This dissertation focuses on the investigation of gas-phase characteristics of cucurbituril host-guest systems using ion mobility spectrometry (IMS) and related techniques. Collision cross-sections (CCS) of alkylammonium complexes of cucurbit[n]uril (CB[n]) are measured to understand the allosteric interactions that induce conformational changes in the complex in the presence of metal cations on one of the portals of the cucurbit[6]uril (CB[6]) host. Cationic species on one CB[6] rim sterically force longer linear alkylammonium guests out of the cucurbituril cavity during complex formation. Similarly, rigid cucurbituril-metal complexes were studied using IMS to demonstrate the effect of long-range ion-neutral interactions on the gas phase mobility of ions. The contributions of charge state and charge distribution to the ion mobility CCS measured using a drift tube ion mobility spectrometer (DTIMS) were studied. This IMS method characterization will help in the study of biomolecules and may answer some of the questions regarding CCS measurements in protein structures, that are still being debated. While most of the studies were done using an IMS system, this dissertation also includes gas phase characterization studies done using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. A novel gas-phase CCS measurement technique - cross sectional areas using Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) was attempted on bigger systems like the [cucurbit[6]uril-n-alkylammonium]+ complexes. Infrared multi-photon dissociation (IRMPD), collision induced dissociation (CID), and sustained off-resonance irradiation (SORI) studies were done on many CB[n] systems, which helped to extract useful structural information about the complexes.

Our group has been studying chiral recognition in gas phase using mass spectrometry for more than 10 years. We are interested in gas phase studies of fundamental interactions because the gas phase avoids complications and masking effects that may arise upon solvation. Therefore, the results of gas phase experiments can be directly compared with those of high-level computational studies. In chapter 2, I studied the roles of hydrogen bonding and pi stacking in gas phase chiral recognition between aromatic crown molecules and aromatic amines. High affinity between host and guest doesn't necessarily result in better recognition. If the affinity is too high, both host enantiomers will bind to the chiral guest very tightly so little discrimination is observed. In order to build an efficient chiral recognition system, we need to select a host and guest that have intermediate binding affinity. Hydrogen bonding is another significant factor that controls the host-guest affinity. In the case of host 1, more hydrogen bonds results in better recognition. We also find that the degree of chiral recognition is greater in the gas phase than in solution. Modeling at the B3LYP/6-31G* level is qualitatively correct, but quantitative agreement with experiment is poor. Inspired by Rekharsky's work which shows successful induced chiral recognition with an achiral host (cucurbituril) in solution, we tested the possibility of applying cucurbiturils as gas phase chiral recognition containers in chapter 5. Conferring chirality on cucurbiturils makes the chiral recognition happen in a restricted space, which might strengthen or hinder the discrimination. By comparing our results with Rekharsky's, we showed the role of solvent in this chiral recognition process. In the gas phase, the enantiodiscrimination does not happen between the "leaving MP" and the "approaching" stronger chiral binder. Because hydrophobic effects are absent in the gas phase, it is possible that the hydrophobic methyl substituent of 2-methylpiperazine and the stronger chiral binder might not be simultaneously included inside the cavity. Therefore, we do not observe enantiodiscrimination in gas phase. The dissociation experiment for the CB[7] ternary complex shows that sec-butylamine binds externally to the CB[7] host. Further, the heterochiral diastereomer is more stable than the homochiral diastereomer. This conclusion is consistent with Rekharsky's result in solution. For more than 15 years, the most common ionization method in our lab has been electrospray ionization. However, ESI is subject to problems with ion suppression, especially when the sample is a mixture or it has a high concentration of salt. The easily ionized molecules tend to scavenge the available charges in the spray solution and dominate the resulting ion population even though other compounds may be present in high abundance. Nanoelectrospray usually yields cold ionization, and analyte suppression can be greatly reduced at nanospray flow rates. Therefore, we constructed a porous polymer monolith (PPM) nanospray emitter similar to that described by Oleschuk et al. and characterized the properties of the PPM emitter. This work is described in chapter 3. Our tests show that this PPM nanospray emitter possesses some special analytical properties: decreased ion suppression, quite stable spray, strong signal intensity and good reproducibility in emitter performance. Chapter 4 deals with the application of the new CRAFTI method to negative ions. CRAFTI stands for cross-sectional areas by Fourier transform ICR. The CRAFTI technique measures collision cross sections, providing a probe of the gas phase conformations of supramolecular complexes. Our preliminary work has shown that CRAFTI is applicable to positive ions, so we further demonstrate the application of the newly-developed method to negative ions in this work. Based on the fact that the experimental cross sections correlate linearly with the theoretical values, we have obtained evidence that CRAFTI is a valid method for negative ions. However, some problems remain. First, we are still working to understand the physical meaning of the CRAFTI cross sections. The absolute values we obtain are generally greater than those obtained from momentum transfer cross section calculations modeled in helium. Second, the precision of the measurements (currently about 2-3%) is still larger than we desire. We need to carefully tune the excitation and isolation amplitudes to make the signal strong and monoisotopic for weak ions. CRAFTI is a very promising and attractive method because FT-ICR provides accurate mass-to-charge measurement along with the cross section measurement. In other words, one technique is sufficient to obtain the shape, size and mass of a molecule simultaneously.

Heterobimetallic catalysts offer large potential for efficient and selective catalysis of a wide range of reactions. Better understanding of these catalytic mechanisms could yield further improvement in their catalytic abilities. Cp(CO)2Fe-Cu(IPr) (IPr = N,N-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) is a catalyst that has been reported to catalyze arene borylation. The catalytic mechanism of this catalyst that had been previously proposed had the initial step being a metal-metal cleavage. However, computational modeling suggested an alternate mechanism that could be more energetically favorable. Rather than a metal-metal cleavage as the initial step, we proposed a photoactivated carbonyl dissociation. To support this proposition, we performed time resolved Fourier transform infrared spectroscopy experiments that found evidence supporting our proposed mechanism. Based on these experimental results, we have proposed a new catalytic cycle. The determination of collisional cross section is a powerful tool in analytical chemistry for distinguishing isomers. Techniques such as ion mobility spectrometry can be used to find the collisional cross section of ions but require specialized equipment. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is a widely used technique for determining ion mass. A technique known as CRoss sectional Area from Fourier Transform Ion cyclotron resonance (CRAFTI) uses a standard FTICR instrument to measure the collisional cross section of ions. This is done by performing a Fourier transform on the data and measuring the Lorenztian width of the peak at the resonant frequency and relating that to the exponential decay of the signal in the time domain. We developed a new data analysis technique that is able to extract just the signal at the resonant frequency in the time domain and directly fit the exponential decay. This new data analysis technique opens new possibilities for expanding the capabilities of CRAFTI measurements, including simultaneous measurement of isomers and a new experimental technique that could measure ions above the mass limit of traditional CRAFTI measurements.

This thesis explores the structures and structural changes of supramolecular host-guest systems, proteins, and other small molecules in the gas phase, utilizing a combination of computational modeling and experimental data. The primary instruments employed were a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) and an ion mobility mass spectrometer (IM-MS). In the IM-MS experiments, the focus was on investigating the binding behavior of cyclodextrin macrocycles—specifically α, β, and γ-cyclodextrin—with per-fluoroalkane substances (PFAS), which are pervasive environmental contaminants. This investigation involved measuring ion-neutral collision cross sections and using computational modeling to determine whether PFAS compounds bind inside or outside the cyclodextrin cavity. The results indicate that only β-cyclodextrin binds PFAS compounds internally, attributed to its seven-fold symmetry and the localized hydrogen bonding network across the macrocycle's secondary face. Conversely, α and γ-cyclodextrin appear to favor collapsing inward, enhancing internal hydrogen bonding while keeping the PFAS bound externally. The FTICR-MS instrument was used for time-resolved CRAFTI (TR-CRAFTI) collision cross section measurements on various systems, including tetraalkylammoniums (TAA), cytochrome C, and β-cyclodextrin host-guest complexes. This involved activating gas-phase ions using sustained off-resonance irradiation (SORI) activation, followed by a variable delay for collisional cooling. Subsequently, a CRAFTI measurement was conducted to obtain a timeresolved view of the collision cross section. Initial findings suggest the feasibility of measuring and modeling structural changes post-activation over varying time scales, ranging from approximately 100 milliseconds to 10 seconds, depending on the size and complexity of the system being studied.

Dans ce travail de thèse, la photoionisation en couche K d’ions multichargés a été étudiée ainsi que la photoionisation en couche de valence d’ions atomiques et de petits ions moléculaires. Les sections efficaces de photoionisation en couche K ont été mesurées pour les ions de la série iso-nucléaire de l’azote, de N+ à N4+, en utilisant le montage de faisceaux ion-photon colinéaires, et la photoionisation en couche de valence des ions Xe+ et Kr+ et des petits ions moléculaires CO2+ et N2+ en utilisant à la fois la technique de faisceaux colinéaires et un piége à ions . Toutes les expériences ont utilisé le rayonnement synchrotron émis par l’anneau de stockage SOLEIL à Saint-Aubin, France. La combinaison des deux techniques permet la mesure sur une échelle absolue des sections efficaces de photoionisation des ions dans l'état fondamental pur.Les sections efficaces expérimentales de photoionisation en couche K sont comparées aux résultats théoriques existants utilisant différentes méthodes : Multi-Configuration Dirac–Fock (MCDF), R-matrice et la Constante d’Ecran par Unité de charge Nucléaire (SCUNC). L’interaction entre l’expérience et la théorie a permis l’identification et la caractérisation des résonances 1s→2p et 1s→3p observées dans les spectres. Les sections efficaces expérimentales de photoionisation en couche de valence mesurées pour les ions Xe+ et Kr+ ont été comparées aux résultats de calculs MCDF obtenus pour le processus de photoionisation directe.La qualité des mesures absolues de section efficace utilisant la technique de faisceaux colinéaires est fortement dépendante de la performance de la source d’ions ECR (Electron Cyclotron Resonance). Afin d'améliorer le courant d'ions dans la région d'interaction, différents systèmes d'extraction des ions à deux et trois électrodes ont été simulés en utilisant les programmes ECRopt et IGUN. / In this thesis work, the K-shell photoionization of multi-charged ions has been studied as well as the valence photoionization of atomic and small molecular ions. The K-shell photoionization cross sections were measured for nitrogen iso-nuclear series, from N+ to N4+ ions using the ion–photon merged beam technique and the valence photoionization cross sections for Xe+ and Kr+ ions and the small molecular ions CO_2^+ and N_2^+ using both the merged beam and ion trap techniques at the SOLEIL synchrotron radiation facility in Saint–Aubin, France. Combination of the two techniques allows for the measurement of the pure ground state ionization cross section on an absolute scale.The experimental K-shell photoionization cross sections are compared with theoretical results obtained from the multi-configuration Dirac–Fock (MCDF), R-matrix and the Screening Constant by Unit Nuclear Charge (SCUNC) methods. The interplay between experiment and theory enables the identification and characterization of the strong 1s→2p and 1s→3p resonances observed in the spectra. The experimental valence photoionization cross sections for Xe+ and Kr+ ions are compared with MCDF calculations results obtained for the direct photoionization process. The quality of the absolute cross section measurements using the merged beam techniques is strongly dependent on the performance of Electron Cyclotron Resonance Ion Source (ECRIS). In order to improve the current of ions in the interaction region, the ions extraction system and transport was simulated by using IGUN program and ECRopt.

L'objectif premier de ce travail de thèse était de développer des analyses métabolomiques non ciblées de vins en bouteilles afin de déchiffrer les informations chimiques relatives à l’évolution de leurs compositions avec le temps. Cette recherche initiale était fondée sur l'hypothèse que, lors de l'analyse, les vins en bouteilles gardent une mémoire chimique des paramètres environnementaux à l’œuvre au moment de leur élaboration (gestion du vignoble, pratiques œnologiques, climat, terroir). Une seconde hypothèse reposait sur la nécessité d’étudier le passé pour anticiper l’évolution de la qualité du vin du point de vue de sa composition chimique. À cet effet et pour la première fois dans la science du vin, la Spectrométrie de Masse à Résonance Cyclotronique des Ions et à Transformée de Fourier (FTICR-MS), la Chromatographie Liquide couplée à la Spectrométrie de Masse (UPLC-Q-TOF-MS), la spectroscopie de Fluorescence d’Excitation et d’Émission (EEMF) et les statistiques multivariées ont été combinées. Le développement méthodologique a révélé l'avantage de coupler les mesures de masses exactes par FTICR-MS à la discrimination des isomères par UPLC-Q-TOF-MS afin d'étendre la gamme des métabolites détectables. Ces outils ont été appliqués à l'identification de marqueurs de vieillissement sur des séries verticales de vins rouges et blancs de Bourgogne, y compris sur des vins très anciens (millésimes inconnus) considérés comme des points extrêmes d'évolution, introduisant ainsi la notion de verticalomics. La caractérisation d'une série de vins blancs de Bourgogne (Chardonnay) a révélé que les espaces chimiques spécifiquement liés à des pratiques œnologiques (SO2 ajouté lors du pressurage, niveau de débourbage ou perméabilité du bouchon) pourraient être déchiffrés, bien que les signatures de millésimes étaient les plus significatives. Des expériences similaires sur les vins de Champagne (Chardonnay, et mélanges de Chardonnay, Pinot noir et Pinot Meunier) après la prise de mousse et le vieillissement sur lattes ont mis en évidence l'effet d'hormesis associé à l'oxygénation du vin. Enfin, les analyses non ciblées d'extraits de raisin et des vins correspondants provenant de différentes appellations et élaborés par le même vigneron ont révélé qu’il était possible de lire des signatures liées au terroir, en particulier après quelques années de vieillissement en bouteille. Plus largement, nos résultats fournissent une description globale sans précédent de la composition chimique du vin et de sa modification par le vieillissement. / The main objective of this work was to develop non-targeted metabolomics analyses of bottled wines in order to decipher chemical informations from the time-related evolution of their composition. This original research was based on the hypothesis that, when analyzed, bottled wines would still hold chemical memories of envionmental parameters (vineyard management, oenological practices, climate, terroir…) at the moment of their elaboration, even after several years of ageing. A second hypothesis was that in order to anticipate the future evolution of the wine quality in terms of chemical composition, it is necessary to know what it was in the past. To that purpose, and for the first time in wine science, Fourier Transform Ion Cyclotron Resonance – Mass Spectrometry (FTICR-MS), Liquid Chromatography coupled with mass spectrometry (UPLC-Q-ToF-MS), Excitation Emission Matrix Fluorescence (EEMF) and multivariate statistics were used in combination. Methodological develoments revealed the advantage of coupling exact mass measurements by FTICR-MS to isomeric discrimination by UPLC-Q-ToF-MS in order to extend the range of detectable metabolites. Such tools were applied to the identification of ageing markers in vertical series of red and white wines from Burgundy, including very old wines (unknown vintages) considered as evolution end points, thus introducing the concept of verticalomics. The characterization of series of white wines from Burgundy (Chardonnay) revealed that chemical spaces specifically related to eonological practices (SO2 addition at pressing, settling level, and permeability of the stopper) could indeed be deciphered although the vintage signatures were confirmed to be the most significant. Similar experiments on Champagne wines (Chardonnay, and blends of Chardonnay, Pinot noir and Pinot Meunier) after the "prise de mousse" and the ageing "sur lattes" further highlighted the hormesis effect associated with the oxygenation of wine. Finally, non-targeted analyses of series of grape extracts and corresponding wines from different appelations – though elaborated by the same winemaker – revealed that terroir-related signatures could be indeed read in wines, in particular after a few years of bottle ageing. Altogether our results provide an unprecedented comprehensive description of the chemical composition of wine and its modification through ageing.

Les sols sont le plus grand réservoir de carbone des écosystèmes terrestres, et la minéralisation des matières organiques par l’activité microbienne représente la majeure partie des flux de CO2 émis à la surface des continents.Dans ce travail, nous avons étudié les matières organiques extraites à l’eau (WEOM), qui correspondent à la fraction la plus réactive des matières organiques du sol (MOS). Nos objectifs étaient (i) d’identifier les liens de la dynamique du WEOM avec les communautés bactériennes, et avec les paramètres physico-chimiques du sol ; (ii) de réaliser une caractérisation chimique précise du WEOM.Il existe un lien fort entre la solubilité des MOS et les structures des communautés bactériennes, et une baisse de leur diversité impacte la dynamique des MOS et du WEOM, et provoque une baisse de la minéralisation des matières organiques. Une étude à l’échelle régionale a également permis d’identifier que les taux de MOS et d’argile contrôlent les quantités de WEOM et leur aromaticité. La caractérisation au niveau moléculaire a montré la présence d’un grand nombre de molécules ubiquistes dans le WEOM. À partir de ces analyses, nous avons également pu décrire les effets du couvert végétal et des propriétés physico-chimiques des sols sur la composition chimique du WEOM. / Soils are the greatest reservoir of C on the continents, and organic matter mineralisation bymicrobial activity represents the major part of the CO2 emitted by terrestrial ecosystems.In this work, we studied water-extractable organic matter (WEOM), which corresponds to themore reactive fraction of soil organic matter (SOM). Our objectives were (i) to identify therelationships of WEOM dynamics with bacterial communities, and with soil physico-chemicalparameters; (ii) to provide a precise chemical characterisation of WEOM.There is a strong link between SOM solubility and the structure of bacterial communities, andan erosion of their diversity has an impact on SOM and WEOM dynamics, and leads to adecrease in organic matter mineralisation. A study at the regional scale then allowed us to identifythat the SOM and clay contents control the quantities of WEOM and its aromaticity. TheWEOM characterisation at the molecular level revealed the presence of a large number ofubiquitous molecules in the WEOM. Based on these analyses, we were also able to describe theeffects of vegetation and soil physico-chemical properties on the chemical composition ofWEOM.

In this thesis work, the K-shell photoionization of multi-charged ions has been studied as well as the valence photoionization of atomic and small molecular ions. The K-shell photoionization cross sections were measured for nitrogen iso-nuclear series, from N+ to N4+ ions using the ion-photon merged beam technique and the valence photoionization cross sections for Xe+ and Kr+ ions and the small molecular ions CO_2^+ and N_2^+ using both the merged beam and ion trap techniques at the SOLEIL synchrotron radiation facility in Saint-Aubin, France. Combination of the two techniques allows for the measurement of the pure ground state ionization cross section on an absolute scale.The experimental K-shell photoionization cross sections are compared with theoretical results obtained from the multi-configuration Dirac-Fock (MCDF), R-matrix and the Screening Constant by Unit Nuclear Charge (SCUNC) methods. The interplay between experiment and theory enables the identification and characterization of the strong 1s→2p and 1s→3p resonances observed in the spectra. The experimental valence photoionization cross sections for Xe+ and Kr+ ions are compared with MCDF calculations results obtained for the direct photoionization process. The quality of the absolute cross section measurements using the merged beam techniques is strongly dependent on the performance of Electron Cyclotron Resonance Ion Source (ECRIS). In order to improve the current of ions in the interaction region, the ions extraction system and transport was simulated by using IGUN program and ECRopt.

Beryllium-7 (Be-7) only decays by electron capture into lithium-7 (Li-7) with a half life of 53 days. We study the effect of ionization on this decay rate. We do so by trapping a Be-7 ion plasma in a cylindrical Malmberg-Penning trap and measuring Be-7 and Li-7 concentrations as functions of time by using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). We have simulated these signals in a 2-dimensional electrostatic particle-in-cell (PIC) code. The two spectrum peaks merge at high ion densities whereas at low ion densities they can be resolved. The merged peak shifts linearly according to the relative abundances of these species. We have also simulated singly-ionized beryllium-7 hydride (BeH+) and Li-7 ion plasmas at high densities. These two separate peaks shift according to their relative abundances. We describe an analytical model that explains how these peaks shift.

In der vorliegenden Arbeit werden Möglichkeiten der Stabilisierung und die photokatalytische Aktivität von Polymorphen des Bismut(III)-oxids, synthetisiert ausgehend von nanoskaligen, polynuklearen Bismutoxidoclustern, beschrieben. Hydrolyse- und Kondensationsstudien werden mit dem Ziel der Aufklärung von Bildungsprozessen von Bismutoxidoclustern ausgehend von bismutnitrat- und bismutsilanolathaltigen Lösungen durchgeführt. Basierend auf polynuklearen Modellverbindungen wird durch deren Hydrolyse und anschließende thermische Behandlung die Darstellung von Nanopartikeln von verschiedenen Polymorphen des Bismut(III)-oxids erreicht. Die Reaktivität der synthetisierten β Bi2O3 Nanopartikel wird zur Synthese von Verbindungen vom Sillenit-Strukturtyp ausgenutzt. Diese Verbindungen sind isostrukturell zum metastabilen γ-Bi2O3. Die isolierten oxidischen Materialien weisen eine hohe photokatalytische Aktivität gegenüber wässrigen Rhodamin B Lösungen bei der Bestrahlung mit sichtbarem Licht auf. Für die β Bi2O3 Nanopartikel wird ebenso die photokatalytische Aktivität gegenüber wässrigen Farbstofflösungen von Indigokarmin, Orange G, Methylorange und Methylenblau sowie wässrigen Schadstofflösungen von Phenol, 4-Chlorphenol, 2,4-Dichlorphenol, 4-Nitrophenol, Triclosan und Ethinylestradiol beschrieben. Die Charakterisierung der synthetisierten Verbindungen erfolgte unter anderem mittels Einkristall-Röntgenstrukturanalyse, Röntgenpulverdiffraktometrie, NMR-Spektroskopie, FTICR-ESI-Massenspektrometrie, UV/Vis-, Infrarot- und Ramanspektroskopie sowie thermischen Analysemethoden. / The present essay describes the stabilization and photocatalytic activity of different polymorphs of bismuth(III) oxide which were prepared starting from nanoscaled, polynuclear bismuth oxido clusters. Hydrolysis and condensation processes of bismuth nitrate as well as bismuth silanolates in solution were performed to provide an insight into the formation process of bismuth oxido clusters. Nanoparticles of different polymorphs of bismuth(III) oxide were obtained by hydrolysis, followed by annealing steps at temperatures of 370 °C and 600 °C starting from polynuclear bismuth compounds, respectively. The high reactivity of the as-prepared β-Bi2O3 nanoparticles was used to synthesize sillenite-type compounds at rather low temperatures which are isostructural to metastable γ-Bi2O3. The isolated oxidic materials show promising photocatalytic activities exemplified by the degradation of aqueous Rhodamine B solutions under visible light irradiation. Additionally, the β- Bi2O3 nanoparticles were tested in photodegradation processes of aqueous solutions containing different dyes such as indigo carmine, orange G, methyl orange and methylene blue as well as typical organic pollutants such as phenol, 4-chlorophenol, 2,4-dichlorophenol, 4-nitrophenol, triclosan and ethinyl estradiol. The characterization of the as-prepared materials was performed using single crystal X-ray diffraction, powder X-ray diffraction analysis, NMR spectroscopy, FTICR- electrospray ionization mass spectrometry, UV/Vis-, IR- and Raman spectroscopy, electron microscopy, nitrogen physisorption as well as thermal analyses.