Browsing by Subject "Photochemistry."
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Item Open Access Cascading logic gates using ion signals generated by photolabile caged compounds(Bilkent University, 2013) Atılgan, AhmetCaged compounds have attracted great attention due to their use in the elucidation of numerous biochemical processes. Photolabile caged compounds release covalently bound moieties upon exposure of ultraviolet light. Releasing the active species in such a controlled manner enables concentration of the molecules to be manipulated in spatiotemporal way. Getting inspired from the knowledge of cellular information transfer through second messenger systems which Ca and Zn ions play important role, we synthesized a photolabile caged Zn(II) compound so that we benefit from its controlled ion release feature, so as to integrate two molecular logic gates physically. For that reason, a molecular logic operation was designed and the released ion was used as information carrier from one logic gate to other. After proving its practicality, we tested same principle for higher molecular logic systems. To do that, photolabile caged Zn(II) compound and previously proved supermolecule with coupled AND logic gates were physically integrated. Results proved that photolabile caged Zn(II) compounds is a useful way to combine two separate logic gates by means of free zinc ions. From this point of view, the approach physical integration of molecular logic gates through a metal ion or compound might be a solution for building more complex molecular logic systems.Item Open Access Fabrication of an on-chip nanowire device with controllable nanogap for manipulation, capturing, and electrical characterization of nanoparticles(Bilkent University, 2008) Uran, CanOne of the major challenges in nanofabrication commonly arises from the necessity to integrate nanostructures (e.g., nanoparticles) on the same chip with microcomponents (e.g., microelectrodes) that are orders-of-magnitude larger in size. For example, in order to make electrical contacts to colloidally synthesized nanoparticles (typically 1-100 nm in size) by integrating them with microelectrodes (typically in the few micrometers range on the critical side), a large size mismatch that easily ranges from 1:10 to 1:10,000 is required to be handled delicately for successful nano-to-micro integration. This necessitates the ability to manipulate and integrate nanoparticles with a sufficient level of precision on the microchip. In this thesis, to provide a convenient solution to this challenging problem, we proposed and demonstrated for the first time an onchip nanowire device that features a controllable nanogap in its architecture for capturing and electrical characterization of nanoparticles in the gap, all fully integrated on the same microchip. Our innovative approach relies on the use of dielectrophoretic electric-field assisted self-assembly of our segmented nanowires to construct a nanoscale device platform. For this purpose, we synthesized gold-silver-gold segmented nanowires and dielectrophoretically aligned them across our microfabricated array of electrodes. Subsequently, we selectively removed the middle silver segment to open a gap in the nanometer size between the self-aligned gold end segments. Using dielectrophoretic assembly once more, we captured nanoparticles in these nanogaps for further electrical characterization. One of the key benefits in our approach was that the aligned nanowires automatically provided electrical contacts to the captured nanoparticles to allow for electrical probing at the nanoscale. Our innovative approach enabled convenient full integration from nanoparticles to nanowires to microelectrodes to macroprobes on a single chip, spanning a size range of more than six orders of magnitude.Item Open Access Nitroolefin functionalized bodipy dyes for protein labeling(Bilkent University, 2013) Turgut, HaticeProtein labeling has significant importance in terms of visualizing dynamics of proteins, cell-cell interactions, mechanisms of life cycles of proteins, etc. Proteins are labeled by either synthetic or natural molecules with purposes such as analysis of 3D structures, determination of turnover number, covalent modifications and tracking protein-protein interactions. In addition to this, sensing and signalling thiol groups have gained popularity recently. Nitroolefin groups on dyes are good Micheal acceptors which undergo fast and selective reaction with thiol moieties. With this knowledge, in this study, we aimed to obtain derivatives of BODIPY dyes having nitroolefin substituents on its different positions. Nitroolefin functionalization of BODIPY dyes was targeted to result in conjugation of nitroolefins with thiol groups such as those belonging to cysteine residues on proteins. Three different nitroolefin functionalized BODIPY dyes have been designed, synthesized and characterized successfully. Incorporating triethylene glycol (TEG) units onto BODIPYs increased water-solubility of the molecules. To prove bioconjugation of the dyes with proteins, absorbance and emission changes were recorded after reaction with both L-cysteine and Bovine Serum Albumin (BSA) and large spectral changes were obtained. The result suggests that nitroolefin functionalization of BODIPY dyes is a promising way to sense biological thiols and hence labeling proteins having thiol groups.Item Open Access Novel multichromophoric energy transfer cassettes based on functionalized BODIPY dyes(Bilkent University, 2012) Çeltek, GizemEnergy necessity is one of the leading problems in the world due to the developing technologies and strategies. There are many energy sources, which are being used for years, however; conversion and transfer of the energy is a problem in many fields due to energy loss. In this manner, the efficiency of energy transfer is very crucial. For this purpose, we have designed multichromophoric molecules, which can absorb the light with donor parts, then transfer the energy to the acceptor site. During this process, energy loss is tried to be prevented by lowering the distance between the donor and acceptor Boradiazaindacene (BODIPY) molecules. Three different energy transfer cassettes are synthesized and characterized. The design of the supramolecule, in means of spectral overlap and distance between the donor and the acceptor site are observed to affect the energy transfer efficiency. Through functional design, these molecules absorb and emit light in different wavelengths. Substation of distyryl and tetrastyryl groups to the acceptor BODIPY core changes the emission and absorption maxima. Increasing number of styryl groups attached to the molecule shifts the spectrum to the red part of the visible region. Through rational design, these molecules can be used in applications of energy transfer and broad spectrum absorber purposes.Item Open Access Optimization of orthogonal reactions on bodipy dyes for one-pot synthesis of light harvesting dendrimers(Bilkent University, 2013) Bekdemir, AhmetFor more than a decade, synthetic organic chemistry has dealt with focusing on highly selective and efficient reactions that can proceed under mild conditions which would then be categorized under the term “orthogonal click chemistry”. These types of reaction have served number of applications for years as in peptide synthesis, homogeneous catalysis and development of supramolecular systems. On the other side, after a partial understanding of how photosynthetic bacteria and plants harvest solar radiation in order to carry their necessary carbon dioxide reduction reaction by converting light to chemical energy, artificial light harvesting systems have captivated a lot attention of scientists. Because today’s one of the biggest and inevitable problems is to discover/invent alternative energy sources/devices for future demands, these artificial light harvesting and solar concentrator systems are highly open for further development and optimization. However, like most other macromolecular systems, synthesis of these kind of devices should be straightforward so as to decrease the cost and to increase the efficiency. At this point, orthogonal click reactions, being mild and efficient synthetic models, can undoubtedly be worthwhile to consider as proper tools for easy preparation of light harvesting molecules. Here we propose a synthesis of thiol, Michael accepting groups, amine and isothiocyanate modified BODIPY dyes for light harvesting cascade preparation. Moreover, the optimization of Michael addition type thiol – ene reaction of these functionalized dyes has been discussed. Among methyl methacrylate, cyanoacetic acid and nitroolefin functionalizations, it was found that nitroolefin attached BODIPY dyes are the most reactive one. The achieved product has been investigated in terms of fluorescence and energy transfer.Item Open Access Photocatalytic nanocomposites for increased optical activity(Bilkent University, 2008) Tek, SümeyraTo combat environmental pollution, photocatalytic decomposition provides degradation of organic and inorganic contaminants near the surface of the photocatalyst nanoparticles by converting optical energy of the absorbed light into chemical energy for the redox reactions. However, photocatalytic activities of such semiconductor metal-oxide nanoparticles are limited with their bandgap energy that allows for optical absorption typically in the ultraviolet spectral range. Yet another limitation is that the photocatalytic activity of these semiconductor nanoparticles is substantially reduced when they are immobilized in solid thin films, resulting from their effectively decreased active surface area. But such immobilized nanoparticles are much more desired in industrial applications, e.g., for mass environmental decontamination and outdoors/indoors self-cleaning on large surfaces. To address these issues, in this thesis, we investigated and demonstrated the spectral behavior and time evolution of optical activity curves of immobilized TiO2 and ZnO nanoparticles. We studied the nanoparticle size effect for the optical activity and demonstrated significant increase in the resulting photocatalysis with decreasing the size of such immobilized nanoparticles for the first time. We obtained optimal excitation conditions for TiO2 and ZnO nanocomposite films separately. We achieved maximum optical recovery levels of 93% for TiO2 nanoparticles and 55% for ZnO nanoparticles at the excitation wavelengths of 310 nm and 290 nm, respectively, after optical irradiation with an excitation density of 7.3 J/cm2 , where we observed no optical recovery for their respective negative control groups (with no nanoparticles). In these comparative spectral studies, we showed strong correlation between the differential optical recovery and the photocatalytic activity. For further substantial enhancement in the near ultraviolet and visible spectral ranges, we also proposed and demonstrated the use of a unique combination of TiO2-ZnO nanoparticles integrated together into the same resin. In this novel approach, we observed higher levels of photocatalytic activity under optical irradiation at and above 380 nm compared to the cases of only TiO2 or only ZnO nanocomposite films with the same total metal-oxide nanoparticle density. At 400 nm in the visible, we accomplished an optical recovery level of ~30% with the combination of TiO2-ZnO nanoparticles together while this level was only ~14% for the TiO2 nanoparticles alone and ~3% for the ZnO nanoparticles alone under identical conditions. Even at 440 nm, we obtained ~20% optical recovery using the TiO2-ZnO photocatalytic synergy, despite the optical activity of the single type of nanoparticles alone close to the zero base-line of their control group. These proof-of-concept experimental demonstrations indicate that such TiO2-ZnO combined nanocomposite films hold great promise for efficient environmental decontamination in daylight.Item Open Access Spectroscopic characterization and charging(Bilkent University, 2008) Tunç, İlknurThe purpose of this work, is to investigate optical and electrical properties of bimetallic alloy and core-shell Au and Ag nanoparticles by optical spectroscopy and XPS, respectively. Several objectives have been pursued in achievement of the goals. First goal is to investigate the tunability of optical properties of bimetallic Au and Ag alloy and core-shell nanoparticles due to changes in composition and structure. The second goal is to study the possibility of charge-storage on single metal particles, especially on Au and Ag, and bimetallic alloy forms of the corresponding nanoparticles in solution. Within this framework, bimetallic Au-Ag alloy and coreshell particles are synthesized, then their electron-storage capacities in aqueous media by introduction of sodium borohydride is followed by spectral shifts in their surface plasmon resonance bands. Moreover, the parameters like composition, structure, affecting the charging ability of particles are reported by means of optical spectroscopy as well. In addition, electron storing/releasing capacities of Au and Ag nanoparticles and their kinetics are investigated. In the second part, main focus is to investigate optical and electric properties by surface modification through incorporating Au and Ag nanoparticles within dielectric shell (silica and titania). Therefore, small Au@SiO2, Ag@SiO2, and Ag@TiO2 core-shell nanoparticles with the metal core size ca. 5-7.5 nm and the shell size ca. 3-7.5 nm are synthesized and optical properties of these nanoparticles are studied. These nanoparticles are also analyzed by XPS under external biasing to get further understanding of their charging capacities. Additionally, we investigated incorporating metal nanoparticles within titania shell to provide enhanced photoactivity through the metal core by means of increased charging capacity.Item Open Access Surface enhanced raman scattering from Au and Ag nanoparticle coated magnetic microspheres(Bilkent University, 2008) Güvenç, Hacı OsmanA novel SERS substrate was prepared by coating Au or Ag nanoparticles onto magnetic microspheres prepared by a modified suspension polymerization method. The micron-sized magnetic microspheres were prepared in two steps: In the first step, inorganic core which consisted of oleic acid coated magnetic magnetite nanoparticles were prepared by co-precipitation method. The second step was the encapsulation of oleic acid coated magnetite nanoparticles by a modified suspension polymerization method. Magnetic microspheres were modified with amine functional groups in order to immobilize Au or Ag nanoparticles onto magnetic microspheres via amine groups of magnetic microspheres, however, a high background signal was obtained in Raman measurements due to the amine groups. Alternatively, Au or Ag nanoparticles were coated directly onto magnetic microspheres by hydroxylamine and sodium borohydrate reduction methods for Au nanoparticle coating and sodium borohydrate for Ag nanoparticle coating. For the first time, Au and Ag nanoparticle coated magnetic microspheres were prepared and used as SERS substrate successfully. The magnetic microspheres were characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), Energy dispersive X-Ray spectroscopy (EDX) attached to SEM, Raman spectroscopy and X-Ray Diffraction (XRD). The average size of magnetic microspheres is measured to be 22 µm from their SEM images. EDX analysis demonstrated that magnetic microspheres were coated with Au or Ag nanoparticles. Moreover, commercially available amine functionalized magnetic microspheres were immobilized with Au nanoparticles and its SERS activity was significantly than the Au nanoparticle coated magnetic microspheres prepared in this study. Enhancement factors for Au and Ag nanoparticle coated magnetic microspheres were calculated to be ca. 105 and 107 , respectively, however, in case of Au nanoparticle immobilized Spherotech magnetic microspheres, enhancement factor was only 2x102 using Rhodamine 6G as SERS probe. Interactions of aspartic acid with Ag and Au nanoparticles were followed by Raman spectroscopy at various pH values. pH dependent interactions of aspartic acid with Au and Ag metals were followed depending on pH for the first time. Protonation or deprotonation of amine or carboxyl groups on aspartic acid depending on pH of the solution affects the interacting functional groups with metal nanoparticles and increase in the signal of the corresponding group was measured. It is found that aspartic acid interacts through amine and carboxyl groups with Ag surface at low pH values and via only carboxyl groups at higher pH values. However, aspartic acid interacts with Au surface through amine and carboxyl groups at all pH values under investigation.Item Open Access Synthesis and characterization of near-ir emissive tetra styryl-BODIPY based light harvesting energy transfer cassettes(Bilkent University, 2011) Köstereli, ZiyaLight harvesting antenna systems are being used to harvest light through its antenna units. Using these systems, light is channeled into an acceptor chromophore and much more concentrated energy is obtained in acceptor unit with a specific wavelength. In this study, we have rationally designed and synthesized two different novel Förster-type light harvesting energy transfer cassettes which have large stokes shifts and emit in near-IR region. The first cassette has four boradiazaindacene (BODIPY) as donor groups and one tetrastyryl-BODIPY as an acceptor group. The second cassette has four distyryl-BODIPY units as donor groups and one tetrastyryl-BODIPY as an acceptor group. Click chemistry is successfully used to combine donor and acceptor groups to each other. Efficient energy transfer from donor groups to acceptor group in both cassettes was observed and characterized using emission spectrum, quantum yields and lifetimes. Energy transfer efficiencies and rate of energy transfer were calculated and it is demonstrated that there is more efficient energy transfer in cassette that has better overlap in donor emission and acceptor absorption spectrum which is in accordiance with expected behaviour for Förster-type of energy transfer cassettes.Item Open Access Titanium dioxide nanostructures for photocatalytic and photovoltaic applications(Bilkent University, 2008) Çakır, DenizIn this thesis, TiO2 nanostructures and their photocatalytic and photovoltaic ap- plications have been investigated by using the ¯rst-principles calculations based on density functional theory. We have concentrated on three di®erent systems, namely TiO2 clusters, nanowires and surfaces. TiO2 is widely used in various applications, since it is chemically stable in di®erent conditions, ¯rm under il- lumination, non toxic, and relatively easy and cheap to produce. Most of the technological applications such as photovoltaic and photocatalytic of TiO2 are mainly related to its optical properties. First of all, structural, electronic, and magnetic properties of small (TiO2)n (n=1{10) clusters have been studied. Various initial geometries for each n have been searched to ¯nd out the ground state geometries. In general, it has been found that the ground state structures (for n=1{9) have at least one dangling or pendant O atom. Only the lowest lying structure of n=10 cluster does not have any pendant O atom. In the ground state structures, Ti atoms are at least 4{fold coordinated for n ¸ 4. Clusters prefer to form three{dimensional and compact structures. All clusters have singlet ground state. The formation energy and HOMO{LUMO gap have also been calculated as a function of the number of TiO2 unit to study the stability and electronic properties. The formation energy increases with increasing size of the cluster. This means that clusters become stronger as their size grows. The interaction of the ground state structure of each (TiO2)n cluster with H2O has been investigated. The binding energy Eb of H2O molecule decreases and oscillates as the cluster size increases. The interaction of the ground state structure of n=3, 4, 10 clusters with more than one H2O molecule has also been studied. We have calculated Eb per adsorbed molecule and we have shown that it decreases with increasing number of adsorbed H2Omolecule (N). When N ¸ 2 for n=3 and N ¸3 for n=4 clusters, H2O molecules bind more strongly to n=10 cluster. The adsorption of transition metal (TM) atoms such as V, Co, and Pt on n=10 cluster has been studied as well. All these elements interact with the cluster forming strong chemisorption bonds, and the permanent magnetic moment is induced upon the adsorption of Co or V atoms. Second of all, structural, electronic and magnetic properties of very thin TiOx (x=1,2) nanowires have been presented. All stoichiometric TiO2 nanowires ex- hibit semiconducting behavior and have non{magnetic ground state. There is a correlation between binding energy (Eb) and the energy band gap (Eg) of these TiO2 nanowires. In general, Eb increases with Eg. In non-stoichiometric TiO nanowires, we have both metallic and semiconducting nanowires. In addition to non{magnetic TiO nanowires, we have also ferromagnetic nanowires. Three{ dimensional (3D) structures are more energetic than planar ones for both stoi- chiometries. The stability of TiOx nanowires is enhanced by the increase of the size and coordination number of Ti and O atoms which tend to possess at least four and two nearest neighbors, respectively. We have also studied the structural and electronic properties of rutile (110) nanowires obtained by cutting bulk ru- tile along the [110] direction with a certain cross section. The bulk nanowires are more energetic than the thin nanowires after a certain diameter. Like thin TiO2 nanowires, all bulk wires are semiconducting and Eg oscillates with the cross section of these (110) nanowires. Third of all, we have studied the interaction of perylenediimide (PDI){based dye compounds (BrPDI, BrGly, and BrAsp) with both the unreconstructed (UR) and reconstructed (RC) anatase TiO2 (001) surfaces. All dye molecules form strong chemical bonds with the surface in the most favorable adsorption struc- tures. The lowest binding energy is 2.60 eV which has been obtained in the adsorption of BrPDI dye on the UR surface. In UR{BrGly, RC{BrGly and RC{ BrAsp cases, we have observed that HOMO and LUMO levels of the adsorbed molecules appear within the band gap and conduction band regions, respectively. Moreover, we have obtained a gap narrowing upon adsorption of BrPDI on the RC surface. Because of the reduction in the e®ective band gap of the surface{dye system and possibly achieved the visible light activity, these results are valuable for photovoltaic and photocatalytic applications. We have also considered the e®ects of the hydration of surface on the binding of BrPDI. It has been found that the binding energy drops signi¯cantly for the completely hydrated surfaces.Fourth of all, we have considered the interaction of BrPDI, BrGly, and BrAsp dye molecules with defect free rutile TiO2 (110) surfaces. All dye molecules form moderate chemical bonds with surface in the most stable adsorption structures. The average binding energy of dye molecules is about 1 eV. Regardless of the type of dye molecules, HOMO and LUMO levels of the adsorbed dye appear within the gap and the conduction band region of defect free surface, respectively. The e®ect of the slab thickness on the interaction strength between the dye and the surface has also been examined. Unlike the four layers slab, BrGly and BrAsp molecules are dissociatively adsorbed on the three layers slab. The interaction between BrPDI and partially reduced rutile (110) as well as platinized surface has been also considered in order to ¯gure out the e®ects of O vacancy and preadsorbed small Ptn (n=1, 3 and 5 ) clusters on the binding, electronic, and structural properties of the dye{surface system. It has been found that BrPDI dye prefers to bind to the O vacancy site for the partially reduced surface case. Transition metal deposition on metal oxides plays a crucial role in various industrial areas such as catalysts and photovoltaic cells. Finally, an extensive study of the adsorption of small Ptn (n=1{8) and bimetallic Pt2Aum (m=1{5) clusters on partially reduced rutile TiO2 (110) has been presented. The e®ect of surface O vacancies on the adsorption and growth of Pt and bimetallic Pt{Au clusters over the defective site of the 4£2 rutile surface has been studied. Struc- tures, energetics and electronic properties of adsorbed Ptn and Pt2Aum clusters have been analyzed. The surface O vacancy site has been found to be the most active site for a single Pt monomer. Other Pt clusters, namely dimer, trimer and so on, tend to grow around this monomer. As a result, O vacancy site behaves as a nucleation center for the clustering of Pt atoms. Small Pt clusters interact strongly with the partially reduced surface. Eb per adsorbed Pt atom is 3.38 eV for Pt1 case and Eb increases as the cluster size grows due to the formation of strong Pt{Pt bonds. Pt clusters prefer to form planar structures for n = 1{6 cases. The calculated partial density of states of Ptn{TiO2 surface has revealed that the surface becomes metallic when n ¸ 3. In the case of bimetallic Pt-Au clusters, Aum clusters have been grown on the Pt2{TiO2 surface. Previously ad- sorbed Pt dimer at the vacancy site of the reduced surface acts as a clustering center for Au atoms. This Pt2 cluster also inhibits sintering of the Au clusters on the surface. The interaction between the adsorbed Au atoms and titania surface as well as previously adsorbed Pt dimer is weak compared to Pt{TiO2 surface interactions. Since charge state of the clusters adsorbed on the oxide surfaces iscrucial for catalysis applications of these clusters, total charge on each atom of the metal clusters has also been calculated. Charge transfer among the cluster atoms and underlying oxide surface is more pronounced for Ptn clusters. Furthermore, the absolute value of total charge on the clusters is greater for Ptn than that of bimetallic Pt{Au case.