Titan, the largest moon of Saturn, is the only known moon with a fully developed nitrogen-rich atmosphere, its ionosphere is detectable as high as 2200 km above its surface and hosts complex organic chemistry. Titan’s atmosphere and ionosphere has striking similarities to current theories of these regions around Earth 3.5 billion years ago. The Cassini spacecraft has been in orbit around Saturn since 2004 and carries a wide range of instruments for investigating Titan’s ionosphere, among them the Langmuir probe, a “space weather station”, manufactured and operated by the Swedish Institute of Space Physics, Uppsala. This thesis presents studies of positive ions, negative ions and negatively charged dust grains (also called aerosols) in Titan’s ionosphere using the in-situ measurements by the Cassini Langmuir probe, supplemented by the data from particle mass spectrometers. One of the main results is the detection of significant (up to about 4000 cm-3) charge densities of heavy (up to about 13800 amu/charge) negative ions and dust grains in Titan’s ionosphere below 1400 km altitude. The dust is found to be the main negative charge carrier below about 1100 km on the nightside/terminator ionosphere, forming a dusty plasma (also called “ion-ion” plasma). A new analysis method is developed using a combination of simultaneous observations by multiple instruments for a case study of four flybys of Titan’s ionosphere, further constraining the ionospheric plasma charge densities. This allows to predict a dusty plasma in the dayside ionosphere below 900 km altitude (thus declaring it a global phenomenon), as well as to empirically estimate the average charge of the negative ions and dust grains to between -2.5 and -1.5 elementary charges. The complete Cassini dataset spans just above 13 years, allowing to study effects of the solar activity on Titan’s ionosphere. From solar minimum to maximum, the increase in the solar EUV flux increases the densities by a factor of ~2 in the dayside ionosphere and, surprisingly, decreases by a factor of ~3-4 in the nightside ionosphere. The latter is proposed to be an effect of the ionospheric photochemistry modified by higher solar EUV flux. Modelling photoionization also reveals an EUV trend (as well as solar zenith angle and corotational plasma ram dependencies) in the loss rate coefficient.

This work focuses on the analysis of plasma irregularities generated during two active space experiments: the injection of an artificial dust layer, and high-power radio waves. The objective of the "first experiment is to examine the effects of artificially created dust layers on the scatter of radars from plasma irregularities embedded in dusty plasma in space. This is an alternate approach for understanding the mechanisms of enhanced radar scatter from plasma irregularities embedded in Noctilucent Clouds and Polar Mesospheric Summer Echoes. The second experiment involves a transmission of high power electromagnetic waves into the ionospheric plasma from the ground, which can excite stimulated electromagnetic emissions offset from the transmitter frequency. These stimulated electromagnetic emissions provide diagnostic information of the ionosphere and thus can be used to investigate fundamental physical principles which govern the earth\'s ionosphere, so that present and future transmission technologies may take into account the complexities of the ionosphere. The interaction altitude of the artificial dust layer and high power radio waves is approximately 250 km and 160 km respectively, thus dealing with uniquely different regions of the ionosphere. Each experiment is discussed separately using theoretical, observational and advanced computational methodologies. The study first investigates plasma turbulence associated with the creation of an artificial dust layer in the earth's ionosphere. Two scenarios are considered for plasma irregularity generation as dust is injected at an oblique angle across the geomagnetic field. The first is a shear-driven plasma instability due to inhomogeneities in the boundary layer between the injected charged dust layer and the background plasma. This begins to appear at very early times once the dust is released into the space plasma, which is of the order or less than the dust charging time period. The second mechanism is free streaming of the charged dust relative to the background plasma. This produces irregularities at times much longer than the dust charging period and also longer than the dust plasma period. Although both mechanisms are shown to produce turbulence in the lower hybrid frequency range, the resulting irregularities have important differences in their physical characteristics. A comparison between the processes is made to determine the consequences for upcoming observations. Both processes are shown to have the possibility of generating turbulence after the release of dust for the regimes of upcoming space experiments over a range of timescales. This work also presents the first observations of unique narrowband emissions ordered near the Hydrogen ion (H+) gyro-frequency (fcH) in the Stimulated Electromagnetic Emission (SEE) spectrum when the transmitter is tuned near the second electron gyro-harmonic frequency (2fce), during ionospheric modification experiments. The frequency structuring of these newly discovered emission lines is quite unexpected since H+ is known to be a minor constituent in the interaction region which is near 160 km altitude. The spectral lines are typically shifted from the pump wave frequency by harmonics of a frequency about 10% less than fcH (" 800 Hz) and have a bandwidth of less than 50 Hz which is near the O+ gyro-frequency fcO. A theory is proposed to explain these emissions in terms of a Parametric Decay Instability (PDI) in a multi-ion species plasma due to possible proton precipitation associated with the disturbed conditions during the heating experiment. The observations can be explained by including several percent H+ ions into the background plasma. The implications are new possibilities for characterizing proton precipitation events during ionospheric heating experiments. / Ph. D.

<p>Lipids are important cellular biomolecules that perform essential functional and biological roles. For instance, lipids in the cell are the compartmentalizer for the cytoplasm and an energy storage unit. The knowledge surrounding lipids is abundant, yet there is still so much to uncover. There are many categories of lipids and within each category the structural composition is extremely diverse. In turn, the dramatic structural complexity of lipids demands analytical methods capable of providing in-depth structural characterization of individual molecular structures. However, lipid structural elucidation has remained challenging, namely due to the presence of isomeric and isobaric species with a complex mixture. In particular, isomeric/isobaric lipid structures arise from variations in class, headgroup, fatty acyl chain, <i>sn</i>-position, and/or carbon-carbon double bond (C=C) position(s). Recently, recent research suggests C=C composition impacts lipid physical properties, metabolic fate, and intermolecular interactions. Thus, analytical strategies capable of localizing sites of unsaturation are of interest in the lipidomics community.</p> <p>Mass spectrometry (MS) is a leading tool for lipid analysis. Electrospray ionization (ESI), a soft ionization method, is the most commonly used method for lipid ionization as a means of taking the ions from liquid-phase to gas-phase without extensive decomposition of the species. Utilizing ESI-MS, lipids can be identified at a sum compositional level via accurate mass measurements. . With tandem mass spectrometers, lipid ions can be further probed, utilizing tandem-MS (MS/MS) to generate structurally informative product ion spectra that facilitate the assignment of lipid molecular structure. More so, gas-phase ion/ion reactions represent a unique MS-based technique that has improved the analysis of lipids structures. Gas-phase ion/ion reactions allow for lipid species to be charge inverted from one polarity to the opposite polarity. This reaction enables lipids to be ionized in a polarity that is optimal for class identification and further investigated in the opposite polarity where more structural information is obtained. All the information provided is captured without the requirement of multiple solution conditions which is necessary when analyzing in both polarities. In the case of charge inverted lipids from positive ion mode to negative ion mode, fatty acyl composition can be obtained; however, C=C information is lacking.</p> <p>MS can also be paired with other analytically technologies to assist with lipid analysis. One of those technologies is liquid chromatography (LC), which allows for the separation of lipids based on different characteristic depending on the column type being used. Reverse-phase LC (RPLC) allows for the separation of lipid molecular species based on structural composition. RPLC-MS/MS benefits from the ability to separate lipids and determine their fatty acyl chain composition but it is difficult to specify C=C location with the use of a synthetic standard that is identical to each molecular species being analyzed.</p> <p>Commonality between the gas-phase ion/ion reactions for charge inversion of lipids and RPLC-MS/MS approaches is the inability to provide C=C coverage. In-solution and unique ion activation techniques have been developed for seeking such information. The Paternò–Büchi reaction is a UV-initiated [2 + 2]-cycloaddition of an excited carbonyl containing compound onto an olefin group. This reaction can be initiated onto the alkene group within an unsaturated lipid aliphatic chain to form an oxetane ring modification. There are two product ions that can be formed upon each unsaturation site due to a lack of regioselectivity the reagent can attach at either side of the C=C. The modified lipids can be taken into gas-phase and collisionally activated via low-energy collision induced dissociation, generating product ions indictive of C=C position(s). The work herein shows the incorporation of the PB reaction into the gas-phases ion/ion reaction and RPLC-MS/MS apparatuses for C=C localization. The methods have been applied to the lipid extracts of bovine liver and human plasma for confident molecule species determination.</p>

<p> Mass spectrometry (MS) is one of the most commonly used analytical techniques in bioanalytical analysis, allowing scientists to characterize molecules with very diverse chemical features. The advance in ionization strategies significantly improves the potential in using MS for that purpose, especially electrospray ionization (ESI) can generate ions directly from solution in ambient conditions, showing high flexibility in coupling with other techniques. Moreover, a hallmark of the ESI of large polymeric molecules is also its tendency to generate a distribution of charge states based on their chemical characteristics, allowing us to exploit the multiple charging phenomenon in various applications. </p> <p>This dissertation introduces the relationships between ESI and multiple charging phenomena with different proposed ionization models, and how condensed-phase and gas-phase approaches affect the multiple charging phenomenon. Moreover, multiply charged ions permit gas-phase ion/ion reactions to occur without neutralizing the ions. Therefore, various ion/ion reactions can be utilized for distinct analytical purposes. Objectively, this dissertation focuses on the investigation of the multiple charging phenomenon from ESI-MS, and the applications from taking the multiply charged ions to perform gas-phase ion chemistry in order to a) manipulate the charges of the targeted ions; b) invert the polarity of the targeted ions; c) and characterization of the ions from the gas-phase ion/ion reactions.</p> <p> The first work demonstrates how multiple components (i.e., complicated mixtures) lead to a highly congested spectrum of ions with overlapped m/z values, resulting from the multiple charging phenomenon after the ESI process. Utilizing ionic reactions can de-congest the spectra via manipulating the charges of the ions to separate the overlapped signals. A universal spectral pattern in the ESI mass spectra is observed while analyzing multiply-charged homopolymers. Various parameters, such as the charges of the ions, widths of polymer distributions, monomer mass, and cationizing agent masses, are investigated to show how they can affect the appearance of the unique patterns, which condense the information of the overall distribution of the homopolymers. Combined with gas-phase charge reduction (i.e., proton transfer reaction), we can characterize the size distribution of polydisperse homopolymer samples.</p> <p>Second, a novel type charge inversion ion/ion reaction summarizing the conversion of multiply charged protein ions to their opposite polarity and still holds multiple charges is reported. The reaction occurs via a single ion/ion collision with highly charged reagent ions, which we usually obtain from biological relevant polymers. Hyaluronic acid (HAs) anions and polyethylenimine (PEI) cations are used as the charge inversion reagents to react with protein ions. Remarkably, inversion of high absolute charge (up to 41) from the reaction is demonstrated. All mechanisms for ion/ion charge inversion involve low-energy ions proceeding via the formation of a long-lived complex. Factors that underlie the charge inversion of protein ions to the opposite polarity with high charge states in reaction with those reagent ions are hypothesized to include: (i) the relatively high charge densities of the HA anions and PEI cations that facilitate the extraction/donation of multiple protons from/to the protein leading to multiply charged protein anions/cations, (ii) the relatively high sum of absolute charges of the reactants that leads to high initial energies in the ion/ion complex, and (iii) the relatively high charge of the ion/ion complex following the multiple proton transfers that tends to destabilize the complex.</p> <p>Third, shotgun MS strategies coupled with different gas-phase ion chemistry and tandem MS to analyze glycolipids are demonstrated. Glycolipids contain both carbohydrates and lipids structure components that it is incredibly challenging to analyze with MS. Isomeric cerebrosides (n-HexCer) and glycosphingosines (n-HexSph), which hold isomerisms in diastereomeric sugar head groups (glucose and galactose), anomeric glycosidic linkages (alpha- or beta-), and isomeric amide-bonded monounsaturated fatty acyl chain (double bond location) are successfully differentiated by dissociating gas-phase ion/ion reaction products, the charge-inverted complex cations. Both relative and absolute quantification of the isomers is also achieved, and analytical performances are evaluated in terms of accuracy, precision, and inter-day precision, allowing us to perform mixture analysis. Porcine brains were used to demonstrate the ability to profile and quantify those isomers from biological extracts. Moreover, a parallel workflow is also proposed for gangliosides, which have more complicated structures among their glycan moiety. Metal cation transfer, proton transfer, and charge inversion reactions are utilized to manipulate the ion types to provide better structural information. The proposed workflow allows us to clean up the mass spectra by neutralizing interfering isobaric ions, differentiate isomeric gangliosides, and perform relative quantitation when the standards are available. The workflow also is used to obtain gangliosides profiles from biological matrices. Overall, work in this dissertation takes advantage of the multiple charging phenomenon and couples with gas-phase ion/ion reactions to achieve various analyses among a wide range of biological-related samples.</p>

No description available.

This thesis describes experimental work towards developing a trapped ion quantum information processor. An existing ion trap apparatus was capable of trapping and laser-cooling single ions or small ion strings of 40 Ca+, and had been used for studies of quantum jumps and natural lifetime measurements in Ca. This thesis describes improvements in this apparatus, which have allowed the stability and the flexibility of experimental control of the ions to be greatly increased. This enabled experiments to read out the spin state of a single trapped ion, and to load ions with isotope selectivity through photoionization. The optical systems were improved by installation of new lasers, optical reference cavities, and a system of acousto-optic modulators for laser intensity switching and frequency control. The photon counting for fluorescence detection was improved, and a new photon time-of-arrival correlation circuit developed. This has permitted rapid and more sensitive detection of micromotion, and hence cancellation of stray fields in the trap. A study of resonant circuits in the low RF, high voltage (10 MHz, 1 kV) regime was carried out with a view to developing a new RF supply for the Paul trap with reduced noise and increased power. A new supply based on a helical resonator was built and used to trap ions. This technique has reduced noise and will permit higher secular frequencies to be attained in the future. A magnetic field B in the ion trap is used to define a quantization axis, and in one series of experiments was required to be of order 100 G to provide a substantial Zeeman splitting. A set of magnetic field coils to control the size and direction of B is described. The design of these posed some problems owing to an unforseen issue with the vacuum chamber. In short, it is magnetizable and acts to first approximation like a magnetic shield. The field coils had to be sufficiently substantial to produce the desired field at the ion even in the presence of this shielding effect, and dark resonance (and other) spectra with Zeeman splitting were obtained to calibrate the field using the ion as a probe. Finally, the thesis describes the successful loading of the ion trap by laser photoionization from a weak atomic beam. This involved two new lasers at 423 nm and 389 nm. Saturated absorption spectroscopy of neutral calcium is first described, then transverse excitation of an atomic beam in our vacuum chamber is used to identify all the main isotopes of calcium and confirm their abundances in our source (a heated sample of natural calcium). Finally, photoionization is used to load the trap. This has three advantages over electron-impact ionization. By avoiding an electron gun, we avoid charging of insulating patches and subsequent electric field drift as they discharge; the flux in the atomic beam and hence calcium (and other) deposits on the electrodes can be greatly reduced; and most importantly, the photoionization is isotope selective. Evidence is presented which suggests that even with an non-enriched source, the rare isotope 43 Ca can be loaded with reasonable efficiency. This isotope is advantageous for quantum information experiments for several reasons, but chiefly because its ground state hyperfine structure can act as a stable qubit.

<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 dir="ltr">Metal ions are typically considered a nuisance for mass spectrometry, as they can introduce chemical noise and distribute an analyte’s signal into multiple peaks. In some cases however, metal ions in biological solutions are either necessary for biomolecular structures, or so ubiquitous in a sample’s native solution conditions that they are difficult to fully remove. In this work, the role of metal ions in biological analytes is explored. For analytes that require metal ions to maintain higher order structures, a mass spectrometry method was developed to determine whether a stable structure is formed from metal ion adducts, or if the metal ion adducts are nonspecifically bound. Electron transfer of these structures reveals complementary fragmentation information, with the added discovery of new radical fragmentation pathways. With mass spectrometry, specific ligand and metal ion affinities can even be determined for analytes at low enough concentrations. In addition to analytes that require metals, an exploration on unwanted metal ion adduction during the electrospray ionization process is shown via gas-phase ion/ion reactions. Observing how specific anionic ligands exchange metals with protons from proteins on a small and controlled scale gives a greater understanding of what solutions can lead to the cleanest results. In addition, this work shows the possibility of finding anionic ligands that will instead exchange protons with metal ions found on proteins. In the gas-phase, these experiments have a high degree of control, leading to a much greater understanding of how metal ions influence mass spectrometry samples.</p>

No description available.

PEGASES est un propulseur à grilles qui accélère à la fois des ions positifs et des ions négatifs pour la poussée. Il nécessite la création d'un plasma ion-ion afin de permettre l'extraction des ions négatifs. Pour obtenir un taux d'ionisation et un taux d'attachement efficaces, le plasma doit être composé de deux températures électroniques : une température élevée pour créer les ions positifs et une faible pour créer les ions négatifs. Ce plasma ion-ion est créé au moyen d'un filtre magnétique qui permet le refroidissement des électrons et qui ralentit leur diffusion. Avec cette méthode, on obtient une forte température électronique près de la zone d'ionisation, avant le maximum de champ magnétique, et une température faible dans la région en aval du filtre magnétique. Plusieurs problèmes se posent alors i) le plasma est excité à la RadioFréquence (RF), celle-ci est susceptible de créer des fluctuations RF du potentiel plasma importantes rendant les mesures de sondes difficiles, ii) les mesures électrostatiques dans les plasmas magnétisés sont rendues difficiles à cause de l'anisotropie des électrons dans un champ magnétique et iii) pour les mesures en plasma ion-ion (caractéristiques courant-tension symétriques) peu de théories existent pour extraire les paramètres plasmas dans nos régime de pressions. Deux diagnostics électrostatiques et un modèle pour extraire les paramètres plasmas dans les plasmas électronégatifs ont été mis au point pendant ma thèse au LPP. Le premier diagnostic est une sonde flottante capacitive permettant la mesure des fluctuations RF du potentiel plasma. Avec ces mesures, la source de PEGASES a été ajustée pour diminuer ces fluctuations. Le second diagnostic est une sonde de Langmuir adaptée pour faire des mesures dans les plasmas électronégatifs magnétisés. Le haut taux de gravure du gaz électronégatif utilisé ainsi que l'anisotropie électronique créée par le champ magnétique impose certaines contraintes sur les matériaux et les dimensions de la sonde de Langmuir. Le modèle reproduit les caractéristiques de sonde de Langmuir dans les plasmas électronégatifs supposant des distributions de Boltzmann. Depuis les courbes I-V mesurées et une procédure d'ajustement de courbe intégrée au modèle analytique il est possible de mesurer i) les températures et les densités des électrons et des ions positifs et négatifs pour les plasmas fortement électronégatifs ($n_-/ n_e>50$), et ii) la température des électrons et les densités des ions positifs et négatifs pour les plasma faiblement électronégatifs ($n_-/ n_e<50$). Ces diagnostics nous ont permis d'étudier l'effet de différents champs magnétiques sur un plasma électropositif et électonégatif. Dans le premier cas, nous avons montré que seul le gradient positif du champ magnétique induit une diminution de la température électronique, le minimum de température électronique est ainsi obtenu au maximum du champ magnétique. Ce minimum de température peut être contrôlé grâce à l'intensité du champ magnétique alors que la pression contrôle la température en amont du filtre. Lorsque qu'un gaz électronégatif est utilisé, un plasma ion-ion est créé environ 1 cm après le maximum de champ magnétique. Les densités d'ions sont relativement constantes au travers du filtre magnétique alors que la densité électronique chute de 3 ordres de grandeur. Contrairement aux plasmas électropositifs où le minimum de température électronique est obtenu au maximum de champ magnétique, la formation du plasma ion-ion est contrôlée par la pression et le ratio de SF6 dans le mélange. Un modèle simple basé sur la mesure des densités et des températures des ions a permis d'évaluer l'efficacité de PEGASES à $T=25$~mN.kW$^{-1}$ et $I_{\rm{sp}}=3790$~s, qui est dix fois moins pour une surface d'éjection quatre fois plus petite que le propulseur ionique à grille T6 de chez QinetiQ qui va propulser la mission Bepi-Colombo.