<p>Fabrication of microarrays using sol-gel immobilization has been utilized as an approach to develop high density biosensors. Microarray fabrication using various printing techniques including pin-printing and piezoelectric ink jet printing methods has been demonstrated. However, only limited characterization to understand the encapsulated biomolecule-material interface has been reported. Herein, Chemical characterization using X-ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR) on pin-printed microarrays of sol-gel derived acetylcholinesterase (AChE) microarrays is reported. Furthermore, the <em>in situ</em> fabrication of microarrays following the sol-gel process using piezoelectric ink jet printing methods was explored. Through techniques measuring solution viscosity, surface tension and particle size, important aspects of bio-ink formulation for piezoelectric ink jet printing were identified. Combined, a greater understanding towards the fabrication and characterization of sol-gel derived microarrays was achieved through this exploratory research.</p> / Master of Science (MSc)

Hyperspectral imaging is an emerging technology in the field of biomedical engineering which may be used as a non-invasive modality to characterize tumors. In this thesis, a hyperspectral imaging system was used to characterize canine mammary tumors of unknown histopathology (pre-surgery) and correlate the results with the post-surgical histopathology results. The system consisted of a charge coupled device (CCD) camera, a liquid crystal tunable filter in the near infrared range (650-1100 nm), and a controller. Spectral signatures of malignant and benign canine mammary tumors were extracted and analyzed. The reflectance intensities of malignant tumor spectra were generally lower than benign tumor spectra over the wavelength range 650-1100nm. Previous studies have shown that cancerous tissues have a higher hemoglobin and water content, and lower lipid concentration with respect to benign tissues. The decreased reflectance intensity observed for malignant tumors is likely due to the increased microvasculature and, therefore, higher blood content of malignant tissue relative to benign tissue. Second derivative method was applied to the reflectance spectra. Peaks at 700, 840, 900 and 970 nm were observed in the second derivative reflectance spectra. These peaks were attributed to deoxy-hemoglobin, oxy-hemoglobin, lipid and water respectively. A Tissue Optical Index (TOI) was developed that enhances contrast between malignant and benign canine tumors. This index is based on the ratio of the reflectance intensity values corresponding to the wavelengths associated with the four chromophores. Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were also applied on the canine spectral dataset and the method was cross-validated. Preliminary results from 22 canine mammary tumors showed that the sensitivity and specificity of the PCA-LDA is method is 86% and 86% respectively. The sensitivity and specificity of the TOI model is 86% and 95% respectively. These results show promise in the non-invasive optical diagnosis of canine mammary cancer. / Electrical and Computer Engineering

This dissertation investigates the electronic spectroscopy of a series of alkyl phenyl ketone radical cations and the dynamics of selective launch states in the strong field regime with tunable near infrared ultrashort laser pulses from 790 nm - 1550 nm coupled to mass spectrometric detection. Our method relies on tunable strong field laser pulses in the range from 1150 nm - 1550 nm to adiabatically ioinized gas phase molecules and prepare ions in the ground ionic state that serve as a launch state for future excitation and control. Adiabatic ionization is capable of transferring little energy to the molecule and producing a majority of a parent molecular ion in comparison to nonadiabatic ionization wherein multiple ionic states can be populated with an accompanying high degree of molecular fragmentation. We measure a dynamic resonance in the low lying electronic states of the acetopheone radical cation via preparation of a launch state with adiabatic ionization followed by a one photon transition within a single pulse duration which facilitates bond dissociation to produce the benzoyl ion. Experiments on acetophenone homologues and derivatives elucidate the structural dependence of the electronic resonance and supporting ab initio calculations identify the dynamic resonance along the molecular torsional coordinate between the ground ionic state, D0, and second excited state, D2. Post ionization excitation within the pulse duration transfers the ground state wavepacket to the D2 surface where the wavepacket encounters a three state conical intersection that facilitates the preferred bond dissociation. Time resolved photodissociation experiments measure the dynamics of the launch state, large amplitude oscillations and extended coherence times support the notion that adiabatic ionization populates a majority of the ground ionic surface. Control of the dissociation products is initiated from the launch state by varying the pump wavelength and probe intensity. Elimination of the D0 wavepacket with a 1370 nm reveals additional secondary dynamics that are attributed to wavepacket motion on the D2 surface. Finally, the effect of para substitution on the acetophenone radical cation is explored as a strategy to control the launch state wavepacket dynamics. Suppresion of the wavepacket dynamics are observed with the addition of alkoxy groups whereas extended coherence of the launch state dynamics approaching ~5 ps is observed upon trifluoromethyl substitution. A possible mechanism for the extended coherenece based on coupled torsional rotors is proposed. / Chemistry

No description available.

No / This paper aims to establish the acid concentration of finely dispersed droplets in hydrocarbon oils. Small quantities of aqueous sulphuric acid (H2SO4) were found to be trapped within hydrocarbon shells, making them inaccessible for concentration evaluation by titration. Fourier transform infrared spectroscopy (FTIR) used in the attenuated total reflection mode (ATR; FTIR-ATR) was applied to study the reaction products of squalane, C30H62, and an API Group I base oil with various concentrations of aqueous H2SO4. The absorbance comparison usually used for estimating acid concentrations was found to fail when small quantities of acid are trapped in the reaction product. It was found that the peak shift and changes in absorbance found for various pure aqueous acid concentrations were useful to establish the remaining concentration of the trapped H2SO4. This paper fulfils the identified need to study acid dissociation-dependent peak shifts of H2SO4 to find the acid concentration of finely dispersed droplets in hydrocarbon oils.

Halogen and nitrogen containing compounds play a key role in the atmospheric chemistry of the Earth. Through a mixed computational and experimental approach, the kinetics of these compounds with radicals common to the atmosphere have been explored. Using fundamental measurements such as the IR absorption cross-section, the rate constants of atmospheric reactions and the properties of product molecules have been derived. These results have been further extended to environmental applications such as the Global Warming Potential for a species. The present results can be used as a calibration for further experiments and as checks on computational predictions of environmental properties. Such modeling can aid in the development of future industrial reagents that are less hazardous to the atmosphere.

The complete role of inositol signaling in plants and humans is still elusive. The plant Arabidopsis thaliana contains fifteen predicted inositol polyphosphate 5- phosphatases (5PTases, E.C. 3.1.3.36) that have the potential to remove a 5-phosphate from various inositol second messenger substrates. To examine the substrate specificity of one of these Arabidopsis thaliana 5PTases (At5PTases), recombinant At5PTase1 was obtained from a Drosophila melanogaster expression system and analyzed biochemically. This analysis revealed that At5PTase1 has the ability to catalyze the hydrolysis of four potential inositol second messenger substrates. To determine whether At5PTase1 can be used to alter the signal transduction pathway of the major drought-sensing hormone abscisic acid (ABA), plants ectopically expressing At5PTase1 under the control of a constitutive promoter were characterized. This characterization revealed that plants ectopically expressing At5PTase1 had an altered response to ABA. These plants have stomata that are insensitive to ABA, and have lower basal and ABA-induced inositol (1,4,5)-trisphosphate [Ins(1,4,5)P₃] levels. In addition, At5PTase1 mRNA and protein levels are transiently regulated by ABA. These data strongly suggest that At5PTase1 can act as a signal terminator of ABA signal transduction. Like the Arabidopsis At5PTase1, a human 5PTase, Ocrl, has the ability to catalyze the hydrolysis of a 5-phosphate from several inositol-containing substrates. The loss of functional Ocrl protein results in a rare genetic disorder known as Lowe oculocerebrorenal syndrome. To gather information concerning the specificity determinants of the Ocrl protein, a structure-function analysis of Ocrl was conducted using a vibrational technique, difference Fourier transform infrared (FT-IR) spectroscopy. Upon the introduction of Ins(1,4,5)P₃ substrate, structural changes in carboxylic acid and histidine residues were observed. The net result of changes in these residues indicates that upon Ins(1,4,5)P₃ introduction, a carboxylic acid-containing residue is protonated, and a histidine residue is deprotonated. This interpretation supports the idea that the deprotonation of the histidine residue is concomitant with the coordination of a divalent cation upon Ins(1,4,5)P₃ introduction. This work allows for the proposal of a new model for the role of the active site histidine of OCRL. / Ph. D.

The targeted design of new catalyst materials can only be accomplished once a fundamental understanding of the interactions between material surfaces and adsorbed molecules is developed. In situ infrared spectroscopy and mass spectrometry methods were employed to probe interactions at the gas-surface interface of oxide-supported metal nanoparticle materials. High vacuum conditions allowed for systematic investigations to describe detailed reaction mechanisms. Specifically, variable temperature infrared spectroscopy was utilized to uncover the binding energetics of CO to the oxide surface of TiO2-based materials. As binding energetics are related to the electronic structure of the adsorption site, differences in evaluated binding enthalpies are hypothesized to probe electronic metal-support interactions that describe charge transfer between the supported metal nanoparticles and TiO2. Cu/TiO2 aerogels were identified as a candidate for more in-depth studies. Flow reactor methods in combination with the surface-based infrared spectroscopy were utilized to elucidate the CO oxidation reaction mechanism over Cu/TiO2 aerogels. Bridging oxygen atoms on TiO2 regions of the material were identified as the active site for catalysis in a Cu-assisted Mars-van Krevelen lattice extraction mechanism. Methanol oxidation was then studied with similar methods to show the complete conversion to CO2 and H2O at high temperatures through the reduction of titania and formation of a formate intermediate. Higher-order carbonaceous alcohols were probed for adsorption and reactivity on Cu/TiO2 aerogels and were observed to follow a similar reaction pathway. The higher-order alcohols, however, were shown to undergo a partial oxidation pathway in the absence of gaseous O2 that is hypothesized to originate from enhanced binding to Cu sites. The decomposition of the chemical warfare agent simulant dimethyl chlorophosphate was also investigated. A hydrolysis pathway to form the significantly less toxic molecule CH3Cl was observed, highlighting the unique promotional effects and chemistry on Cu/TiO2 aerogels. The results presented exemplify both the influence of electronic metal-support interactions on catalysis and the versatile reactivity of Cu/TiO2 aerogels. / Doctor of Philosophy / Interactions between small gaseous molecules and material surfaces have very important implications for applications regarding the environment, industry, and military/public safety. The mechanisms in which gases interact with a solid surface can determine how the material can be functionally used as catalysts. Scientists and engineers start to build a fundamental understanding of what makes a catalyst successful for different applications by understanding the location and strength of interactions. A catalyst's surface acts to lower activation barriers and provide low-energy pathways for interacting molecules to chemically change, by breaking bonds for molecular decomposition and/or forming new bonds. The vibrations of chemical bonds that break and form on surfaces are probed with infrared spectroscopy at the gas-surface interface to study molecular adsorption and reactivity. In addition, a flow cell reactor is used to characterize reaction progress and identify products in real-time. A class of reactive nanoparticulate materials is utilized as a model system on which to study various chemical reactions for important applications including small molecule oxidation for industrial detoxification and clean energy applications, as well as the decomposition of chemical warfare agents. Reaction mechanisms for the oxidation of carbon monoxide and alcohols were elucidated through the utilization of the methods described above. In addition, the decomposition of a chemical warfare agent simulant is characterized. The discoveries and understanding of important chemical properties presented in this dissertation will aid in the synthesis of effective next-generation catalyst materials.

The advancements of chemists, engineers, and material scientists has yielded an enormous and diverse library of high-performance materials with varying chemical and physical properties that can be used in a wide array of applications. A molecular-level understanding of the nature of gas–surface interactions is critical to the development of next generation materials for applications such as gas storage and separation, chemical sensing, catalysis, energy conversion, and protective coatings. Quartz crystal microbalance (QCM) and in situ infrared (IR) spectroscopic techniques were employed to probe how topological features of a material as well as structural differences of the analytes affect gas sorption. Detailed studies of the interactions of three categories of molecules: aromatic hydrocarbons, triatomic ambient gases, and chemical warfare agents, with metal-organic frameworks (MOFs) and polyurethane coatings were conducted to build structure–property relationships for the nature and energetics of gas sorption within each material. Differences in the molecular structure of the guest compounds were found to greatly influence how, and to what extent each molecule interacts with the MOF or polyurethane film. Specifically, IR studies revealed that transport of aromatic compounds within the zirconium-based MOF, UiO-66 was limited by steric restrictions as molecules passed through small triangular apertures within the pore environment of the MOF. In contrast, the smaller triatomic molecules, CO2, SO2, and NO2, were able to pass freely through the MOF apertures and instead reversibly adsorbed inside the MOF cavities. Specifically, SO2 and NO2 were observed to preferentially bind to undercoordinated zirconium sites located on the MOF nodes. In addition, uptake of CO2, SO2, and NO2 was also aided by dispersion forces within the confined pore environments and by hydrogen bond formation with μ3 OH groups of the MOFs. Dimethyl chlorophosphate (DMCP), a nerve agent simulant that contains several electronegative moieties, was also found to strongly adsorb to undercoordinated zirconium; however, unlike in the aromatic and triatomic molecule systems, DMCP remained permanently bound to the MOFs, even at high temperatures. Finally, QCM studies of mustard gas simulant uptake into polyurethane films of varying hard:soft segment compositions revealed that dipole-dipole and dipole-induced dipole interactions were responsible for favorable absorption conditions. Furthermore, the ratio of hard and soft segment components of the polyurethane had a minor impact on simulant adsorption. Higher hard-segment content resulted in a more crystalline film that reduced simulant uptake, whereas the rubbery, high soft segment polyurethane allowed for greater vapor absorption. Ultimately, molecular-level insight into how the chemical identity of a guest molecule impacts the mechanism and energetics of vapor sorption into both MOFs and polymeric films can be extended to other relevant systems and may help identify how specific characteristics of each material, such as size, shape, and chemical functionality impact their potential use in targeted applications. / Doctor of Philosophy / The nature in which specific gases interact with materials will largely dictate how the material can be utilized. By understanding where and how strongly gas molecules interact with a material, scientists and engineers can rationally design new and improved systems for targeted applications. In the research described in this thesis, we examined how the chemical structure of three different groups of compounds, which have relevance in many industrial, environmental, and defense-related applications, affected the type and strength of interaction between the gas and material of interest. From these studies, we have identified how key properties and features within the examined materials such as size, shape, and chemical composition, lead to significant differences in how vapor molecules interacted with the materials. For example, benzene, toluene, and xylene, which are incredibly important chemicals in industry, were found to be restricted by narrow passageways as they moved through materials with small pores. In contrast, small gases present in the environment from combustion exhaust such as CO₂, SO₂, and NO₂ were able to freely traverse through the passageways, and instead weakly interacted with specific chemical groups inside the cavities of the material. On the same material however, a third class of compounds, organophosphorus-containing chemical warfare agent mimics, irreversibly reacted with chemical groups of the surface, and remained bound even after exposure to high temperatures. Ultimately, the work presented in this thesis is aimed at providing key fundamental insights about specific classes of materials on how, and how strongly they interact with targeted hazardous vapors, which can be utilized by synthetic chemists to design next generation materials.

Diborane (B2H6) is a hydride gas often employed in high-purity industrial surface processes such as chemical vapor deposition or epitaxial layer growth. The use of diborane at industrial scales is complicated by the formation of higher-order borane contaminants in pure diborane gas via a complex series of gas-phase reactions. An advanced, rationally designed sorbent could stabilize diborane through interfacial interactions, dramatically reducing the decomposition rate without permanently trapping the molecule. However, the design of such a sorbent would require a nuanced understanding of diborane's fundamental surface chemistry, about which little is known. In the work presented in this thesis, a novel ultra-high vacuum (UHV) system was designed and employed to characterize the fundamental interactions of diborane with a variety of surfaces. In situ Fourier-transform infrared (FTIR) spectroscopy and temperature-programmed desorption (TPD) experiments were used in conjunction with density-functional theory (DFT) calculations to elucidate binding geometries and interaction mechanisms. On non-functionalized model surfaces such as CaF2 or amorphous carbon, diborane adsorbed only at cryogenic temperatures. Hydroxylated surfaces such as amorphous silica (SiO2) adsorbed significantly more diborane, which remained at slightly higher temperatures. FTIR spectra indicated the presence of hydrogen bonding between diborane and surface hydroxyl groups. DFT calculations revealed that the interaction takes the form of a novel bifurcated dihydrogen bond. In contrast with previous reports, diborane exhibited only weak interactions with the surface hydroxyl groups of silica. DFT calculations further elucidated that the irreversible reaction of diborane with surface hydroxyls is only possible in the presence of a second nucleophile (such as adventitious water). On the metal-organic framework (MOF) UiO-66 NH2, unique chemistry was observed in which diborane reacted with the –NH2 groups of the MOF linkers, yielding stable surface-bound products. DFT calculations determined the reaction mechanism to be dissociative adsorption of diborane, resulting in two amine-bound –BH3 moieties. Importantly, it was found that these fragments persisted at room temperature and could only leave the surface via the reverse reaction. The discovery that diborane can be stored as separate fragments that re-combine to yield the parent molecule has important implications for the development of new diborane sorbents. We hypothesize that surfaces designed with fixed, precisely spaced nucleophiles could enable the reversible storage of diborane. / Doctor of Philosophy / Diborane (B2H6) is a useful but hazardous gas employed in both academia and industry, often in processes that require ultra-high-purity source gases. However, diborane reacts with itself at room temperature, making the contamination of pure diborane very difficult to avoid. This problem could potentially be solved with a specially designed solid material that would sequester diborane without destroying it, but the design of such a material would require a much better understanding of diborane's chemistry with surfaces than currently exists. In this work, we employed ultra-high vacuum (UHV) methods to study the interactions between diborane and a variety of surfaces, with the ultimate goal of determining guiding principles for the design of diborane-stabilizing sorbents. Among the materials we studied were inorganic carbon, silica (SiO2), and a class of advanced microporous materials known as metal-organic frameworks (MOFs). Inorganic materials were found not to interact meaningfully with diborane. A novel hydrogen bond was discovered between diborane and the surface of silica, but the interaction was found to be too weak to provide significant stabilization. Most MOFs behaved similarly to silica. The MOF UiO-66-NH2, however, was found to react with diborane. Through a combination of computer simulations and UHV experiments, the precise nature of the reaction was determined. On the surface of UiO 66 NH2, diborane splits into two surface-bound BH3 molecules, where it is trapped until the reaction reverses. Importantly, it was found that BH3 can only leave the surface by recombining into diborane—effectively storing diborane on the surface to be released later. We hypothesize that this useful chemistry is due to the fixed distance between chemical groups on the MOF surface. This discovery suggests a promising strategy for the design of advanced diborane sorbents.