Master of Science / Department of Chemistry / Daniel A. Higgins / Single molecule tracking (SMT) measurements have been applied to the study of molecular mobility in sol-gel-derived silica gradient films in this thesis. Such gradient films have broad potential applications in controlled adhesion and transport of cells, vesicles and polymers; separation of complex chemical mixtures and in the development of new catalysts. Silica films were prepared by “infusion-withdrawal dip-coating”. In this method, a suitable substrate is slowly withdrawn from a silica sol of time varying composition. The deposition reservoir is initially filled with a sol derived from one silica precursor (tetramethoxysilane). A second sol, prepared from a different precursor (methyltrimethoxysilane), is then infused into the deposition reservoir, as the mixed sol is withdrawn. Films thus prepared were initially characterized by bulk fluorescence spectroscopy, infrared (IR) microscopy, contact angle goniometry, spectroscopic ellipsometry and surface profilometry. The fluorescence, IR and contact angle data all demonstrate the presence of a gradient in the methyl content of the silica film. The primary objective of the work performed under this thesis was to investigate the diffusion of Nile Red molecules in and on these films, as a function of position along the gradient, by SMT methods. Histograms of the mean-square displacement of the molecules depict the presence of at least two distinct populations: one incorporating fixed (entrapped or adsorbed) molecules and the other clearly reflecting the presence of mobile molecules. The latter population was observed to vary along the gradient dimension and also changed as the films aged over the course of five days. Molecular mobility is attributed to the presence of liquid-like silica oligomers in the films. Spatial variations in the observed mobility are tentatively assigned to variations in oligomer viscosity along the gradient. Film viscosity also changes as the polymerization of the oligomers continues during film aging.

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.

The typical strategy for atmospheric analysis of volatile organic compounds (VOCs), is to collect discrete samples which are then transported to a laboratory for analysis. This method has limited spatial and temporal resolution, and can be both costly and time consuming. To overcome these limitations, a mobile monitoring platform was developed for real-time quantitative chemical analysis. This work describes the development of membrane introduction mass spectrometer and identi es the necessary requirements to make a reliable and e ective instrument for in-situ chemical analysis. These include, the integration of a membrane interface with a miniaturized mass spectrometer, development of a data management strategy, reducing the e ects of isobaric interferences and employing an internal standard for quantitative measurements. Furthermore, the negative e ects of environmental variables, such as the Earth's magnetic eld, were examined and e ectively eliminated. In addition, this work demonstrates quantitative mapping of atmospheric VOCs in real-time, which allows rapid identi cation of chemical plumes and therefore, areas of potential concern. Both lab and eld-based comparisons of iv membrane introduction mass spectrometer data and traditional whole air sampling canister data were undertaken. The primary eld site was near Ft. McMurray, AB where baseline data was collected around a steam assisted gravity drainage (SAGD) facility and surrounding public roads. Monitoring for fugitive emissions at this facility and surrounding bitumen mining and processing operations is demonstrated. Field data were also obtained, near an industrial site in Ft.Saskatchewan, AB, that demonstrate the e cacy of an adaptive sampling strategy. Finally, chemical ionization was investigated as a soft ionization strategy to improve chemical selectivity for the analysis of complex hydrocarbon mixtures. The development of an in-line liquid chemical ionization reagent delivery system is presented and proposed as an e ective strategy for eliminating interferences arising from biogenic terpenes and alkyl aromatics. In all, this thesis presents the design and implementation of a mobile membrane introduction mass spectrometer for atmospheric chemical analysis. Results that improve performance and demonstrate the novelty of the data-type are provided, along with avenues for future development. / Graduate / 0486 / 0799 / 0608

The work presented in this Thesis describes the design, synthesis and reactivity of a symmetric and various asymmetric Schiff-base macrocycles that are capable of forming a wedge-shaped “Pacman” conformation upon metal binding. Chapter One introduces catalysts for small molecule transformation as well as transition metal complexes of pyrrole-containing macrocycles. Further to this, Pacman systems, including previous work from Love and co-workers, and complexes capable of secondary coordination-sphere control will be discussed. Chapter Two details the design and synthesis of two asymmetric macrocycles that both contain one neutral and one N₄-donor imine-pyrrole binding pocket, H₂LP and H₂LNMe. The synthesis and characterisation of the series of complexes [M(LP)] and [M(LNMe)] (M = Pd, K₂, Co, VCl, TiCl, Mg, Fe and Mn) and their characteristics highlighted, including the formation of a supramolecular cyclic hexamer. Chapter Three presents the modification of the above ligands at the meso-group, the N-substituent and the non-pyrrolic binding pocket to give H2LFP and H₂LFNMe, H₂LNMes and H₂L(NH)NMe respectively. Palladium and cobalt complexes of these macrocycles were prepared and characterised. Chapter Four describes the design and synthesis of the ligand H₄LEt as well as the synthesis and characterisation of tin-alkyl and mononuclear calcium complexes of LEt, as well as the heterobimetallic complexes [SnMe₂(M)(THF)(LEt)] (M = Zn or Fe). The homobimetallic complexes [M₂(LEt)] (M = Co, Mg and NbCl) are also presented along with a magnesium-cubane structure of LEt in which the cubane is encapsulated by two, bowl-shaped macrocycles. Chapter Five provides a summary of the work presented in this thesis. Chapter Six describes the full experimental details and analytical data for all compounds synthesised in this work.

In this work organic molecules, namely derivatives of BODIPY and poly-para-phenyls are investigated on different metal surfaces by means of LT-STM. These molecule are important for the development of molecular electronics and spintronics. I show that aza-BODIPY molecules form a weak chemical bond with the Au(111) substrate and the molecular structure significantly changes upon adsorption. Due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of ±1 V. The temperature dependent formation of different molecular nanostructures formed by polyparaphenyls and Au adatoms is discussed. The diffusing Au adatoms act as coordination centers for the cyano groups present on one end of the molecules. The structure of the super molecular assemblies completely changes in a temperature range of only 60 K. Furthermore, I investigate in this work the hybridization of atomic orbitals within the molecular ligand. The Kondo resonance of a Co atom incorporated into an other aza-BODIPY derivative is investigated in detail on Ag(100). The hybridization of the atomic Co orbital with the organic ligands molecular orbitals is shown by spectroscopy measurements with submolecular resolution. The changing line shape of the Kondo resonance for the molecule-substrate system is discussed. This data is compared to measurements of Co incorporated in another molecular binding motive and on different metal samples to show the importance of the local environment for molecular materials. / In dieser Arbeit werden organische Moleküle, Derivate von BODIPY und poly-para-Phenyl, auf verschiedenen Metalloberflächen mittels Tief-Temperatur Rastertunnelmikroskopie (LT-STM) untersucht. Diese Moleküle sind wichtig für die Entwicklung von molekularer Elektronik und Spintronik. Ich zeige, dass aza-BODIPY-Moleküle eine schwache chemische Bindung mit dem Au(111)- Substrat eingehen und die molekulare Struktur bei der Adsorption deutlich verändert wird. Wegen der geringen Rauigkeit der Au(111)-Oberfläche wird bereits bei einer angelegten Spannungen über ±1 V die Diffusion der Moleküle beobachtet. Die temperaturabhängige Bildung verschiedener molekularer Nanostrukturen aus poly-para-Phenyl und frei beweglichen Goldatomen wird diskutiert. Die diffundierenden Goldatome agieren hierbei als Koordinationszentren für die Cyanogruppen am einen Ende der Moleküle. Die Struktur der supramolekularen Anordnungen verändert sich dabei in einem Temperaturbereich von nur 60 K vollkommen. Außerdem beschäftige ich mich in dieser Arbeit mit der Hybridisierung atomare Orbitale im molekularen Verbund. Die Kondo-Resonanz eine Co-Atoms, welches in einem anderen aza-BODIPY-Derivat gebunden ist, wird detailliert auf der Ag(100)-Oberfläche untersucht. Die Hybridisierung des atomaren Co-Orbitals mit den molekularen Orbitalen des organischen Liganden wird an Hand von Spektroskopiemessungen mit submolekularer Auflösung gezeigt. Die veränderte Form der Kondo-Resonanz für dieses Molekül-Substrat-System wird diskutiert. Diese Daten werden mit Messungen an Co-Atomen in anderen molekularen Bindungsschemen und auf anderen Substraten verglichen um dieWichtigkeit der lokalen Umgebung für molekulare Materialien zu verdeutlichen.

<p>Electroporation is a biological cell's natural reaction to strong electric fields, where transient pores are created in the cell membrane. While electroporation holds promise of being a safe and effective tool for enhancing molecular delivery in numerous medical applications, it remains largely confined to preclinical research and clinical trials due to an incomplete understanding of the exact mechanisms involved. Muscle fibers are an important delivery target, but traditional theoretical studies of electroporation ignore the individual fiber geometry, making it impossible to study the unique transverse and longitudinal effects from the pulse stimulus. In these long, thin muscle fibers, the total reaction of the fiber to the electric field is due to fundamentally different effects from the constituent longitudinal and transverse components of the electric field generated by the pulse stimulus. While effects from the transverse component have been studied to some degree, the effects from the longitudinal component have not been considered. </p><p>This study develops a model of electroporation and delivery of small molecules in muscle tissue that includes effects from both the transverse and longitudinal components of the electric field. First, an asymptotic model of electric potential in an individual muscle fiber is derived that separates the full 3D boundary value problem into transverse and a longitudinal problems. The transverse and longitudinal problems each have their own respective source functions: the new "transverse activating function" and the well known longitudinal activating function (AF). This separation enhances analysis of the different effects from these two AFs and drastically reduces computational intensity. Electroporation is added to the asymptotic fiber model, and simplified two-compartment mass transport equations are derived from the full 3D conservation of mass equations to allow simulation of molecular uptake due to diffusion and the electric field. Special emphasis is placed on choosing model geometry, electrical, and pulsing parameters that are in accordance with experiments that study electroporation-mediated delivery of small molecules in the skeletal muscle of small mammals.</p><p>Simulations reveal that for fibers close to the electrodes the transverse AF dominates, but for fibers far from the electrodes the longitudinal AF enhances uptake by as much as 2000%. However, on the macroscopic tissue level, the increase in uptake from the longitudinal AF is no more than 10%, given that fibers far from the electrodes contribute so little to the total uptake in the tissue. The mechanism underlying the smaller effect from the longitudinal AF is found to be unique to the process of electroporation itself. Electroporation occurs on the short time scale of polarization via the transverse AF, drastically increases membrane conductance, and effectively precludes further creation of pores from charging of the membrane via the longitudinal AF. The exact value of enhancement in uptake from the longitudinal AF is shown to depend on pulsing, membrane, and tissue parameters. Finally, simulation results reproduce qualitative, and in some cases quantitative, behavior of uptake observed in experiments.</p><p>Overall, percent increase in total tissue uptake from the longitudinal AF is on the order of experimental variability, and this study corroborates previous theoretical models that neglect the effects from the longitudinal AF. However, previous models neglect the longitudinal AF without explanation, while the asymptotic fiber model is able to detail the mechanisms involved. Mechanisms revealed by the model offer insight into interpreting experimental results and increasing efficiency of delivery protocols. The model also rigorously derives a new transverse AF based on individual fiber geometry, which affects the spatial distribution of uptake in tissue differently than predicting uptake based on the magnitude of the electric field, as used in many published models. Results of this study are strictly valid for transport of small molecules through small non-growing pores. For gene therapy applications the model must be extended to transport of large DNA molecules through large pores, which may alter the importance of the longitudinal AF. In broader terms, the asymptotic model also provides a new, computationally efficient tool that may be used in studying the effect of transverse and longitudinal components of the field for other types of membrane dynamics in muscle and nerves.</p> / Dissertation

During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequencing is presented. The method has been applied to several projects and further development by others has enabled even higher sample throughputs. Amplification of single cell genomes is a prerequisite for sequence analysis. Paper 2 evaluates four commercially available kits for whole genome amplification of single cells. The results show that coverage of the genome differs significantly among the protocols and as expected this has impact on the downstream analysis. In Paper 3, single cell genotyping by exome sequencing is used to confirm the presence of fat cells derived from donated bone marrow within the recipients’ fat tissue. Close to hundred single cells were exome sequenced and a subset was validated by whole genome sequencing. In the last paper, a new method for phasing (i.e. determining the physical connection of variant alleles) is presented. The method barcodes amplicons from single molecules in emulsion droplets. The barcodes can then be used to determine which variants were present on the same original DNA molecule. The method is applied to two variable regions in the bacterial 16S gene in a metagenomic sample. Thus, two of the papers (1 and 4) present development of new methods for increasing the throughput and information content of data from massively parallel sequencing. Paper 2 evaluates and compares currently available methods and in paper 3, a biological question is answered using some of these tools. / <p>QC 20160127</p>

This thesis is focused on understanding the interactions between molecules and surface-enhanced Raman scattering (SERS) substrates that are typically unresolved due to the diffraction limit of light. Towards this end, we have developed and tested several different sub-diffraction-limited imaging techniques in order to observe these interactions. First, we utilize an isotope-edited bianalyte approach combined with super-resolution imaging via Gaussian point-spread function fitting to elucidate the role of Raman reporter molecules on the location of the SERS emission centroids. By using low concentrations of two different analyte molecules, we find that the location of the SERS emission centroid depends on the number and positions of the molecules present on the SERS substrate. It is also known that SERS enhancement partially results from the molecule coupling its emission into the far-field through the plasmonic nanostructure. This results in a particle-dictated, dipole-like emission pattern, which cannot be accurately modeled as a Gaussian, so we tested the applicability of super-resolution imaging using a dipole-emission fitting model to this data. To test this model, we first fit gold nanorod (AuNR) luminescence images, as AuNR luminescence is primarily coupled out through the longitudinal dipole plasmon mode. This study showed that a three-dimensional dipole model is necessary to fit the AuNR emission, with the model providing accurate orientation and emission wavelength parameters for the nanostructure, as confirmed using correlated AFM and spectroscopy. The dipole fitting technique was next applied to single- and multiple-molecule SERS emission from silver nanoparticle dimers. We again found that a three-dimensional dipole PSF was necessary to accurately model the emission and orientation parameters of the dimer, but that at the single molecule level, the movement of the molecule causes increased uncertainty in the orientation parameters determined by the fit. Finally, we describe progress towards using a combined atomic force/optical microscope system in order to position a carbon nanotube analyte at known locations on the nanoparticle substrate. This would allow for the simultaneous mapping of nanoparticle topography and exact locations of plasmonic enhancement around the nanostructure, but consistently low signal-to-noise kept this technique from being viable. / text

<p>Highly correlated quantum chemical methods have been appliedto study the photophysical properties of substituted benzenes.With the inclusion of spin-orbit coupling, the phosphorescencesof these molecules have been calculated usingMulti-CongurationalSelf- Consistent Field (MCSCF) quadraticresponse theory. The Herzberg-Teller approximation has beenadopted to evaluate the vibronic contributions tophosphorescence.</p><p>The performance of hybrid density functional theory (DFT) atthe B3LYP level is examined in comparison to the MP2, CCSD andCCSD(T) methods for the geometry and permanent dipole moment ofp-aminobenzoic acid. The time-dependent DFT/B3LYP method isapplied to calculate the two-photon absorption of a series ofZinc-porphyrin derivatives in combination with a two-statemodel. The transitions between excited singlet and tripletstates of Zinc and Platinum based organometallic compounds havebeen computed using DFT quadratic response theory. The resultsare used to simulate the non-linear propagation of laser pulsesthrough these materials utilizing a dynamical wave propagationmethod.</p>

L'adhésion cellulaire est un processus biologique fondamental contrôlé par des liaisons moléculaires spécifiques entre ligands et récepteurs attachés à des surfaces. La formation et la rupture de ces liens dépendent de facteurs cinétiques, mécaniques et structurels. Le but de ce travail était d'observer comment l'interaction ICAM-1 (Inter- Cellular Adhesion Molecule 1) - anti ICAM-1 pouvait être modifiée en jouant i) sur la multivalence de molécules impliquées dans la liaison ii) sur la topographie de surface et iii) sur la mobilité des ligands. A cette fin, on a principalement utilisé une chambre à flux laminaire, complété par une détection de molécule unique par fluorescence. L'étude sur les effets de multivalence, utilisant des monomères et dimères d'ICAM-1, a été réalisée en absence ou en présence d'une force mécanique, montrant la plus grande stabilité des liaisons divalentes. En outre, un renforcement avec la force et le temps a été trouvé et décrit avec une fonction à deux paramètres, montrant, pour les liaisons divalentes, un comportement intermédiaire entre rupture parallèles et successives des liaisons monovalentes. La fréquence d'adhésion des liaisons monovalentes et divalentes présente différentes valeurs causées par la différence de longueur de ces molécules. Les expériences d'adhésion ont été effectuées en variant la topographie du substrat à l'échelle nanométrique pour les molécules étudiées. Une comparaison des cinétiques de liaisons sur ces surfaces ne montrent pas de différences soit dans la formation ou dans la rupture. Dans l'écoulement, le temps de contact entre les molécules est contrôlé par la convection de microsphères. Des résultats récents montrent qu'un temps minimum est requis pour former la liaison (Robert et al. 2011). Pour tester cette prédiction, les ligands sont ancrés à une bicouche lipidique (SLB) pour étudier comment la diffusion peut modifier l'adhésion. Expérimentalement, les fréquences d'adhésion des liaisons ont montré un comportement similaire pour les SLB fixes et fluides. Toutefois, une simulation numérique 2D prédit un effet sur la formation de la liaison, même lorsque la diffusion des ligands est faible. Il semblerait que la diffusion joue un rôle dans la dissociation de la liaison, limitant fortement la dissociation de la bicouche fluide. Cet effet peut être expliqué par la présence éventuelle de liaisons multiples dues à l'accumulation des ligands sur la surface de contact. La chambre à flux laminaire et le suivi de particule individuelle a permis de mieux comprendre les mécanismes d'adhésion et le comportement de l'interaction des molécules d'ICAM-1 au niveau de molécule individuelle, lorsque l'environnement moléculaire a été modifiée. Des travaux similaires peuvent être effectuées sur d'autres molécules d'adhésion afin d'atteindre une connaissance beaucoup plus large des mécanismes d'adhésion, ou sur les liaisons entre TCR et pMHC qui sont extrêmement importantes dans la réponse immunitaire.