Structure determination of macromolecular protein assemblies remains a challenge for well-established experimental methods. In this thesis, an emerging structural technique, ion mobility-mass spectrometry (IM-MS) is explored. An assessment of collision cross section (CCS) measurement accuracy using travelling-wave IM (TWIMS) instrumentation was carried out (Chapter 3). Through the collation of a protein complex CCS database and the development of a calibration framework for TWIMS, significant improvements to CCS measurement accuracy have been achieved. Next, the advantages and limitations of using IM-MS to generate restraints for structure characterisation were explored. Computational tools designed to exploit IM-MS data for structural modelling were developed and tested on a training set of systems (Chapter 4). These include two heteromeric protein complexes, and an oligomeric intermediate involved in beta-2-microglobulin aggregation. Further structural information can be attained by using gas-phase dissociation techniques, such as collision-induced dissociation (CID). The effects of charge state on CCS and the gas-phase dissociation pathway of complexes were investigated (Chapter 5). This highlighted the possibility of using CID in conjunction with supercharging to manipulate dissociation pathways to achieve more useful structural information. Finally, the gas-phase structures of globular and intrinsically disordered protein complexes were probed by IM-MS and molecular dynamics (MD) simulations (Chapter 6). Experimental observations were recapitulated remarkably closely by simulations, including gas-phase structural collapse and the ejection of monomer subunits when the energy of the system was increased sufficiently. Overall, this research has contributed to the IM-MS field by providing the framework for improved CCS measurements of large protein complexes and the use of restraints from IM-MS for structural modelling. Significantly, IM-MS has been used in combination with charge manipulation, CID and MD simulations to reveal further insights into the gas-phase structures, stabilities and dissociation pathways of multimeric protein complexes.

Ion mobility (IM) spectrometry is a gas-phase electrophoretic technique in which ions are separated on the basis of their relative mobility in the presence of a weak electric field gradient and a buffer gas. Ion mobility-mass spectrometry (IM-MS) has the capability of separating ions based on m/z, size and shape, providing additional structural information compared to using mass spectrometry on its own. In this thesis, IM-MS has been used to investigate organic and organometallic complexes and identify reactants, intermediates and products in reaction mixtures. Collision cross sections (CCS) have been measured for three salen ligands, and their complexes with copper and zinc using travelling-wave ion mobility-mass spectrometry (TWIMS) and drift tube ion mobility-mass spectrometry (DTIMS), allowing a comparative size evaluation of the ligands and complexes. CCS measurements using TWIMS were determined using peptide and TAAH calibration standards with good intra-day and inter-day reproducibility. TWIMS measurements gave significantly larger CCS than DTIMS derived data in helium, indicating that the choice of calibration standards is important in ensuring the accuracy of TWIMS derived CCS measurements. The CCS data obtained from IM-MS measurements have been compared to CCS values obtained from X-ray coordinates and modelled structures. The analysis of small organic and organometallic molecules has been extended to investigations of the potential of IM-MS for reaction monitoring and structural studies of the components of catalytic cycles. Reaction mixtures of an organocatalysed Diels-Alder cycloaddition reaction have been monitored using IM-MS and high-field asymmetric waveform ion mobility-mass spectrometry (FAIMS-MS). Reactant, product, catalyst and reaction intermediates, including an intermediate not previously detected, were identified and the catalyst and intermediates monitored over time. An organometallic catalytic cycle using a palladium catalyst has been analysed using IM-MS and the CCS of reactants, intermediates and products have been measured and compared to theoretical CCS calculations. Good agreement was observed between measured and calculated data. Species not amenable to electrospray ionisation were covalently bound to an ionisable tag containing a quaternary ammonium ion allowing the tagged molecules to be detected by IM-MS.

This dissertation presents efforts to expand the role of mass spectrometry (MS) in structural biology. Determination of quaternary structure of a protein complex has been hindered by limited fragmentation from collision-induced dissociation (CID). As an alternative, surface-induced dissociation (SID) was implemented for a quadrupole - time-of-flight instrument in the Wysocki laboratory. This research tested the hypothesis that SID should produce fragmentation reflective of subunit organization. Furthermore, ion mobility (IM) was used to prove the direct relationship between precursor conformation and observed dissociation patterns, and the relationship between activation and product ion conformation. The structure and dynamics of a dimeric small heat shock protein (sHSP) with no solved structure was investigated. The importance of N- and C-terminal domains for dimerization was determined, and the dimers were shown to exchange subunits. From exchange kinetics it is proposed that subunit exchange is unrelated to heat shock activity. SID was used to elucidate the subunit architecture of heterogeneous protein assemblies, including one previously solved protein structure and two formerly uncharacterized proteins. The heterohexamer toyocamycin nitrile hydratase dissociated into trimers, revealing the hexamer to be a dimer of trimers. The bacterial ribonuclease toxin:antitoxin tetramer was shown to have an antitoxin dimer at its core, with flanking individual toxin subunits. The examples presented here are the first clear proof that SID results can clearly indicate the substructure of a protein assembly.IM was used to study the conformation of precursor and product ions. A greater understanding of the relationship between precursor conformation and observed dissociation patterns was developed. Different charge states of a dodecameric sHSP were found to have significantly different conformations, which were directly reflected in SID spectra. IM comparison of CID and SID product ions showed that the same charge state of a product ion from either method has the same CCS. This suggests the product ion conformation is dependent upon ion charge state, and independent of activation method and collision energy. The cause and effect relationship between precursor conformation and MS/MS patterns, and activation and product ion conformation were clearly illustrated. Together, this body of research expands the role of MS for structural biology.

The use of laser desorption as a sample introduction method for solid phase microextraction (SPME) has been investigated in this research project. Three different types of analytical instruments, mass spectrometry (MS), ion mobility spectrometry (IMS) and gas chromatography (GC) were employed as detectors. The coupling of laser desorption SPME to these three instruments was constructed and described in here. <br /><br /> Solid phase microextraction/surface enhanced laser desorption ionization fibers (SPME/SELDI) were developed and have been coupled to two IMS devices. SPME/SELDI combines sampling, sample preparation and sample introduction with the ionization and desorption of the analytes. Other than being the extraction phase for the SPME fiber, the electro-conductive polymer coatings can facilitate the ionization process without the involvement of a matrix assisted laser desorption/ionization (MALDI) matrix. The performance of the SPME coatings and the experimental parameters for laser desorption SPME were investigated with the SPME/SELDI IMS devices. The new SPME/SELDI-IMS 400B device has a faster data acquisition system and a more powerful data analysis program. The optimum laser operation parameters were 250 <em>&mu;J</em> laser energy and 20 <em>Hz</em> repetition rate. Three new SPME coatings, polypyrrole (PPY), polythiophene (PTH) and polyaniline (PAN) were developed and evaluated by an IMS and a GC. The PPY coating was found to have the best performance and was used in most of the experiments. The characteristics of the PPY and the PTH SPME/SELDI fiber were then assessed with both IMS and MS. Good linearity could be observed between the fiber surface area and the signal intensity, and between the concentration and the signal intensities. <br /><br /> The ionization mechanism of poly(ethylene glycol) 400 (PEG) was studied with the SPME/SELDI-IMS 400B device. It was found that the potassiated ions and sodiated ions were both present in the ion mobility spectra. The results obtained with quadrupole time-of-flight (QTOF) MS confirmed the presence of both potassiated and sodiated ions. This result suggested that cationization is the main ionization process when polymers are directly ionized from the PPY coated silica surface. Four PEGs with different average molecular weights and poly(propylene glycol) 400 were also tested with this SPME/SELDI device. The differences between the ion mobility spectra of these polymers could be used for the fast identification of synthetic polymers. <br /><br /> The SPME/SELDI fibers were then coupled to QTOF MS and hybrid quadrupole linear ion trap (QqLIT) MS, respectively. Improved sensitivity could be achieved with QqLIT MS, as the modified AP MALDI source facilitated the ion transmission. The application of method for analysis of urine sample and the bovine serum albumin (BSA) digest were demonstrated with both PPY and PTH fibers. The LOD for leucine enkephalin in urine was determined to be 40 <em>fmol &mu;L^-1</em> with PTH coated fiber; and the LOD for the BSA digest was 2 <em>fmol &mu;L^-1</em> obtained with both PTH and PPY fibers. <br /><br /> A new multiplexed SPME/AP MALDI plate was designed and evaluated on the same QqLIT MS to improve the throughput, and the performance of this technique. The experimental parameters were optimized to obtain a significant improvement in performance. The incorporation of diluted matrix to the extraction solution improved the absolute signal and S/N ratio by 104X and 32X, respectively. The incorporation of reflection geometry for the laser illumination improved the S/N ratio by more than two orders of magnitude. The fully optimized high throughput SPME/AP MALDI configuration generated detection limit improvements on the order of 1000-7500X those achieved prior to these modifications. This system presents a possible alternative for qualitative proteomics and drug screening. <br /><br /> Laser desorption SPME as a sample introduction method for the fast analysis of non-volatile synthetic polymers was also demonstrated here. The coupling of laser desorption SPME to GC/FID and GC/MS was performed, and the advantage of laser desorption over traditional thermal desorption was demonstrated in this research. Laser desorption PEG 400 was observed more effcient than thermal desorption. Good separation was obtained even with a 1-m or 2-m column. These results demonstrate the potential of laser desorption SPME as a sample introduction method for the fast GC analysis of non-volatile compounds such as synthetic polymers.

In this dissertation, the ion mobility technique is used to determine the structures of small acetylene cluster ions, (C2H2)1-3+, mass-selected from the largest ever reported ionized acetylene clusters. The technique is also used to characterize the reaction of acetylene clusters with water in an effort to elucidate thermochemistry and kinetics of some interesting ion-molecule reactions suspected to occur in interstellar clouds and other interplanetary bodies.A combination of ion mobility measurements, collision induced dissociation (CID), and theoretical calculations are used to provide the most conclusive evidence for the frequently hypothesized trimerization of ionized acetylene to form the benzene ion. The results also provide evidence for the isomerization of the acetylene dimer ion, (C2H2)2+, to form the cyclobutadiene and vinylacetylene ions.Investigation of the reactions of acetylene radical ions (C2H2∙+) with water reveals competing kinetics for two primary, C2H4O∙+ and C2H3O+, and a secondary, H+(H2O)n, product with an overall reaction rate coefficient of 2.0 × 10-11 cm3s-1. By comparing experimentally observed reactions to theoretically (G3MP2) predicted thermochemistry, the C2H4O∙+ ion is suggested to be the ethenolium ion (vinyl alcohol ion, CH2CHOH∙+) and the C2H3O+ ion is suggested as either the 1-hydroxy-ethenylium (CH2COH+) or cyclic 2H-oxirenium (c-CH2CHO+) ion. Investigation of the temperature dependence of the equilibrium constant for the association reaction (C2H2)3 + + (H2O)n-1 ↔ (C2H2)3∙+(H2O)n using the van't Hoff plot revealed binding energies and reaction entropies identical to those recently published for the benzene+/water system thus providing even more evidence for the formation of benzene ions from ionized acetylene clusters.We also provide a density functional (UB3LYP/Wachters+ f) investigation of Fe+, Co+, and Ni+(C2H2)n clusters (where n = 1-3) to supplement mass spectrometric analysis of the acetylene-solvated cations. For the Co+(C2H2)n clusters, the mass spectrum revealed an intriguing behavior of oscillating magic numbers which we suspect to be the consequence of a Co+-mediated polymerization reaction to form covalent Co+CnHn complexes. The UB3LYP/Wachters+f predicted barrier and exothermicity for the initial step of the proposed trimerization reaction are 25.4 and 101.4 kcal/mol respectively. Our results suggest the efficiency of this reaction is facilitated by cooperative interactions and favorable orientations of acetylenes in the cluster.

In this dissertation, the ion mobility mass spectrometry technique is used to study the possible mechanisms of formation of polyaromatic hydrocarbons (PAHs) and polyaromatic nitrogen-containing hydrocarbons (PANHs) via the ion-molecule reactions of acetylene neutrals with different aromatic cations, in order to infer the possible mechanisms of formation of PAHs and PANHs in different environments such as interstellar media under different ionizing conditions. Furthermore, this technique is used to probe structures, address the thermochemistry, and measure the kinetics of the product ions originated from these reactions. Reactions of benzene radical cations with acetylene produce styrene and naphthalene-type cations at high temperatures. The second order rate constant of this reaction is found to be in the order of 10-14 cm3.s-1 with a barrier of 3.5 kcal.mol-1. Under low temperature regime, benzene radical cation acts as a catalyst to initiate the formation of higher complex hydrocarbons through the associative charge transfer to the acetylene clusters, (C2H2)n+, n= 6-10. Phenylium cation reactions with acetylene is found to be four orders of magnitudes faster than those of benzene radical cation, as predicted theoretically. In these systems the second addition of acetylene molecule is found to follow the Bittner-Howard mechanism. Phenylacetylene and styrene radical cations reactions with acetylene are also studied and the addition of one acetylene molecule to the radical cation is observed. The second order rate constant of the product ions is found to be in the order of 10-13 and 10-14 cm3.s-1 for the phenylacetylene and styrene radical cations respectively. Ion molecule reactions of pyridine cation, benzonitrile cation and pyrimidine radical cation with acetylene are studied. Formation of complex organics with fused nitrogen atom in an aromatic ring is reported. Condensation products of acetylene via the ion-molecule reactions are observed with pyridine cation of up to five acetylene molecules onto the pyridine cation at room temperature. Meanwhile, condensation of only two acetylene molecules is observed for benzonitrile cation and pyrimidine radical cation respectively. In the later case, these condensation reactions are observed with hydrogen abstraction. Ion mobility measurements, collisional induced dissociation (CID) and ab initio calculations are combined to probe the possible structures of the reaction products. Formation of PAHs over nanoparticle surfaces is carried out by studying polymerization of acetylene over Pd nanocatalyst and supported Pd nanocatalyst over MgO and CeO2 prepared by the LVCC technique under different temperature conditions. C8H10 species are formed at 400 oC. However, at 600 oC, production of C16H10 (pyrene isomer) is found to be the major catalytic product. Self polymerization of acetylene at different temperatures is presented as well. Our results of the ion-molecule reactions, associative charge transfer (ACT) and catalytic polymerization over catalysts surfaces’ of acetylene interacting with different aromatic and heterocyclic cations could explain the different possible pathways of formation of complex organics in different ionizing environments in carbon-rich interstellar media in space.

Characterizing the interactions of solvent molecules with ions is fundamental in understanding the thermodynamics of solution chemistry. These interactions are difficult to observe directly in solution because the number of solvent molecules far exceed that of ions. This lend the gas phase to be the ideal medium in the study ion-solvent interactions on a molecular level. Ionized polycyclic aromatic hydrocarbon (PAH) molecules can readily form hydrogen bonds with neutral solvent molecules in aqueous and interstellar medium. Previous research has been done for stepwise solvation of small molecules such as benzene+, pyridine, and phenylacetylene. The similarity in these results show that these organic ions can be considered prototypical model systems for aromatic ion-neutral solvent interactions. The goal of this dissertation is to demonstrate that naphthalene can act as a prototypical model of PAH ions for ion-solvent interactions. Two types of experiments are considered throughout this dissertation using ion mobility mass spectrometry: (1) ion-neutral equilibrium thermochemistry and (2) mobility measurements. For thermochemistry experiments, the naphthalene radical cation was injected into the drift cell containing helium and/or neutral solvent vapor and the enthalpy and entropy changes were measured by varying the drift cell temperature and measuring the equilibrium constants. The results of these studies showed that small polar molecules bind to naphthalene with similar energy based on the measured by the enthalpy changes. Unsaturated aliphatic molecules behave similarly, but with much lower binding energy. Aromatic ions tend to bind to the naphthalene with lower binding energy than that observed with the benzene ion. The results for small polar molecules were compared to similar studies using the phenyl cation. The second series of experiments required the coexpansion of the naphthalene and benzene or pyridine. Injecting theses dimers into the drift cell allowed the measurement of reduced mobility on the dimers at a series of temperatures. These were used to calculate the average collision cross section and thus give insight in to the structure of these aromatic dimers. Structures were determined by comparing these results to those predicted by DFT calculations.

La spectrométrie de masse tandem est une technique analytique versatile, notamment utilisée dans le champ de la protéomique pour dériver la séquence de peptides. Cette thèse vise à contribuer au développement de méthodes intégrées à la spectrométrie de masse afin d’apporter des informations structurales sur les ions moléculaires, intermédiaires réactionnels ou produits de réactions. La fragmentation des peptides protonés est induite par collisions avec une gaz rare (CID). Des multiples fragments sont observés et la séquence peptidique peut être dérivée de la mesure de la masse de séries d’ions analogues. Les mécanismes de fragmentation par CID des peptides protonés sont très complexes, constituant un champ de recherche important. Dans ce contexte, le couplage de deux techniques comme la spectrométrie de masse et la spectroscopie infrarouge a été utilisé pour caractériser des ions fragments (an et bn) de peptides. Divers signatures infrarouges identifiées dans les gammes spectrales 1000-2000 et 3000-3800 cm-1 et caractéristiques de différents motifs structuraux ont mis en évidence la permutation de la séquence de la chaîne peptidique pour les ions an. Dans le cas des ions bn, la formation d’une structure macrocyclique s’appuie sur la formation spécifique d’un complexe produit d’une réaction avec NH3, que nous avons caractérisé par spectroscopie infrarouge. L’objectif ultime de cette thèse était de mettre en place une approche multimodale sur un spectromètre de masse unique, intégrant la séparation par mobilité ionique et la spectroscopie infrarouge d’ions moléculaires en permettant la caractérisation structurale par spectroscopie infrarouge des ions simultanément sélectionnés en masse et par mobilité ionique. La technique de mobilité ionique mise en œuvre est de type « Differential Ion Mobility spectrometry » (DIMS). Nous aurions souhaité pouvoir exploiter l’IMS sur des ions fragments de peptides, mais la technique DIMS ne le permettait pas. Nous avons choisi d’explorer la séparation et la caractérisation des monosaccharides cationisés par Li+, Na+ et K+. Dans le cas des complexes de Li+, les résultats spectroscopiques et de mobilité ionique sont cohérents avec les structures les plus stables prédites par la théorie. Ces calculs de chimie quantique permettent aussi d’interpréter une signature spectrale spécifique de complexes de Li+ avec des anomères de glucose. / Tandem mass spectrometry is a versatile analytical technique, used in particular in the field of proteomics to derive peptide sequence. This thesis aims to contribute to the development of integrated approaches to mass spectrometry to provide structural information on molecular ions, which can either be reaction intermediates or reaction products. The fragmentation of protonated peptides is induced by multiple collisions with rare gas atoms (CID). Multiple fragments are observed and the peptide sequence is derived from the measurement of the mass difference between two consecutive analogous ions. Fragmentation mechanisms of the protonated peptides under CID conditions constitute an intense research field. In the frame of this PhD thesis, mass spectrometry and infrared spectroscopy were coupled to characterize the fragment ions (an and bn) peptides. Several infrared signatures were found in the 1000-2000 and 3000-3800 cm-1 spectral ranges characteristic of different structural motifs. In the case of the an ions, these IR signatures provide evidence of the permutation of the sequence of the peptide chain. In the case of the middle size bn ions, the formation of a macrocyclic structure relies on the specific formation of an ion-molecule complex with NH3, whose structure has been characterized by IR spectroscopy.The ultimate objective of this thesis was to develop a multimodal approach based on a single mass spectrometer, which incorporates ion mobility spectrometry and infrared spectroscopy in order to characterize the structure of mobility- and mass-selected molecular ions. The ion mobility technique used is the "Differential Ion Mobility spectrometry" (DIMS). Peptide fragment ions could not be studied using this new set-up. We chose to study the separation and characterization of cationized monosaccharides with Li+, Na+ or K+. In the case of lithiated complexes, the spectroscopic and ion mobility data are consistent with the low energy structures predicted by theory, allowing in particular the interpretation of an IR specific signature characteristic of some Li+ complexes of glucose anomers.

A utilização de ozônio como agente oxidante tem apresentado resultados positivos para a degradação de contaminantes orgânicos em subsuperfície. O ozônio apresenta alta reatividade, tanto com os compostos orgânicos de interesse quanto com os compostos inorgânicos presentes no meio, principalmente com os íons metálicos constituintes da matriz sólida, mobilizando os para a água subterrânea. Este estudo detectou e quantificou os íons metálicos de interesse presentes na matriz solida, sendo estes: Fe, Al, Mn, Cr, Pb, Ni e Zn. Também foram determinados os íons que foram mobilizados da matriz sólida, a partir da injeção do ozônio em solo proveniente de uma área contaminada por compostos orgânicos. / The use of ozone as an oxidizing agent has shown positive results for the degradation of organic contaminants in the subsurface. Ozone is highly reactive with both the organic compounds of interest as with inorganic compounds present in the environment, especially with the metal ions of the solid matrix constituents, mobilizing them into groundwater. This study detected and quantified the metal ions of interest present in the solid matrix, namely: Fe, Al, Mn, Cr, Pb, Ni and Zn. lons that have been mobilized from the solid matrix due to the ozone injection in soil from a contaminated area for organic compounds were also determined.

Ion mobility spectrometry is a powerful technique for the study related to molecule. The work of tow major applications are introduced in this paper. The first application is the optimization of parameters in CCS. The accurate calculation of the collision cross section for multiple molecules is a long-time interested topic in the research for substances detection in micro scale. No reliable analytical approach to calculate the collision cross section has been established to date. Different approaches rely on different mechanism will provide different results in significant extent. This work introduce a method for the determination of parameters in the Lennard Jones potential. Experimental data combined with numerical computation was the fundamental strategy during the optimization of the parameters. In the experiment, electrospray is used as the ion source of IMS while a nebulizer was utilized to electrify the aromatic compounds. New parameters show no less accuracy and equal efficiency while can explain the physical meaning of the collision more clearly. The second application is the trace detection of explosives with very low concentration. The detection of explosives is an important topic in security, while the detection will be difficult due to the low vapor pressure of explosives. In this work, two types of devices are designed for the trace detection of explosives at an extremely low concentration. TNT is selected as the explosives in the experiment. The experiment succeed to reach a sensitivity of 1 part per quintillion, and even find out a linear relationship between the logarithm of TNT concentration and TNT vapor pressure.