Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Cancer is one of the leading causes of death in the world. Billions of dollars are spent to treat cancer every year. This clearly shows the need for developing improved treatment techniques that are affordable to every person. Early diagnosis and imaging of tumors is equally important for the battle against this disease. This dissertation will discuss new approaches for discovering and developing novel detection and treatment techniques for cancer using organic ligands, and Fe/Fe3O4 core/shell magnetic nanoparticles. A series of o-phenylenediamine derivatives with nitro-, methyl- and chloro- substituents were synthesized and studied their ability to act as anticancer agents by using steady-state, UV/Vis-, and fluorescence spectroscopy. In the absence of zinc(II), intercalation with DNA is the most probable mode of interaction. Upon addition of zinc(II), DNA-surface binding of the supramolecular aggregates was observed. The interaction of the supramolecular (-ligand-Zn2+-)n aggregates with MDA 231 breast cancer cells led to significant cell death in the presence of UVA at λ=313 nm displaying their potential as anticancer agents. Bimagnetic Fe/Fe3O4 core/shell nanoparticles (MNPs) were designed for cancer targeting after intratumoral or intravenous administration. Their inorganic center was protected by dopamine-oligoethylene glycol ligands. TCPP (4-tetracarboxyphenyl porphyrin), a fluorescent dye, was attached to the dopamine-oligoethylene glycol ligands. These modified nanoparticles have the ability to selectively accumulate within the cancerous cells. They are suitable candidates for local hyperthermia treatment. We have observed a temperature increase of 11 ºC in live mice when subcutaneously injecting the MNPs at the cancer site and applying an alternating magnetic field The system is also suitable for Magnetic Resonance Imaging (MRI), which is a diagnostic tool to obtain images of the tumors. Our superparamagnetic iron oxide nanoparticles have the ability to function as T1 weighted imaging agents or positive contrasting agents. We were able to image tumors in mice using MRI. Various proteases are over-expressed by numerous cancer cell lines and, therefore, of diagnostic value. Our diagnostic nanoplatforms, designed for the measurement of protease activities in various body fluids (blood, saliva, and urine), comprise Fe/Fe3O4 core/shell nanoparticles featuring consensus sequences, which are specific for the target protease. Linked to the consensus sequence is a fluorescent organic dye (e.g. TCPP). Cleavage of the sequence by the target protease can be detected as a significant increase in fluorescence occurring from TCPP. We were able to correlate our diagnostic results with cancer prognosis.

Doctor of Philosophy / Department of Chemistry / Ryszard J. Jankowiak / The constituents of oxygen-evolving photosystem II core complexes—antenna proteins (CP43 and CP47) and reaction center (RC)—have been the subject of many studies over the years. However, the various issues related to electronic structure, including the origin/composition of the lowest-energy traps, origin of various emission bands, excitation energy transfer (EET), primary charge separation (CS) processes and pigment site energies remain yet to be fully resolved. Exploiting our state-of-the-art techniques such as low-T absorption, fluorescence, and hole burning (HB) spectroscopies, we resolved some of the issues particularly related to CP47 and isolated RC protein complexes. For example, we demonstrated that the fluorescence origin band maximum (~695 nm) originates from the lowest-energy state ~693 nm of intact CP47. In intact CP47 in contrast to destablished protein complexes, the band (~695 nm) does not shift in the temperature range of 5–77 K unless hole-burning takes place. We also studied a large number of isolated RC preparations from spinach, and wild-type Chlamydomonas reinhardtii (at different levels of intactness), as well as its mutant (D2-L209H), in which the active branch pheophytin (PheoD1) has been genetically replaced with chlorophyll a (Chl a). We showed that the Qx-/Qy-region site-energies of PheoD1 and PheoD2 are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803]. Finally, we demonstrated that the primary electron donor in isolated algal RCs from C. reinhardtii (referred to as RC684) is PD1 and/or PD2 of the special Chl pair (analogous to PL and PM, the special BChl pair of the bacterial RC) and not ChlD1. However, the latter can also be the primary electron donor (minor pathway) in RC684 depending on the realization of the energetic disorder. We further demonstrate that transient HB spectra in RC684 are very similar to P+QA - PQA spectra measured in PSII core, providing the first evidence that RC684 represent intact isolated RC that also possesses the secondary electron acceptor, QA. In summary, a new insight into possible charge separation pathways in isolated PSII RCs has been provided.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Porin A from Mycobacterial smegmatis (MspA) is an octameric trans-membrane channel protein and is one of the most stable porins known to date. MspA has been successfully isolated and purified to obtain liquid extracts and crystals using a modified extraction procedure. A full analytical assessment has been carried out to authenticate its’ structure, including gel electrophoresis, spectroscopy (fluorescence, UV, FTIR, NMR), HPLC, Bradford protein assay, dynamic light scattering and X-ray crystallography. Nanoscopic vesicle formation of MspA molecules in aqueous media has been thoughroughly investigated. Temperature dependent dynamic light scattering experiments reveal that size of such vesicles is dependent on temperature but is independent of ionic strength of the medium. Zeta potential measurements reveal a steady build up of positive charge on the vesicle surface with increasing temperature. For the first time, wild type (WT) MspA has been utilized as a channel forming agent. This phenomenon has future potential in DNA sequencing and the development of antimycobacterial drugs. Channel activity of WT MspA and mutant A96C MspA has been investigated and has shown to form stable channels across DPhPC lipid bilayers. Blocking of the channel current via external molecules (i.e. channel blocking) is an extremely important process, which helps to evaluate the biosensor ability of the pore. In this regard, two Ruthenium based compounds, Ru(QP-C2)38+ (i.e. RuC2) and Ru(bpy)32+have been successfully employed as channel blocking agents. Both compounds show evidence for channel blocking of WT MspA. However, these results are not reproducible. Three dimensional aggregation behavior of RuC2-MspA vesicles have been thoughroughly investigated. It is evident that addition of RuC2 significantly increases vesicle size and polydispersity of MspA aggregates in solution. The results provide explanations onto the lack of channel blocking ability of MspA by RuC2. Development of a ‘greener’ dye sensitized solar cell with the use of MspA as an electron carrier is investigated for the first time. A series of Ru(II)-phenanthroline-based dyes have been synthesized as non-toxic dyes in this regard. Chemical binding between the dyes and MspA has been achieved successfully. Two types of solar cell prototypes, i.e. TiO2-based (Grätzel type) and FTO-based have been developed and tested. Significant current generation and conversion efficiencies have been achieved for both cell types. This marks the first development of a protein-based photovoltaic device, which has the potential to be developed as a new class of “hybrid soft solar cells”.

Doctor of Philosophy / Department of Chemical Engineering / Jennifer L. Anthony / Ionic liquids are low melting salts composed of an organic cation and an inorganic or organic anion. Ionic liquids are of interest for their wide range of applications and unique properties, such as the negligible vapor pressure of some types of ionic liquids, and the ability to modify ionic liquid properties by selection of the cation or anion. It has been hypothesized that over one million binary ionic liquids (meaning a single cation/anion pair) are possible. Due to the vast number of potential combinations, it should be possible to design ionic liquids specifically for an application of interest. One potential application is their use as protein solvents. However there is little understanding of how ionic liquids affect proteins. This research examined the solubility and secondary structure of the hydrophobic corn protein zein in seven ionic liquids and three conventional solvents as a function of temperature and solvent properties. Zein’s solubility in the solvents was measured gravimetrically from 30 to 60 degrees Celsius. Solubility was then related to solvent properties to gain an understanding of what solvent properties are important, and how to design an ionic liquid to dissolve zein. It was found that a good solvent for zein has a small molecular volume, a low polarity, and is a weak hydrogen bond acceptor. Infrared spectroscopy with curve fitting was used to examine the secondary structure of zein as a function of both solvent and temperature from 25 to 95 degrees Celsius. It was found that most of the ionic liquids change zein’s secondary structure, but those secondary structure changes were not affected by temperature. Aprotic ionic liquids increase the amount of β-turn secondary structure through non-polar interactions between the mixed aromatic-alkyl imidazolium cations and the non-polar portions of the zein. Strong hydrogen bond accepting molecules were found to increase the amount of β-turn secondary structure. It is hypothesized from this research that suitable solvents for zein will have a small molar volume, low polarity, and be poor hydrogen bond acceptors. This combination of properties will enhance zein’s solubility and limit secondary structure changes that can harm protein properties.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Recent development of a variety of superparamagnetic and ferromagnetic iron/iron oxide (Fe/Fe₃O₄) nanoparticles with different surface chemistry have been widely studied for numerous biological applications such as drug delivery, as diagnostics, hyperthermia and magnetic resonance imaging. The wide applications of Fe/Fe₃O₄ nanoparticles are possible since they exhibit favorable properties as high magnetization ability, are smaller than 100 nm in size, they can be coated with several ligands which allow drug delivery at a specific site and are biocompatible. By using Fe/Fe₃O₄ nanoparticles as drug delivery agents treatment costs and side effects can be reduced, however treatment efficacy can be increased. We have demonstrated that Fe/Fe₃O₄ nanoparticles can be utilized in different methods depending on their properties, to be used as therapeutic agents for cancer treatment. In one method we have taken advantage of the Fe/Fe₃O₄ nanoparticles magnetic ability to produce hyperthermia (heat) in cancer cells when subjected to an alternative magnetic field. Here we use the cell based delivery system since the size of the nanoparticles are small they can be taken up by monocyte/ macrophage like cells for systemic transportation to the inflamed cancer cite. The hyperthermia study was conducted in mice with pancreatic cancer. This study demonstrated that the life expectancy of the mice increased by 31%. In the next method we took the advantage of the surface chemistry of the Fe/Fe₃O₄ nanoparticles and changed it with dopamine-peptide and dopamine-thiosemicarbazone ligands. The advantage of the peptide is to deliver the nanoparticle to its target site and the thiosemicarbazone analogue is used as an iron chelator that would initiate apoptosis in cancer cells. This nanoplatform was tested in 4T1 breast cancer cell line and normal fibroblast cell line and demonstrated that it was effective towards the cancer cell line than the normal cell line at a ratio of 5:1 of thiosemicarbazone analogue : dopamine on the nanoparticle. However further studies are needed to be done to clarify the effectiveness of this nanosystem.

Master of Science / Department of Chemistry / Christopher T. Culbertson / Chemical separation involves selective movement of a component out of a region shared by multiple components into a region where it is the major occupant. The history of the field of chemical separations as a concept can be dated back to ancient times when people started improving the quality of life by separation of good materials from bad ones. Since then the field of chemical separation has become one of the most continually evolving branches of chemical science and encompasses numerous different techniques and principles. An analytical chemist’s quest for a better way of selective identification and quantification of a component by separating it from its mixture is the cause for these ever evolving techniques. As a result, today there are numerous varieties of analytical techniques for the separation of complex mixtures. High Performance Liquid Chromatography (HPLC), Gas Chromatography (GC), Capillary Electrophoresis (CE) and Gel Electrophoresis are a few out of a long list. Each these techniques manipulates the different physical and chemical properties of an analyte to achieve a useful separation and thus certain techniques will be suited for certain molecules. This work primarily focuses on the use of Capillary Electrophoresis as a separation technique. The mechanism of separation in Capillary Zone Electrophoresis and principles of UV detection will discussed in chapter one. Chapter two contains a discussion about the application of Capillary Electrophoresis (CE) on microfluidc devices. This will include sections on: microfabrication techniques of PDMS and photosensitized PDMS (photoPDMS), a UV detector for microfluidic devices and its application for the detection of wheat proteins. In Chapter three we report the experimental part of this project which includes; investigations on the effect of UV exposure time and thermal curing time on feature dimensions of photoPDMS microfluidic device, investigations on the injection and separation performances of the device, characterization of a UV detector set up and its application for the separation and detection of wheat gliadin proteins. The results of these investigations are presented in chapter four.

Master of Science / Department of Chemistry / Emily McLaurin / Cu-doped ZnSe/CdSe core/shell nanocrystals were synthesized using the growth doping method. Upon shell growth, the nanocrystals exhibit dual emission. The green luminescence peak is assigned as band edge emission and the broad, lower energy red peak is due to Cu dopant. Although, the oxidation state of Cu in the nanocrystals is debated, the emission is explained as recombination of a hole related to Cu²⁺ with an electron from the conduction band. The emission changed in the presence of dodecanethiol. Generally, the band edge emission intensity decreases and the Cu emission intensity increases. One explanation is the thiol acts as a hole trap, preventing hole transfer to the conduction band. Samples were obtained with varying amounts of Cd²⁺. In the presence of larger amounts of Cd²⁺, the nanocrystals had “thicker shells”, and both the band edge and Cu emission were less sensitive to thiol. The sensitivity likely decreased because the shelled, larger nanocrystals have fewer surface defects resulting in more available electrons.

Master of Science / Department of Chemistry / Kenneth Klabunde / Remediation of the indoor environment led to the development of novel catalysts which can absorb light in the visible range. These catalysts were prepared using the wet chemistry method known as sol-gel chemistry because preparation via sol-gel provides a homogeneous gel formation, which can be treated via supercritical drying to produce an aerogel. These aerogels have been found to have high surface areas when a combination of titania/silica is used. The increase in surface area has been shown to enhance the activity of the catalysts. Mixed metal oxide systems were prepared using titanium isopropoxide and tetraethyl orthosilicate to yield a 1:1 system of titania/silica (TiO2/SiO2). These systems were doped during the initial synthesis with transition metals (Mn or Co) to create mixed metal oxide systems which absorb light in the visible light range. These materials were assessed for potential as heterogeneous catalysts via gas-solid phase reactions with acetaldehyde. Degradation of acetaldehyde as well as the formation of CO2 was monitored via gas chromatography-mass spectrometery. To increase the activity, visible light was introduced to the system. Experiments have shown that a 10 mol % manganese doped titania/silica system, in the presence of light, can degrade acetaldehyde. The cobalt doped counterpart showed dark activity in the presence of acetaldehyde resulting in the formation of CO2 without the addition of visible light. In the hope of increasing surface area a mixed solvent (toluene/methanol) synthesis procedure was applied to the manganese doped catalyst. The resulting materials were of a low surface area but showed a significant increase in degradation of acetaldehyde. Examination of the interactions between mixed metal oxide systems and semivolatile organic compounds (SVOCs) was studied. The pollutant, triphenyl phosphate, was dissolved in n-pentane and exposed to 10 mg of a given catalyst. These reactions were monitored using UVVis. All systems but the manganese doped titania/silica system resulted in the observation of no activity with triphenyl phosphate. The manganese doped catalyst shown a peculiar activity, the increase in absorbance of the triphenyl phosphate peaks as well as the formation of a new peak.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / A family of three 2-aminopyrazine derivatives were prepared and co-crystallized with thirty carboxylic acids. Our theoretical charge calculations and experimental results from 90 reactions demonstrated that decreasing the charge on the hydrogen-bond acceptor sites results in a decrease of the supramolecular yield (the frequency of occurrence of the desired outcome). However, synthon crossover (undesired connectivity) was observed 7/12 times and was unavoidable due to competitive binding sites present in the N-heterocyclic bases chosen. To avoid synthon crossover, we used a strategy based on geometric bias. We utilized hydrogen-bonding two-point contacts and halogen-bonding single-point contacts for supramolecular reactions with the 2-aminopyrazine family of compounds. The desired two-point contact and single-point contact (N•••I or N•••Br) appeared in 9/9 times even in the presence of other potentially interfering intermolecular interactions. In addition, the role of charge in controlling the presence/absence of proton transfer was also highlighted. To establish a hierarchy in halogen-bonding interactions we designed and synthesized a library of eight molecules equipped with two different halogen bond donors and combined with variety of halogen-bond acceptors. 11 Halogen-bonded co-crystals were obtained; however, positional disorder of I/Br atoms obscures a complete analysis. This problem was solved by introducing asymmetry in the halogen-bond donor molecules. Finally, successfully demonstrated an unprecedented hierarchy in halogen-bond interactions based on electrostatics. We developed high-yielding Suzuki-Miyaura coupling reactions of tetraboronic pinacolyl ester cavitand to iodoarenes with a range of functional groups (electron withdrawing/donating group and a heterocycle) that show robustness and versatility, making it a ‘launch pad’ for the synthesis of many new cavitands in a facile manner. We have also successfully demonstrated cavitand functionalization from tetraaldehyde to tetraoximes using ‘solvent assisted grinding’, irrespective of the position of the aldehyde. Finally, we prepared tetra-substituted pyridyl and carboxylic acid cavitands having an ellipsoidal cavity capable of encapsulating asymmetric guest molecules and was subsequently obtained the first of its kind, C[subscript]2v symmetric molecular capsule with encapsulated asymmetric guest molecule.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / The photochromic spirodihydroindolizine/betaine (DHI/B) system has been reinvestigated applying picosecond, microsecond, stationary absorption measurements, and NMR-kinetics. The first surprise was that the electronic structure of the betaines is quite different than commonly assumed. The photochemical ring-opening of DHIs to betaines is a conrotatory 1,5 electrocyclic reaction, as picosecond absorption spectroscopy confirms. The (disrotatory) thermal ring-closing occurs from the cisoid betaine. The lifetime of the transoid betaine is 60 s at 300 K, whereas the lifetime of the cisoid isomer is of the order of 250 microseconds. According to these results, the electrocyclic back reaction of the betaines to the DHI is NOT rate determining, as previously thought, but the cisoid-transoid-isomerization of the betaine. Although the presence of a second nitrogen atom increases the photostability of the spirodihydroindolizine-pyridazine/betaine-system remarkably, the photochemical reaction mechanism appears to be exactly the same for spirodihydroindolizine-pyridazine/betaine-system. A nondestructive photoswitch or an information recording systems has been explored using styryl-quinolyldihydroindolizines. Both isomers DHI and betaine are fluorescent. When the blue betaine is stabilized in a thin polymethyl methacrylate (PMMA) matrix, it is stable for several hours even in room temperature and very stable at 77K. Although irradiation of visible light = 532 nm allows the photo-induced reaction of the Betaine back to the DHI, a nondestructive read-out can be performed at λ = 645 nm upon excitation with λ = 580 nm. Image recording (write) and read-out, as well as information storage (at 77K) have been demonstrated. Charged and maleimide-functionalized DHI/B systems have beed synthesized for use as photochemical gates of the mycobacterial channel porin MspA. Positively charged and maleimide functionalized DHI groups that were attached to the DHI/B-system permit the binding of the photoswitch to selective positions in the channel proteins due to the presence of a cysteine moiety. An inexpensive new method for the large scale synthesis of coelenterazine is developed. A modified Negishi coupling reaction is used to make pyrazine intermediates from aminopyrazine as an economical starting material. This method permits the use of up to 1g coelenterazine per kg body weight and day, which turns the renilla transfected stem cells into powerful light sources.