xiv, 195 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / We explore the reconstruction of B-state vibrational wave packets in I 2 from simulated two-color nonlinear wave packet interferometry data. As a simplification of earlier proposals, we make use of different vibrational energy ranges in the B-state--rather than different electronic potential surfaces--for the short-pulse preparation and propagation of both target and reference wave packets. Numerical results from noisy interferograms indicate that experimental reconstruction should be possible with high fidelity (>0.99). Time-resolved coherent nonlinear optical experiments on small molecules in low-temperature host crystals are exposing valuable information on quantum mechanical dynamics in condensed media. We make use of generic features of these systems to frame two simple, comprehensive theories that will enable the efficient calculation of their ultrafast spectroscopic signals and support their interpretation in terms of the underlying chemical dynamics. Both treatments rely on the identification of normal coordinates to unambiguously partition the well-structured guest-host complex into a system and a bath and expand the overall wave function as a sum of product states between fully anharmonic vibrational basis states for the system and approximate Gaussian wave packets for the bath degrees of freedom. The theories exploit the fact that ultrafast experiments typically drive large-amplitude motion in a few intramolecular degrees of freedom of higher frequency than the crystal phonons, while these intramolecular vibrations indirectly induce smaller-amplitude--but still perhaps coherent--motion among the lattice modes. The equations of motion for the time-dependent parameters of the bath wave packets are fairly compact in a fixed vibrational basis/Gaussian bath (FVB/GB) approach. An alternative adiabatic vibrational basis/Gaussian bath (AVB/GB) treatment leads to more complicated equations of motion involving adiabatic and nonadiabatic vector potentials. Numerical tests of the FVB/GB are presented. We consider two bilinearly coupled harmonic oscillators with varying coupling strengths and initial conditions and show that the mixed quantum/semiclassical theory compares favorably with the exact results. Linear absorption spectra and wave-packet interferometry signals calculated using the theory are presented. This dissertation includes previously published coauthored material. / Committee in charge: David Herrick, Chairperson, Chemistry; Jeffrey Cina, Advisor, Chemistry; Thomas Dyke, Member, Chemistry Michael Kellman, Member, Chemistry; Hailin Wang, Outside Member, Physics

A presente tese tem por objetivo inicial estudar a reatividade de ésteres de Si, N, S e seus análogos em fase gasosa para obter informações detalhadas do mecanismo destas espécies quando submetidas a ataque nucleofílico, sobretudo no que tange a competição entre as vias de substituição nesses centros e no carbono. Esses estudos são realizados experimentalmente através da técnica de espectrometria de massas por transformada de Fourier e ressonância ciclotrônica de íons (FT-ICR) e amparados por cálculos de estrutura eletrônica. Os resultados obtidos indicam que, para o Si, as alcoxissilanas reagem com os nucleófilos através de um aduto pentacoordenado que desloca, preferencialmente, um alcóxido. De forma minoritária, pode ocorrer o deslocamento de outro ligante gerando silóxidos ou carbânions. Neste estudo, foi caracterizada uma reação inédita de troca de Me por F nos silóxidos mediada por NF3. Os estudos dos ésteres de nitrogênio indicam que as reações de eliminação são mais favoráveis que as de substituição e que a substituição no nitrogênio, apesar de ser considerada mais favorável pelos cálculos, não é observada. Esse comportamento foi elucidado através do uso de dinâmica molecular e indica que o complexo de entrada para a via de reação no nitrogênio não é formado devido à repulsão sofrida pelo nucleófilo pelos oxigênios que rodeiam o centro de N. Resultados teóricos semelhantes foram encontrados para os ésteres de enxofre e, em adição aos resultados experimentais disponíveis, indicam que não só a dinâmica de reação exerce um papel importante nesses sistemas, como também sugerem uma compensação entre o caráter dinâmico e a termoquímica destes sistemas. Para nucleófilos fracos que não são favoráveis do ponto de vista termoquímico, a formação do complexo de entrada não é impedida pela repulsão, dado que esses nucleófilos não costumam ter centros nucleofílicos com carga muito localizada. O oposto ocorre com nucleófilos fortes, que procederiam pelo caminho de substituição no S por uma via praticamente sem barreira, mas não o fazem já que a repulsão do nucleófilo é muito intensa. Em uma segunda etapa a solvatação dos íons F-, Br- e I- foram estudadas na fase gasosa a partir da espectroscopia dissociação no infravermelho. A partir da formação por uma fonte de eletrospray de agregados altamente solvatados, foi possível determinar o efeito dos íons na organização das moléculas de solvente, determinar a mudança da solvatação interna para solvatação de superfície e determinar o número de hidratação em fase gasosa para os íons Br- e F-. Além disso, tanto os resultados experimentais quanto teóricos mostram que a natureza do íon influencia a primeira camada de solvatação e que a carga formal tem um efeito predominante em longo alcance, podendo organizar até centenas de moléculas de solventes. Por fim, realizamos a adaptação do sistema de aquisição do FT-ICR do laboratório. Isso não só confere um sistema atualizado ao nosso instrumento, como possibilita que novos experimentos, como a espectroscopia de íons, possam ser realizados no nosso grupo de pesquisa. / This thesis comprises the study of the reactivity of gas-phase ions in the gas-phase and the structural modifications observed for gas-phase ions as a function of progressive solvation by spectroscopic techniques. In the first part, we describe the gas-phase reactivity of Si, N, and S esters and their analogs towards simple nucleophiles and a detailed analysis of the competition between different reaction channels namely substitution vs. elimination. These studies were carried out by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and supported by theoretical calculations. Our results suggest that alkoxysilanes react with nucleophiles via a pentacoordinated adduct that results in alkoxide displacement as the major reaction channel. The displacement of other ligands can also occur to yield siloxides or carbanions. As part of these studies, we also report a Me/F exchange reaction in siloxide ions mediated by NF3. Results obtained for the nitrogen esters show elimination-type reactions to be the most favorable pathway followed by nucleophilic displacement. No displacement was observed at the nitrogen center in spite of the fact that calculations predict this channel to be the most favorable pathway. This behavior was further explored by ab initio molecular dynamics calculations that show that the entrance complex for the nitrogen pathway is avoided because of the strong electrostatic repulsion exerted by the oxygen atoms as the nucleophile approaches the N center. Similar theoretical results were obtained for the sulfur esters. Comparison of these calculations with the experimental results also suggests that the reaction dynamics play an important role in these systems. Furthermore, we propose that a combination of thermochemical and dynamic balance hinders substitution at the heteroatom. For strong nucleophiles that could undergo substitution at the S center via a barrierless pathway, the reaction is hindered by the strong repulsion experienced by these nucleophiles. In the second part, we study the structure of gas-phase solvated F-, Br- and I- by infrared dissociation spectroscopy. The highly solvated clusters were generated by electrospray ionization and their structures probed to gather information regarding the short and long-range effect of these ions on the solvation network. Solvation parameters such as the number of water molecules needed for a switch from internal to surface solvation and the hydration numbers for F- and Br- were determined. Theoretical and experimental results show that the solvation pattern of the first solvation shell for these ions depends on the nature of the ion while the ion charge prevails in determining the long-range pattern. This pattern effect is shown to prevail up to hundreds of solvent molecules. Finally, a new data acquisition and control system is described for our FT-ICR spectrometer. This system not only updates the original instrument but it also brings in new capabilities to the spectrometer such as the ability to carry out gas-phase ion dissociation spectroscopy.

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.

The gas-phase ion chemistry of hydroxyl- and amino-substituted polycyclic aromatic hydrocarbons (PAHs) and their protonated counterparts were studied using mass spectrometry. Ions were generated using an electron ionization (EI) source and the unimolecular chemistry of metastable ions was studied by performing mass-analysed ion kinetic energy spectrometry (MIKES) experiments with a magnetic sector tandem mass spectrometer. Collision-induced dissociation (CID) experiments were used in conjunction with MIKES experiments to determine ion structure. The ten molecules studied were: 1-naphthol, 2-naphthol, 1-naphthylamine, 2-naphthylamine, 1-aminoanthracene, 2-aminoanthracene, 1-phenanthrol, 9-phenanthrol, 1-hydroxypyrene and 1-aminopyrene. Since it is believed that larger PAHs, on the order of more than 50 carbon atoms, populate the interstellar medium, the goal of this study was to attempt to extrapolate the results from smaller systems to larger ones. The trends found include: hydroxy-substituted PAH radical cations lose carbon monoxide spontaneously and amino-substituted PAH radical cations lose HCN. Mechanisms for both processes are proposed, and it appears from the present results that this process should extrapolate to larger PAHs. Another trend found was that all the remaining fragment ions were always a closed ring. Protonated amino-substituted PAHs were generated by electrospray ionization using a quadruple time-of-flight mass spectrometer. By protonating 1-naphthol and 2-naphthol using methane in the high-pressure EI source, it was found that they lost exclusively H2O. As for 2-naphthylamine, 1-aminoanthracene and 2-aminoanthracene, it was found that 2-naphthylamine lost NH3 and a hydrogen atom, NH3being the dominant channel. However, as the ion size 3 increases, the hydrogen-loss channel became the dominant channel. This means that larger PAHs will likely lose exclusively a hydrogen atom to reform the parent radical cation.

It is unclear whether all intercalation techniques truly lead to the insertion of atoms between the graphite layers, or also lead to other effects which contribute to expansion. The objective of this project is to better understand the effects caused by different intercalation methods. Three intercalation methods were explored to determine the method which incurs the least damage to the surface and microstructure of the graphite intercalated compounds, yet achieves the best intercalation and therefore expansion. All the main findings are summarised below:  The gas phase sample had virtually no mass loss at the point where expansion took place. Therefore the intercalation was very efficient, producing large expansion without significant mass loss.  The mass loss that only occurs at the sublimation of iron chloride (320 ºC) indicates the excessive "un-intercalated" or residual iron chloride.  After oxidation, before purification, the gas phase sample has 25 % residual mass; this also proves the presence of impurities and residual iron chloride in the exfoliated sample. For the Hummers and electrochemical samples, expansion and mass loss occur over a wide temperature range, this indicates that graphite oxide was formed rather than the theoretically expected "insertion of atoms between the sheets".  The mass losses before 200 ˚C of the samples of the Hummers and electrochemical methods are more evidence that graphite oxide and graphite surface complexes with oxygen were produced.  The Hummers and electrochemical intercalation methods show similar expansion and mass loss curves, therefore it can be concluded that the reaction mechanism for both these methods is alike.  The gas phase method yields the best expansion of 250 % using the TMA, whereas both the other methods deliver approximately 220 %.  Using microwave expansion the electrochemical intercalation method yields the best bulk volume expansion of 1500 %, with the gas phase sample delivering a volume expansion of 1450 %. The Hummers samples are extremely damaged. This is clear from the several and deep oxidation pits visible throughout the basal plane of these samples. The basal plane and the edges are even eroded before purification and oxidation. This intercalation technique employs oxidisers in the preparation method which additionally oxidises the samples. This explains why the Hummers method renders the most damage. The residual material on the gas phase sample acts as catalysts making the sample very reactive and consequently damaging the surface during oxidation. The partially oxidised purified gas phase sample visibly shows the pits and roughened edges. There are two “types” of intercalation. The first intercalation “type” is the actual insertion of atoms or molecules between the graphite layers, whereas the other “type” of intercalation is the production of graphite oxide. The compound comprises carbon, oxygen and hydrogen, obtained by treating graphite with strong oxidisers. The functional groups usually found in graphite oxide are carbonyl (C=O), hydroxyl (-OH), phenol amongst others and also some impurities of sulphur when sulphuric acid is used. Both these intercalation types lead to expansion. It is recommended that a more efficient method for removal of residual material in the gas phase samples be explored. It is also recommended that more research be done to determine the reaction mechanisms during the three different intercalation methods. The graphite surface complexes of the intercalated compounds and the evolved gases during expansion should be analysed. / Dissertation (MEng)--University of Pretoria, 2015. / tm2015 / Chemical Engineering / MEng / Unrestricted

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Cílem této práce bylo prostudovat vliv předpolymerace na vybraný komerční MgCl2–nosičový TiCl4 katalyzátor (tzv. Zieglerův-Nattův). Výsledkem práce bylo nalezení optimálních podmínek, které umožní ideálně využít této techniky k modifikaci struktury a morfologie zvoleného katalyzátoru a dosažení stabilnějšího průběhu polymerace a lepších vlastností produkovaného polypropenu. U předpolymerací byl studován vliv teploty, koncentrace triethylhliníkového kokatalyzátoru a externího donoru, množství polyolefinu syntetizovaného během předpolymerace (tzv. stupeň předpolymerace) na následné chování předpolymerovaného katalyzátoru při plynofázní polymeraci propenu.

A mixture-fraction-based thermodynamic equilibrium approach for modeling gas-phase combustion was adapted and used in FIRETEC, a wildfire computational fluid dynamics model. The motivation behind this work was the desire to incorporate the features of complex chemistry calculations from the thermodynamic equilibrium model into FIRETEC without significantly increasing the computational burden of the program. In order to implement the mixture-fraction-based thermodynamic equilibrium approach, a sub-grid pocket model was developed to simulate the local mixture fraction of sub-grid flame sheets. Numerical simulations of wildfires were performed using FIRETEC with the new sub-grid, mixture-fraction-based pocket model to model gas-phase combustion. The thermodynamic equilibrium model was used to calculate flame temperatures and combustion products, including CO2 and CO, for sub-grid, gas-phase combustion in FIRETEC simulations. Fire spread rates from simulations using the new sub-grid combustion model were 25-100% higher than fire spread rates from previous FIRETEC simulations, but the successes of modeling propagating fire lines and calculating detailed equilibrium combustion products from simulated sub-grid flame sheets demonstrated the feasibility of this new approach. Future work into the fine-tuning of pocket model parameters and modifying the conservation equation for energy in FIRETEC was recommended.

<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>

<div>Heightened awareness regarding the implication of disturbances in lipid metabolism with respect to prevalent human-related pathologies demands analytical techniques that provide unambiguous structural characterization and accurate quantitation of lipids in complex biological samples. The diversity in molecular structures of lipids along with their wide range of concentrations in biological matrices present formidable analytical challenges. Modern mass spectrometry (MS) offers an unprecedented level of analytical power in lipid analysis, as many advancements in the field of lipidomics have been facilitated through novel applications of and developments in electrospray ionization tandem mass spectrometry (ESI-MS/MS). ESI allows for the formation of intact lipid ions with little to no fragmentation and has become widely used in contemporary lipidomics experiments due to its sensitivity, reproducibility, and compatibility with condensed-phase modes of separation, such as liquid chromatography (LC). Owing to variations in lipid functional groups, ESI enables partial chemical separation of the lipidome, yet the preferred ion-type is not always formed, impacting lipid detection, characterization, and quantitation. Moreover, conventional ESI-MS/MS approaches often fail to expose diverse subtle structural features like the sites of unsaturation in fatty acyl constituents or acyl chain regiochemistry along the glycerol backbone, representing a significant challenge for ESI-MS/MS. To overcome these shortcomings, various charge manipulation strategies, including charge-switching, have been developed to transform ion-type and charge state, with aims of increasing sensitivity and selectivity of ESI-MS/MS approaches. Importantly, charge manipulation approaches afford enhanced ionization efficiency, improved mixture analysis performance, and access to informative fragmentation channels.</div><div><br></div><div>Here, gas-phase ion/ion chemistry was developed to transform conventional lipid ion types formed upon direct ESI into structurally informative ion types entirely within the mass spectrometer. Explicitly, gas-phase anionic to cationic charge switching chemistries were first developed for fatty acid profiling, as unambiguous structural elucidation and relative quantitation were achieved. Extensions of this gas-phase charge switch derivatization strategy to glycerophospholipids (GPLs), including ether GPLs, and fatty acid esters of hydroxy fatty acids demonstrates the versatility and flexibility of the ion/ion platforms. In an alternate approach, gas-phase proton transfer ion/ion reactions were employed for the gas-phase separation, concentration, and identification of cardiolipins (CLs) from total lipid extract. In total, benefits for lipid structure elucidation and enhanced detection efficiencies have been demonstrated utilizing the reported gas-phase ion/ion platforms.</div>