This thesis concerns heating and current drive in tokamak plasmas using the fast magnetosonic wave in the ion cyclotron range of frequencies. Fast wave heating is a versatile heating method for thermonuclear fusion plasmas and can provide both ion and electron heating and non-inductive current drive. Predicting and interpreting realistic heating scenarios is however difficult due to the coupled evolution of the cyclotron resonant ion velocity distributions and the wave field. The SELFO code, which solves the coupled wave equation and Fokker-Planck equation for cyclotron resonant ion species in a self-consistent manner, has been upgraded to allow the study of more advanced fast wave heating and current drive scenarios in present day experiments and in preparation for the ITER tokamak. Theoretical and experimental studies related to fast wave heating and current drive with emphasis on fast ion effects are presented. Analysis of minority ion cyclotron current drive in ITER indicates that the use of a hydrogen minority rather than the proposed helium-3 minority results in substantially more efficient current drive. The parasitic losses of power to fusion born alpha particles and beam injected ions are concluded to be acceptably low. Experiments performed at the JET tokamak on polychromatic ion cyclotron resonance heating and on fast wave electron current drive are presented and analysed. Polychromatic heating is demonstrated to increase the bulk plasma ion to electron heating ratio, in line with theoretical expectations, but the fast wave electron current drive is found to be severely degraded by parasitic power losses outside of the plasma. A theoretical analysis of parasitic power losses at radio frequency antennas indicates that the losses can be significantly increased in scenarios with low wave damping and with narrow antenna spectra, such as in electron current drive scenarios. / QC 20100506

Studies of protein and peptide expression are vital in order to understand complex biological systems. As demonstrated in this thesis, on-line packed capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS) is a useful analytical tool for such studies. A proteomics method, based on global tryptic digestion and subsequent separation and detection of the peptides by LC-FTICR MS, was developed for qualitative analysis of body fluids. Initial experiments on cerebrospinal fluid (CSF) provided results that were comparable or superior to those achieved by more time- and sample-consuming techniques. The method was also successfully applied on plasma and amniotic fluid. One of the major challenges in proteomics is the broad dynamic range of proteins in biological matrices. The advantages of removing high-abundant components from CSF and plasma prior to MS were demonstrated. In order to search for potential biomarkers, mass chromatograms of CSF from patients suffering from amyotrophic lateral sclerosis (ALS) and controls were compared using an in-house constructed pattern recognition program. ALS-specific patterns were observed, and four out of five unknown samples were correctly assigned. Alternative strategies to quantitatively compare two pools of samples rely on differential chemical labeling. The performance of one such method, quantification-using-enhanced-signal-tags, was investigated in complex sample analysis. The experimental intensity ratios were proven to be consistent with the prepared concentration ratios of abundant proteins in CSF. Finally, the thesis reports on the first experiments where electron capture dissociation (ECD) was successfully incorporated in on-line LC-MS experiments. ECD and nozzle-skimmer fragmentation were applied to a sample of endocrine peptides extracted from mouse pancreatic islets. The two fragmentation methods provided complementary information. However, the method needs further optimization before it can be applied in the analysis of more complex samples, such as body fluids.

Magnetic nozzles, like Laval nozzles, are observed in several natural systems and have application in areas such as electric propulsion and plasma processing. Plasma flowing through these nozzles is inherently tied to the field lines and must separate for momentum redirection or particle transport to occur. Plasma detachment and associated mechanisms from a magnetic nozzle are investigated. Experimental results are presented from the plume of the VASIMR® VX-200 device flowing along an axisymmetric magnetic nozzle and operated at two ion energies to explore momentum dependent detachment. The argon plume expanded into a 150m3 vacuum chamber where the background pressure was low enough that charge-exchange mean-free-paths were longer than experiment scale lengths. This magnetic nozzle system is demonstrated to hydrodynamically scale up to astrophysical plasmas, particularly the solar chromosphere, implying general relevance to all systems. Plasma parameters were mapped over a large spatial range using measurements from multiple plasma diagnostics. The data show that the plume does not follow the magnetic field lines. A mapped integration of the ion flux shows the plume may be divided into three regions where 1) the plume briefly follows the magnetic flux, 2) diverges quadratically before 3) expanding with linear trajectories. Transitioning from region 1→2, the ion flux departs from the magnetic flux suggesting ion detachment. An instability forms in region 2 driving an oscillating electric field that causes ions to expand before enhancing electron cross-field transport through anomalous resistivity. Transitioning from region 2→3 the electric field dissipates, the trajectories linearize, and the plume effectively detaches. A delineation of sub-to-super Alfvénic flow aligns well with the inflection points of the linearization without a change in magnetic topology. The detachment process is best described as a two part process: First, ions detach by a breakdown of the magnetic moment when the quantity |v/fcLB| becomes of order unity. Second, the turbulent electric field enhances electron transport up to a factor of 4±1 above collisional diffusion; electron cross-field velocities approximate that of the ions and depart on more centralized field lines. Electrons are believed to detach by breakdown of magnetic moment further downstream in the weaker magnetic field.

The subject of this thesis is high-precision mass-measurements performed with Penning trap mass spectrometers (PTMS). In particular it describes the SMILETRAP I PTMS and the final results obtained with it, the masses of 40Ca and that of the proton. The mass of 40Ca is an indispensible input in the evaluation of measurements of the bound electron g-factor, used to test quantum electrodynamical calculations in strong fields. The value obtained agrees with available literature values but has a ten times higher precision. The measurement of the proton mass, considered a fundamental physical constant, was performed with the aim of validating other Penning trap results and to test the limit of SMILETRAP I. It was also anticipated that a measurement at a relative precision close to 10-10 would give insight in how to treat certain systematic uncertainties. The result is a value of the proton mass in agreement with earlier measurements and with an unprecedented precision of 1.8×10-10. Vital for the achieved precision of the proton mass measurement was the use of the Ramsey excitation technique. This technique, how it was implemented at SMILETRAP I and the benefits from it is discussed in the thesis and in one of the included papers. The second part of the thesis describes the improved SMILETRAP II setup at the S-EBIT laboratory, AlbaNova. All major changes and upgrades compared to SMILETRAP I are discussed. This includes, apart from the Ramsey excitation technique, higher ionic charge states, improved temperature stabilization, longer run times, different reference ions, stronger and more stable magnetic field and a more efficient ion detection. Altogether these changes should reduce the uncertainty in future mass determinations by an order of magnitude, possibly down to 10-11. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 9: Accepted.

Nós calculamos o efeito da interação elétron-fonons longitudinais óticos (LO) sobre a energia de transição ls &#8594 2p+ entre os níveis de uma impureza doadora, localizada em um poço quântico de GaAs-AlxGa1-xAs. Nossos resultados para a energia de transição em função do campo magnético aplicado mostram claramente, que a saturação da energia de transição (efeito pinning) ocorre na energia dos fônons LO, em boa concordância com recentes dados experimentais. Obtemos também a massa de cíclotron de polarons confinados em fios quânticos quase-unidimensionais, com potencial de confinamento parabólico. Observamos que o comportamento da massa é diferente daquele para sistemas bi-dimensionais e que esta diferença é maior quanto maior o potencial de confinamento. Para a heterojunção de GaAs-AlGaAs e GaAs-GaSb, investigamos a importância da interação elétron-fonons interfaciais sobre a massa de cíclotron. Verificamos que a contribuição dos fonons interfaciais é fundamental nas regiões próximas às resonâncias, onde domina o espectro. Finalmente, calculamos a energia de ligação de uma impureza hidrogenóide, localizada no centro de um ponto quântico circular de GaAs-AlGaAs. Na ausência de campo magnético aplicado, obtivemos uma expressão analítica para a função de onda do elétron ligado. Notamos, que a influência do campo magnético sobre a energia de ligação é fraca nas regiões de pequenos raios, devido ao forte potencial de confinamento. / We calculate the effects of the electron-longitudinal optical (LO) phonons interaction on the intra donor ls &#8594 2p+ transition energy in GaAs-AlGaAs quantum wells structures. Our results to the transition energy as a function of the magnetic Field strength, show that the pinning effect occur in the phonon LO energy in good agreement with recent experimental data. The cyclotron mass of polarons confined in quasi.one.dimensional quantum-well wires with parabolic confinement potential, is also obtained. The behavior of electrons effective mass with magnetic field is different, of the two-dimensional systems, and the difference increase when the confinement potential increase. To heterojunctions of GaAs-AlAs and GaAs-GaSb, we investigate the electroninterfacials optical (IO) phonons interactions on the effective cyclotron mass. We find that the electron-IO-phonons interaction is fundamental near the resonances, where they dominate the spectra. Finally, the ground state binding energy of donor impurity, placed in the center of a circular quantum dot is calculated. Without magnetic field, we obtained the analytic expression to the bound electron wave function. The influence of the magnetic field on the donor binding energy is weaker, when the radius of the quantum dot became smaller.

Es wurde eine Elektron-Zyklotron-Resonanz-Ionenquelle mit einer Mikrowellenfrequenz von2,45 GHz für die Produktion intensiver Ströme einfach geladener Metallionen entwickelt. Deren Beladung mit Metalldampf erfolgt über ein integriertes zylindrisches Sputtermagnetron, welches speziell für diese Aufgabe entworfen wurde. Die entstandene MECRIS, engl. Magnetron Electron Cyclotron Resonance Ion Source, vereinigt die ECR-Ionenquellentechnologie mit der Magnetron-Sputtertechnologie auf bisher einzigartige Weise und verkörpert so ein neues Metallionen-Quellenkonzept. Unter Verwendung eines Al-Sputtertargets konnte die Funktionsfähigkeit der MECRIS an dem Beispiel der Al+-Ionenerzeugung erfolgreich demonstriert werden. Der extrahierbare Al+-Ionenstrom wurde über einen neuartigen, im Rahmen der Arbeit entwickelten, Hochstrom-Faraday-Cup gemessen. Auf Basis numerischer Berechnungen wurde das Gesamtmagnetfeld so ausgelegt, dass die Permanentmagnete des Magnetrons und die Spulen der ECR-Quelle eine Minimum-B-Struktur erzeugen, welche einen effektiven Elektroneneinschluss nach dem magnetischen Spiegelprinzip ermöglicht. Gleichzeitig wird durch eine geschlossene ECR-Fläche, mit der magnetischen Resonanzflussdichte von 87,5 mT, eine optimale Heizung der Plasmaelektronen realisiert. Die mithilfe einer Doppel-Langmuir-Sonde gemessene Elektronentemperatur steigt in Richtung Quellenmitte an und beträgt maximal 11 eV. Geheizte Elektronen erlauben die effiziente Stoßionisation der Al-Atome, welche mit einer Rate von über 1E18 Al-Atome/s eingespeist werden und eine höchstmögliche Dichte von 2E10 1/cm³ aufweisen. Die MECRIS erzeugt hauptsächlich einfach geladene Ionen des gesputterten Materials (Al+) und des Prozessgases (Ar+). Der Al+-Ionenextraktionsstrom ist über die Erhöhung der Prozessparameter Sputterleistung, Mikrowellenleistung, Spulenstrom und Extraktionsspannung um eine Größenordnung bis auf maximal 135 μA steigerbar, was einer Stromdichte von 270 μA/cm² über die Extraktionsfläche von rund 0,5 cm² entspricht. Dies steht im Einklang mit der Prozessparameterabhängigkeit der anhand der Sonde bestimmten Plasmadichte, welche einen größtmöglichen Wert von etwa 6E11 1/cm³ annimmt. Das Verhältnis von extrahiertem Al+- zu Ar+-Ionenstrom kann durch Optimierung der Prozessparameter von 0,3 auf maximal 2 angehoben werden. Sondenmessungen des entsprechenden Ionendichteverhältnisses bestätigen diesen Sachverhalt. Um möglichst große Extraktionsströme und Al+/Ar+-Verhältnisse zu generieren, muss die ECR-Fläche demnach in dem Bereich der höchsten Al-Atomdichte in der Targetebene lokalisiert sein. Gegenüber dem alleinigen Magnetronplasma (ohne Mikrowelleneinspeisung) können mit dem MECRIS-Plasma um bis zu 140 % höhere Al+-Ionenströme produziert werden. Aus Sondenuntersuchungen geht hervor, dass dies eine Folge der um etwa eine Größenordnung gesteigerten Plasmadichte und der um rund 7 eV größeren Elektronentemperatur des MECRIS-Plasmas ist. Das MECRIS-Plasma wurde außerdem mittels optischer Emissionsspektroskopie charakterisiert und durch ein globales sowie ein zweidimensionales Modell simuliert. Die gewonnenen Prozessparameterabhängigkeiten der Plasmadichte, Elektronentemperatur sowie Al+- und Ar+-Ionendichte stimmen mit den Sondenergebnissen überein. Teilweise treten jedoch Absolutwertunterschiede von bis zu zwei Größenordnungen auf. Die Erhöhung der Sputterleistung und Extraktionsspannung über die derzeitigen Grenzen von 10 kW bzw. 30 kV sowie die Optimierung der Extraktionseinheit hinsichtlich minimaler Elektrodenblindströme bietet das Potential, den Al+-Ionenstrom bis in den mA-Bereich zu steigern. / An electron cyclotron resonance ion source working at a microwave frequency of 2.45 GHz has been developed in order to generate an intense current of singly charged metal ions. It is loaded with metal vapor by an integrated cylindrical sputter magnetron, which was especially designed for this purpose. The MECRIS (Magnetron Electron Cyclotron Resonance Ion Source) merges ECR ion source technology with sputter magnetron technology in a unique manner representing a new metal ion source concept. By using an Al sputter target, the efficiency of the MECRIS was demonstrated successfully for the example of Al+ ion production. The extractable ion current was measured by a newly developed high-current Faraday cup. On the basis of numerical modeling, the total magnetic field was set in a way that the permanent magnets of the magnetron and the coils of the ECR source are forming a minimum-B-structure, providing an effective electron trap by the magnetic mirror principle. Simultaneously, optimal electron heating is achieved by a closed ECR-surface at resonant magnetic flux density of 87.5 mT. Electron temperature increases towards the center of the source to a maximum of about 11 eV and was measured by a double Langmuir probe. Due to the heated electron population, efficient electron impact ionization of the Al atoms is accomplished. Al atoms are injected with a rate of more than 1E18 Al-atoms/s resulting in a maximum Al atom density of 2E10 1/cm³. The MECRIS produces mainly singly charged ions of the sputtered material (Al+) and the process gas (Ar+). The Al+ ion extraction current is elevated by one order of magnitude to a maximum of 135 μA by increasing the process parameters sputter magnetron power, microwave power, coil current, and acceleration voltage. Related to the extraction area of about 0.5 cm², the highest possible Al+ ion current density is 270 μA/cm². A corresponding process parameter dependency was found for the plasma density showing a peak value of about 6E11 1/cm³, which was deduced from probe measurements. The ratio of the extracted Al+ ion current to the Ar+ ion current can be enhanced from 0.3 to a maximum of 2 by optimization of the process parameters. This was confirmed by probe investigations of the appropriate ion density ratio. In conclusion, the ECR-surface needs to be located in the area of the highest Al atom density in the target plane in order to improve the extraction current and Al+/Ar+ ratio. The MECRIS plasma produces an Al+ ion current, which is up to 140 % higher compared to that of the sole sputter magnetron plasma (without microwave injection). As revealed by probe measurements, this effect is due to the higher plasma density and electron temperature of the MECRIS plasma, leading to a difference of one order of magnitude and 7 eV, respectively. Additionally, the MECRIS plasma has been characterized by optical emission spectroscopy and simulated by a global and a two-dimensional model. Retrieved process parameter dependencies of plasma density, electron temperature, Al+ ion density, and Ar+ ion density coincide with probe findings. Although a discrepancy of the absolute values of partly up to two orders of magnitude is evident. Potentially, the Al+ ion current can be enhanced to the mA-region by optimizing the ion extraction system for minimal idle electrode currents and by rising sputter magnetron power as well as acceleration voltage above the actual limits of 10 kW and 30 kV, respectively.

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

QC 20100622

Mass-selected infrared multiple photon spectroscopy (IRMPD), Fourier transform ion cyclotron resonance (FT-ICR) kinetic experiments, RRKM and electronic structure calculations have been performed in order to propose a complex mechanism involving the formation of the proton-bound dimer of water (H5O2+) from 1,1,3,3-tetrafluorodimethyl ether. It has been found that the reaction is facilitated by a series of sequential exothermic bimolecular ion-molecule reactions. Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate which decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). The 1,4-elimination of hydrogen fluoride is found to be strongly supported by the results of both RRKM theory and electronic structure calculations. Lastly, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition and product species was obtained using MP2/aug-cc-pVQZ//MP2(full)/6-31G(d) level of theory. Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and two of the protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. It was found that the formation of a proton-bound dimer (PBD) of caffeine and ammonia was elusive under the experimental conditions. The low binding energy of the caffeine and ammonia PBD is responsible for the perceived difficulty in obtaining an IRMPD spectrum. The IRMPD spectrum of the PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also obtained. The spectrum of protonated caffeine showed the dominant existence of a single isomer, whereas the spectrum of protonated theophylline showed a mixture of isomers. The mixture of isomers of protonated theophylline resulted as a consequence of proton-transport catalysis (PTC) occurring within the PBD of theophylline and ammonia. All calculated harmonic spectra have been produced at the B3LYP/6-311+G(d,p) level of theory with fundamental frequencies scaled by 0.9679; calculated anharmonic spectra have also been provided at the same level of theory and were found to greatly improve the match with the IRMPD spectra obtained in all cases. Ionic hydrogen bond (IHB) interactions, resulting from the association of caffeine and theophylline with their protonated counterparts, forming proton-bound homodimers, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. It is found that the IRMPD spectra of the proton-bound homodimers of caffeine and theophylline are complicated resulting from the existence of several pairs of enantiomers separated by a narrow range of relative Gibbs free energies (298 K) of 15.6 and 18.2 kJ mol-1, respectively. The IRMPD spectrum of the proton-bound homodimer of theophylline is dominated by a unique isomer facilitated by formation of a bidentate IHB. Formation of this interaction lowers the relative Gibbs free energy of the ion to 9.75 kJ mol-1 below that of the most favourable pair of enantiomers. The IRMPD spectrum of the PBD of caffeine is complicated by the existence of at least two pairs of enantiomers with the strong likelihood of the spectral contributions of a third pair existing. The most favourable enantiomeric pair involves the formation of a O-H+⋯O IHB. However, verification of a pair of enantiomeric PBDs containing a N-H+⋯O IHB is also observed in the IRMPD spectrum of the PBD of caffeine due to the presence of three free carbonyl stretching modes located at 1731, 1751 and 1785 cm-1. The mass-selected IRMPD spectra of the sodium cation-bound dimers (SCBD) of caffeine and theophylline also have been obtained. Both the mass-selected IRMPD spectra and electronic structure calculations predict the most likely structure of the SCBDs of caffeine and theophylline to form by an efficient O⋯Na+⋯O interaction between C=O functional groups possessed by each monomer. The frequencies of the C=O-Na+ stretch are found to be nearly identical in the IRMPD spectra for both of the SCBDs of caffeine and theophylline at 1644 and 1646 cm-1, respectively. However, the degenerate free C=O symmetric and asymmetric stretches for the SCBDs of caffeine and theophylline found at 1732 and 1758 cm^(-1), respectively, demonstrating a red-shift for caffeine possibly linked to a steric interaction absent in theophylline. Free rotation about the O⋯Na+⋯O bond is found to greatly decrease the complexity of the IRMPD spectra of the SCBDs of caffeine and theophylline and demonstrates excellent agreement between the IRMPD and calculated spectra. Electronic structure calculations have been done at the MP2(full)/aug-cc-pCVTZ/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory using the aug-cc-pCVTZ basis set for Na+ and all Na+-interacting heterotatoms, and the 6-311+G(2d,2p) basis set for all non-interacting atoms within the SCBDs, in order to provide accurate electronic energies. Currently, installation and implementation of a pulsed electrospray high pressure ion source mated to an existing high pressure mass spectrometer (HPMS) is underway. The new ion source will greatly increase the range of possibilities for the study of ion-molecule reactions in the McMahon laboratory. One of the unique features of the new design is the incorporation of a gas-tight electrospray interface, allowing for more possibilities than only the study of cluster-ion equilibria involving hydration (H2On⋯S+), where S+ is an ion produced by electrospray. Other small prototypical biological molecules such as amines and thiols can be used without concern for the toxicity of these species. Another unique design feature allows electrosprayed ions to associate with neutral solvent species in an electric field free reaction chamber (RC). This ensures that values of equilibrium constants determined are truly representative of ions in states of thermochemical equilibrium. The existing HPMS in the McMahon laboratory is limited to the study of small volatile organic molecules. The new ion source will permit the exploration of systems involving non-volatile species, doubly charged ions and many biologically relevant molecules such as amino acids, peptides, nucleobases and carbohydrates.

Mass-selected infrared multiple photon spectroscopy (IRMPD), Fourier transform ion cyclotron resonance (FT-ICR) kinetic experiments, RRKM and electronic structure calculations have been performed in order to propose a complex mechanism involving the formation of the proton-bound dimer of water (H5O2+) from 1,1,3,3-tetrafluorodimethyl ether. It has been found that the reaction is facilitated by a series of sequential exothermic bimolecular ion-molecule reactions. Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate which decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). The 1,4-elimination of hydrogen fluoride is found to be strongly supported by the results of both RRKM theory and electronic structure calculations. Lastly, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition and product species was obtained using MP2/aug-cc-pVQZ//MP2(full)/6-31G(d) level of theory. Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and two of the protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. It was found that the formation of a proton-bound dimer (PBD) of caffeine and ammonia was elusive under the experimental conditions. The low binding energy of the caffeine and ammonia PBD is responsible for the perceived difficulty in obtaining an IRMPD spectrum. The IRMPD spectrum of the PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also obtained. The spectrum of protonated caffeine showed the dominant existence of a single isomer, whereas the spectrum of protonated theophylline showed a mixture of isomers. The mixture of isomers of protonated theophylline resulted as a consequence of proton-transport catalysis (PTC) occurring within the PBD of theophylline and ammonia. All calculated harmonic spectra have been produced at the B3LYP/6-311+G(d,p) level of theory with fundamental frequencies scaled by 0.9679; calculated anharmonic spectra have also been provided at the same level of theory and were found to greatly improve the match with the IRMPD spectra obtained in all cases. Ionic hydrogen bond (IHB) interactions, resulting from the association of caffeine and theophylline with their protonated counterparts, forming proton-bound homodimers, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. It is found that the IRMPD spectra of the proton-bound homodimers of caffeine and theophylline are complicated resulting from the existence of several pairs of enantiomers separated by a narrow range of relative Gibbs free energies (298 K) of 15.6 and 18.2 kJ mol-1, respectively. The IRMPD spectrum of the proton-bound homodimer of theophylline is dominated by a unique isomer facilitated by formation of a bidentate IHB. Formation of this interaction lowers the relative Gibbs free energy of the ion to 9.75 kJ mol-1 below that of the most favourable pair of enantiomers. The IRMPD spectrum of the PBD of caffeine is complicated by the existence of at least two pairs of enantiomers with the strong likelihood of the spectral contributions of a third pair existing. The most favourable enantiomeric pair involves the formation of a O-H+⋯O IHB. However, verification of a pair of enantiomeric PBDs containing a N-H+⋯O IHB is also observed in the IRMPD spectrum of the PBD of caffeine due to the presence of three free carbonyl stretching modes located at 1731, 1751 and 1785 cm-1. The mass-selected IRMPD spectra of the sodium cation-bound dimers (SCBD) of caffeine and theophylline also have been obtained. Both the mass-selected IRMPD spectra and electronic structure calculations predict the most likely structure of the SCBDs of caffeine and theophylline to form by an efficient O⋯Na+⋯O interaction between C=O functional groups possessed by each monomer. The frequencies of the C=O-Na+ stretch are found to be nearly identical in the IRMPD spectra for both of the SCBDs of caffeine and theophylline at 1644 and 1646 cm-1, respectively. However, the degenerate free C=O symmetric and asymmetric stretches for the SCBDs of caffeine and theophylline found at 1732 and 1758 cm^(-1), respectively, demonstrating a red-shift for caffeine possibly linked to a steric interaction absent in theophylline. Free rotation about the O⋯Na+⋯O bond is found to greatly decrease the complexity of the IRMPD spectra of the SCBDs of caffeine and theophylline and demonstrates excellent agreement between the IRMPD and calculated spectra. Electronic structure calculations have been done at the MP2(full)/aug-cc-pCVTZ/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory using the aug-cc-pCVTZ basis set for Na+ and all Na+-interacting heterotatoms, and the 6-311+G(2d,2p) basis set for all non-interacting atoms within the SCBDs, in order to provide accurate electronic energies. Currently, installation and implementation of a pulsed electrospray high pressure ion source mated to an existing high pressure mass spectrometer (HPMS) is underway. The new ion source will greatly increase the range of possibilities for the study of ion-molecule reactions in the McMahon laboratory. One of the unique features of the new design is the incorporation of a gas-tight electrospray interface, allowing for more possibilities than only the study of cluster-ion equilibria involving hydration (H2On⋯S+), where S+ is an ion produced by electrospray. Other small prototypical biological molecules such as amines and thiols can be used without concern for the toxicity of these species. Another unique design feature allows electrosprayed ions to associate with neutral solvent species in an electric field free reaction chamber (RC). This ensures that values of equilibrium constants determined are truly representative of ions in states of thermochemical equilibrium. The existing HPMS in the McMahon laboratory is limited to the study of small volatile organic molecules. The new ion source will permit the exploration of systems involving non-volatile species, doubly charged ions and many biologically relevant molecules such as amino acids, peptides, nucleobases and carbohydrates.