Theses (M.S.)--Marshall University, 2006. / Title from document title page. Includes abstract. Document formatted into pages: contains xii, 76 pages. Bibliography: p. 71-76.

With more atoms in a system, coupling between quantum states complicates the system dynamics. We shine intense laser pulses on three systems with increasing complexity: a molecule, a dimer, and a solid. For single molecules, a 400 nm photon excites NO_2 and initiates a dissociation process. We probe the dynamics using a strong laser pulse to ionize the molecule, and detect the resulting electrons and ions. The evolution of the NO-O molecular bond was directly measured in our experiment. For dimers, a laser pulse removes three electrons from (CO)_2. The dimer breaks up into C^+, O^+ and CO^+. Compared to a monomer, CO^{2+} in the dimer has a new prompt dissociation pathway that produces fragments with higher kinetic energy. Calculation shows that the Coulomb field of the neighboring CO^+ modifies the electronic state of the dimer, giving rise to a prompt channel. Coupling between different charge state configurations results in a new dimer electronic state, which leads to dissociation with higher kinetic energy. For solids, coupling among many atoms creates bands and a bandgap that plays the role of the ionization potential and reduces the threshold for electron-hole pair generation. Thus, solids are a good medium for high-order harmonic generation at the high repetition rates needed for frequency combs. We generate up to the 7th harmonic in silicon and zinc oxide with femtosecond pulses from a thulium fiber laser.

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La théorie de la dynamique des processus chimiques élementaires cherche à décrire quantitativement les collisions réactives à l'échelle atomique. Les mouvements des noyaux étant extrêmement difficiles à traiter dans le formalisme quantique, les tomes sont souvent considérés comme des objets classiques. Cepandant, les effets purement quantiques jouent un rôle majeur dans certaines situations, alors que la description classique les néglige. Cette thèse apporte de nouvelles perspectives sur l'inclusion, dans le formalisme clasique, de forts effets quantiques, à savoir la quantification des mouvements internes des réactifs et produits. / The goal of chemical reaction dynamics theory is the quantitative description of reactive molecular collistions at the atomic scale. Since nuclear motions are difficult to study quantum mechanically, nuclei are often considered as classical object. However, quantum effects may play a major role in some situation, and the standard classical description does not take them into account. This thesis brings new perspectives on the inclusion into the classical treatment of one of the strongest qunatum effects, the quantization of reagents and products.

L'anomalie isotopique de l'ozone observée au début des années 1980 a été la première manifestation de fractionnement isotopique indépendant de la masse d'origine chimique. Attribuée au départ, essentiellement au processus de formation de l'ozone, les travaux récents mettent en évidence d'autres contributions telles que la photodissociation. Cette thèse utilise une approche théorique basée sur des calculs ab initio de chimie et dynamique quantique pour déterminer les sections efficaces d'absorption et leurs variations isotopiques. Ces sections efficaces permettent d'étudier la photodissociation de l'ozone par irradiation du soleil (flux actinique) ; ce qui permet une évaluation précise du processus de photodissociation à l'enrichissement isotopique de l'ozone. Ces résultats pourront être intégrés dans un modèle global prenant en compte à la fois les processus de formation et de destruction de l'ozone. / The ozone isotopic anomaly observed in early 1980s has been the first occurance of mass independent fractionation of chemical origin. Assigned first, essentially to the ozone formation process, recent works show additional contributions such as the photolysis process. This thesis uses a theoretical approach based on ab initio quantum chemistry and dynamics computations to obtain the absorption cross sections and their isotopic variations. The absorption cross sections allow to study ozone's photodissociation by solar irradiation (actinic flux) ; which enables an accurate evaluation of the photodissociation process in ozone's isotopic enrichment. Obtained results could be integrated in a global model that takes into account both ozone's formation and destruction processes.

Selective gas-phase dissociation strategies have been developed for the characterization of cross-linked peptides and proteins in quadrupole ion trap mass spectrometers. An infrared chromogenic cross-linker (IRCX) containing a phosphotriester afforded rapid differentiation of cross-linked peptides from unmodified ones in proteolytic digests of cross-linked proteins by selective infrared multiphoton dissociation (IRMPD). Only the cross-linked peptides containing the chromogenic phosphate underwent IRMPD and unmodified peptides were not affected by IR irradiation. IRMPD of IRCX-cross-linked peptides yielded uncross-linked y-ion sequence tags of the constituent peptides due to secondary dissociation of all primary product ions which contained the chromophore, thus allowing successful de novo sequencing of the cross-linked peptides. Peptides cross-linked via a two-step conjugation strategy through the formation of a bis-arylhydrazone (BAH) bond were selectively dissociated by ultraviolet radiation at 355 nm. The BAH-cross-linked peptides could be distinguished from not only unmodified peptides but also dead-end modified peptides based on the selectivity of ultraviolet photodissociation. In a complementary approach, electron transfer dissociation of BAH-cross-linked peptides resulted in preferential cleavage of the hydrazone bond which produced two modified peptides. These modified peptides were subsequently interrogated by CID which allowed for the original site of cross-linking to be pinpointed. IRMPD was implemented in a dual pressure linear ion trap to demonstrate successful photodissociation of peptides having modest absorptivities. Peptides were observed to efficiently dissociation by IR irradiation exclusively in the low pressure cell whereas no dissociation was observed in the high pressure cell due to extensive collisional cooling. IRMPD provided greater sequence coverage of the peptides than CID and yielded product ion mass spectra which were predominantly composed of singly charged product ions which simplified spectral interpretation. IRMPD was further applied for the sequencing of small-interfering RNA. Complete sequence coverage was obtained and the results were compared to CID. / text

Les disques protoplanétaires entourant les jeunes étoiles sont les embryons des systèmes planétaires. A différentes phases de leur évolution, ils peuvent subir d'importantes pertes de masse par photoévaporation : des photons énergétiques, issus de l'étoile centrale ou d'une étoile voisine, chauffe le disque qui perd en masse sous l'échappement des particules. Cependant, ce mécanisme et la physique sous-jacente n'ont que peu été contraints par les observations. Les objectifs de cette thèse sont d'étudier la photoévaporation dans le cas particulier où elle est due à des photons FUV, d'identifier les principaux paramètres physiques (densité, température) et processus (chauffage et refroidissement) impliqués, et d'estimer son impact sur l'évolution dynamique des disques. L'étude repose sur le couplage observations - modélisations des disques photoévaporés par les photons UV en provenance d'étoiles massives proches. Ces objets, appelés "proplyds", ont leur disque entouré d'une large enveloppe nourrie des flots de photoévaporation. A l'aide d'un modèle 1D d'une région de photodissociation, j'ai développé un modèle pour l'émission dans l'infrarouge lointain des proplyds. Ce modèle a été utilisé pour interpréter les observations, issues principalement de Herschel, pour quatre proplyds. Il apparait que les conditions physiques en surface de leur disque sont similaires: une densité de l'ordre de 10 6 par cm cube et une température d'environ 1000 K. Cette température est maintenue par un équilibre dynamique : si la surface se refroidit, la perte de masse diminue et l'enveloppe se réduit. L'atténuation UV produite par l'enveloppe diminue alors et le disque, recevant plus de photons UV, chauffe. La majorité du disque peut s'échapper sous forme de flots de photoévaporation avec des taux de perte de masse de quelques 10 -7 masse solaire par an ou plus, en accord avec les observations précédentes des traceurs du gaz ionisé. A la suite de ce travail, j'ai développé un modèle hydrodynamique 1D pour étudier l'évolution dynamique d'un disque en photoévaporation par un champ de rayonnement externe. [...] / Protoplanetary disks are found around young stars, and represent the embryonic stage of planetary systems. At different phases of their evolution, disks may undergo substantial mass-loss by photoevaporation: energetic photons from the central or a nearby star heat the disk, hence particles can escape the gravitational potential and the disk loses mass. However, this mechanism, and the underlying physics regulating photoevaporation, have not been well constrained by observations so far. The aims of this thesis are to study photoevaporation, in the specific case when it is driven by far-UV photons, to identify the main physical parameters (density, temperature) and processes (gas heating and cooling mechanisms) that are involved, and to estimate its impact on the disk dynamical evolution. The study relies on coupling observations and models of disks being photoevaporated by UV photons coming from neighbouring massive star(s). Those objects, also known as "proplyds", appear as disks surrounded by a large cometary shaped envelope fed by the photoevaporation flows. Using a 1D code of the photodissociation region, I developed a model for the far-IR emission of proplyds. This model was used to interpret observations, mainly obtained with the Herschel Space Observatory, of four proplyds. We found similar physical conditions at their disk surface: a density of the order of 10 6 cm and a temperature about 1000 K. We found that this temperature is maintained by a dynamical equilibrium: if the disk surface cools, its mass-loss rate declines and the surrounding envelope is reduced. Consequently, the attenuation of the UV radiation field by the envelope decreases and the disk surface, receiving more UV photons, heats up. Most of the disk is thus able to escape through photoevaporation flows leading to mass-loss rates of the order of 10 -7 solar mass per year or more, in good agreement with earlier spectroscopic observations of ionised gas tracers. Following this work, I developed a 1D hydrodynamical code to study the dynamical evolution of an externally illuminated protoplanetary disk. [...]

La photopolymérisation radicalaire contrôlée (P2RC) est un domaine en plein essor en science des matériaux. En effet, ce procédé permet d’envisager la synthèse de polymères à architecture complexe dans des conditions douces et constitue une approche de choix pour élaborer des couches de polymères microstructurées. Dans ce contexte, l’extension des techniques RAFT, ATRP et NMP à un mode photochimique est principalement étudiée. Au cours de cette thèse, nous nous sommes intéressés en particulier à la technique de NMP2 (Nitroxide Mediated Phototopolymerization). Typiquement nous avons préparé des alcoxyamines photosensibles pour un contrôle de la polymérisation sous irradiation. Une attention spéciale a été portée sur la compréhension du mécanisme régissant le procédé et sur des relations structure/réactivité. De plus les meilleurs candidats ont été testés en NMP2 et plus particulièrement pour la conception de motifs structurés de polymères sur surface. Enfin, de nouvelles approches ont été explorées pour effectuer une NMP2 avec notamment l’ESCP (Enhanced Spin Capturing Polymerization). / Controlled radical photopolymerization represents a rapidly emerging field in material science. This process is characterized by important advantages and provides the possibility to prepare complex polymer architectures in mild conditions such as patterns. In recent years, the development of controlled radical photopolymerizations, such as RAFT, ATRP and NMP, is recognized as particularly interesting and powerful. In this context, we focused our research to the development of the NMP2 polymerization. In line with this research context, the topic of this thesis was to prepare alkoxyamines for a photochemical control. Particular attention has been focused on understanding the mechanism governing the process and structure/reactivity relationships. In addition, the best candidates were tested in NMP2 process and more particularly to the preparation of polymer patterns on surface. Finally, new approaches have been explored to perform NMP2 such as ESCP (Enhanced Spin Capturing Polymerization).

La spectrométrie de masse est devenue un outil indispensable pour la recherche en protéomique, notamment grâce au développement récent de nouveaux spectromètres de masse comme l’Orbitrap et de nouvelles méthodes de dissociation. La stratégie « bottom-up » (analyse des mélanges de peptides protéolytiques) est la plus utilisée par son efficacement et sa simplicité par rapport à la stratégie top-down (analyse des peptides plus longs ou des protéines intactes), mais cette dernière permet une caractérisation plus complète des isoformes de protéines et des modifications post-traductionnelles.Les méthodes de dissociation utilisant des photons, comme la photodissociation dans le domaine ultra-violet (UVPD) et la dissociation multiphotonique infrarouge (IRMPD), ont reçu une grande attention comme approches alternatives aux méthodes de dissociation par collision. L'absorption du photon UV à haute énergie peut être « diluée » sur l'ensemble du peptide ou de la protéine et provoque une fragmentation étendue du squelette peptidique (liaisons C-C), tandis que les photons IR à faible énergie augmentent progressivement l'énergie interne et dissocient préférentiellement les liaisons amide (C-N) les plus labiles.Cette thèse est centrée sur le développement de méthodes et les applications pour une caractérisation structurale de biomolécules par des méthodes d'activation utilisant des photons. L'intérêt de combiner des photons infrarouges à faible énergie et des photons UV à haute énergie dans un spectromètre de masse Orbitrap, pour la caractérisation de petites protéines, a été évalué. En outre, la dissociation infrarouge multiphotonique a été implémentée dans un piège à ions électrostatique afin d’étendre les méthodes de fragmentation aux macromolécules de très haut poids moléculaires dans le domaine mégadalton. L'une des principales avancées de cette thèse a été d'adapter ces méthodes de spectrométrie de masse aux objets biomoléculaires, allant des petits peptides (dans la gamme de masse de kilodalton) à des fibres de protéines entières (dans la gamme de masse de mégadalton) / The structural characterization of proteins often required them to be fragmented into small units containing only few amino acids. In bottom-up approach, proteins are cleaved into small peptides by enzyme then these peptides are subjected to further fragmentation in a collision cell of a tandem mass spectrometer. However, in top-down approach, proteins can directly be dissociated (without enzyme) into small fragments by collision, electron and photon-driven dissociations. Photon-based activation methods including ultraviolet photodissociation (UVPD) and infrared multiphoton dissociation (IRMPD) have received great attention as an alternative to electron-driven and collision induced dissociation methods. Absorption of the high-energy UV photon is dispersed over the whole peptide or protein and stimulates extensive C?Ca backbone fragmentation while the low-energy IR photons gradually increases the internal energy and thus favorably dissociates the most labile amide (C?N) bonds. This thesis focuses on the method development and applications for characterizing biomolecules by photon-based activation methods. The interest of combining high-energy UV photons and low-energy IR photons in an Orbitrap mass spectrometer, for protein and post-translationally modified peptide characterization, has been evaluated. Moreover, infrared multiphoton dissociation has been implemented in a gated electrostatic ion trap to push forward the limit of fragmentation methods to large megadalton ions. One of the main breakthroughs in this thesis is the ability to adapt these method developments and applications to biomolecular objects ranging from small peptides (in kilodalton mass range) to entire protein fibrils (in megadalton mass range)

Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-inducedfluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption. The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore of the green fluorescent protein (GFP), p-hydroxybenzylidene-2,3-dimethylimidazolone (HBDI). The body of work in this dissertation highlights the integration of gas-phase spectroscopy and mass spectrometry to elucidate the fundamental photophysical properties of biological and related ions.