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.

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.

Knowledge gaps related to mass transfer processes involved in passive air sampling of semivolatile organic compounds and factors potentially influencing passive sampling rates (PSRs) were addressed with controlled laboratory experiments, mass transfer modeling, and a field sampling campaign. The observed non-uniform SVOC distributions within porous passive sampling media (PSMs) contradict an assumption in an earlier passive air sampling theory and proved the existence of a kinetic resistance on the PSM side. This resistance can affect PSRs as revealed by a new PAS model which is based on fundamental laws of mass transfer in air and porous media. By considering mass transfer processes within the PSM, the model is able to explain the large variations of field calibrated PSRs with temperature and between SVOC species and the two-stage uptake process, which cannot be addressed by the earlier PAS theory. Because the PSM side kinetic resistance invalidates the assumption that depuration compounds added to the PSM prior to deployment are subject to the same kinetic resistance as the sampled SVOCs, PSRs derived from the loss rates of depuration compounds can differ from the actual PSRs of the sampled SVOCs. Using such PSRs could thus introduce additional uncertainty to PAS-derived air concentrations. Experiments using XAD-resin and silica-gel filled mesh cylinder as PSMs for the uptake of SVOCs and water vapor respectively revealed that sorbent in the inner portion of the PSM does not take part in chemical uptake; PSRs are thus proportional to the interfacial transfer area but not the amount of the sorbent. Accordingly, thinner PSM can be used to reduce the amount of sorbent while keeping or even increasing the PSRs. Optimized designs of PASs could be tested time efficiently using the gravimetrical approach based on water vapor uptake by silica gel.

Knowledge gaps related to mass transfer processes involved in passive air sampling of semivolatile organic compounds and factors potentially influencing passive sampling rates (PSRs) were addressed with controlled laboratory experiments, mass transfer modeling, and a field sampling campaign. The observed non-uniform SVOC distributions within porous passive sampling media (PSMs) contradict an assumption in an earlier passive air sampling theory and proved the existence of a kinetic resistance on the PSM side. This resistance can affect PSRs as revealed by a new PAS model which is based on fundamental laws of mass transfer in air and porous media. By considering mass transfer processes within the PSM, the model is able to explain the large variations of field calibrated PSRs with temperature and between SVOC species and the two-stage uptake process, which cannot be addressed by the earlier PAS theory. Because the PSM side kinetic resistance invalidates the assumption that depuration compounds added to the PSM prior to deployment are subject to the same kinetic resistance as the sampled SVOCs, PSRs derived from the loss rates of depuration compounds can differ from the actual PSRs of the sampled SVOCs. Using such PSRs could thus introduce additional uncertainty to PAS-derived air concentrations. Experiments using XAD-resin and silica-gel filled mesh cylinder as PSMs for the uptake of SVOCs and water vapor respectively revealed that sorbent in the inner portion of the PSM does not take part in chemical uptake; PSRs are thus proportional to the interfacial transfer area but not the amount of the sorbent. Accordingly, thinner PSM can be used to reduce the amount of sorbent while keeping or even increasing the PSRs. Optimized designs of PASs could be tested time efficiently using the gravimetrical approach based on water vapor uptake by silica gel.

Open and throughfall precipitation samples were collected at Haliburton Forest for a total of nine events from July – November of 2009. The following species were analyzed quantitatively: NO3-, SO42-, Cl-, HCOO-, C2O42-, NH4+, Na+, K+, Ca2+, and Mg2+. Wet deposition inputs to the system were quantified and the sources of wet-deposited species were probed. The throughfall method was employed to quantify inputs to the forest floor and probe canopy-precipitation interactions. Leaf wash samples at three heights aided in the interpretation of throughfall data and allowed for an examination of vertical profiles of dry deposition to the canopy. Results suggest possible nitrate foliar leaching during the growing season, although this appears to cease during senescence. This finding supports previous evidence that Haliburton Forest has shifted from nitrogen-limitation toward nitrogen-saturation and estimated total atmospheric N inputs to the system are close to the proposed critical load of 10 kg N ha-1 yr-1.

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.

Open and throughfall precipitation samples were collected at Haliburton Forest for a total of nine events from July – November of 2009. The following species were analyzed quantitatively: NO3-, SO42-, Cl-, HCOO-, C2O42-, NH4+, Na+, K+, Ca2+, and Mg2+. Wet deposition inputs to the system were quantified and the sources of wet-deposited species were probed. The throughfall method was employed to quantify inputs to the forest floor and probe canopy-precipitation interactions. Leaf wash samples at three heights aided in the interpretation of throughfall data and allowed for an examination of vertical profiles of dry deposition to the canopy. Results suggest possible nitrate foliar leaching during the growing season, although this appears to cease during senescence. This finding supports previous evidence that Haliburton Forest has shifted from nitrogen-limitation toward nitrogen-saturation and estimated total atmospheric N inputs to the system are close to the proposed critical load of 10 kg N ha-1 yr-1.

Doctor of Philosophy / Department of Mechanical and Nuclear Engineering / Kevin B. Lease / The overall goal of this study was to assess the effects of surface chemistry on adhesion of polymeric systems underwater. The adhesion is quantified by the thermodynamic work of adhesion (W) when two surfaces are approached and the energy release rate (G) when the surfaces are separated. For some polymeric systems there is a difference between W and G, referred to as adhesion hysteresis. For this study an experimental approach based upon Johnson-Kendall-Roberts (JKR) theory of contact mechanics was utilized to evaluate how surface chemistry affects the adhesion behavior (both W and adhesion hysteresis) in the presence of water. The interfacial interactions were also studied in air and contrasted to those obtained underwater. To accomplish the overall goal of this research, this study was divided into two phases where smooth model surfaces with disparate surface chemistries were used. The model surfaces in the first part included poly(dimethysiloxane) (PDMS), glass surfaces chemically functionalized to display hydrophilic to medium to hydrophobic characteristics, and thin films of wood-based biopolymers. The functionalities used to modify glass surfaces included polyethylene oxide (PEO) with hydrophilic nature; amine, carbomethoxy, and mercapto (thiol) with intermediate characteristics; cyclohexyl, fluorocarbon, and methyl with hydrophobic behavior. In addition to these surfaces, flat PDMS and clean glass surfaces were also used for means of comparison. The wood-derived polymers included two different cellulose types (natural cellulose and regenerated cellulose) as well as one lignin surface (from hardwood milled lignin). These surfaces were probed with native PDMS hemispheres, which are hydrophobic. The results showed that in air the value of W for all model surfaces was independent of the surface chemistry, except fluorocarbon which was lower. Underwater W was significantly affected by the surface hydrophilicity/ hydrophobicity. The adhesion hysteresis both in air and underwater was significantly dependent on the structure of the probed surface. For the second phase PDMS hemispheres were chemically modified with amine functionality to probe model surfaces with hydrophilic and intermediate behavior. These surfaces included glass surfaces functionalized with PEO and amine as well as PDMS sheets that were functionalized with amine. Native PDMS flat surfaces were also used for means of comparison. The results showed that for the selected surfaces both W and hysteresis were affected by the surface chemistry in both media.

Doctor of Philosophy / Department of Chemistry / Duy H. Hua / Three research projects are described in this dissertation and they consist of the discovery of norovirus protease inhibitors, modification of graphene oxides (GO) for the detection of norovirus, and design and fabrication of nanoelectronic device based on nanocarbon fibers for the detection of breast cancer proteases, legumain and cathepsin B. A novel class of tripeptidyl anti-noroviral compounds which strongly inhibit NV3CL[superscript]pro in enzyme and cell based assays was discovered. An example of one of the most active compounds is (1-{3-methyl-1-[2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester, which showed an IC₅₀ value of 0.14 ± 0.2 μM (enzyme assay) and EC₅₀ value of 0.04 ± 0.02 μM (cell based assay). This compound has an aldehyde warhead, a P1 glutamine surrogate, a P2 leucine, a P3 L-1-napthylalanine and an N-terminal carboxybenzyl cap. The corresponding bisulfite adduct, 2-[2-(2-benzyloxycarbonylamino-3-naphthalen-1-yl-propionylamino)-4-methyl-pentanoylamino]-1-hydroxy-3-(2-oxo-pyrrolidin-3-yl)-propane-1-sulfonic acid monosodium salt, has a comparable activity in enzyme and cell based assays (IC₅₀ 0.24 ± 0.1 μM; EC₅₀ 0.04 ± 0.03 μM). (1-{3-methyl-1-[2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester and its ketoamide derivative, (1-{1-[2-isopropylcarbamoyl-2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-3-methyl-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester, exhibited very good broad spectrum anti-viral activity, especially in human rhino virus and severe acute respiratory syndrome bioassays. We demonstrated that the surface of graphene oxide can be chemically modified with t-butylester and carboxylic acid functionalities. Fourier transform infrared spectroscopy, Raman spectroscopy and solid state nuclear magnetic resonance spectroscopy confirmed the presence of t-butylester and carboxylic acid functional groups. One sided oligonucleotide functionalized graphene oxide was synthesized using a solid state technique. A carboxylic acid functionalized graphene oxide was deposited onto the surface of electronic chips to bridge two gold electrodes, using a direct deposition technique. The carboxylic acid functionalized graphene oxide displayed semi-conductive properties and its use in an electronic biosensor device to detect noroviral RNA was investigated. Novel redox-active protease substrate peptides H₂N-(CH₂)₄CO-Ala-Ala-Asn-Leu-NHCH₂-ferrocene and H₂N-(CH₂)₄CO-Leu-Arg-Phe-Gly-NHCH₂-ferrocene were synthesized successfully and used in an alternating current voltammetry technique to facilitate the detection of the cancer related protease enzymes legumain and cathepsin B. After attachment of these peptides to the tips of carbon nanofiber nanoelectrode arrays, the presence of active protease enzymes could be detected as manifest by an exponential decay in current signal detect when monitored by alternating current voltammetry, at initial enzyme concentrations of 80.1 nM (legumain) and 30.7 nM (cathepsin B). The peptide cleavage sites were confirmed by analyses of the cleaved fragments using high performance liquid chromatography and mass spectrometry. Results showed that the cleavage of H₂N-(CH₂)₄CO-Ala-Ala-Asn-Leu-NHCH₂-ferrocene at the C-terminal side of asparagine residues by legumain and cleavage of H₂N-(CH₂)₄CO-Leu-Arg-Phe-Gly-NHCH₂-ferrocene at the C-terminal side of arginine residues by cathepsin B. Legumain exhibited a specificity constant (k[subscript]cat/K[subscript]m) of 11.3 x 10ᶟ M⁻¹S⁻¹ while cathepsin B exhibited a higher value of specificity constant (4.3 x 10⁴ M⁻¹S⁻¹) which agreed with the values obtained from fluorescence enzyme assay.

Doctor Of Philosophy / Department of Chemistry / Christer Aakeröy / Crystal engineering, or non-covalent synthesis in the solid state, requires an understanding of intermolecular forces, and the hydrogen bond has become a reliable non-covalent tool in the construction of supramolecular architectures. In the same way that synthetic chemists refer to a “yield” to quantify a desired product, crystal engineers typically determine the successful formation of a supramolecular product according to the frequency or occurrence of preferred intermolecular interactions between molecules under certain reaction conditions, thus, the supramolecular yield. These non-covalent reactions can be effectively carried out using supramolecular reagents (SR’s). A family of ditopic bis-imidazol-1-yl/benzimidazol-1-yl compounds were synthesized and used as SR’s in combination with a variety of dicarboxylic acids to produce binary solids in 100% yield through the primary acid···imidazol-1-yl/benzimidazol-1-yl synthons even in the presence of potentially disruptive intermolecular interactions. We furthermore noted that secondary C–H···O interactions within and between 1-D chains were of equal structural importance based upon an analysis of the metrics displayed by these interactions. The use of these SR’s as ligands with neutrally charged metal complexes was also investigated. SR’s containing benzimidazol-1-yl and carboxamide moieties were synthesized and combined with two different carboxylic acids to make ternary solids through acid···benzimidazol-1-yl and carboxamide···acid hydrogen bonds using a hierarchical approach – the best donor-best acceptor, second best donor-second best acceptor guidelines. These SR’s were also employed as ligands for high-yielding syntheses of linear metal complexes where neighboring complexes are linked via carboxamide···carboxamide hydrogen bonds. Asymmetric SR’s possessing two different N-heterocycles were synthesized and employed in the construction of ternary supermolecules with a high degree of structural selectivity and specificity when introduced to two different carboxylic acids. The stronger acid interacts at the more basic site, while the weaker acid hydrogen-bonds with the less basic nitrogen atom. Finally, an SR containing three different binding sites was designed and synthesized with the aim of producing quaternary co-crystals.