<p>The purpose of this thesis research was to examine the gas-phase reactions of 2- methoxypropene (MOP) with protonated nitrogen-containing compounds, specifically pyridine, and aniline derivatives, in a linear quadrupole ion trap mass spectrometer. In addition, to maintain consistency with past experiments, several previously investigated sulfoxides were included in this study. The analytes were protonated via atmospheric pressure chemical ionization (APCI) in a linear quadrupole ion trap spectrometer, transferred into the ion trap, isolated, and then allowed to react with MOP inside the ion trap. </p> <p>All the protonated sulfoxides examined reacted with MOP to generate a stable adduct, as expected. They also transferred a proton to MOP. All protonated anilines reacted in the same manner with MOP. The diagnostic adduct formation reaction is proposed to involve proton transfer from the protonated analyte to MOP followed by addition of the neutral analyte to protonated MOP. In sharp contrast to sulfoxides and anilines, protonated pyridines were unreactive toward MOP. Therefore, the formation of a stable adduct is diagnostic for both sulfoxides and anilines but these compounds can be differentiated from pyridines due to the lack of reactivity of their protonated forms toward MOP. </p>

<p dir="ltr">In mass spectrometry, analyte molecules are ionized by various mechanisms, such that they can be manipulated by electric and magnetic fields. By performing such manipulations, the mass to charge (<i>m/z</i>) ratio of the analyte molecules can be measured. Many methods for ion manipulation that allow for such <i>m/z </i>determination have been developed in the form of different mass analyzers. These include but are not limited to magnetic/electric sector instruments, time-of-flight (TOF) mass analyzers, 3D quadrupole ion traps, quadrupole mass filters, linear quadrupole ion traps (LITs), Fourier-transform ion cyclotron resonance (FT-ICR) instruments, Orbitrap mass analyzers, and electrostatic linear ion traps (ELITs). Each of these mass analyzers has unique advantages and disadvantages resulting from its specific mechanism of operation, allowing each of these to find a niche in mass spectrometry applications. The ELIT is a mass analyzer composed of two opposing ion mirrors, which cause trapped high energy ions to oscillate along a linear axial trajectory. The oscillation period of ions in the ELIT is dependent on injection energy, the potential energy and electrode geometry of the ELIT, and the ion <i>m/z</i> ratio. As such, mass spectra can be measured by measuring the frequency of ion packets in the ELIT in Fourier-transform (FT) operation mode, or by or by allowing ions to separate spatially in an <i>m/z </i>dependent manner before detection via a microchannel plate (MCP) in multiple-reflection time-of-flight (MR-TOF) mode of operation. The ability to perform two orthogonal mass analysis techniques in a single mass analyzer is one key advantage of the ELIT. Both FT-MS, and MR-TOF mode of operation are high-resolution techniques, making the ELIT unique in its excellent performance characteristics despite low complexity and manufacturing cost. Additionally, the ELIT can be used to perform high-resolution ion isolations, which makes it especially attractive for tandem-MS.</p><p dir="ltr">In chapter 1, the operating principles for MR-TOF and FT-MS modes of operation in an ELIT are discussed. In chapter 2 and 3, the performance, limitations, and applications of the mirror-switching isolation technique in the ELIT are discussed. Given the high-resolution performance of the ELIT for both mass analysis and ion isolation, it is clear that the ELIT has great potential for tandem-MS applications which require high-resolution in either the precursor selection, mass analysis step, or both. In chapters 4, 5, and 6, the implementation and development of infrared multi-photon dissociation, and surface-induced dissociation techniques in the ELIT are discussed, and it is shown that the ELIT can be used to as a standalone tandem mass spectrometer. While not performed on the ELIT instrument, the charge-based valet parking technique discussed in chapter 7 applies to tandem-MS as a whole, as it is shown to improve fragment yield in ETD. Finally, in chapter 8, the future directions of development for the ELIT mass analyzer are discussed.</p>

<p>High-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) are powerful tools for the characterization of the molecular structures of components of both simple and complex mixtures. MS and MS/MS have played key roles in many fields, including proteomics, metabolomics, and petroleomics. This thesis focuses on the development of tandem mass spectrometric methods for the structural characterization of asphaltenes and small isomeric molecules. In addition, this thesis also presents a method to address a sampling bias in asphaltene analysis. </p>

<p>This thesis covers the four topics discussed in each of the following paragraphs. It is unified by the dual ability of ambient ionization mass spectrometry as a useful analytical tool allowing for monitoring of chemical reactions, in addition to its capability to accelerate reaction rates using the same equipment under accelerating or non-accelerating conditions. The ability to manipulate reactions and monitor the subsequent effects to the rate of the reactions can provide vital information for many industrial arenas. Current process analytical technology (PAT) is extremely time-consuming, and typically costly due to dependence on analysis conducted at the end stage of production. Additionally, many chemical reactions found to be useful in pharmaceutical or manufacturing industries are labor intensive and require harsh conditions such as heat or expensive catalysts. Several methods have been developed to overcome these current limitations, while providing vital information on short-lived intermediates, degradation products, and accelerated reaction rates. A sampling device was developed and coupled with nESI allowing for monitoring of heterogeneous chemical reactions by mass spectrometry without the additional requirement of separation (filters, chromatography, etc.) In addition, this technique maintains the high sensitivity, specificity, speed and structural elucidation provided by mass spectrometry analysis. The analysis provided kinetic profiles of all reactants, intermediates, products and coproducts throughout the course of the reaction.</p><p> The ability to effectively control chemical reactions and their rates is a priority across several fields of study. Several factors affecting reaction rates, such as heat and catalysts selected, have been well studied. However, there has been recent interest in exploring the capabilities for reaction acceleration in charged microdroplets. It is known that reaction rates on the surface of a droplet greatly differ from reactions occurring in the droplet. The Katritzky transamination reaction was used as a model to identify the effects of the air-solution interface on reaction acceleration by varying the air-liquid surface to volume ratio. The significant increase in reaction rate constants was further enhanced by solid–solution interfacial effects observed after addition of glass nanoparticles.</p><p> The effective degradation of non-polar hydrocarbons is an environmental concern as they are the main composition of waste generated from petroleum processing. Saturated alkanes are relatively stable molecules which present a challenge for analysis by mass spectrometry without the use of extreme experimental conditions. A rapid analysis method by paper spray ionization was developed that allows for the oxidation products of saturated alkanes to be monitored by MS in under two minutes. This method relies on the generation of a hydroxyl radical by reacting iron (III) chloride with aqueous hydrogen peroxide on the principle of Fenton’s chemistry. The presence of this radical in direct contact with an alkane produces several oxidation products which can be easily monitored by MS. The reagents are added to a paper triangle sequentially, creating a thin film which allows reaction acceleration in relatively small volumes analyzed directly from paper at atmospheric pressure.</p><p> The dimerization of 4-ethynylaniline derivatives in acetonitrile was monitored by nano electrospray ionization mass spectrometry. Dimer products formed by electrocyclization and radical processes were observed that are not detected as a corresponding bulk reaction. This gas-phase reaction has been interrogated in a solution phase analog with radical initiators and characterized by ¹H NMR. This work demonstrates that compounds can be synthesized by the electrospray process. Future studies may reveal how this observation affects the interpretation of the MS results involving electrospray.</p>

<p>Mass spectrometry-based techniques have been widely used in reaction monitoring due to their high sensitivity and ability to offer structure information by tandem mass spectrometry. We applied nanoelectrospray mass spectrometry (nanoESI-MS) to simultaneously monitor pre-catalysts, catalytic intermediates, reagents, and products of palladium catalyzed Suzuki-Miyaura cross-coupling reactions. A set of Pd cluster ions related to the monoligated Pd (0) active catalyst is detected, and its deconvoluted isotopic distribution reveals contributions from two neutral molecules. One is assigned to the generally accepted Pd (0) active catalyst, seen in MS as the protonated molecule, while the other is suggested to correspond to a deactivated form of Pd catalyst. Oxidative stress testing of the synthetic model catalyst XPhos Pd cyclo-octadiene, performed using oxygen and Fe(III), supported this assignment. Thus, the make-up of the monoligated set of Pd (0) ions appears to indicate the oxidation state of the system. The formation and removal of the oxidative addition intermediate during the catalytic cycle was monitored to provide information on the progress of the transmetalation step. </p> <p> </p> <p><a>Recently, microdroplets created by ambient ionization source have been used as reaction vessels to accelerate organic reactions. Field desorption mass spectrometry under ambient conditions is applied to study solution-phase organic reactions in micro-volumes. Compared to nanoelectrospray, it is noteworthy that radical cations and formation of radical cation products are observed. Three reactions, the hydrazone formation by phenyl hydrazine and indoline-2,3-dione, the Katritzky reaction between a pyrylium salt and anisidine, and the Hantzsch synthesis of 1,4-dihydropyridine, were investigated by this system and reaction acceleration was observed to different extents. The increase in rate relative to that for the corresponding bulk reactions is attributed to solvent evaporation which increases concentration, and to the increase of surface-to-volume ratio with enhanced interfacial reaction rate constants. Later work in this thesis describes explicit solvent calculations to study the energies and structures of the hydrazone formation reaction from phenylhydrazine and indoline-2,3-dione in acidic methanol with density functional tight binding (DFTB) methods. Additionally, the thesis covers MS based methods for determination of isoaspartate and aspartate in peptide by gas-phase chemistry and detection of S-nitrosoglutathione in exhaled breath condensate sample.</a></p>

<p>The notion of autonomous laboratories is of much interest to the chemical science community.  Promises of increased efficiency and throughput of discovery, beyond that of automated platforms, has already begun to be fulfilled by autonomous continuous flow reactors and desktop robots.  For fully autonomous laboratories to be further realized, various components in these systems require automation.  Herein this work, are presented multiple data-driven statistical methods for automating and optimizing various chemical systems and processes.  Presented are: the development and deployment of a general stochastic optimization algorithm, a machine learning-based solvent selection pipeline for organic transformations, a generalized data-dependent scoring methodology for antibody assay development, the prototyping of an automated platform for ion-molecule reactions inside a linear ion trap, and a review on recent developments for machine learning and mass spectrometry.  In summary, these works present various components for furthering the automation of chemistry.</p>

<p dir="ltr"><i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) is a Gram-negative bacterium responsible for many infections in immunocompromised humans. This multi-drug resistance human pathogen can form biofilms, which help protect it from not only clinical treatment but also from main homeostasis and metabolism. Understanding biofilm structures is critical to help combat biofilm formation and develop better ways to treat <i>P. aeruginosa</i> infections. A molecule that helps biofilm formation and virulence infections for <i>P. aeruginosa</i> is pyocyanin, which is believed to be correlated with the invasiveness of the bacteria and the stabilization of biofilms. To better understand the role of pyocyanin in assisting <i>P. aeruginosa</i> with survival, we applied optical imaging to study pyocyanin in biofilms and under blue light treatment. Using nonlinear optical imaging methods, we could successfully detect the aggregation of pyocyanin in biofilms. Furthermore, we discovered that pyocyanin protects <i>P. aeruginosa</i> from blue light inactivation. In addition, we found that blue light treatment alters the structure of pyocyanin, leading to irreversible changes that produce distinct spectra in UV-Vis and fluorescence signals. <i>These results provide new insights into how pyocyanin protects </i><i>P. aeruginosa</i> in blue light treatment. Further investigation would lead to better treatment strategies for more effective treatment of <i>P. aeruginosa</i> and biofilms for various infections.</p>

<p>Mass spectrometry (MS) alone or coupled with high-performance liquid chromatography (HPLC) or gas chromatography (GC) is a versatile analytical tool that is routinely employed for identification of unknown compounds in complex mixtures. MS operates by separating ionized analytes based on their mass-to-charge (<i>m/z</i>) ratios. If the analyte can be ionized without complete fragmentation, MS provides molecular weight information and, if performed at high resolution, elemental compositions for the ionized analytes. Tandem mass spectrometry (MSⁿ, n <u>></u> 2 where each MS step corresponds to an ion isolation or separation event) also provides structural information of ionized analytes. With this approach, structural information of the ionized analytes is obtained by isolating the ionized analytes of interest and subjecting them to fragmentation experiments, such as collision-activated dissociation (CAD). The ions of interest can also be isolated and allowed to react with gaseous molecules to generate product ions (ion-molecule reactions). </p> The experiments described in this dissertation focused on the development of tandem mass spectrometry methods based on CAD and/or gas-phase ion-molecule reactions for the differentiation of acyl, <i>N</i>- and <i>O</i>-glucuronide drug metabolites and for identification of primary carbamates as potentially mutagenic impurities. Further, by using a previously published method titled Distillation, Precipitation, Fractionation Mass Spectrometry (DPF MS), the chemical compositions of five crude oil samples, including heavy, medium, and light crude oils with different API gravities, were determined. Additionally, the gravimetric percentages of different compound classes found in these crude oils are reported as well as the correlations found between API gravities and the chemical compositions of crude oils.

The application of neutral dicopper helicates to the encapsulation of a number of anions was investigated. Two dicopper salen derived helicates were studied which contained phenolic and either iminophenyl (1) or oxime (2) donor groups. UV-visible spectroscopy was used to determine the binding stoichiometry and formation constants of the anion complexes. Complex binding was supported by electrospray ionisation mass spectrometry. Receptor 1 possessed a remarkable selectivity for sulfate in isopropanol (IPA) for which a log K value of 5.07 ± 0.24 was obtained. Receptor 2 bound all anions studied more strongly than 1. Crystal structural data supports the proposition that there is a steric barrier to contraction of 1 from the bulky iminophenyl groups. Receptor 2 was not restricted by the small oxime moieties allowing for optimum copper-anion interactions.

<p>Ion soft landing is a preparative mass spectrometry technique that enables intact deposition of polyatomic ions onto surfaces. The ability to select ions with well-defined mass, charge, and kinetic energy, along with precise control over size, shape, and position of the ion beam in the deposition process distinguishes ion soft landing from traditional synthetic and surface preparation approaches. A wide range of projectile ions including molecular ions, non-covalent complexes, clusters, and ionic fragments generated in the gas phase have been used in soft-landing studies to address both the fundamental questions related to ion-surface interactions and enable applications of hyperthermal beams.</p> <p>Since the first soft landing instrument was implemented by Cooks and co-workers in 1977, significant advances have been achieved in preparative mass spectrometry instrumentation. Current instrument development efforts are focused on obtaining high ion currents, increasing the experimental throughput, and developing capabilities for layer-by-layer deposition. In chapter 2 and 3, two novel instrumentation approaches are introduced, which improve the ion flux and experimental throughput of ion soft landing research. In particular, soft landing of ions of both polarities enables the bottom-up construction of ionic materials. Meanwhile, a rotating wall mass analyzer substantially increases the mass range of mass-selective deposition and disperses multiple species on the same surface thereby increasing the experimental throughput. These instrumentation developments open up the opportunities to explore research topics in the field of catalysis, energy storage and production, biology, and quantum sciences.</p> <p>In chapter 4, I describe a novel <i>in situ</i> spectroelectrochemistry approach for studying structural changes of electroactive species during electrochemical processes. In these experiments, ion soft landing is used to prepare well-defined ions at electrochemical interfaces. In addition, understanding of the gas-phase properties of cluster ions is important for their application in ion soft landing research. Ions can be prepared in the proper physical and chemical state via gas-phase chemistry approaches, and the favorable properties and reactivities of ions can thereby be harnessed using ion soft landing. In chapter 5 and 6, gas phase properties of host-guest complexes of cyclodextrins and polyoxometalates and molybdenum halide clusters are discussed.</p>