state of interested macromolecules, a temperature-controlled ATR – FTIR spectroscopy based method was developed to explore the interaction between urea and the collapsed state of macromolecule. LCST measurements revealed that the solubility of PDEA increases with increasing urea concentrations, whereas PNIPAM salts-out from the solution monotonically, despite the fact that both polymers have similar molecular structures. Temperature gradient ATR-FTIR measurements were carried out to further investigate this discrepancy. First, no favourable urea accumulation towards the collapsed form of macromolecules was observed up to 6.0 M urea, which puts doubt on the urea clouding mechanism. Moreover, at elevated (> 3.0 M) urea concentrations, the collapsed form of the PNIPAM and PDEA accumulated towards the cooler parts of temperature gradient in solution, indicating the preferred form of the macromolecule is the soluble (uncollapsed) form. These surprising results indicate that both PNIPAM and PDEA prefers the soluble form at elevated urea concentrations above the LCST. As a molecular mechanism, the urea molecules act as a "glue" between the amide groups of PNIPAM, bringing intra- and inter-molecular parts of the macromolecule into close proximity, and act as a collapsed form of macromolecules. Apparently, such a mechanism is not valid for the PDEA. Our findings shed new light not only on aqueous phase phenomena, but also on the aggregated (collapsed) phase of macromolecules in aqueous medium. Item Open AccessThe pursuit of an ideal coordination environment of the catalytic site for water splitting(Bilkent University, 2022-07) Ahmad, Aliyu Aremu; Karadaş, FerdiThe construction of catalysts from cheap materials and exquisite tuning of the coordination environment of the active site is pivotal to the development of a highly active sustainable water-splitting catalyst. Although recent years have seen tremendous growth in the application of Prussian Blue Analogues (PBAs) as non-noble catalysts for water splitting, the effect of the structural coordination of the active sites on the activity of a Prussian blue (PB) catalyst is yet to be explored. Herein, using two simple synthetic strategies, we show that manipulating the coordination environment of the catalytic sites affects the morphology, electronic properties, and eventually the catalytic activity of PBAs. Moreover, this study mimics natural photosynthesis by using solar light as an energy source. First, we demonstrate that the water oxidation activity and stability of a Co–Fe PBA can be tuned by coordinating bidentate capping ligands to the catalytic cobalt sites. Structural characterization studies reveal that the ligand decorated structures are of relatively lower dimensionality and they retained their network structures even after photocatalysis. Photocatalytic water oxidation studies indicate that coordination of one equivalent ligand group to the catalytic cobalt sites (CoL–Fe) results in an enhancement of about 50 times in upper-bound turnover frequency (TOF), while coordination of two equivalent ligand groups to the catalytic cobalt sites (CoL2–Fe) lead to an inactivity, which is attributed to the lack of coordination of water molecules to the catalytic sites. In addition, computational studies support experimental observation by showing that bidentate pyridyl groups enhance the susceptibility of the rate-determining Co(IV)-oxo species to the nucleophilic water attack during the critical O−O bond formation. We found in the second study that the replacement of [Fe(CN)6]3− unit with a square planar [Ni(CN)4]2− building block drastically changes the electronic environment and catalytic properties by converting the PB structure from 3D to a 2D layered structure, and we utilized it for the first time for photocatalytic hydrogen evolution reaction. We synthesized a 2D cyanide-coordination compound [Co–Ni] and performed a complete structural and morphological characterization that fully supports our synthetic claim. Relying on its exposed facets, layered morphology, and abundant surface-active sites, [Co–Ni] can efficiently convert water and sunlight to H2 in the presence of a ruthenium photosensitizer with an optimal evolution rate of 30,029 μmol g−1 h −1, greatly exceeding that of 3D PBA frameworks and top-ranked catalysts operating under the same condition. Furthermore, [Co–Ni] retains its structural integrity throughout a 6-hour photocatalytic cycle, which is confirmed by XPS, XRD and Infrared analysis. Overall, these two strategies signify the importance of the coordination environment of the active sites in exploiting structure/morphology and optimizing the activity of the catalyst. Item Open AccessCO2 activation on MnOx /Pd(111) model catalyst(Bilkent University, 2022-07) Anıl, Arca; Özensoy, EmrahCO2 is an atmospheric pollutant (i.e., a greenhouse gas) and it can be converted into valuable chemicals such as methanol, methane, and formic acid. However, CO2 reduction is a challenging process due to the thermodynamic stability of CO2. In this work, we focus on the activation of CO2 by using an atomically well-defined MnOx/Pd(111) planar model catalyst. Pd(111) surface can dissociatively adsorb hydrogen molecules, but CO2 does not strongly bind to the Pd(111) surface. On the other hand, MnOx nano-structures can facilitate the activation of CO2 due to the presence of acid and base sites on the metal oxide surface. Therefore, MnOx/Pd(111) was chosen as a model catalyst to investigate catalytic CO2 activation. A multifunctional ultra-high vacuum system with quadrupole mass spectrometer (QMS), X-ray photoelectron spectrometer (XPS), and low energy electron diffraction (LEED) was used to perform the experiments. Manganese thin film growth mechanism on Pd(111) surface was determined by using XPS. Manganese was evaporated on Pd(111) substrate at two different temperatures (i.e., 85 K and 300 K). Formation of products after the dosing of the reactants on the MnOx/Pd(111) surface was examined via temperature programmed desorption (TPD). For both cases, formed manganese oxide thin film was investigated by using XPS to estimate the relative, Mn0, Mn2+ and Mn3+ surface concentrations. Prepared manganese film on Pd(111) at 300 K could activate CO2 to CO, which is a valuable chemical for the chemical industry. To prepare smaller clusters, manganese was evaporated on the Pd(111) single crystal surface at 85 K. At moderate manganese coverage, carbonate CO32- formation was detected on the MnOx/Pd(111) interfacial sites. Item Open AccessThe formation of Liesegang patterns of cobalt hexacyanoferaate Prussian blue analogue in polyacrylamide gels(Bilkent University, 2022-01) Tootoonchian, Pedram; Baytekin, BilgeThe formation of patterns in nature has always fascinated scientists who try to understand the mechanism behind this complex phenomenon. Liesegang patterns (LPs) are one category of periodic precipitations patterns formed by the reaction- diffusion (RD) system, studied and modeled by chemists and mathematicians for over a century. The majority of the focus has been on understanding the formation of these patterns, modeling them, and studying the effect of different gel types, gel concentrations, and inner and outer concentrations on various systems. There are only a few examples in the literature showing the effect of temperature, electric or magnetic field, and mechanical force on LPs and controlling the pattern formation by these external stimuli, and more importantly, showing a possible application of these systems. In this work, we show a novel approach to form LPs in a hydrogel medium, track the band formation with temperature, characterize each band, and last but not least, suggest a useful application for these LPs. This study mainly concentrates on the pattern formation of cobalt Prussian blue, but LPs of some other Prussian Blue Analogues (PBAs) are also shown. First, we propose a new method to form PBAs LPs formation. Then, we track the band formation by changing the system's temperature. To understand the effect of temperature on the microscale, we characterize each band using SEM, EDX, and XPS to analyze particles size and Co/Fe ratio. Finally, we use each band as electrocatalysts for water oxidation reactions in water splitting. Item Open AccessNovel glycerol dry reforming catalysts with monometallic and bimetallic active sites(Bilkent University, 2021-09) Akyürek, Salim Can; Özensoy, EmrahNovel glycerol dry reforming catalysts with monometallic (Ru) and bimetallic (Ru and Ni or Ru and Co) active sites which are supported on a custom-design ternary mixed oxide support material (i.e., Al2O3-TiO2-ZrO2, AZT) with varying compositions were examined. Characterization of the synthesized catalytic system was carried out with XRD, Raman, BET, XPS, ICP-MS, SEM, and EDX techniques. Structure of the Ru active sites as a function of Ru loading was also investigated with in-situ FTIR spectroscopy via CO adsorption. Catalytic reactivity results revealed that 1 wt.% Ru/AZT70 catalyst can outperform the 1 wt.% Ru/La2O3-ZrO2 catalyst in GDR reaction, where the latter catalyst is known to be the best catalyst in the literature for GDR reaction. 0.5wt.% Ru/AZT70 catalyst showed close activity compared to 1wt.% Ru/AZT70 catalyst. Furthermore, catalytic promotional effect of Ni for low Ru loadings in GDR reaction was also demonstrated. Item Open AccessHighly-dispersed iridium catalysts with sub-nanometer diameters for carbon monoxide oxidation(Bilkent University, 2021-09) Hosseini, Seyedsaber; Özensoy, EmrahNovel catalytic architectures composed of catalytic centers with sub-nanometer diameters for CO oxidation reaction were designed, synthesized, and characterized. Accordingly, well-dispersed iridium precious metal active sites were supported on various catalytic support materials. Namely, magnesium oxide (MgO), ceria (CeO2), lanthana-zirconia (La2O3–ZrO2) and titania-zirconia (TiO2–ZrO2) systems were chosen as different support systems. The favorable catalytic effect of highly-dispersed Ir active sites with sub-nanometer diameters were demonstrated in flow-mode catalytic performance tests, where the lower loadings of highly dispersed Ir sites showed comparable catalytic activity in CO oxidation to that of bigger Ir clusters with higher metal loading. Furthermore, influence of the catalyst pre-treatment conditions (e.g., reduction in H2, oxidation in O2, and calcination in air) on the catalyst structure and performance were also studied via XRD, Raman, BET, XPS, TEM, EDX, and in-situ FTIR spectroscopy techniques. Our results indicate that in all the catalytic systems, high-dispersion Ir sites can be generated on supports where Ir exists as small clusters with < 1 nm particle size. Moreover, catalyst pretreatment conditions revealed noticeable alterations in the catalyst structure in terms of average support particle size, reduction extent of the support, specific surface area, pore volume, pore size, and Ir oxidation state. Finally, catalytic performance results indicated that under reaction conditions yielding close to 100% CO conversion, 0.2 and 0.5 wt.% Ir catalysts led to comparable performance to that of 1 wt.% Ir catalyst demonstrating the advantage of catalytic systems with highly dispersed sub-nanometer diameter active sites with extremely low metal loading. Item Open AccessSynthesis of novel photoactive nanoparticles towards phototherapy(Bilkent University, 2021-09) Duah, Ishmeal Kwaku; Tuncel, DönüşNanomaterial-based compounds are attracting a lot of interest because many functionalities such as photoactive units, drugs and targeting groups can be combined on one platform to fight against infectious diseases and cancer. Recently, conjugated polymer-based nanomaterials have proven to be effective photosensitizers for antibacterial and photodynamic cancer therapies owing to their unique electronic and optical properties, including high singlet oxygen generation capacity, strong light-harvesting ability and its tunable optical spectrum. In this study, novel cross-linked conjugated polymer nanoparticles-based photosensitizers namely conjugated polymer-porphyrin nanoparticles (CPPN) and cross-linked conjugated polymer nanoparticles (PCP) were synthesized. The nanoparticles were prepared via nanoprecipitation using cucurbituril-(CB6)-catalyzed azide-alkyne cycloaddition (CB6-AAC) reaction. Conjugated polymer-porphyrin nanoparticles (CPPN) are advantageous than micelles incorporating porphyrin systems. For micelles containing porphyrin systems, the phototherapy effect of the porphyrin can only be seen after the porphyrin is released by conditions such as a change in pH, which is not the case for conjugated polymer-porphyrin nanoparticles (CPPN). The nanoparticles demonstrated high reactive oxygen species (ROS) generation efficiency which is evident in the antibacterial and anticancer photodynamic therapy (PDT) experiments. From the antibacterial photodynamic therapy experiment, when Gram-negative (Escherichia coli, E. coli) and Gram-positive (Bacillus subtilis, B. Subtilis and Staphylococcus aureus, S. aureus) bacteria were incubated with CPPN (20 µg/mL) and irradiated with white light (22 mW/cm2) for 10 min, more than 3.5-log reduction in colony-forming units (CFUs) was recorded for CPPN. Furthermore, when E. coli and B. subtilis were treated with PCP (24 µg/mL) and illuminated with light, about 3-log killing efficiency was recorded. However, in the dark, the nanoparticles demonstrated minimal dark cytotoxicity against the model bacteria. In addition, the anticancer photodynamic effect of CPPN and PCP on MCF-7 breast cancer cells was investigated. When MCF-7 breast cancer cells were treated with PCP in the dark and under light irradiation, almost all cells were alive for both cases. It may be that PCP could not generate enough reactive oxygen species to kill the cells. When MCF-7 breast cancer cells were treated with CPPN in the dark, the cell viability was 96% and upon irradiation with light for 20 minutes, the cell viability decreased to about 4%. Moreover, conjugated polymer-porphyrin-gold nanoparticles (CPPN-Au) and cross-linked conjugated polymer-gold nanoparticles (PCP-Au) nanoparticles were prepared, but due to the instability of the nanoparticles, they could not be used in phototherapy. Item Open AccessElectrochemical noise investigation of lithium based batteries(Bilkent University, 2021-09) Karaoğlu, Gözde; Ülgüt, BurakWith the widespread use of portable technological devices such as smart phones, laptops, tablets and smart watches, and electric cars in recent years, the need for energy is also increasing. Batteries based on lithium chemistry are the primary choice of the portable technology industry due to their small size, light weight, rechargeability and high energy density, and therefore, the interest in lithium-based batteries has been an important academic research topic. Electrochemical noise measurements are commonly used measurement methods in the corrosion research. In recent years, electrochemical noise measurements have been employed as a non-destructive testing method, especially in lithium-based batteries, but the measurement methods and analyses methods presented in the literature are insufficient. In this thesis, electrochemical noise measurement methods and common analyses methods in lithium-based batteries are summarized, a new approach how to make accurate noise measurement and analysis, and under which conditions lithium-based batteries show noise increase is introduced. The use of lithium alloy as the anode material in rechargeable batteries causes its energy density to be less than the energy density provided by pure metallic lithium used in non-rechargeable batteries. For this reason, the use of pure metallic lithium in rechargeable batteries is extremely important for industrial development. The examination of pure metallic lithium batteries with electrochemical noise, which is a non-destructive measurement method during charging and discharging, and imaging with optical microscope in situ and after death with spectroscopic analysis methods are presented. Item Open AccessTotal synthesis of biologically active fungal natural products daldiquinone and bulgarein, and intramolecular Diels-Alder reactions for fluoranthene synthesis(Bilkent University, 2021-06) Ahmadlı, Dilgam; Türkmen, Yunus EmreNatural products continue to play a significant role in drug discovery and be a substantial source for novel pharmaceutical drugs. Total synthesis of biologically active natural products is critical for deciphering how natural products regulate cellular and other biological processes and, structure determination. In addition, the total synthesis of natural products has also been a stimulus for the discovery of new methodologies and reactions. The fungal natural product daldiquinone (15), which possesses a highly oxidized binaphthyl skeleton, was isolated in 2018 from Daldinia concéntrica, and was shown to have antiangiogenesis activity against HUVECs with an IC50 value of 7.5 M. Another fungal natural product bulgarein (1) was first isolated in 1976 from the fungus Bulgaria inquinans, and was shown to induce topoisomerase I-mediated DNA cleavage. However, as in the case of daldiquinone (15), total synthesis of bulgarein (1) has yet to be reported. In this work, we report the first total syntheses of daldiquinone (15) and bulgarein (1) starting from the commercially available 1,8-DHN (1,8-dihydroxynaphthalene, 1,8-naphthalenediol) via a concise route. Pd-catalyzed Suzuki coupling and C-H arylation reactions between functionalized naphthalenes and hypervalent iodine-mediated double oxidation of phenol to o-quinone were employed as key steps. Thanks to their thermal stability and electronic properties, fluoranthene derivatives have widespread medicinal chemistry and organic optoelectronics applications. A significant number of fluoranthene-based natural products are known, including bulgarein (1). Although many procedures have been developed to synthesize fluoranthenes, practical and modular strategy for synthesizing many substituted unsymmetrical fluoranthenes is still desirable. In this work, we report a novel approach to achieve modular syntheses of fluoranthene derivatives based on intramolecular Diels-Alder reaction. Item Open AccessSynthesis & characterization of mesoporous zinc cobaltite thin films and its electrochemical application for OER(Bilkent University, 2021-07) Kalaycı, Nesibe Akmanşen; Dağ, ÖmerTransition metal cobaltite materials were widely used as electrode material due to their excellent electrochemical performance, flexibility to be prepared with different morphologies and, high surface area. In this thesis, mesoporous zinc cobaltite thin films were synthesized in cubic spinel structure via molten-salt assisted surfactant assembly (MASA) method with a high surface area and its electro-catalytic performance in oxygen evolution reaction (OER) was analyzed. Clear and homogenous aqueous solution of surfactants (P123 and CTAB), zinc nitrate hexahydrate and cobalt(II) nitrate hexahydrate (as precursors) are coated on glass substrate to obtain mesophases, thereafter mesophases are calcined to synthesize mesoporous zinc cobaltite (denoted as m-ZnCo) as powder. m-ZnCo-60 (with a total salt/P123 ratio of 60) samples were synthesized with a smooth film morphology and maximum surface area of 102 m2/g. The mesophases with different compositions were analyzed using X-Ray Diffraction (XRD) technique. The line(s) between 1.5 and 2°, 2θ, in the XRD pattern is an indication for the formation of ordered lyotropic liquid crystalline mesophase. Aging of the mesophase was monitored via XRD and POM techniques to establish its stability. The stable mesophases were used to synthesize m-ZnCo film and powder samples. The powder samples were collected after calcination process and characterized by XRD, N2 adsorption-desorption, SEM, HR-TEM techniques. The precursor solutions were spin coated on half of 1cm x 2cm size FTO glasses, then calcined and used in three-electrode system as working electrodes. The electrocatalytic performance of the materials was analyzed by cyclic voltammetry (CV), chronopotentiometry (CP), and chronoamperometry (CA) experiments for oxygen evolution reaction (OER). All electrodes were stable up to 100 mA/cm2 current density and displayed minimum Tafel slope value of 41 mV/dec. Mesoporous zinc cobaltite materials were also synthesized through precursor solutions without CTAB. Removing CTAB from the synthesis results films with rougher surface and reduced crystallinity. Same techniques were also employed for characterization. The prepared electrodes of non-CTAB samples exhibited a lower Tafel slope of 40 mV/dec and overpotential of 256 mV at 1mA/cm2 current density. In addition, silica templated mesoporous zinc cobaltite was synthesized by adding TMOS to the precursor solution of ZnCo-60 to increase the surface area, the calcined samples were denoted m-ZnCo-60-S20-300 (S20 is represents 20 TMOS/P123 mole ratio). The m-ZnCo-60-S20-300 sample has the highest specific surface area of 215 m2/g. However, despite having higher surface area due to high resistance of silica material, silicated samples exhibited higher overpotential values.