In this dissertation, I use Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to study the structure and energetics of gas phase ions. Infrared multiphoton dissociation spectroscopy (IRMPD) is a technique for measuring the IR spectrum of gas phase ions in a Penning trap. I use this technique to investigate the conformation of cucurbituril complexes, terminal diamines, and protonated amino acids. Cross sectional areas by Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) is a technique developed by the Dearden lab to measure the cross section of gas phase ions. In this work, I further develop a fundamental understanding of this technique. I investigate the role that dissociation plays in this and other FTICR-MS techniques. I also show that the principles of the CRAFTI technique can be used to measure the pressure inside the cell of an FTICR-MS. This technique, linewidth pressure measurement (LIPS), allows for a quantitative measurement and comparison of CRAFTI cross sections. To demonstrate the improvements to the technique, I measure the CRAFTI cross sections for the 20 standard amino acids and compare these to literature values measured by ion mobility measurements.

This dissertation investigates Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques to study the impact of molecular structure on conformation and binding energetics. A novel method to determine collison cross sectional areas using FTICR (CRAFTI), initially developed by the Dearden lab, was applied to study the conformations of molecular systems with unique structural attributes in an attempt to explore the molecular range of CRAFTI. The systems chosen for CRAFTI studies include crown-ether alkylammonium complexes and biogenic amino acids. The results were found to be consistent with expected behavior, and strongly correlated with experimental measurements made using ion mobility spectrometry (IMS) and predictions from computations. The analytical sensitivity of CRAFTI was highlighted by its ability to distinguish the normal and branched structural isomers of butylamine. Besides conformation characterization, quantitative evaluation of binding was undertaken on metal ion-cryptand complexes on the FTICR instrument using sustained off-resonance irradiation-collision-induced dissociation (SORI CID) method. Complex formation and dissociation was found to be a strong function of both guest and host sizes which impacted steric selectivity, and polarizability. The results demonstrate the ability of FTICR to simultaneously determine structure, conformation and binding thereby providing comprehensive molecular characterization.

The use of mass spectrometry in the biosciences has undergone huge growth in re- cent years due to sustained effort in the development of new ionisation techniques, more powerful mass analysers and better bioinformatic tools. These developments mean that it is now possible to introduce complex crude biological-mixtures into a mass spectrometric platform and to obtain detailed information about the sample. The front-end sample handling techniques used for sample preparation have, for the most part, not changed despite the recent advances in hyphenation of liquid- chromatography and mass spectrometry required to tackle the issue of increased sample complexity. In this thesis the possibility of using Digital Microfluidics (DMF) for front-end sample preparation prior to mass-spectrometric analysis of protein samples has been investigated. DMF is a micro-electromechanical system (MEMS) technology used for manipulation of sub-microlitre droplets. The movement of discrete droplets of liquid is exploited using the Coulombic forces arising due to free charge polarisation. Droplets can be split, joined, dispensed and moved over a sub-surface electrode array. In this thesis a range of DMF devices have been designed, manufactured and coupled with mass spectrometric platforms for protein analysis. A variety of techniques for mass spectrometry- based analysis of biological samples from the fluidic chips have been investigated. A robotic system has been developed to automate sample introduction, manipulation and removal. Finally the application of on-chip sample purification and enzymatic digestion have been demonstrated, providing proof of concept for digital microfluidic sample preparation in mass spectrometry-based proteomics.

Humic substances (HS) are described as a complex mixture of organic molecules formed by incomplete decomposition of plant, animal and microbial matter. They are found in soil, water and air and have many environmental roles, e.g. water retention and metal ion binding in soil. Despite their importance, the molecular composition of HS is poorly understood. This is mostly because of an inability to separate individual molecules from these complex mixtures and then characterise them by standard analytical methods such as NMR and MS. In order improve the understanding of these important mixtures I have studied them using a high-resolution analytical method, Fourier transform ion-cyclotron resonance mass spectrometry (FTICR MS). Initial efforts focussed on testing the, fast, automated data analysis of the large data sets produced. Two pieces of software were compared and the reliability of the formulae assigned by these was critically evaluated. This confident formula assignment was then applied to study the consequences of different ionisation and instrumental parameters on the mass spectra obtained. The use of laser desorption/ionisation (LDI) without the need to employ a matrix required in matrix assisted laser desorption/ionisation (MALDI) was explored. A comparison of LDI and electrospray ionisation (ESI) FTICR MS of natural organic matter samples showed that these methods ionise complementary sets of compounds. The LDI ionised compounds were characterised as aromatics or condensed aromatics and compounds belonging to lower oxygen classes (maximum number at O8), while ESI ionised higher oxygen classes (maximum number at O16) with a vast majority of compounds classified as aliphatic based on their modified aromaticity index. MALDI and LDI spectra produced very similar data with over 90% matching formulas implying that fragmentation is not caused by LDI, as taught previously. My work showed that to maximize the coverage by FTICR MS of the molecular space occupied by these complex mixtures, multiple ionization methods must be used. As a particularly convenient and readily deployable ionization technique, LDI should be included in standard analytical protocols for FTICR MS analysis of NOM. I have explored different parameters and experimental settings to obtain a fuller coverage of the molecular space of NOM, this showed that different experimental conditions enhance peak intensities in different m/z regions of the FTICR MS spectra and that information can be obtained outside of the narrow 200-700 m/z window. To gain chemical and structural information about humic substances beyond what is currently known, experiments aimed to label HS using different isotopes and at specific sites were developed and tested. Two methylation reactions were of particular interest. A methylation that selectively targeted carboxylic acid groups and incorporated deuterium in the form of CD3 groups. An international standard, Suwannee River fulvic acid, was methylated and analysed by high-resolution mass spectrometry in order to gain information on the number and distribution carboxylic acid groups. This proved challenging due to the reactivity of the unknown molecules being difficult to determine in advance. Additionally, the peak separation being reduced to as low as 1.5 mDa pushed the instrument resolution and assignment confidence to their limits. The second methylation method explored used 13CH3I, a nonselective agent reacting with any labile proton, particularly attaching 13CH3 groups to carboxylic, phenolic and alcoholic OH groups. I prepared a methylated sample of fulvic acid from a Red Moss raised bog (Balerno, near Edinburgh) ready for analyses by high field NMR. This investigation yielded structures of a number of phenolic compounds for the first time by NMR.

Dans le cadre de la qualité environnementale des matériaux, il est essentiel d'apporter la preuve que les matériaux à base de ciments adjuvantés ne relarguent pas ou peu de matières organiques lors de leur contact avec l'eau constituant une solution lixiviante. Les additifs organiques, tels que les agents de mouture et les superplastifiants, constituent deux classes d'adjuvants organiques utilisés de manière systématique dans la fabrication ou la formulation des matériaux cimentaires, notamment quand ils sont en contact avec l'eau potable (conduites et châteaux d'eau). Pour évaluer le piégeage de ces composés organiques par une pâte de ciment CEM I, cinq montages de lixiviation dynamique CTG-LEACHCRETE ont été mis en place et adaptés pour l'étude de pâtes de ciment formulées avec des adjuvants organiques. La seconde partie de ce travail a pour objectif de mettre au point des techniques analytiques sensibles pour la détection de traces des constituants du superplastifiant et de l'agent de mouture directement dans les produits de la lixiviation de pâtes de ciment (les lixiviats) grâce aux techniques de spectrométrie de masse MALDI-TOF et Py-THM-MS. Enfin, l'application du protocole global de "lixiviation dynamique couplée à la spectrométrie de masse" nous permet d'apprécier la présence des composés organiques suite à des essais de lixiviation de pâtes de ciment formulées avec de l'agent de mouture et du superplastifiant. Cette démarche nous a permis d'obtenir de nombreux résultats donnant des informations sur les mécanismes de piégeage des différents additifs organiques par une pâte de ciment / Evidence that materials used by the industry are not damageable for the environment has become a major issue. In cement industry, organic admixtures such as grinding aids or superplasticizers ar widely used. In particular, they constitute cementitious materials in concrete contacting water like in water pipes and water tower. It is therefore essential to test whether these organic coumpounds are enventually dissolved into water by leaching. In this aim, five different dynamic leaching tests were developed and applied to a CEM I cement paste formulated with organic admixtures. In paralell, highly sensitive analytical methods based on MALDI-TOF and Py-THM-MS mass spectrometry techniques were designed in order to detect traces of leached superplasticizers or grinding aids. The dynamic leaching tests coupled to mass spectrometry allowed us to detect the presence of organic compounds in the leachate, and to better understand the mechanisms involved in the trapping of additives into a cement paste

In my dissertation, I use a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR-MS) to investigate supramolecules. Cross-sectional areas by Fourier transform ICR (CRAFTI), a novel technique for measurements of collision cross sections by FTICR, is demonstrated for the first time. The CRAFTI method measures the total "dephasing cross section" for removal of the ions from the coherent packet in the FTICR cell, including contributions not only from momentum transfer but also from reactive collisions including those leading to collisional dissociation. Experimental CRAFTI collision cross sections correlate linearly with theoretically computed results and with results obtained using ion mobility measurements. Different collision gases, including Xe, N2, Ar, and SF6, are all appropriate for the CRAFTI technique when the experiments are done at proper kinetic energies. The CRAFTI technique was applied to characterize the molecular shape of complexes of alkyl mono- and n-alkyldiamine with cucurbit[n]uril in the gas phase. The CRAFTI results are consistent with corresponding computational geometries. The CRAFTI technique was combined with SORI-CID (sustained off-resonance irradiation collision induced dissociation) for characterization of complexes of α,ω-alkyldiammonium with cucurbit[n]urils (n=5, 7 and 8) and cucurbituril derivatives. The results demonstrate that for bigger cucurbiturils, the complexes have the alkyldiamine tails threaded through the cavity of the host; for smaller cucurbiturils, the complexes have the tails of the alklydiamines external to the portal of the host.Capping molecules for larger CBn to form larger containers were also investigated. Using SORI-CID methods, CB7, a bigger cucurbituril cage, was found to form a more stable complex with Gu+ (guanidinium). Several neutral guests (benzene, fluorobenzene and toluene) were trapped in CB7 cavity to form inclusion complexes.

In this dissertation, I used Fourier transform ion cyclotron resonance mass spectrometry (FTICR) and ion mobility spectrometry (IMS) to study the structure and energetics of supramolecular complex ions in the gas phase. Using the CRAFTI (cross sectional areas by Fourier transform ion cyclotron resonance) technique developed by Dearden’s lab we observed that complexes with alkali cations capping the portals of cucurbit[5]uril (CB[5]) bind halide anions size-selectively in the gas phase. Our data suggest that Cl– binds inside the CB[5] cavity, Br– binds both inside (with Na+ions capping the portals of CB[5]) and outside (when K+caps CB[5]), and I– binds weakly outside. Although geometry optimization at the M06-2X/6-31+G* level of ab initio theory suggests internal anion binding is energetically favored over external binding, we believe the externally-bound complexes observed experimentally must be due to large energetic barriers hindering the passing of large anions through the CB[5] portal, preventing access to the interior. Calculation of the barriers to anion egress using MMFF//M06-2X/6-31+G* theory supports this idea. Collision cross section (CCS) measurements using the CRAFTI method for CB[5] complexes with various alkali metals and different neutral guests (methanol, ethanol, formic acid, and acetonitrile) along with the results of mass spectra from FTICR show that both the sizes and the resulting charge densities of the alkali metal ions affect the relative tendency of the guests to bind inside CB[5]. The CCS values suggest that methanol, formic acid, and acetonitrile are internally bound CB[5] while ethanol is bound outside the CB[5] host. The relative abundances of the paired peaks in the obtained mass spectra indicate that the inclusion of formic acid and methanol are enhanced when K+ ions cap the complexes, whereas the inclusion of acetonitrile is enhanced when Cs+ ions cap the complexes. The relative abundance of ethanol complexes increases when Na+ ions cap the complexes. CRAFTI CCS values for singly- and doubly-charged cucurbit[n]uril (n = 5, 6, and 7), decamethylcucurbit[5]uril (mc5), and cyclohexanocucurbit[5]uril (CB*[5]) complexes of alkali metal cations (Li+-Cs+) show +2 complex ions have CCS values ranging between 94-105% of those of their +1 counterparts (increasing with metal ion size). These results are consistent with CCS values were calculated using the projection approximation (PA). Ion mobility measurements of the same complexes find the CCS of +2 complexes to be in all cases 9-12% larger than those of the corresponding +1 complexes, with little metal ion dependence. Trajectory method (TM) calculations of CCS for the same structures consistently yield values 7-10% larger for the +2 complexes than for the corresponding +1 complexes and little metal ion dependence which agrees with experimental values.

Détermination des interactions microscopiques entre les actinides et les substances humiques présentes dans l’environnementUne quantité pondérable de plutonium a été introduite dans l’environnement lors d’essais nucléaires ou d’accidents civils. Les zones contaminées, nécessitant une surveillance particulière, sont devenues des lieux d’études très intéressants pour comprendre le comportement du plutonium dans l’environnement. Jusqu’à peu de temps encore, il était admis que le plutonium introduit dans les sols était relativement immobile en raison de sa propension à se sorber fortement sur les roches et de sa faible solubilité dans l’eau. Cependant, des études menées sur des zones contaminées montrent que les substances humiques, omniprésentes dans l’environnement, peuvent influencer la spéciation d’un métal et donc sa migration. C’est pourquoi, il est indispensable de connaître l’influence des substances humiques sur la spéciation du plutonium pour comprendre le transport de celui-ci dans un milieu naturel. Toutefois, en raison de la nature complexe et hétérogène de la matière organique naturelle, il est difficile de décrire de façon microscopique les interactions entre substances humiques et le plutonium. En effet, les substances humiques forment un mélange hétérogène de supra-molécules polydispersées produites par des réactions chimiques ou biochimiques durant la transformation naturelle de matière organique animale, végétale ou microbienne.Le but de ces travaux est d’évaluer à l’échelle de moléculaire les phénomènes de complexation des actinides par la matière organique naturelle. Ces recherches s’organisent autour de deux axes : la caractérisation de dizaines de milliers de molécules dans chaque échantillon de substances humiques naturelles et la détermination des molécules responsables de la vectorisation des actinides dans l’environnement.La mise au point d'une méthodologie a permis de mettre en évidence, pour la première fois, quelques molécules responsables de la complexation des actinides dans des échantillons de matière organique naturelle. Les résultats obtenus montrent l’influence de l’origine du prélèvement de la matière organique sur le type de molécules complexantes. Cette étude montre, également, que la vectorisation des actinides par la matière organique résulte d’une interaction avec un ensemble de molécules présentant des affinités plus ou moins forte pour le métal. Ces résultats semblent être en accord avec les modélisations macroscopiques NICA-DONNAN (approches continue) utilisés actuellement. / Large amount of plutonium has been introduced into the environment as a result of nuclear weapons testing, and nuclear power-plant accidents. Contaminated areas, which need a particular survey, have become a very interesting place to study and understand the plutonium behaviour in the environment. Until few years ago, it was admitted that plutonium introduced into subsurface environment is relatively immobile, owing to its low solubility in ground water and strong sorption onto rocks. However, studies of contaminated areas show that humic substances, which are ubiquitous in environment, can alter the speciation of metal ion, e.g. plutonium, and thus their migration. These humic substances are major components of the natural organic matter in soil and water as well as in geological organic deposits such as lake sediments, peats and brown coals. They are complex heterogeneous mixtures of polydispersed supra-molecules formed by biochemical and chemical reactions during the decay and transformation of plant and microbial remains. The knowledge of the impact of humic substances on the plutonium migration is required to assess their transport in natural systems. However, due to the complex and heterogeneous nature of humic substances, there are a lot of difficulties in the description of microscopic interactions. The aim of this PhD thesis is to evaluate as precisely as possible interactions between actinides and humic substances. This work is divided in two parts: on the one hand humic substances will be separated to identify each component, on the other hand the speciation of actinides with characterized humic substances will be studied. In the first part of this study, new methods are developed to study the speciation of actinides with humic substances using two kinds of mass spectrometers: an ICP-MS and a high resolution mass spectrometer using various ionization devices (ESI, APCI, DART, APPI) in order to determine all active molecules for the complexation.In the second part, a new way of humic substances separation had been developed using an electrophoresis capillary apparatus. This efficient separation technique allows to simplify the characterisation of the complex heterogeneous mixtures without changing speciation of the chemical system.This study will lead to point out some molecules responsible for complexation of actinides by the humic substances.

This dissertation investigates non-covalent macromolecular chemistry using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques. The included studies reveal the impact of molecular structure on conformation and binding energetics. Supramolecules that might be too heavy to be dissociated in single collision-induced dissociation (CID) were dissociated using sustained off-resonance collision induced dissociation (SORI-CID) techniques. Relative binding energies and thresholds were evaluated for various macromolecular host-guest systems. Besides the non-covalent binding energies, conformation characterization was undertaken by a novel method to determine collision cross sectional areas using FTICR (CRAFTI, and multi-CRAFTI), initially developed by the Dearden lab. The systems chosen for further understanding of macromolecular interactions include calixarene-alkali metal complexes, cucurbit[5]uril-alkali halide complexes and cryptand-alkali metal complexes. The results were found to be consistent with expected behavior, and strongly correlated with predictions from computations. Size- and shape selectivity, as well as host-guest polarizability, are the main factors that govern the non-covalent macromolecular interactions that control complex conformation and dissociation. The results demonstrate the ability of FTICR to simultaneously determine binding energy, structure and conformation, which are the most important aspects for determination of comprehensive molecular characterization.

This dissertation expounds on the investigations of the structure and chemistry of peptides and supramolecular host-guest systems in the gas phase. These investigations used two different kinds of analytical instrument: Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and ion mobility mass spectrometry (IM-MS, IMS). These investigations were complemented by chemical modeling. The FTICR was used to radially trap ions with its 4.7 T magnet, which allowed the ions to undergo sustained off-resonance irradiation collision-induced dissociation (SORI-CID). A subsequent event then measured the collision cross sections (σ) of the targeted precursor ion and one of the selected product ions. These experiments were repeated multiple times to measure σ for as many precursor/product pairs as possible. A similar kind of experiment was performed in the IM-MS instrument, through in-source collision-induced dissociation and size-based ion separation in the instrument’s mobility region. When the precursor/product σ ratios were compared, the values obtained by both methods were in good agreement with each other. Application of the FTICR-based technique to [2.2.2]-cryptand+Cs+ caused the externally bound Cs+ to migrate into the cryptand’s cavity. Further development of the FTICR-based technique allowed me to perform the post-SORI σ measurements in a time-resolved fashion. Data collected in this manner revealed that collisionally activated peptides refold over a 5 – 10 second timescale, as determined by their σ shrinking with time. These experiments allowed for observation of a peptide refolding. The IM-MS instrument was applied to a supramolecular chemistry problem surrounding cucurbit[7]uril (CB7), and its ability to bind two identical guests within its cavity. Literature precedent and conventional wisdom suggested that only one guest would bind within CB7’s cavity while the other guest would be bound externally. When ion mobility cross sections (Ω) were obtained for [CB7 + Guest2]2+ systems, it was discovered that both guests could be bound within CB7’s cavity. This was possible because the guests possessed the correct shape and chemistry to favor dispersive interactions between CB7’s cavity and the adjacent guest, and ion-dipole interactions with CB7’s carbonyl-lined portal.