Ozone is a heavily monitored pollutant. Ozone is not directly emitted into the atmosphere, but rather the product of chemical reactions. Ground level ozone occurs when nitrogen oxides (NOx) and volatile organic compounds (VOCs) react with each other in the presence of sunlight. The primary precursors of ozone are anthropogenically emitted, and as a result, tropospheric ozone has cost millions of dollars in damages and has hurt the health of countless people. This dissertation is a collection of work that aims to provide insight into atmospheric reactions that result in tropospheric ozone and the instrumentation to study such reactions. While these reactions are well studied, this research is novel in its attempt to understand water vapor's influence in tropospheric ozone reactions. As the troposphere continues to get warmer and wetter from global climate change, water vapor will play a larger role in tropospheric reactions, which in turn may perturb the global reactions. Work is presented on the self-reaction of β-hydroxyethyl peroxy radical (β-HEP), an ozone precursor, and the increase in reaction rate catalyzed by water vapor. β-HEP serves as a model system for understanding the roles of water vapor in perturbing the kinetics and product branching ratio of ozone forming reactions. The self-reaction rate coefficient of β-HEP was investigated between 274-296 K with 1.0 × 1015 to 2.5 × 1017 molecules cm-3 of water vapor at 200 Torr total pressure by slow-flow laser flash photolysis coupled with UV time-resolved spectroscopy and long-path, wavelength-modulated, diode-laser spectroscopy. The overall rate constant is expressed as the product of temperature-dependent and water vapor-dependent terms giving k(T,H2O) = 7.8 × 10-14(e8.2 (±2.5) kJ/RT )(1 + 1.4 × 10-34 × e92 (±11) kJ/RT [H2O]). The results suggest that formation of a β-HEP-H2O complex is responsible for the observed water vapor enhancement of the self-reaction rate coefficient. A new discharge flow mass-spectrometer was engineered in collaboration with the California Institute of Technology and NASA's Jet Propulsion Laboratory. This instrument allows for rapid study of water vapor influence on the kinetics of atmospheric reactions. This instrument will be used in further studying the β-HEP + NO reaction as a function of water vapor concentration.

<p> The interaction mechanisms of an ion beam with a solid target are identified. Basic parameters associated with ion scattering, charge neutralization, inelastic energy losses and secondary ion production are described. Low energy (1-20 kev) experimental studies on these topics are reviewed. A low energy ion mass spectrometer is described. The ion beam is generated by an existing kev ion accelerator and is directed to a newly constructed UHV target chamer. The energy and angular distributions of the backscattered particles are measured with a hemispherical electrostatic analyser and a channeltron detector. A high precision goniometer allows target rotation about two perpendicular axes by angles of 180° and 90° with an accuracy and repeatability of 0.1°. The interaction chamber is bakeable to 250°c and was designed for an ultimate pressure of 10^-11 torr. The data acquisition system chamber scans the energy spectrum automatically so that the radiation dosage at the target is equalized for all channels. </p> / Thesis / Master of Engineering (MEngr)

No description available.

Gastroparesis is a disorder characterized by delayed gastric emptying due to chronic abnormal gastric motility. Prokinetic agents such as domperidone and metoclopramide are the cornerstone in treatment of gastroparesis. Although these medications have been used for decades, essential information about their metabolism is not available. Lack of knowledge about the metabolites formed in the body upon administration of the aforementioned medications as well as the enzymes involved in their metabolism limits key information needed to make sound medical decisions. Accurate and comprehensive identification of the metabolites along with reaction phenotyping of prokinetic agents will ensure safe and effective use of these drugs and hence enhance the clinical outcome. The thesis starts with an introductory chapter which comprises a comprehensive literature review on gastroparesis and the available pharmacological treatment options. The chapter also emphasizes the importance of metabolic profiling of prokinetic agents (domperidone and metoclopramide) and its impact on enhancing the safety and efficacy of these medications. Chapter 2 of this project was aimed to determine phase oxidative and conjugative metabolites of domperidone in the plasma and urine of gastroparesis patients using tandem mass spectrometry. First, the metabolites were identified in in-vitro human subcellular fractions. The knowledge gained in this experiment helped identifying the metabolites in the biological fluids of patients. In total, 12 metabolites including 7 new metabolites were identified, 5 of which were not reported previously. Chapter 3 aimed to identify the cytochrome P450 (CYP) enzymes responsible for the metabolism of metoclopramide. The parent depletion approach was used and a novel LC-MS/MS method was developed and validated to enable metoclopramide quantification. CYP2D6 was showed to the predominant isoform in metoclopramide metabolism; other isoforms also contribute to a minor extent. Chapter 4 discusses the possibility of potential drug-drug interaction (DDI) in the current management practice of gastroparesis. We identified and investigated some frequently used drug combinations that are known to share common metabolic pathways. Domperidone in combination with pioglitazone and ondansetron was evaluated. Results showed that pioglitazone inhibited domperidone metabolism in-vitro. Our experiments did not predict a DDI for the domperidone - ondansetron combination. In summary, the ultimate goal of this thesis was to improve the management of gastroparesis by increasing information about the metabolic disposition of prokinetic agents and to investigate the magnitude of putative drug combinations. The knowledge provided by this work will help in making more effective and less hazardous clinical decisions which will ultimately lead to more successful gastroparesis management. / Pharmaceutical Sciences

The variation in the carbon isotope composition of the cap rock of Texas and Louisiana sulphur wells was investigated by means of a simultaneous collection mass spectrometer. These rocks showed anomalously large depletions in C-13. The isotope depletion in the decarboxylation of pyruvic acid, both by chemical means and by bacteria, was measured and the isotope composition of the carbon dioxide released was found to be similar to that of the cap rock. The hypothesis is advanced that the carbonate of the cap rock may have originated by the precipitation of carbon dioxide released in the bacterial decarboxylation of an organic substrate. / Thesis / Master of Science (MSc)

This thesis presents axially symmetric equivalents of three-dimensional rf ion traps. Miniaturization in mass spectrometry has focused on miniaturizing mass analyzers. Decrease in mass analyzer size facilitates reduction of the size of other components of a mass spectrometer, especially the radio frequency electronics and vacuum system. Miniaturized mass analyzers are made using advanced microfabrication techniques. Due to micromachining limitations, it is not possible to fabricate ion traps with exact axial symmetry. The motivation for this thesis is to investigate newer three-dimensional geometries which do not possess axial symmetry, but are equivalent in performance to axially symmetric ion traps. We introduce a 3D geometry called square ion trap(SIT) having a ring electrode made off our square shaped planar surfaces and square shaped endcap electrodes resembling a cuboid. Initially, a SIT geometry is taken and it will be investigated if this unknown 3D geometry can be made equivalent to a well characterized, axially symmetric ion trap like the CIT. The purpose of showing equivalence will be to understand the ion dynamics and fields inside the new 3D SIT. This thesis consists of five chapters. In Chapter 1, we present the necessary background information required to understand the operation of a mass spectrometer. The Paul trap geometry is introduced followed by the derivation of equation of ion motion inside the Paul trap. The Mathieu stability plot and the modes of operation of a mass spectrometer are briefly discussed. The chapter ends by outlining scope of the thesis. Chapter 2 describes the computational methods employed by us in the thesis. First, the geometry of square ion trap is introduced. Then the boundary element method(BEM) which is used to compute the charge distribution on the electrode surfaces is discussed. This is followed by the three-dimensional Green’s function which should be employed for non-axially symmetric structures. The method to calculate potential and field inside the ion trap from charge distribution is shown. Calculation of multipole coefficients for non-axially symmetric traps using charge distribution is shown. The methods used to generate ion trajectory and stability plot are discussed. The Nelder-Mead simplex method used for optimization is also presented. To verify our numerical methods of charge calculation, we have taken standard textbook problems and compared our results with those presented therein. The multipoles calculation, field and ion trajectory was verified by comparing the results for the Paul trap and cylindrical ion traps. Chapter 3 presents the results for axially symmetric equivalents of 3D rf ion traps. SIT geometry of dimensions equivalent to the CIT0 are taken and field and multipoles are studied in it. Then optimization is applied to create a CIT geometry equivalent to the SIT under study. Axial field and ion trajectory was compared and observed to be matching. Finally, stability plot was generated for both SIT and its equivalent CIT and was found to present a close match. Chapter 4 presents the numerical results obtained for three-dimensional rf ion trap equivalent of CIT. In this chapter, we have considered two standard geometries, the CIT0 and the CITopt. Optimization was applied to create SIT geometries equivalent to the CIT0 and the CITopt respectively. Comparison of fields and ion trajectory confirmed the fact that non-axially symmetric traps can be created equivalent to any axially symmetric ion trap. We have also considered another case of axially symmetric circular planar ion trap which has an annular ring electrode and two planar endcap electrodes. Square equivalent of circular planar trap was created by the optimizer and its equivalent was verified by ion trajectory comparison. Chapter 5 summarizes the thesis with a few concluding remarks.

The interaction of active molybdenum field emission microcathode arrays with oxygen, water, carbon dioxide, methane, hydrogen and helium gases was studied. Experiments were setup to measure the emission characteristics as a function of gas exposures. The resulting changes in the surface work function of the tips were determined from the Fowler-Nordheim plots. The kinetics of the FEA-gas interaction were studied by observing the ion species originating from the array during and after gas exposures with a high resolution quadrupole mass spectrometer. With the work function data and the mass spectrometry information, the mechanisms responsible for emission degradation and subsequent device recovery after exposures have been determined. The data obtained was used in estimating the device lifetimes under various vacuum environments. Also it was found that the gas exposure effects are similar in dc and pulsed modes of operation of the arrays, thus permitting the use of dc mode testing as an effective acceleration method in establishing the device lifetimes under various vacuum conditions. The vacuum conditions required for the long term emission current stability and reliability of vacuum microelectronic devices employing FEAs are established. Exposure of Mo field emitter arrays to oxygen bearing species like oxygen, water and carbon dioxide resulted in serious emission current degradation. Whereas, exposure to methane and hydrogen caused a significant increase in emission current. The control of residual gases like 02, C02 and H20 in the vacuum envelope is essential for the emission current stability and long term reliability of vacuum microelectronic devices employing field emission microcathode technology.

<div>Amongst the various classes of mass analyzers, the quadrupole ion trap (QIT) is by far the most versatile. Although it can achieve only modest resolution (unit) and mass accuracy (101-102 ppm), it has high sensitivity and selectivity, can operate at pressures exceeding 10-3 torr, is tolerant to various electrode imperfections, and has single analyzer tandem mass spectrometry (MS/MS) capabilities in the form of product ion scans. These characteristics make the QIT ideal for mass spectrometer miniaturization, as most of the fundamental performance metrics of the QIT do not depend on device size. As such, the current drive in miniature systems is to adopt miniature ion traps in various forms – 3D, linear, toroidal, rectilinear, cylindrical, arrays, etc.</div><div><br></div><div>Despite being one of the two common mass analyzers with inherent MS/MS capabilities (the other being the Fourier transform ion cyclotron resonance mass spectrometer), it is commonly accepted that the QIT cannot perform one-dimensional precursor ion scans and neutral loss scans - the other two main MS/MS scan modes - or two-dimensional MS/MS scans. The former two are usually conducted in triple quadrupole instruments in which a first and third quadrupole are used to mass select precursor and product ions while fragmentation occurs in an intermediate collision cell. The third scan can be accomplished by acquiring a product ion scan of every precursor ion, thus revealing the entire 2D MS/MS data domain (precursor ion m/z vs. product ion m/z). This, however, is not one scan but a set of scans. Because the ion trap is a tandem-in-time instrument rather than a tandem-in-space analyzer, precursor ion scans, neutral loss scans, and 2D MS/MS are, at best, difficult.</div><div><br></div><div>Yet miniature mass spectrometers utilizing quadrupole ion traps for mass analysis would perhaps benefit the most from precursor scans, neutral loss scans, and 2D MS/MS because they generally have acquisition rates (# scans/s) an order of magnitude lower than their benchtop counterparts. This is because they usually use a discontinuous atmospheric pressure interface (DAPI) to reduce the gas load on the backing pumps, resulting in a ~1 scan/s acquisition rate and making the commonly-used data-dependent acquisition method (i.e. obtaining a product ion scan for every abundant precursor ion) inefficient in terms of sample consumption, time, and instrument power. Precursor and neutral loss scans targeting specific molecular functionality of interest - as well as 2D MS/MS – are more efficient ways of moving through the MS/MS data domain and thus pair quite readily with miniature ion traps.</div><div><br></div><div>Herein we demonstrate that precursor ion scans, neutral loss scans, and 2D MS/MS are all possible in a linear quadrupole ion trap operated in the orthogonal double resonance mode on both benchtop and portable mass spectrometers. Through application of multiple resonance frequencies matching the secular frequencies of precursor and/or product ions of interest, we show that precursor ions can be fragmented mass-selectively and product ions ejected simultaneously, preserving their relationship, precursor ion -> product ion + neutral, in the time domain and hence allowing the correlation between precursor and product ions without prior isolation. By fixing or scanning the resonance frequencies corresponding to the targeted precursor and product ions, a precursor ion scan or neutral loss scan can be conducted in a single mass analyzer. We further show that 2D MS/MS - acquisition of all precursor ion m/z values and a product ion mass spectrum for every precursor ion, all in a single scan - is possible using similar methodology. These scan modes are particularly valuable for origin-of-life and forensic applications for which the value of miniature mass spectrometers is readily evident.</div>

This thesis presents results of investigations that have been carried out to understand dynamics in nonlinear Paul trap mass spectrometers. Of the three problems that have been taken up for study in this thesis, the first concerns understanding early/delayed ejection of ions in mass selective boundary ejection experiments. The second looks at the differential resolution observed in forward and reverse scan resonance ejection experiments. The third study explores a coupled nonlinear resonance within the nominally stable region of trap operation. The method of multiple scales has been to elucidate dynamics associated with early and delayed ejection of ions in mass selective ejection experiments in Paul traps. We develop a slow flow equation to approximate the solution of a weakly nonlinear Mathieu equation to describe ion dynamics in the neighborhood of the stability boundary of ideal traps (where the Mathieu parameter qz = qz* = 0.908046). For positive even multipoles in the ion trapping field, in the stable region of trap operation, the phase portrait obtained from the slow flow consists of three fixed points, two of which are saddles and the third is a center. As the qz value of an ion approaches qz*, the saddles approach each other, and a point is reached where all nonzero solutions are unbounded, leading to an observation of early ejection. The phase portraits for negative even multipoles and odd multipoles of either sign are qualitatively similar to each other and display bounded solutions even for qz > qz*, resulting in the observation of delayed ejection associated with a more gentle increase in ion motion amplitudes, a mechanism different from the case of the positive even multipoles. The second study investigates constraints on pre-ejection dynamical states which cause differential resolution in resonance ejection experiments using Paul traps with stretched geometry. Both analytical and numerical computations are carried out to elucidate the role of damping and scan rate in influencing coherence in ion motion associated with the forward and reverse scan. It has been shown that in the forward scan experiments, for a given damping, low scan rates result in coherent motion of ions oof a given mass at the jump point. At this point, the amplitude and phase of ions of a given mass, starting at different initial conditions, become effectively identical. As the scan rate is increased, coherence is destroyed. For a given scan rate, increasing damping introduces coherence in ion motion, while decreasing damping destroys this coherence. In reverse scan experiments, for a given damping, very low scan rates will cause coherent ion motion. Increasing the scan rate destroys this coherence. The effect of damping in reverse scan experiments is qualitatively similar to that in the forward scan experiments, but settling times in the forward scan are shorter, leading to improved coherence and resolution. For mass spectrometrically relevant scan rates and damping values, significantly greater coherence is obtained in the forward scan. In the third study we investigate the weakly coupled and nonlinear Mathieu equations governing ion motion in axial and radial directions in a Paul trap in the neighborhood of a nonlinear resonance point at az* = -0.2313850427 and qz* = 0.9193009931$. Using harmonic balance based approximate averaging up to second order; we obtain a slow flow that, we numerically demonstrate, approximates the actual ion dynamics. We find that the slow flow is Hamiltonian. We study the slow flow numerically with the objective of exploring and displaying some of the possible types of interesting ion motions. In particular, we choose specific but arbitrary parameter values; study the stability of the individual radial and axial motion invariant manifolds; examine the rather large times associated with escape of ions; notice regions in the averaged phase space wherein trajectories do not, in fact, escape; observe apparently chaotic dynamics preceding escape for ions that do escape; and note that trajectories that do not escape appear to be confined to 4-tori. We conclude with some comments on the implications for practical operation of the Paul trap near this resonant point.

Plasma enhanced chemical vapor deposition systems are massively deployed to grow numerous thin film coatings including hydrogenated amorphous silicon. A new deposition chamber was designed, procured, and constructed to investigate the plasma properties of a 100% silane (SiH4) glow discharge with varying chamber pressure and inter-electrode spacing. A Hiden EQP1000 ion mass spectrometer sampled the plasma from the substrates point of view. Ion energy distributions were obtained using four different excitation sources +DC, –DC, radio frequency (at 13.56 MHz), and the DC Saddle Field (DCSF) in the tetrode configuration. The shape of the ion energy distributions was constant for the capacitively coupled +DC, –DC, and rf (at higher pressures of 75 and 160 mTorr) glow discharges. The shape of the ion energy distributions for the DCSF plasma exhibited a double peak or saddle structure analogous to radio frequency plasmas. The width between the peaks (peak separation) was controlled by the pressure and the semi-transparent cathode to semi-transparent anode distance. Ion energy distributions from the DCSF plasma concurred with rf and +DC ion energy distributions at specific pressures and inter-electrode distances. This result demonstrates the versatility of the DCSF glow discharge system. Moreover, control of the peak separation is modeled to be iii equivalent to controlling the critical ratio (ion transit time in the sheath to the electron oscillating period), and/or the inferred electron oscillating sheath potential. The DCSF possesses a fusion of rf and +DC methods. The long high energy tail or constant background are indicative of a +DC high voltage sheath in which there is an increasing fraction of collisionless ions as the anode-cathode distance increases. These collisionless ions are provided by the oscillating electrons (or rf nature) of the DCSF method. Higher order silane (silicon containing) ions increase in relative intensity with increasing inter-electrode spacing for the +DC, –DC, and rf plasmas. These higher order silane ions are also detected in the DCSF plasma, and can be reduced at either lower pressure or lower cathode to anode or cathode to substrate distances.