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.

Doctor of Philosophy / Department of Chemistry / Jun Li / Reduction in electrode size down to nanometers dramatically enhances the detection sensitivity and temporal resolution. Here we explore nanoelectrode arrays (NEAs) and nanoparticles in building high performance biosensors. Vertically aligned carbon nanofibers (VACNFs) of diameter ~100 nm were grown on a Si substrate using plasma enhanced chemical vapor deposition. SiO[subscript]2 embedded CNF NEAs were then fabricated using techniques like chemical vapor deposition, mechanical polishing, and reactive ion etching, with CNF tips exposed at the final step. The effect of the interior structure of CNFs on electron transfer rate (ETR) was investigated by covalently attaching ferrocene molecules to the exposed end of CNFs. Anomalous differences in the ETR were observed between DC voltammetry (DCV) and AC voltammetry (ACV). The findings from this study are currently being extended to develop an electrochemical biosensor for the detection of cancerous protease (legumain). Preliminary results with standard macro glassy carbon electrodes show a significant decrease in ACV signal, which is encouraging. In another study, NEA was employed to capture and detect pathogenic bacteria using AC dielectrophoresis (DEP) and electrochemical impedance spectroscopy (EIS). A nano-DEP device was fabricated using photolithography processes to define a micro patterned exposed active region on NEA and a microfluidic channel on macro-indium tin oxide electrode. Enhanced electric field gradient at the exposed CNF tips was achieved due to the nanometer size of the electrodes, because of which each individual exposed tip can act as a potential DEP trap to capture the pathogen. Significant decrease in the absolute impedance at the NEA was also observed by EIS experiments. In a final study, we modified gold nanoparticles (GNPs) with luminol to develop chemiluminescence (CL) based blood biosensor. Modified GNPs were characterized by UV-Vis, IR spectroscopy and TEM. We have applied this CL method for the detection of highly diluted blood samples, in both intact and lysed forms, which releases Fe[superscipt]3[superscript]+ containing hemoglobin to catalyze the luminol CL. Particularly, the lysed blood sample can be detected even after 10[superscript]8 dilution (corresponding to ~0.18 cells/well). This method can be readily developed as a portable biosensing technique for rapid and ultrasensitive point-of-care applications.

This thesis presented a microfluidic preparation of bubbles-templated micro-size materials. In particular, this thesis focused on the microfluidic formation and dissolution of CO2 bubbles. First, this thesis described pH-regulated behaviours of CO2 bubbles in the microfluidic channel. This method opened a new way to generate small (<10 µm in diameter) with a narrow size distribution (CV<5%). Second, the microfluidic dissolution of CO2 bubbles possessed the important feature: the local change of pH on the bubble surface. This allowed us to encapsulate the bubbles with various colloidal particles. The bubbles coated with particles showed a high stability against coalescences and Ostwald ripening. The dimensions and shapes of bubbles with a shell of colloidal particle were manipulated by the hydrodynamic and chemical means, respectively. Third, we proposed a microfluidic method for the generation of small and stable bubbles coated with a lysozyme-alginate shell. The local pH decrease at the periphery of CO2 bubbles led to the electrostatic attraction between lysozyme on the bubble surface and alginate in the continuous phase. This produced the bubbles with a shell of biopolymers, which gave a long-term stability (up to a month, at least) against the dissolution and coalescence. Fourth, we presented a single-step method to functionalize bubbles with a variety of nanoparticles. The bubbles showed the corresponding properties of nanoparticles on their surface. Further, we explored the potential applications of these bubbles as contrast agents in ultrasound and magnetic resonance imaging.

Dissolved organic matter (DOM) is comprised of a complex array of molecular constituents that are linked to many globally-relevant processes and yet this material is still largely molecularly uncharacterized. Research presented here attempted to probe the molecular complexity of this material from both Arctic and temperate climates via multifaceted and novel approaches. DOM collected from remote Arctic watersheds provided evidence to suggest that permafrost-disturbed systems contain more photochemically- and biologically-labile material than undisturbed systems. These results have large implications for predicted increasing temperatures where widespread permafrost melt would significantly impact stores of organic carbon in polar environments. In attempting to address the complexities and reactivity of DOM within global environments, more information at the molecular-level is necessary. Further research sought to unravel the molecularly uncharacterized fraction via use of nuclear magnetic resonance (NMR) spectroscopy in conjunction with hyphenated and varied analytical techniques. Directly hyphenated high performance size exclusion chromatography (HPSEC) with NMR was explored. This hyphenation was found to separate DOM into structurally distinct fractions but proved limited at reducing DOM heterogeneity. Of the many high performance liquid chromatography (HPLC) techniques tested, hydrophilic interaction chromatography (HILIC) was found the most effective at simplifying DOM. HILIC separations utilizing a sample from Florida resulted in fractions with highly resolved NMR signals and substantial reduction in heterogeneity. Further development with a 2D-HILIC/HILIC system to achieve additional fractionation was employed. This method produced fractions of DOM that were homogenous enough to produce excellent resolution and spectral dispersion, permitting 2D and 3D NMR experiments to be performed. Extensive NMR analyses of these fractions demonstrated strong evidence for the presence of highly oxidized sterols. All fractions, however, provided 2D NMR spectra consistent with oxidized polycyclic structures and support emerging data and hypotheses suggesting that cyclic structures, likely derived from terpenoids, are an abundant, refractory and major component of DOM. Research presented within this thesis demonstrates that HILIC and NMR are excellent co-techniques for the analysis of DOM as well as that oxidized sterols and other cyclic components with significant hydroxyl and carboxyl substituents are major constituents in DOM.

In this work the methodology is developed to study spreading and penetration of a custom ink-jet ink formulation, containing hydrophobic cationic crystal violet dye, ethoxylated surfactant, and ink solvent marked by lithium salt. With a new technique utilizing Time-of-Flight Secondary Ion Mass Spectrometry imaging, the ink component distribution and its effect on print quality of uncoated and coated papers are evaluated. High spatially resolved images obtained by ToF-SIMS illustrate differentiation of individual ink components, with ink solvent spreading more than the dye in all paper samples. Uncoated papers show greater and more irregular spreading leading to poor edge definition and poor print quality. Large separation of the dye from the solvent in the vertical direction of multipurpose and photo glossy ink-jet paper suggests a step-wise progression of ink penetration: ink flows through a more porous structure in the x-direction before advancing to the next sublayer in the z-direction of paper.

Snow and ice can significantly affect the environmental fate of contaminants. This thesis presents a laboratory technique for measuring mercury in metamorphosing snow, and a computer model for organic contaminants in a seasonally ice covered ocean. The laboratory method to study the fate of mercury in snow was developed using laboratory-made snow of controlled composition made in a cold room, aged and melted, with mercury quantified in air, snow, and dissolved and particulate fractions of the melt water. It was found that the method gave a mass balance for mercury, and can be used to look at mercury fate in snow representative of different environments. The fugacity based fate and transport model for organic contaminants in a seasonally ice-covered ocean was parameterized to Barrow Strait, and tested against environmentally derived net air to sea water fluxes. It was found that the model could reproduce these environmental data.

In this work the methodology is developed to study spreading and penetration of a custom ink-jet ink formulation, containing hydrophobic cationic crystal violet dye, ethoxylated surfactant, and ink solvent marked by lithium salt. With a new technique utilizing Time-of-Flight Secondary Ion Mass Spectrometry imaging, the ink component distribution and its effect on print quality of uncoated and coated papers are evaluated. High spatially resolved images obtained by ToF-SIMS illustrate differentiation of individual ink components, with ink solvent spreading more than the dye in all paper samples. Uncoated papers show greater and more irregular spreading leading to poor edge definition and poor print quality. Large separation of the dye from the solvent in the vertical direction of multipurpose and photo glossy ink-jet paper suggests a step-wise progression of ink penetration: ink flows through a more porous structure in the x-direction before advancing to the next sublayer in the z-direction of paper.

Snow and ice can significantly affect the environmental fate of contaminants. This thesis presents a laboratory technique for measuring mercury in metamorphosing snow, and a computer model for organic contaminants in a seasonally ice covered ocean. The laboratory method to study the fate of mercury in snow was developed using laboratory-made snow of controlled composition made in a cold room, aged and melted, with mercury quantified in air, snow, and dissolved and particulate fractions of the melt water. It was found that the method gave a mass balance for mercury, and can be used to look at mercury fate in snow representative of different environments. The fugacity based fate and transport model for organic contaminants in a seasonally ice-covered ocean was parameterized to Barrow Strait, and tested against environmentally derived net air to sea water fluxes. It was found that the model could reproduce these environmental data.

Atmospheric ammonia contributes to a number of environmental problems, but many questions regarding the behaviour of ammonia in the atmosphere remain. Field studies were performed to investigate the gas-particle partitioning of ammonia, the surface-atmosphere exchange, and to compare measurements with an online chemical transport model and offline thermodynamic models. A state-of-the-art instrument, Quantum Cascade Tunable Infrared Laser Differential Absorption Spectrometer (QC-TILDAS), with a novel sampling technique was used to measure ammonia. The detection limit of the instrument was found to be 690 ppt at 1 Hz and 42 ppt when averaged to 5 minutes. The uncertainty in the measurement is 10 % based on calibration from a permeation tube source. Laboratory and field tests show the ammonia time response to be slower at lower mixing ratios, and when the ambient relative humidity is high. Observations from the first field campaign discussed, the Border Air Quality and Meteorology Study (BAQS-Met), were compared to a chemical transport model AURAMS (A Unified Regional Air quality Modeling System). The model was often biased low in ammonia and ammonium and predicted an incorrect diurnal profile. Observations suggest a coupling between gas-particle and surface-atmosphere equilibria whereby a large atmospheric condensation sink induces emission of ammonia from the surface. A simple approach at representing the ammonia bi-direction flux more closely matched the observations, indicating that a fully coupled bi-directional flux parameterization in chemical transport models is necessary to accurately predict atmospheric ammonia. A suite of instrumentation during the CalNex 2010 field campaign allowed for in-depth analysis of gas-particle partitioning and estimation of aerosol pH. Observations were compared to predictions from the thermodynamic equilibrium models ISORROPIA and E-AIM. Deviations form equilibrium were found during periods of high levels of aerosol nitrate and positive net charge. The gas-particle partitioning was found to be very sensitive to aerosol pH.