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Neste trabalho, as fragmentações de 2-aroilbenzofuranos e de neolignanas diidrobenzofurânicas (NDB) foram investigadas empregando espectrometria de massas sequencial com ionização por eletrospray (ESI-MS/MS). Os compostos estudados foram sintetizados e, em seguida, suas vias de fragmentação em condições de dissociação induzida por colisão (CID) foram associadas às suas respectivas estruturas. Além das relações estrutura-fragmentação, espectrometria de massas de múltiplos estágios (MSn) e dados termoquímicos, obtidos por Química Quântica Computacional, foram também utilizados para a elucidação das vias de fragmentação. Para os 2-aroilbenzofuranos protonados, os resultados demonstraram que dois íons acílios, provenientes de rearranjos de hidrogênio competitivos, são os mais intensos nos espectros de íons produtos. O íon acílio [M+HC6H6]+ foi o mais intenso para todos os 2-aroilbenzofuranos investigados devido ao fato de que sua decomposição requerer energia crítica maior que a de outras vias de fragmentação competitivas. No caso das NDBs, os resultados indicaram que perdas de CH3OH e CO são comuns aos compostos analisados, tanto na forma protonada como na forma desprotonada. Entretanto, as perdas de CH3OH a partir de NDB protonadas envolvem migração de carga, enquanto que para moléculas desprotonadas, a perda de metanol é um processo remoto à carga. A perda de ceteno (C2H2O) diretamente da molécula protonada é uma via diagnóstica das NDB acetiladas, enquanto que os íons produtos [M+HC3H6O2]+ ou [M+HC6H6O]+ são diagnósticos das NDB que apresentam saturação entre C7 e C8. Para NDBs desprotonadas, íons produtos formados por perdas de CH3 são diagnósticos de grupos metoxila ligados ao anel aromático. A presença do grupo acetil também levou à formação de alguns íons diagnósticos devido à mudança no sítio de desprotonação. Por sua vez, clivagens da cadeia lateral remotas à carga são fragmentações diagnósticas de NDBs que apresentam saturação entre C-7 e C-8. As estruturas dos íons propostos foram suportadas por dados termoquímicos (entalpia e energia de Gibbs). Os resultados deste trabalho contribuem para o conhecimento da química em fase gasosa desses compostos e auxiliarão na identificação dos mesmos diretamente de misturas. / In this work, the fragmentation of 2-aroylbenzofuran and dihydrobenzofuran neolignans (DBN) was investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS). The studies compounds were synthesized and their fragmentation pathways under collision-induced dissociation (CID) were associated with their respective structures. Besides the structure-fragmentation correlations, multiple-stage mass spectrometry (MSn) and thermochemical data, which were estimated by Quantum Computational Chemistry, were also employed in the elucidation of the fragmentation pathways. For protonated 2-aroylbenzofuran, the results demonstrated that two acylium ions, which arises from two competitive hydrogen rearrangements, are the most intense in the product ion spectra. The acylium ion [M+HC6H6]+ was the most intense for all the investigated 2-aroylbenzofuran, since its decomposition requires a higher critical energy as compared to other competitive fragmentation processes. In the case of DBNs, our results indicated that eliminations of CH3OH e CO are common to the analyzed compounds in their protonated and deprotonated forms. However, eliminations of CH3OH from protonated DBNs involve charge migration, whereas elimination of CH3OH from deprotonated DBNs is a fragmentation remote to the charge site. Elimination of ketene (C2H2O) directly from the protonated molecule is diagnostic for acetylated DBNs, whereas the product ions [M+HC3H6O2]+ or [M+HC6H6O]+ are diagnostic for DBNs displaying a saturated bond between C7 and C8. For deprotonated DBNs, product ions resulting of CH3 losses are diagnostic for methoxyl groups attached to the aromatic ring. The presence of the acetyl group also led to the formation of some diagnostic ions due to the change of the deprotonation site. For compounds that display a saturated bond between C-7 and C-8, cleavages of the side chain of DBNs are also diagnostic. The structures of the proposed ions were supported by thermochemical data (enthalpy and Gibbs energy). The results of this work will contribute to the knowledge of the gas-phase ion chemistry of these compounds and will aid in their identification directly from mixtures.

Neste trabalho, as fragmentações de 2-aroilbenzofuranos e de neolignanas diidrobenzofurânicas (NDB) foram investigadas empregando espectrometria de massas sequencial com ionização por eletrospray (ESI-MS/MS). Os compostos estudados foram sintetizados e, em seguida, suas vias de fragmentação em condições de dissociação induzida por colisão (CID) foram associadas às suas respectivas estruturas. Além das relações estrutura-fragmentação, espectrometria de massas de múltiplos estágios (MSn) e dados termoquímicos, obtidos por Química Quântica Computacional, foram também utilizados para a elucidação das vias de fragmentação. Para os 2-aroilbenzofuranos protonados, os resultados demonstraram que dois íons acílios, provenientes de rearranjos de hidrogênio competitivos, são os mais intensos nos espectros de íons produtos. O íon acílio [M+HC6H6]+ foi o mais intenso para todos os 2-aroilbenzofuranos investigados devido ao fato de que sua decomposição requerer energia crítica maior que a de outras vias de fragmentação competitivas. No caso das NDBs, os resultados indicaram que perdas de CH3OH e CO são comuns aos compostos analisados, tanto na forma protonada como na forma desprotonada. Entretanto, as perdas de CH3OH a partir de NDB protonadas envolvem migração de carga, enquanto que para moléculas desprotonadas, a perda de metanol é um processo remoto à carga. A perda de ceteno (C2H2O) diretamente da molécula protonada é uma via diagnóstica das NDB acetiladas, enquanto que os íons produtos [M+HC3H6O2]+ ou [M+HC6H6O]+ são diagnósticos das NDB que apresentam saturação entre C7 e C8. Para NDBs desprotonadas, íons produtos formados por perdas de CH3 são diagnósticos de grupos metoxila ligados ao anel aromático. A presença do grupo acetil também levou à formação de alguns íons diagnósticos devido à mudança no sítio de desprotonação. Por sua vez, clivagens da cadeia lateral remotas à carga são fragmentações diagnósticas de NDBs que apresentam saturação entre C-7 e C-8. As estruturas dos íons propostos foram suportadas por dados termoquímicos (entalpia e energia de Gibbs). Os resultados deste trabalho contribuem para o conhecimento da química em fase gasosa desses compostos e auxiliarão na identificação dos mesmos diretamente de misturas. / In this work, the fragmentation of 2-aroylbenzofuran and dihydrobenzofuran neolignans (DBN) was investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS). The studies compounds were synthesized and their fragmentation pathways under collision-induced dissociation (CID) were associated with their respective structures. Besides the structure-fragmentation correlations, multiple-stage mass spectrometry (MSn) and thermochemical data, which were estimated by Quantum Computational Chemistry, were also employed in the elucidation of the fragmentation pathways. For protonated 2-aroylbenzofuran, the results demonstrated that two acylium ions, which arises from two competitive hydrogen rearrangements, are the most intense in the product ion spectra. The acylium ion [M+HC6H6]+ was the most intense for all the investigated 2-aroylbenzofuran, since its decomposition requires a higher critical energy as compared to other competitive fragmentation processes. In the case of DBNs, our results indicated that eliminations of CH3OH e CO are common to the analyzed compounds in their protonated and deprotonated forms. However, eliminations of CH3OH from protonated DBNs involve charge migration, whereas elimination of CH3OH from deprotonated DBNs is a fragmentation remote to the charge site. Elimination of ketene (C2H2O) directly from the protonated molecule is diagnostic for acetylated DBNs, whereas the product ions [M+HC3H6O2]+ or [M+HC6H6O]+ are diagnostic for DBNs displaying a saturated bond between C7 and C8. For deprotonated DBNs, product ions resulting of CH3 losses are diagnostic for methoxyl groups attached to the aromatic ring. The presence of the acetyl group also led to the formation of some diagnostic ions due to the change of the deprotonation site. For compounds that display a saturated bond between C-7 and C-8, cleavages of the side chain of DBNs are also diagnostic. The structures of the proposed ions were supported by thermochemical data (enthalpy and Gibbs energy). The results of this work will contribute to the knowledge of the gas-phase ion chemistry of these compounds and will aid in their identification directly from mixtures.

<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>

Identification of trace unknown analytes in complex samples remains a significant challenge for analytical chemistry. Mass spectrometry (MS) and analytical separations techniques can now be used to develop and support a new analytical strategy called non-target analysis which aims to provide comprehensive identification and quantification of all detectable chemical species in a complex sample. This thesis addresses challenges currently limiting the utility of this non-target approach by developing analytical methods for acquiring MS data suitable for identification of trace unknowns and investigating current tools available for unknown identification from MS spectral data. Liquid chromatography (LC) - MS, a widely used technique in trace analysis, was used to develop an analytical method capable of simultaneously acquiring high resolution MS and tandem mass spectrometry (MS/MS) data for hundreds of metabolites in urine. An emerging separation technique called high field asymmetric waveform ion mobility spectrometry (FAIMS) was also investigated, as an alternative to LC, for the identification of non-target analytes in urine. Modifications were carried out to the FAIMS-MS source interface allowing for transmission of small metabolite ions from FAIMS to MS. The challenge of direct electrospray (ESI) in urine analysis using ESI-FAIMS-MS was addressed by using sample dilution and extending MS data acquisition time using FAIMS. This allowed for higher quality MS data to be acquired for low abundance urinary metabolites than was possible by LC-MS and the complete elimination of ionization suppression in dilute urine samples. Insight gained into ESI suppression in complex samples allowed for two methods of semi-quantification to be proposed for non-target analytes in complex samples without using unavailable chemical standards. To address the challenge of unknown identification, faced throughout this thesis, an integrated approach was implemented to identify metabolites based only on spectral data without the usual requirement of availability of chemical standards. This approach combined spectral libraries, literature reports on ion chemistry and de novo identification based on gas phase ion chemistry with a detailed fragmentation study on nucleic acid bases, notably protonated uracil. Together, the instrumental methods and approaches to data analysis described allowed for the identification of 110 abundant chemical species detected in urine. / Natural Sciences and Engineering Research Council of Canada, Ontario Ministry of Training, Colleges and Universities, Canadian Foundation for Innovation

<p dir="ltr">Originating from J. J. Thomsons original work and the development of electrospray ionization (ESI) by John B. Fenn, mass spectrometry offers a versatile analytical tool to measure beyond an ion’s m/z, especially for biomolecules. Gas-phase ion/ion reactions within a mass spectrometer offers an attractive approach to study biomolecules as they take place on the millisecond and sub millisecond time scale, have high efficiency, allow oppositely charged ions to interact with each other in a controlled manner, and a allows for selection of each reactant prior to the reaction via ion isolation. This can be used to probe gas-phase chemistry that can reflect reactions in solution, however gas-phase reactions have no solvent effects and happen faster, making it a simpler experiment. Here, a variety of gas-phase ion/ion reactions and ion trap methodologies are described to study mostly lipids with a minor amount of transmetalation at the beginning.</p><p dir="ltr">First, a series of multivalent metals complexed to neutral ligands are demonstrated to form ion-pairs with tetraphenylborate anions via ion/ion reactions. The resulting products were subjected to collision induced activation (CID) to observe their involvement in transmetalation, complementary density functional theory (DFT) calculations are provided as well. Next, sequential ion/ion reactions were performed to convert isomeric phosphoinositol phosphates dianions to monocations to reveal structural characterization and isomeric differentiation utilizing tandem MS and dissociation kinetics. The following two chapters after, reports on complementary efforts to separate lipids in the gas-phase of different mass and charge but similar mass-to-charge (m/z) resulting in overlapping m/z signals. The first report demonstrates a physical approach where singly and double charged lipids are separated in space from each other, trapped simultaneously such that no information is lost. The second utilizes a lanthanide, Yb3+ trication complex that underwent ion/ion reactions with singly and doubly charged lipid anions of similar m/z that result in different m/z products for each singly and doubly charged lipids. Lastly, a sequential ion/ion approach utilizing hexa(ethylene glycol) dithiol as a novel reagent to charge invert structurally uninformative lipid cations to structurally informative anions with subsequent carbon-carbon double bond localization.</p>

<p>During the past fifty years, mass spectrometry, often hyphenated with chromatography, has developed into the most widely used technique for the quantitative and qualitative analysis of increasingly complex mixtures of (bio)organic molecules.</p> <p>One important aspect of this development concerns the relationship between the structure (atom connectivity) of a molecule and the mass spectrum obtained by electron ionization (EI). In this context, from 1960 - 1990, a wealth of studies has appeared that uses a variety of novel experimental techniques, often in conjunction with isotope labelling, to probe the structure, stability, reactivity and dissociation characteristics of the radical cations generated by EI of various classes of molecules. One highlight was the discovery of surprisingly stable distonic ions and the role they play in the dissociation chemistry of ionized molecules.</p> <p>However, mechanistic proposals based upon experimental observations can often only be considered as tentative. Synergy between experiment and theory would be ideal to remedy this situation, but it was not until recent spectacular advances in computer technology and software that this approach could be implemented. It has led to the growing realization that many rearrangement reactions of radical cations in the rarefied gas-phase involve catalysis. Proton-transport catalysis (PTC) is a prime example : here, a neutral species induces an ion to isomerize via hydrogen-bridged radical cations (HBRCs) as intermediates. An exemplary case described in this thesis concerns the ion-molecule reaction of the cyanamide ion with a single H₂O molecule : experiment and theory indicate that the H₂O molecule catalyzes the swift transformation of NH₂-CN^·⁺ into the more stable carbodiimide ion HN=C=NH^·⁺.</p> <p>The thesis exploits the synergy of tandem mass spectrometry and computational chemistry to study the role of catalysis in the association and dissociation reactions of several systems of radical cations. During these studies, a new type of a catalyzed reaction was discovered: "ion-catalysis", where an organic cation promotes the otherwise prohibitive rearrangement of a neutral. Ion-catalysis is proposed to explain the unexpected loss of NH₂O^· from low-energy N-hydroxyacetamide ions CH₃C(=O)NHOH^·⁺ : the molecular ion rearranges into the HBRC [O=C-C(H₂)--H--N(H)OH]^·⁺ whose acetyl (cation) component catalyzes the transformation NHOH^· --> NH₂O^·. Another highlight involves a hybrid reaction, in which both the ion and the neutral component of an incipient HBRC catalyze one another to rearrange into more stable isomers.</p> <p>Catalysis may also play an important role in astrochemistry and a question addressed in this context is whether pyrimidine, a key component of DNA, may be generated by ion-molecule reactions. It appears that the acrylonitrile ion (AN) does not react with HCN to produce ionized pyrimidine, instead it isomerizes by PTC. However, the reaction of the ion with its neutral counterpart does not involve catalysis, but rather cyclization into the pyrimidine ion ! A related topic concerns the structures of covalently bound dimers of the ubiquitous interstellar molecules HCN and HNC. Neutralization-Reionization Mass Spectrometry in conjunction with model chemistry calculations leaves little doubt that the elusive dimers HN=C=C=NH and HC=N-C=NH are kinetically stable in the rarefied gas-phase, whereas HC=N-N=CH is not.</p> <p>The structure of ions may also be probed by interactions with selected neutral molecules rather than dissociative collision experiments (MS/MS). An exciting case involves the differentiation of isomeric heterocyclic ions by ion-molecule reactions with dioxygen. Here, too, model chemistry calculations play an essential role in understanding the mechanism and the scope of the reaction.</p> / Doctor of Philosophy (PhD)

<p dir="ltr">Interfaces play an important role in a broad range of physical, chemical, and biochemical processes. For example, nutrient transport from and to cells happens at the cellular membrane interface, the corrosion of metals occurs due to chemical reactions at the solid/air interface, and the development of waterproof clothing relies on the modification of the clothing surface with hydrophobic species. The importance and complexity of interfaces make a detailed understanding of the interfacial physicochemical processes central to both the fundamental science and the development of new technologies. Specifically in the fields of energy storage/production and heterogeneous catalysis, understanding the transformations of the active species on surfaces leads to the development of high-performance, stable interfaces. In the thesis presented herein, ion soft landing was used as a preparative technique to understand the chemical changes that ions undergo on surfaces. Ion soft landing is a mass spectrometry technique in which polyatomic ions are deposited onto surfaces while preserving their chemical structure and charge state. The advantage of using ion soft landing to study interfaces is that it enables the preparation of well-defined ionic interfaces by the deposition of mass-selected ions on a defined surface area with high control over the amount of deposited material. Because ion soft landing uses purified ion beams formed in the gas phase, it also allows to study the chemical properties of the analytes in the absence of counterions or solvent molecules. Collectively, these capabilities make ion soft landing a powerful approach for preparing ionic interfaces and studying their chemical properties. A new direction in ion soft landing research takes advantage of gas phase ion chemistry techniques, such as collision-induced dissociation, to generate well-defined reactive fragment ions as unique building blocks for studying chemistry at interfaces. <b>Chapter 2 </b>of this thesis discusses the development of an ion soft landing instrument that enables high transmission of fragment ions for their deposition onto surfaces. Ion soft landing of reactive fragment ions opens up possibilities for studying their stability and reactivity on surfaces providing a path to the controlled preparation of unique ionic interfaces. <b>Chapters 3 </b>and <b>4 </b>describe an unusual spontaneous ligand loss observed for soft landed [Ni(bpy)₃]²⁺⁰, an ion of interest in the field of catalysis, and its stabilization by codeposition with anions. We compared the reactivity of [Ni(bpy)₃]²⁺on surfaces against that of [Ni(bpy)₂]²⁺and [Ni(bpy)]⁺species (both formed by ligand removal in the gas phase). This comparison indicates that the dissociation of [Ni(bpy)₃]²⁺ occurs both due to its reorganization on a surface and by charge-reduction. Both processes substantially reduce ligand binding energy and facilitate ligand loss from the complex.</p><p dir="ltr"><b>Chapter 5 </b>diverges from ion soft landing and instead presents a gas-phase ion chemistry study on the stability of cucurbituril-viologen host-guest complexes to better understand the intrinsic properties that influence the strength of their interaction. We found that there is a “perfect fit” size of the host that maximizes interactions with the guest thus increasing its stability. In addition, guests of smaller sizes that are better incorporated into the host have a substantial stability compared to those that have functional groups extending outside of the protecting cavity of the host. The results of this work reveal a strategy to stabilize viologens in the gas phase for the preparation of functional interfaces using ion soft landing.</p><p dir="ltr">Finally, <b>Chapter 6 </b>shows the results of a work at the teaching/learning interface, specifically regarding an undergraduate research project developed for the Analytical Chemistry I course (CHM323) at Purdue University. The goal of this project was to further develop students’ scientific skills on planning, problem-solving, and critical thinking to assess the performance of two analytical techniques. Specifically, the project described in <b>Chapter 6 </b>was designed in such a way that students had to do research on appropriate analytical techniques to quantify ascorbic acid in an unknown sample, propose an experimental protocol, perform it in the laboratory, and concisely summarize the results of their work in a lab report.</p><p dir="ltr">In summary, the work presented in this thesis encompasses three areas. First, it shows the advantages of using fragment ions produced in the gas phase to study the complex physicochemical processes occurring at interfaces. Second, it presents a study on the gas-phase stability of viologen-based host-guest complexes with the prospect of making viologens accessible for the preparation of functional interfaces using ion soft landing. Finally, it describes an undergraduate laboratory project aimed at developing the scientific skills of students in an analytical chemistry course.</p>