Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / The preparation of mesoporous/macroporous silica materials and polarity gradient thin film are introduced in this thesis. These porous silica materials and gradient materials have the potential applications as stationary phases for chemical separations, as materials for combinatorial catalysis and as absorbent/adsorbent layers for use in chemical or biological sensors. Single molecule spectroscopy is used to probe the chemical interaction between single dye molecule and porous silica matrix. Bulk fluorescence spectroscopy is used to investigate the properties of gradient film. In Chapter one, the applications of single molecule spectroscopic methods to sol-gel silica materials are reviewed, which covers a subset of the recent literature in this area and provided salient examples of the new information that can be obtained by single molecule studies. In Chapter two, both the sample preparation and experiment setup are covered. In Chapter three, the preparation of mesoporous silica film is presented. Single molecule spectroscopy is used to probe the mass transport and molecule-matrix interactions in mesoporous thin-film systems. Three different dyes of varying size, charge, and hydrophilicity are used. Silica films with/without surfactant or containing different kind surfactant are studied. The results provide new information on mass transport through the films, evidence of reversible surface adsorption, and quantitative information on variations in these phenomena with film hydration. In Chapter four, a new model describing how to explore the actual dye concentration in single molecule experiment with considering the molecule orientation is presented, which is verified to be correct by both experimental and simulated data. In Chapter five, the growth process of Methylsilsesquioxane (MSQ) particle is studied by single molecule spectroscopy, in which, the MSQ particle is treated as “native” dye molecule. In Chapter six, silica films incorporating polarity gradients are produced by using “infusion-withdrawal dip-coating” method. The gradient film is characterized by bulk fluorescence spectroscopy, water contact angle and FTIR. In Chapter seven, a brief conclusion is drawn and future directions are presented.

Doctor of Philosophy / Department of Chemistry / Christopher T. Culbertson / As the field of separation science evolves so do the techniques, tools and capabilities of the discipline. The introduction of microfluidics stemmed from a desire to perform traditional analyses faster and on a much smaller scale. The small device sizes exploited in microfluidics permits the investigation of very small volumes of very dilute samples yielding information inaccessible by traditional macroscale techniques. All of the chapters presented in this dissertation illustrate attempts to supplement current microscale techniques with new tools, techniques and analysis schemes for looking at biologically relevant analyses. In chapter two I present the development and characterization of an amphiphilic polymer that has potential as a material for the fabrication of microfluidic devices. This material is composed of a poly(dimethylsiloxane)-poly(ethylene oxide) block copolymer and is dramatically more hydrophilic than the other polymeric materials currently used for the fabrication of microfluidic templates, mainly poly(dimethylsiloxane). Biomolecules such as proteins are notoriously hydrophobic and will tend to adsorb to other hydrophobic surfaces thus the use of a hydrophilic material may serve to reduce or eliminate this problem. The amphiphilic material is of a suitable durability for micromolding and molded channel architectures can be sealed between two layers of the material by simple conformal contact permitting the execution of high speed electrophoretic separations. Chapter three contains initial results obtained while investigating the fluorescent labeling and electrophoretic separation of ecdysteroids. Ecdysteroids are hormones found in insects that are responsible for controlling the process of molting. Here we attempted to analyze these molecules by employing a reactive fluorescent probe, BODIPY FL® hydrazide, that would target the α,β-unsaturated ketone group on the steroid, permitting its analysis by capillary electrophoresis with laser induced fluorescence detection. While optimistic initial results were obtained with the labeling and analysis of similar functional groups on model compounds such as progesterone, labeling of the ecdysteroid molecules was never achieved to a degree that would permit reliable analysis. In chapter four I report the development and use of a microimmunoaffinity column for the analysis of insect serine protease inhibitors, or serpins. These proteins play a very important role in the regulation of insect immune responses and their activity may play an integral role in the effective transmission of the malaria parasite by the mosquito Anopheles gambiae. A microimmunoaffinity column was constructed from magnets, poly(dimethylsiloxane), fused silica capillary and Protein A coated magnetic microspheres. In these initial studies, purified antibodies to serpin protein, as well as purified serpin protein, were used to prepare and investigate the ability to isolate, preconcentrate, and elute serpin proteins for subsequent analysis. By implementing this miniaturized system which incorporates very small fluid volumes we hoped to extend this technique to the analysis of very small samples, and eventually to the analysis of individual small insects. Our work indicates that it is possible to isolate, elute, and detect serpin protein on a traditional western blot membrane. Chapter five presents the development of a novel polymer blend for the fabrication of paper-based microfluidic devices and use of these devices in the performance of diagnostically relevant clinical assays. We took the concept of paper-based microfluidic devices and improved upon the current photoactive polymers used for their fabrication by developing a polymer blend using an acryloxy modified siloxane polymer as well as a commercially available photoactive adhesive, Norland Optical Adhesive 74. This blended polymer resulted in a dramatic reduction in fabrication time as well as improved resolution permitting the reliable patterning of small feature sizes. We also report for the first time a demonstration of these devices performing a two-step spatially separated online chemical derivatization facilitating the analysis of urinary ketones. These devices are predominantly used for the analysis of urine, and their application was extended to the quantitation of nitrite in saliva for the purposes of hemodialysis monitoring. While varied in application, all of the data presented in this dissertation exploits the power of miniaturization to improve current methods of analysis and to extend macroscale techniques to trace biological analytes.

Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-inducedfluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption. The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore of the green fluorescent protein (GFP), p-hydroxybenzylidene-2,3-dimethylimidazolone (HBDI). The body of work in this dissertation highlights the integration of gas-phase spectroscopy and mass spectrometry to elucidate the fundamental photophysical properties of biological and related ions.

This work has explored the capability of a mixed film composed of oligonucleotides and oligomers to improve the selectivity for the detection of fully complementary oligonucleotide targets in comparison to partially complementary targets which have one and three base-pair mismatched sites. The intention was to introduce a “matrix isolation” effect on oligonucleotide probe molecules by surrounding the probes with oligomers, thereby reducing oligonucleotide-to-oligonucleotide and/or oligonucleotide-to-surface interactions. This resulted in a more homogeneous environment for probes, thereby minimizing the dispersity of energetics associated with formation of double-stranded hybrids. The mixed film was constructed by immobilizing pre-synthesized oligonucleotides onto a mixed aminosilane layer and then growing the oligomer portion by surface-initiated atom transfer radical polymerization (ATRP) of 2-hydroxy methacrylate (PHEMA). The performance of the mixed film was compared to films composed of only oligonucleotides in a series of hybridization and melt curve experiments. Surface characterization techniques were used to confirm the growth of the oligomer portion as well as the presence of both oligonucleotides and oligomer components. Polyatomic bismuth cluster ions as sources for time-of-flight secondary ion mass spectrometry experiments could detect both components of the mixed film at a high sensitivity even though the oligomer portion was at least 200-fold in excess. At the various ionic strengths investigated, the mixed films were found to increase the selectivity for fully complementary targets over mismatched targets by increasing the sharpness of melt curves and melting temperature differences (delta Tm) by 2- to 3-fold, and by reducing non-specific adsorption. This resulted in improved resolution between the melt curves of fully and partially complementary targets. A fluorescence lifetime investigation of the Cy3 emission demonstrated that Cy3-labeled oligonucleotide probes experienced a more rigid microenvironment in the mixed films. These experiments demonstrated that a mixed film composed of oligonucleotides and PHEMA can be prepared on silica-based substrates, and that they can improve the selectivity for SNP discrimination compared to conventional oligonucleotide films.

A photolabile terpolymer containing 6-nitroveratyloxycarbonyl (NVOC) protected amine, epoxy and trimethoxysilyl functionality in 1:3:2 monomer ratio was synthesized to template glass surfaces for specific site directed coupling of non-probe oligomers and probe oligonucleotides. Non-probe oligomers were introduced to the surface to control the environment of the probes by reducing probe-to-probe and probe-to-surface interactions. The trimethoxysilyl group served as the anchoring site for the terpolymer to be covalently bound to glass and silicon wafers. Amine terminated non-probe oligomers were coupled to the epoxy sites and thiolated 19-mer SMN1 probes were directed to the deprotected amine sites via the heterobifunctional linker, sulfosuccinimidyl-4-[maleimidomethyl]cyclohexane-1-carboxylate (sulfo-SMCC). Characterization of the terpolymer was done using 1H NMR, 13C NMR, MALDI-ToF and elemental analysis. NVOC deprotection was monitored by UV absorption, and surface characterization of the bound terpolymer on silicon wafers was investigated with XPS, ToF-SIMS, ellipsometry and static contact angle. Neutral polyethylene glycol (PEG), negatively charged methacrylic acid (MAA) oligomer and dC20 oligonucleotides were used as non-probe oligomers. The probe density on the surface was estimated to be 2.2 ± 0.3 x 10^12 molecules/cm2 and the presence of the oligomers on the surface did not significantly affect probe immobilization efficiency. The mixed films were functional for target hybridization and its selectivity towards partially-mismatched targets was investigated at different solution pH, ionic strength and temperature. It was demonstrated that pH can be tuned to ameliorate non-specific adsorption and ionic strength governed the selectivity of the surfaces. Improved selectivity was achieved at high salt concentration (1 M NaCl) on PEG and dC20 mixed films at room temperature. The MAA surface did not show significant improvements in selectivity. This indicated that charge of the oligomers does not dominate control of selectivity. The results suggested that the terpolymer construct played a role in depression of the melting temperature of the hybridized duplex to within 5 to 10 oC of room temperature. With the melting temperature shifted closer to room temperature, it is possible to improve selectivity for room temperature detections of single nucleotide polymorphism.

L’étude qui suit porte sur l’évaluation du risque écotoxicologique du cérium, l’élément le plus exploité de la famille des lanthanides. La présence grandissante de ce métal dans notre quotidien rend possible son relargage dans l’environnement. Il est donc primordial de comprendre l’impact qu’il aura sur les organismes vivant dans un système aquatique. Une approche centrée sur le modèle du ligand biotique a été utilisée pour évaluer adéquatement l’interaction entre le cérium et un ligand biotique à la surface de l’algue unicellulaire Chlamydomonas reinhardtii. Pour mener une étude sur le risque écotoxicologique d’un élément métallique il faut, avant tout, comprendre la spéciation (répartition sous ses différentes formes chimiques) de l’élément en question. Les premières sections du mémoire vont donc traiter des expériences qui ont été menées pour évaluer la spéciation du cérium dans les conditions expérimentales d’exposition à C. reinhardtii. Il sera question de faire la distinction entre la forme particulaire du métal et sa forme dissoute, de caractériser ces changements par spectroscopie ainsi que d’évaluer le pouvoir complexant de la matière organique naturelle. Les résultats montrent une importante déplétion du métal dissout en solution à pH neutre et basique et une forte interaction avec la matière organique naturelle, peu importe le pH de la solution. Ensuite, les expériences de bioaccumulation seront expliquéesen comparant l’effet du pH, de la présence d’un ion compétiteur et de la présence de matière organique naturelle sur les paramètres d’internalisation du cérium. Les résultats indiquent qu’à pH acide, le comportement du cérium est plus prévisible qu’à pH neutre. Néanmoins, en tenant compte de la complexité des milieux naturels, l’interaction du métal avec les molécules complexantes va diminuer son risque d’interaction avec un organisme vivant. / The following study is on the ecotoxicological risk evaluation of cerium, the most widely exploited element of the lanthanide family. The increasing presence of this element in our everyday lives renders possible its release in the environment. It is therefore of primary importance to understand the impact this metal will have on living organisms in aquatic environments. An approach centered on the biotic ligand model was used here to evaluate the interaction between cerium and a biotic ligand at the surface of the unicellular algae Chlamydomonas reinhardtii. To study the ecotoxicological risk of a metallic element one must understand the speciation (partitioning between its multiple chemical species) of the element in question. The first chapters of this thesis will discuss the experiments performed to evaluate cerium speciation under exposure conditions C. reinhardtii. The issue will be to distinguish between the particulate and dissolved species of the metal, to characterise these changes by spectroscopy, as well as to evaluate the complex formation capacity of the metal with natural organic matter. Results indicate an important depletion of dissolved metal in neutral and alkaline solutions as well as a strong interaction with natural organic matter, regardless of solution pH. Bioaccumulation experiments will then be explained and will compare the effects of pH, the presence of competing ions and the presence of natural organic matter on cerium uptake. Results show that cerium’s behaviour is more predictable under acidic pH conditions. Nonetheless, considering the complexity of the natural environment, the interaction of the metal with natural ligands will most likely reduce the risk of cerium’s interaction with living organisms.

Plusieurs tests médicaux, comme celui du dépistage du cancer du sein, se basent sur l’observation de section tissulaire sous un microscope. Ces tests se basent sur l’interprétation d’un spécialiste et les résultats peuvent varier d’un expert à un autre dû la subjectivité des observations. L’utilisation d’une technique analytique offrant une quantification et une identification de cibles moléculaires dans une section tissulaire permettrait aux experts de produire des diagnostics plus objectifs et diminuerait possiblement le nombre de faux diagnostics. Les travaux présentés dans ce mémoire portent sur le développement d’une technique SPRi-MALDI-IMS permettant l’imagerie en deux dimensions de protéines contenues dans une section tissulaire. La MALDI-IMS est la technique de choix pour l’imagerie de biomolécules dans les sections tissulaires. Par contre, elle ne parvient pas à elle seule à quantifier de façon absolue le matériel adsorbé à la surface. Donc, le couplage de la MALDI-IMS avec la SPRi permet la quantification absolue de protéines en deux dimensions et crée une technique répondant aux besoins des experts médicaux. Pour ce faire, nous avons étudié, l’effet de la chimie de surface sur la nature et la quantité de matériel adsorbé à la surface du capteur. De plus, la cinétique de transfert des protéines du tissu vers le capteur a dû être optimisée afin de produire des empreintes correspondant au tissu d’origine, afin d’atteindre la gamme dynamique des instruments SPRi et MALDI-IMS. La technique résultante de ces optimisations permet d’obtenir les premières images quantitatives et qualitatives de protéines en deux dimensions d’une seule section tissulaire. / Several medical tests, such as breast cancer screening, are based on the observation of tissue section under a microscope. These tests rely on the interpretation of a specialist and the results can vary due to subjectivity of these analyses. Using an analytical technique able to quantify and identify molecular targets in a tissue section would enable experts to produce more objective diagnostic and possibly reduce the number of misdiagnosis. The work presented in this thesis focuses on the development of a SPRi-MALDI-IMS technique for imaging proteins in a tissue section. MALDI-IMS is the contemporary technique of choice for biomolecule imaging in tissue sections. However, absolute quantification of material absorbed to the surface cannot be performed using MALDI-IMS. The absolute quantification of proteins in two dimensions was successfully achieved by coupling of the MALDI-IMS with SPRi. Accordingly, we investigated by studying the nature of the surface chemistry and the amount of material adsorbed on the sensor’s surface. In addition, the kinetics of the protein transfer had to be optimized to produce imprints corresponding to the transferred tissue and to reach the dynamic ranges of both SPRi and MALDI-IMS instruments. The resulting technique led to quantitative and qualitative images of proteins in two dimensions of a single tissue section. It is envisioned that SPRi-MALDI-IMS can eventually meet the needs of medical experts for pathological screening.

Les éléments de terres rares (REEs) sont de plus en plus utilisés dans une multitude d’applications, notamment la fabrication d’aimants, de batteries rechargeables et les écrans de téléviseurs. Ils sont pour la plupart des métaux trivalents peu solubles dans les eaux naturelles. Comme pour les métaux divalents, le risque écologique des REEs est très probablement étroitement lié à leurs spéciations chimiques. Cependant, le comportement du samarium (Sm) dans les matrices environnementales est très peu connu et il n'existe actuellement aucune technique pour évaluer sa spéciation chimique. Dans cette optique, la technique d'échange d'ions (IET) sur la résine Dowex a été optimisée pour mesurer le samarium libre en solution. Les temps d'équilibre ont d'abord été déterminés pour des solutions tamponnées de samarium (Sm 6,7x10-8 M ; MES 1,0 mM M ; pH 6,0) en présence du nitrate de sodium (de 0,01M à 0,5 M). Pour ces diverses forces ioniques, l’équilibre thermodynamique n’est atteint que pour NaNO3 0,5M. Un autre mode d’utilisation de la résine (mode dynamique) a donc été développé pour tenir compte des conditions environnementales et évaluer efficacement le samarium libre. Les impacts des ligands organiques tels le NTA, l’EDTA, le citrate, l’acide malique et l’acide fulvique Suwannee River Standard I (SRFA) ont été étudiés par l’IET en mode dynamique. Une grande corrélation a été trouvée plus entre les taux d’accumulation de samarium sur la résine d’échange pour différents rapports NTA : Sm, EDTA : Sm, SRFA : Sm et le samarium libre. Par contre, aucune corrélation significative n’a été observée pour les ligands citrate et acide malique compte tenu des complexes qu’ils forment avec le samarium et qui s’adsorbent aussi sur la résine Dowex. Les concentrations Sm3+ mesurées par la technique IET ont été fortement corrélées avec celles prédites par le modèle WHAM 7.0 en utilisant la constante de stabilité obtenue par titration de SRFA par extinction de la fluorescence. Par ailleurs, la formation de colloïdes de samarium en fonction du pH influe grandement sur la détermination du samarium libre et doit être prise en compte dans la spéciation du samarium. L'IET assisté par des techniques auxiliaires comme le dosage par extinction de la fluorescence et le SP-ICPMS pourrait être une technique utile pour évaluer les concentrations de Sm biodisponible dans les eaux naturelles. / Samarium is present in several high technology products such as magnets, lasers, etc., however little is known about to what extent it can pollute environmental matrices. For divalent metals such as Cd, Cu and Ni, toxicity has often been closely correlated with the free ion concentration. Unfortunately, there are currently no techniques available for evaluating the speciation of samarium in environmental matrices. In this study, an economical and easy to use ion exchange technique (IET) using a resin has been studied for use in measuring free samarium. In order to optimize the IET for free samarium determinations, equilibrium times were first determined for pH buffered solutions of samarium (6.7x10 8 M Sm, 1.0 mM MES, pH 6.0) in the presence of different concentrations of sodium nitrate (NaNO3: 0.01 M to 0.5 M). Equilibrium was only attained for the highest concentration of NaNO3. Therefore, another technique using dynamic measurements on the Dowex resin was developed. Thus, the impacts of different organic ligands such as EDTA, citrate, malic acid and Suwannee River fulvic acid Standard I (SRFA) have been investigated using IET in dynamic mode. The calibration of the technique using different concentrations of NTA, EDTA, citrate, malic acid and fulvic acid (SRFA) allowed the determination of accumulation rates. Strong correlations were found between accumulation rates and the free samarium when using EDTA and NTA to control free samarium. The correlation was very low in case of citrate and malic acid suggesting that their complexes with samarium were adsorbed on the resin. Finally, fluorescence quenching titrations (FQT) and SP-ICPMS were used to determine samarium speciation. The free samarium determined by IET is strongly correlated to that calculated by WHAM 7.0 using the stability constant from FQT and that from Sonke (2006). However, the free Sm resulted from IEC-SP-ICPMS technique has been overestimated once compared to that found using VMinteQ or WHAM 7.0 models. The Sm particulates determined by SP-ICPMS have demonstrated that pH has a great influence on Sm exchange on resin and has to be considered while measuring free samarium. Thus, the IET should be associated to other techniques such as fluorescence quenching titration and SP-ICPMS for evaluating the bioavailable Sm concentrations in natural waters.

Master of Science / Department of Food Science / Weiqun Wang / We previously selected a purple-fleshed sweetpotato p40 clone that has been shown to protect against colorectal cancer in a murine model. This study is to identify anthocyanins by using HPLC/MS-MS and assess the stability during various coking conditions. P40 possesses a high content of anthocyanins up to 13 mg/g dry matter. Total 12 acylated anthocyanins with caffeic, ferulic, and p-hydrobenzoic acid have been identified on either cyanidin or peonidin bases. The top three major anthocyanins are cyanidin 3-caffeoyl-p-hydroxybenzoyl sophoroside-5-glucoside, peonidin 3-caffeoyl sophoroside-5-glucoside, and cyanidin 3-(6'' -caffeoyl-6''-feruloylsophoroside)-5-glucoside, which account for an half of the total anthocyanin contents. Seven non-, mono-, or di-acylated cyanidin species and five mono- or di-acylated peonidin species contribute for 69% and 31% of total anthocyanins, respectively. Over 80% of total anthocyanins measured by acid hydrolysis were cyanidin derivatives. Therefore, as a cyanidin-predominated variety, p40 is unique when compared with other reported purple-fleshed sweetpotatoes that usually contain more peonidin than cyanidin. While baking does not impact overall contents of anthocyanins, steaming, high pressure cooking, microwaving, and frying significantly reduce 20% of total anthocyanin contents. Mono-acylated anthocyanins show a higher resistance against heat than di- and non-acylated. Among of which, cyaniding 3-p-hydroxybenzoylsophoroside-5-glucoside exhibits the best thermal stability. Better understanding of dietary anthocyanins and their stabilities may lead to the development of a functional anthocyanin-enriched sweetpotato product for health benefits.

Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.