One of the most fundamental challenges in analytical mass spectrometry (MS) is the efficient conversion of neutral molecules into intact gas-phase ions. In this thesis, I investigate the capabilities of various new and established ionization techniques including (a) the Array of Micromachined UltraSonic Electrosprays (AMUSE), (b) Direct Analysis in Real Time (DART) and (c) Electrospray Ionization (ESI) for bioanalytical and biomedical analysis purposes. The AMUSE is a MicroElectroMechanical System (MEMS)-based device that was created as an alternative, and more sensitive approach for ion generation in an array format. In the AMUSE, the processes of droplet formation and DC droplet charging are separated allowing ionization of liquid samples using low charging voltages and a wide variety of solvents. Our analytical characterization work with the AMUSE showed that ion generation with this device was indeed possible, and that incorporation of a Venturi device increased signal stability and sensitivity due to enhanced droplet desolvation and increased ion transfer efficiency. A detailed investigation to determine the optimal source parameters for ionization of aqueous solutions of model compounds including reserpine, leucine enkephalin and cytochrome C was carried out and it was found that ionization was possible even without the application of a DC charging potential. Subsequent experiments using the thermometer ion method to characterize the AMUSE from a more fundamental point of view, showed that AMUSE ions are lower in internal energy than ESI ions, opening interesting possibilities for the mass spectrometric study of labile species. Furthermore, it was found that it was possible to manipulate the internal energy of the ion population by varying the parameters that most strongly affect desolvation and focusing. Our studies with DART were directed at investigating its analytical potential for application to the identification of active ingredients (AIs) in low quality combination medicines and counterfeit antimalarials that are commonly sold in regions of the world (particularly Southeast Asia) where drug resistant malaria is endemic as their use may engender increased resistance against the few remaining effective antimalarials.

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Clostridium thermocellum is a thermophilic bacterium that converts biomass to ethanol directly; however, high sensitivity of this bacterium toward ethanol limits its commercial utility. To elucidate the effect of ethanol on the growth of this bacterium a metabolite analysis of C. thermocellum was performed. The hypothesis of the project was that exogenous ethanol alters the metabolite profile of C. thermocellum. For metabolite analysis, capillary electrophoresis-electrospray ionization-mass spectrometry method (CE-ESI-MS) was developed due to highly polar and charged nature of metabolites. To increase the sensitivity of CE-ESI-MS, several parameters at the ESI interface were optimized. The application of 50% isopropanol as a sheath liquid increased sensitivity for metabolite analysis dramatically. Trimethylamine acetate (pH 10) was used as background electrolyte (BGE) due to its ability to separate the structural isomers of glucose phosphate. For metabolite sample preparation, novel methods for quenching and CE compatible metabolite extraction protocols were developed. Newly developed protocols were applied to metabolite analysis of wild type (WT) and ethanol adapted (EA) strains of C. thermocellum grown in batch cultures. Significant differences were found in key intracellular metabolites such as NAD+ and pyruvic acid. Intracellular concentrations of NAD+ were low in EA cells compared to WT cells and pyruvic acid was only detected in EA cells. To further understand the effect of ethanol on metabolite fluxes, WT and EA cells were grown in increasing concentrations of ethanol and the metabolite profile for each ethanol treatment was obtained. Significant changes were found in intracellular metabolite concentrations. Metabolic data showed that the glycolysis process in WT cells was obstructed due to exogenous ethanol which was evident from accumulation of G6P. On the other hand, no such accumulation of G6P was observed in the EA strain; however pyruvate began to accumulate in EA strain. These changes in intracellular metabolite concentrations due to perturbation of exogenous ethanol supported the hypothesis. Also, this investigation revealed a correlation between ethanol and metabolite profile changes and was able to explain a possible mechanism of growth inhibition of C. thermocellum which will certainly help genetic engineers to develop superior strains of C. thermocellum for commercial cellulosic ethanol production.

Lignin, one of main components in the woody cell walls, is a complex heterogeneous biopolymer, which provides structural support and transportation of water in plants. It is highly recalcitrant to degradation (both chemically and environmentally) and protects cellulose from being degraded/hydrolyzed. Due to the structural complexity of native lignin, complete characterization and elucidation of lignin’s structure remains very challenging. The overarching goal of this work is to develop mass spectrometry based analytical methods to contribute to a better understanding of lignin structures. This dissertation will focus on the development and application of High-Resolution Accurate-Mass (HRAM) Mass Spectrometry (MS) as main analytical technique for studying lignin model compounds, including understanding the ionization behavior, studying corresponding fragmentation patterns and extracting structural information for structural elucidation eventually. Analytical methods were also developed to study the post-pretreatment products of the synthetic trimeric model compound using High-Performance Liquid Chromatography (HPLC) coupled with High-Resolution Accurate Mass (HRAM) Mass Spectrometry (MS). The first project of this dissertation focuses on mass spectral the characterization of lignin models from the in vitro oxidative coupling reactions. Three specific trimeric compounds were isolated and their ionization behaviors were investigated using HRAMMS via electrospray ionization (ESI). The reaction parameters of the in vitro oxidative coupling reaction were critical in alternating the linkage profiles of resulting dehydrogenation polymers (DHPs). Reaction parameters were tuned to obtain desired DHP linkages profile. Upon the isolation of three different trimeric compounds, a systematic comparison of ionization efficiency of three trimeric compounds was carried out using ESI-HRAM-MS under different ionization conditions. The second project was aimed to design a synthetic route for a lignin model compound that will be a good representation for native lignin during the pretreatment process. The model compound of interest has not been obtained previously through chemical synthesis. Due to the reactivity of cinnamyl alcohol, which contains the unsaturated side chain, this new synthesis strategy was developed based on the known aldol-type reaction route. A versatile synthesis procedure for preparation of β-O-4 oligomeric compounds was designed and implemented to include the most important functional groups (phenolic alcohol, aryl glycerol β-aryl ether bond and unsaturated side chain) in the resulting model compound. This new synthesis route also allowed incorporation of different monolignols. In the third project, Fenton chemistry was applied to a synthetic lignin model compound. Due to the non-specificity in the post pretreatment product profile, nontargeted analytical strategy was developed and applied to study the post-pretreatment products of the model compound using HPLC-HRMS. The results from this dissertation showed a significant difference in ionization behavior between three structurally different model compounds and indicated that primary structures of lignin compounds can largely affect corresponding electrospray ionization properties as well as fragmentation pattern. The work in this dissertation provides analytical techniques for non-targeted analysis of complex lignin samples and an insightful understanding of Fenton’s reaction pretreatment upon lignin model compound.

Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to monitor organometallic reactions. It is fast at generating spectrum, soft to fragile organometallic compounds and sensitive to intermediates in low concentration. When coupled with the pressurized sample infusion (PSI) that helps to continuously inject reacting solution to the MS, both an inert-gas atmosphere and real-time reaction monitoring can be achieved. Also collision induced dissociation (CID) of MS can be used to probe the relative binding affinities of phosphine ligands in ruthenium complexes. PSI ESI-MS can be coupled with Fourier transform infrared spectroscopy (FTIR) to monitor the rhodium-catalyzed hydroacylation simultaneously. This technique expands the dynamic range to 5 magnitudes. The effect of mass-transfer in heterogeneous hydrogenation of charge-tagged alkyne was also studied by PSI ESI-MS. In this study cross area, stirring effect, catalyst loading and hydrogen concentration were considered and tested. Also in the study an interesting finding reveals in heterogeneity of the solution. Relative binding affinities of different phosphine ligands were attained from comparing the relative intensities of fragmentation products from MS/MS. And the phosphine ligand substitution reaction was monitored by the ESI-MS in a real-time manner. A competitive dissociative substitution mechanism was proposed and confirmed by the simulation and modeling of COPASI. / Graduate

Over the past decades, electrospray ionization for mass spectrometry (ESI-MS) has become one of the most commonly employed techniques in analytical chemistry, mainly due to its broad applicability to polar and semipolar compounds and the superior selectivity which is achieved in combination with high resolution separation techniques. However, responsiveness of an analytical method also determines its suitability for the quantitation of chemical compounds; and in electrospray ionization for mass spectrometry, it can vary significantly among different analytes with identical solution concentrations. Therefore, we investigated the ESI-response behavior of 56 nitrogen-containing compounds including aromatic amines and pyridines, two compound classes of high importance to both, synthetic organic chemistry as well as to pharmaceutical sciences. These compounds are increasingly analyzed employing ESI mass spectrometry detection due to their polar, basic character. Signal intensities of the peaks from the protonated molecular ion (MH+) were acquired under different conditions and related to compound properties such as basicity, polarity, volatility and molecular size exploring their quantitative impact on ionization efficiency. As a result, we found that though solution basicity of a compound is the main factor initially determining the ESI response of the protonated molecular ion, other factors such as polarity and vaporability become more important under acidic solvent conditions and may nearly outweigh the importance of basicity under these conditions. Moreover, we show that different molecular descriptors may become important when using different types of instruments for such investigations, a fact not detailed so far in the available literature.

The presented master thesis is devoted to the investigation of reaction intermediates in homogeneous gold catalysis. Electrospray ionization mass spectrometry (ESI-MS) was used as the primary research technique in this study. Delayed reactant labeling was used as the main method. I have focused mainly on the hydration of 1-phenyl-1-propyne catalyzed by the gold complex [Au(IPr)(MeCN)]BF4 (IPr = 1,3-bis(2,6-di-iso-propylphenyl)imidazol-2- ylidene). I have detected two main intermediates containing one or two gold atoms, respectively (monoaurated and diaurated intermediate). I have obtained rate constants for the degradation of the reaction intermediates and their half-lives. I have derived kinetic isotope effects for the formation and the decomposition of the detected intermediates. I have shown that the kinetics of the degradation of both intermediates is identical, therefore I conclude that hydration of alkynes catalyzed by gold complex [Au(IPr)(MeCN)]BF4 proceeds most probably via neutral monoaurated intermediates. These neutral intermediates are detected by ESI-MS as protonated (monoaurated intermediate) or tagged by a second gold cation (diaurated intermediate). Key words: gold catalysis, reaction intermediates, electrospray ionization, mass spectrometry.

A crescente demanda por água doce de boa qualidade, associada ao aumento na frequência de florações tóxicas de cianobactérias em reservatórios utilizados para consumo humano, levou à publicação da Portaria nº. 518/04 pelo Ministério da Saúde. Entre outros parâmetros de potabilidade, as empresas fornecedoras de água tratada devem realizar o monitoramento de cianotoxinas. Para tanto, métodos analíticos rápidos e precisos para a determinação destes compostos são imprescindíveis. Neste contexto, o presente trabalho teve como objetivo empregar a cromatografia líquida acoplada à espectrometria de massas para o estudo das principais cianotoxinas em território nacional: microcistinas, anatoxina-a(s), cilindrospermopsina e saxitoxinas. Os resultados obtidos estão distribuídos em capítulos específicos dedicados a cada grupo de toxinas. Dessa forma, o primeiro capítulo apresenta um estudo de fragmentação na fase gasosa de ânions de microcistinas em um equipamento do tipo orbitrap. É demonstrado que o modo negativo de ionização por electrospray fornece informações estruturais importantes e complementares ao modo positivo de ionização. Uma abertura seletiva do peptídeo cíclico é proposta e mecanismos discutidos, o que facilita a interpretação de resultados durante a caracterização de variantes desconhecidas. O modelo de fragmentação desenvolvido foi utilizado para identificar a variante [Leu1]MC-LR em um extrato de Microcystis spp. O segundo capítulo descreve metodologias qualitativas de LC/MS para o monitoramento e identificação do organofosforado natural anatoxina-a(s), cuja análise é prejudicada pela ausência de padrões comerciais. A cromatografia de interação hidrofílica foi empregada e mecanismos de fragmentação na fase gasosa propostos, discutindo-se os íons característicos desta estrutura química. Tal modelo permitiu a identificação desta toxina nas cepas de Anabaena oumiana ITEP-25 e ITEP-26 pela primeira vez. O terceiro capítulo disserta sobre os mecanismos de fragmentação na fase gasosa da toxina cilindrospermopsina quando ionizada por electrospray na forma de aduto com metais alcalinos. Diferenças nas vias de fragmentação são demonstradas de acordo com o raio atômico do metal formador do aduto, com implicações práticas na sua determinação cromatográfica. Já o quarto capítulo discute os mecanismos de fragmentação de variantes sulfatadas de saxitoxinas (GTX1e4, GTX2e3, dcGTX2e3, GTX5) após ionização por electrospray no modo positivo e negativo. É demonstrado pela primeira vez que uma conformação estrutural específica do grupamento sulfato explica a intensa eliminação de SO3 observada para as variantes GTX1, GTX2 e dcGTX2 no modo positivo de ionização. Por outro lado, o modo negativo de ionização apresenta vantagens uma vez que a dissociação na fonte é insignificante se comparada à dissociação observada no modo positivo. Como resultado, métodos quantitativos no modo negativo podem apresentar maior sensibilidade, permitindo a detecção destas toxinas em amostras ambientais em quantidades mais baixas. De maneira geral, conclui-se que a cromatografia líquida acoplada à espectrometria de massas é ferramenta poderosa para a análise quali e quantitativa das principais cianotoxinas, podendo ser amplamente empregada para o monitoramento de água para consumo humano. / The increasing occurrence of toxic cyanobacterial blooms in reservoirs used to supply drinking water for human consumption has prompted the publication of resolution 518/04 by the Brazilian Ministry of Health. Among other quality requirements, the monitoring of cyanotoxins in treated water is mandatory for companies responsible for potable water distribution. Therefore, precise and rapid analytical methods are essential. In this context, the aim of this work is to employ liquid chromatography coupled to mass spectrometry to study the most important cyanotoxins in our country: microcystins, anatoxin-a(s), cylindrospermopsis and saxitoxins. The obtained results are distributed in four chapters, each one dedicated to a single group of toxins. In this way, chapter one presents the gas-phase fragmentation behavior of deprotonated microcystins in an Orbitrap instrument. It is demonstrated that electrospray negative ionization can provide significant structural information about microcystins. These results are complementary to the positive ionization mode. A selective ring opening process is proposed and possible mechanisms are discussed, which may facilitate data interpretation when unknown variants are considered. The general fragmentation model was further applied to the characterization of [Leu1]MC-LR in a Microcystis spp. cell extract. The second chapter describes qualitative analytical methods for the identification of anatoxin-a(s), a natural organophosphate whose determination is hampered by the lack of commercial standards. Hydrophilic interaction liquid chromatography was employed and fragmentation mechanisms proposed, identifying the characteristic product ions of this toxin. The developed methods were further used to identify anatoxin-a(s) for the first time in Anabaena oumiana strains ITEP-25 and ITEP-26. The third chapter presents data related to the gas-phase fragmentation behavior of cylindrospermospin when this toxin is ionized as metal adducts. Different fragmentation pathways are accessed depending on the atomic radius of the metal cation involved. Practical implications for the chromatographic analysis of this toxin are presented. The last chapter describes the fragmentation behavior of sulphate-containing saxitoxin variants (GTX1&4, GTX2&3, dcGTX2&3, GTX5) after electrospray ionization in both the positive and negative modes. A mechanism for the intense SO3 elimination from [M+H]+ ions from GTX1, GTX2 and dcGTX2 is proposed for the first time and relies on a specific structure conformation. On the other hand, the negative ionization mode shows much less in-source dissociation when compared to the positive mode. As a consequence, methods based on negative ionization might be more sensitive for sulfate-containing variants, allowing the detection of lower amounts of these toxins in environmental samples. At the end, it can be concluded that liquid chromatography is a well-suited and powerful technique for the qualitative and quantitative analysis of cyanotoxins, being an invaluable contribution to water safety evaluation.

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