<p>This dissertation presents several examples of diverse applications of mass spectrometry. For example, high-resolution mass spectrometry was utilized for qualitative and quantitative chemical characterization of ionized compounds in petrochemical samples, specifically, in condensate-like oil samples. Further, the ability to use tandem mass spectrometry to rapidly detect trace amounts of short-lived reaction intermediates in solution reactions is demonstrated. Finally, selective tandem mass spectrometry methods based on diagnostic gas-phase ion-molecule reactions were developed for the identification of carboxylic acid functionalities in protonated analytes.</p>

A multiplexed method for performing MS/MS on multiple ions simultaneously in a miniature rectilinear ion trap (RIT) mass spectrometer has been developed. This method uses an ion encoding procedure that relies on the mass bias that exists when ions are externally injected into an RIT operated with only a single phase RF applied to one pair of electrodes. The ion injection profile under such conditions ions is Gaussian-like over a wide range of RF amplitudes, or low mass cutoff (LMCO) values, during ion accumulation. We show that this distribution is related to ion m/z and is likely caused by ions having an optimal range of pseudo-potential well depths for efficient trapping. Based on this observation, precursor ion intensity changes between two different injection LMCO values can be predicted, and these ion intensity changes are found to be carried through to their corresponding product ions, enabling multiplexed MS/MS spectra to be deconvoluted. The gas-phase reactions of a series of coordinatively unsaturated [Ni(L)n]y+ complexes, where L is a nitrogen-containing ligand, with chemical warfare agent (CWA) simulants in a miniature rectilinear ion trap mass spectrometer were investigated as part of a new approach to detect CWA. Results show that the metal complex ions can react with low concentrations of several CWA simulants, including dipropyl sulfide (simulant for mustard gas), acetonitrile (simulant for the nerve agent tabun), and diethyl phosphite (simulant for nerve agents sarin, soman, tabun, and VX), thereby providing a sensitive means of detecting these compounds. The [Ni(L)n]2+ complexes are found to be particularly reactive with the simulants of mustard gas and tabun, allowing their detection at low parts-per-billion (ppb) levels. These detection limits are well below the median lethal doses for these CWAs, which indicates the applicability of this new approach, and are about two orders of magnitude lower than electron ionization detection limits on the same mass spectrometer. The use of coordinatively unsaturated metal complexes as reagent ions offers the possibility of further tuning the ion-molecule chemistry so that desired compounds can be detected selectively or at even lower concentrations. Mass spectrometry has become a tool for studying noncovalently bound complexes. Specifically, electrospray ionization mass spectrometry (ESI-MS) has found increasing use for the determination of affinity (Ka) or dissociation (Kd) constants. Direct measurement of the equilibrium components by ESI-MS is the most straightforward approach for determining binding equilibrium constants, but this approach is prone to error and has some inherent limitations. Transferring complexes from solution to the gas phase may perturb the equilibrium concentrations and/or different ionization efficiencies may cause the resulting ion signals not to reflect actual solution concentrations. Furthermore, ESI only works under a limited range of solvent conditions (i.e. low ionic strengths), which limits the broad applicability of this approach. We propose an approach based on covalent labeling in the context of metal-catalyzed oxidation (MCO) reactions that, when combined with MS, overcomes such limitations when determining metal-ligand binding constants. The MCO-MS approach will provide concurrent information regarding metal binding site and metal-protein binding affinity. Optimization of the MCO reaction through isotopic mass tags will permit enhanced identification of modified residues. Application of this method to study the affinity and binding interactions of other divalent metals with β2m are likely to provide insight into the specificity of copper for causing β2m amyloid formation.

No description available.

Popular catalytic cycles, such as the Heck, Suzuki, and Negishi, utilize metal centers that oscillate between two oxidation states (II/0) during the three main steps of catalysis: reductive elimination, oxidative addition, and transmetallation. There has been a push to use less toxic, cheaper metal centers in catalytic cycles, leading to interest in first-row transition metals, such as nickel and cobalt. With these metals, the cycles can potentially pass through the +1 oxidation state, which acts as reactive intermediates, undergoing oxidative additions to form products, potentially with radical characteristics. The oxidative addition steps of catalytic cycles are critical to determining overall rates and products, however in many cases, these steps have not been amenable to study, in either condensed phase or gas phase, in the past. Through the use of electron transfer dissociation (ETD) technology on a modified Thermo Electron LTQ XLTM mass spectrometer, it is possible to generate intermediates in these catalytic cycles, including those in unusual oxidation states. Using sequentially coupled ion/ion-ion/molecule reactions, the reduced, reactive intermediate can be readily generated, isolated, and studied.As a model set of reactions, the mono- and bis-phenanthroline complexes of Fe(I), Co(I), Ni(I), Cu(I), and Zn(I) were formed by reduction of the corresponding M(II) species in an ion/ion reaction with the fluoranthenyl radical anion. The chemistry of the M(I) species was probed in ion/molecule reactions with allyl iodide. In order to explore ligand effects and the scope of oxidative addition reagents further, bipyridine and terpyridine were studied with these five first-row transition metal complexes while using an acetate series and other substrates for oxidative additions. Through these studies, the roles of the metal and ligand in dictating the product distributions and reaction rates were assessed. Metal electron count, ligand flexibility, and coordination number are critical factors. The overall reactivity is in accord with density functional theory calculations and mirrors that of proposed intermediates in condensed-phase catalytic cycles. In addition, second- and third-row transition metals (Ru(I), Pd(I), and Pt(I)) were explored with bipyridine, mono- and bis-triphenylphosphine, and 1,2-bis(diphenylphosphino)benzene ligation schemes. A variety of oxidative addition reagents were surveyed to determine the scope of reactivity and preference toward metal-carbon bond formation or carbon radical formation.

As part of this project and in preparation for future experimental studies of gas-phase ion-molecule reactions, extensive modification and characterization of the crossed molecular beam machine in the Department of Chemistry, University of Canterbury has been carried out. This instrument has been configured and some preliminary testing completed to enable the future study of gas-phase ion-molecule collisions of H⁺₃ and Y⁻ (Y = F, Cl, Br) with dipole-oriented CZ₃X (Z = H, F and X = F, Cl, Br). Theoretical calculations (ab initio and density functional theory) are reported on previously experimentally characterized Na + CH₃NO₂, Na + CH₃NC, and K + CH₃NC systems, and several other systems of relevance. All gas-phase experimental and theoretical studies have the common theme of studying collision orientation dependence of reaction under singlecollision conditions. Experimental measurements, theoretical simulations and calculations are also reported on some selected ferrous (Fe²⁺) high-spin (S=2) crystals, in an attempt to resolve microscopic contributions of two fundamental macroscopic tensor properties: the electric-field gradient (efg); and the mean square displacement (msd) in the case when more than one symmetry related site of low local point-group symmetry contributes to the same quadrupole doublet. These determinations have been made using the nuclear spectroscopic technique of Mössbauer spectroscopy, and complemented with X-ray crystallographic measurements.

<div>This dissertation details three studies which utilize nontraditional applications of electrospray ionization mass spectrometry. The first study explores and discusses the limitations of identifying unknown drug metabolites using ion-molecule reactions performed inside a mass spectrometer and coupled with high performance liquid chromatography. Ultimately, it was concluded that some highly-efficient, MS² ion-molecule reactions coupled with some drug metabolites would be sufficiently sensitive for <i>in vivo</i> drug metabolism studies. However, this study also concluded that the rate of false-positives and false-negatives may be higher than previous publications suggest.</div><div><br></div><div>The next study analyzed sulfur-containing compounds under atypical negative mode electrospray ionization mass spectrometry conditions. After noting that low analyte flow rates during electrospray ionization experiments on ethanethiol resulted in significant oxygen incorporation, the aim of this study was to understand the chemistry behind the oxygen incorporation and search for ways to experimentally limit the degree of oxygen inclusion. The atypical conditions were ultimately shown to induce significant ozonolysis and other oxidation reactions. Ultimately, only the use of high flow rates or switching to a different ionization technique were successful in mitigating the oxidation product formation. A new reaction mechanism for the oxidation of ethanethiol with ozone was proposed. Quantum chemical calculations were used to support the mechanism.</div><div><br></div><div>Finally, electrospray ionization mass spectrometry was used to analyze mixtures of selenium and/or tellurium in amine-thiol solvent systems. Selenium and tellurium are essential components in many thin film solar cells and other photovoltaics and amine-thiol solvent systems have been identified as a key solution processing strategy for synthesizing selenium and tellurium thin films. However, the reaction between selenium/tellurium and the amine-thiol solvent system is poorly understood and requires detailed study before large-scale industrial synthesis can be achieved. In this study, the dissolution mechanisms for selenium and tellurium in two different amine-thiol solvent systems were explored and discussed. The role of the basicity of the amine, the relative concentrations of the thiol, and the presence of co-dissolved chalcogens were all studied and used to propose dissolution mechanisms. The results of the experiments were used to control the synthesis of lead-selenium-tellurium alloy nanoparticles and could inform further studies on controlling metal chalcogenide synthesis through the appropriate choice of amine-thiol solvents.<br></div>

This thesis describes the study of a range of ion-molecule reactions at very low collision energies using a newly developed experimental technique which involves the reaction of velocity-selected beams of translationally cold neutral molecules with very low kinetic energy ion ensembles. These studies have been enabled by the construction of a new apparatus for trapping and laser-cooling gas phase atomic ions (⁴⁰Ca⁺). The laser-cooling process results in the formation of ordered, low kinetic energy, lattice-like ion structures, also known as "Coulomb crystals". The properties of single and multicomponent Coulomb crystals (which may also involve molecular ions), and their manipulation via modulation of the applied fields, are explored experimentally and with the use of molecular dynamics simulations. Variations in the laser-cooling parameters are shown to result in different steady-state populations of the electronic states of ⁴⁰Ca⁺ involved with the laser cooling cycle, and these are modelled within an appropriate theoretical framework. The imaging of ⁴⁰Ca⁺ fluorescence as a function of time allows the study of various ion-molecule reactions at collision energies around 300 K, with single ion sensitivity. These reaction studies are extended to low-temperature (collision energies close to 1 K), by combination of the ion trap apparatus with a bent quadrupole guide velocity-selector. Ion-molecule collision energies are shown to be variable over a short range through a change in the quadrupole guide voltage, or the ion trapping parameters; the effect of these modulations on the rate constant is explored for Ca⁺ + CH₃F. Bimolecular rate constants for the reactions of ⁴⁰Ca⁺ with CH₃F, CH₂F₂ and CH₃Cl have been determined for a range of ⁴⁰Ca⁺ state populations, allowing resolution of the global rate contributions from the ground and combined excited states. These results are analysed in the context of capture theories and ab initio electronic structure calculations. In each case, suppression of the ground state rate constant is explained by the presence of either a submerged or real barrier on the ground state potential surface. Rates of reaction from the combined excited states are generally found to be in line with capture theories, and in some cases variation is found between the high and low collision energy regimes. Molecular product ions generated in these experiments have been shown to be sympathetically-cooled into the crystal structure, and subsequently identified through resonance-excitation mass spectrometry. Molecular ions were also produced by multiphoton laser ionisation of a thermal background gas of OCS molecules. An ion-molecule reaction involving a molecular ion, that of charge transfer between OCS⁺ and ND₃, has been studied at a collision energy near 1 K for the first time using sympathetically-cooled OCS⁺ and velocity-selected ND₃. These experiments illustrate the generality of the techniques described herein, and should lead to many possibilities for future studies.

<p> Mass spectrometry (MS) has become one of the most powerful and versatile tools for chemical analysis due to its ultra-high sensitivity, high throughput, ease of automation, and the large amount of information obtained. Nowadays, MS is extensively used in many tasks, such as identification and quantitation of drug metabolites, analysis of the products of biomass pyrolysis, and study of reactive intermediates, to name a few. However, these mass spectrometric analyses are not without challenges. For example, the requirement for quantifying trace amounts of substances in a complex mixture constantly pushes the detection limit of mass spectrometers, and the increased sample complexity demands higher and higher mass resolution. Therefore, MS is constantly evolving to address more difficult analytical challenges. A variety of MS techniques have been developed over the years, including soft ionization methods that facilitate mass spectrometric analysis of macromolecules, such as proteins and antibodies that enables the development of new therapeutic agents, benchtop high-resolution mass spectrometers, such as the orbitraps that can be used to analyze some of the most complex mixtures, and portable mass spectrometers which can be used in the home and garden and even in cancer surgery. Besides its applications in chemical analysis, MS can serve as a unique tool for the fundamental study of gas-phase ion/molecule reactions, these gas-phase reactions can be used to better understand the reactivities of many reactive intermediates and to obtain structural information for unknown analytes.</p><p></p><p> This thesis is aimed at addressing challenges involved in mass spectrometric analyses of isomeric drug metabolites (Chapter 4), quantitation of drug metabolites by using tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS) (Chapter 5), delineating cellulose depolymerization mechanisms upon fast pyrolysis by using pyrolysis-tandem mass spectrometry (py-MS/MS) (Chapter 6), and studying the reactivities of vinyl cation intermediates (Chapter 7). An overview of the dissertation research is given in Chapter 1, the instrumentation and principles of linear quadrupole ion trap (LQIT) mass spectrometer are discussed in Chapter 2, and the organic synthesis performed for several studies is detailed in Chapter 3.</p>

A espectroscopia de ressonância ciclotrônica de íons foi usada para estudar reações de íons alcóxido, hidróxido, fluoreto, íon-radical óxido, acetileto e amideto com formiatos de alquila; o último íon reage também com N,N-dimetilformamida. Em todos os casos ocorre uma reação de descarbonilação, dando origem a um íon solvatado, que as evidências experimentais indicam ser unido por ponte de hidrogênio. Deslocamentos nucleófilos de grupos ligados ao esqueleto formílico podem ocorrer em casos adequados e em casos especiais ocorre ainda a formação de íons formiato. Os íons solvatados formados a partir de íons fluoreto e alcóxido com formiatos de alquila reagem com álcoois, podendo-se desta meneira estabelecer uma ordem de capacidade de solvatação para os álcoois alifáticos simples. A ordem estabelecida foi: CH3OH < C2H5OH < iso-C3H7OH < tert-C4H9OH. Foram determinadas constantes relativas de velocidade para as reações de vários íons negativos com formiatos de alquila, em sistemas onde se forma mais de um produto. Nos casos mais favoráveis (reações de íons fluoreto) foram calculadas constantes de velocidade absolutas para os vários canais de reação. / Ion-cyclotron resonance spectroscopy has been used to study the reactions between alkoxide, hydroxide, fluoride, O-, acetylide and amide ions with alkyl formates; the last ion reacts also with N,N-dimethylformamide. In all systems a decarbonylation occurs, giving rise to a solvated product ion, held by a hydrogen bond, as evidenced experimentally. Nucleophilic displacement of the formyl group substituents may occur in favorable cases and in a few particular systems the formation of formate ion is observed. The solvated ions formed through the reaction of fluoride or alkoxide ions with alkyl formates can react further with alcohols to establish the intrinsic clustering ability of simple aliphatic alcohols. The order of solvating ability is shown to follow the order CH3OH < C2H5OH < iso-C3H7OH < tert-C4H9OH. In systems where parallel reactions occur, relative rate constants were determined; in the most favorable cases (reactions of fluoride ions), absolute rate constants for the various reaction channels were calculated.

A espectroscopia de ressonância ciclotrônica de íons foi usada para estudar reações de íons alcóxido, hidróxido, fluoreto, íon-radical óxido, acetileto e amideto com formiatos de alquila; o último íon reage também com N,N-dimetilformamida. Em todos os casos ocorre uma reação de descarbonilação, dando origem a um íon solvatado, que as evidências experimentais indicam ser unido por ponte de hidrogênio. Deslocamentos nucleófilos de grupos ligados ao esqueleto formílico podem ocorrer em casos adequados e em casos especiais ocorre ainda a formação de íons formiato. Os íons solvatados formados a partir de íons fluoreto e alcóxido com formiatos de alquila reagem com álcoois, podendo-se desta meneira estabelecer uma ordem de capacidade de solvatação para os álcoois alifáticos simples. A ordem estabelecida foi: CH3OH < C2H5OH < iso-C3H7OH < tert-C4H9OH. Foram determinadas constantes relativas de velocidade para as reações de vários íons negativos com formiatos de alquila, em sistemas onde se forma mais de um produto. Nos casos mais favoráveis (reações de íons fluoreto) foram calculadas constantes de velocidade absolutas para os vários canais de reação. / Ion-cyclotron resonance spectroscopy has been used to study the reactions between alkoxide, hydroxide, fluoride, O-, acetylide and amide ions with alkyl formates; the last ion reacts also with N,N-dimethylformamide. In all systems a decarbonylation occurs, giving rise to a solvated product ion, held by a hydrogen bond, as evidenced experimentally. Nucleophilic displacement of the formyl group substituents may occur in favorable cases and in a few particular systems the formation of formate ion is observed. The solvated ions formed through the reaction of fluoride or alkoxide ions with alkyl formates can react further with alcohols to establish the intrinsic clustering ability of simple aliphatic alcohols. The order of solvating ability is shown to follow the order CH3OH < C2H5OH < iso-C3H7OH < tert-C4H9OH. In systems where parallel reactions occur, relative rate constants were determined; in the most favorable cases (reactions of fluoride ions), absolute rate constants for the various reaction channels were calculated.