La compréhension de l'irradiation à l'échelle du nanomètre dans les systèmes biomoléculaires nécessite l'observation de caractéristiques nouvelles auxquelles les développements techniques actuels nous permettent d'accéder. Ce travail se situe au coeur de la construction du nouveau dispositif DIAM Dispositif d’Irradiation d’Agrégats de Molécules biologiques développé à l’Institut de Physique Nucléaire de Lyon. Le développement d’une source d’agrégats associée à un spectromètre de masse à double focalisation a permis l’obtention des premiers faisceaux d’agrégats moléculaires protonés sélectionnés en masse. De plus, un système de détection innovant a été développé et validé dans des expériences de dissociations d’agrégats d’eau protonés par collision sur un gaz. Les résultats obtenus contribuent à la connaissance de la stabilité et de la structure des petits agrégats d’eau protonés et des agrégats mixtes d’eau et de pyridine protonés / Nanoscale characterization of irradiation in biomolecular systems requires observation of novel features which are now achievable with the recent technical progress. This work is a central part in the development of DIAM which is a new experimental set-up devoted to irradiation of biomolecular clusters at the Institut de Physique Nucléaire de Lyon. The development of the cluster source and of a double focusing mass spectrometer leads to the production of intense beams of mass selected protonated molecular clusters. Combined with this mass selected cluster beams an innovative detection technique is demonstrated in collision induced dissociation experiments. The results contribute to the knowledge of the stability and the structure of the small protonated water clusters and mixed clusters of water and pyridine

L'étude des Hydrocarbures Aromatiques Polycycliques (PAH) a connu un intérêt croissant depuis une trentaine d'années, en raison notamment de leur possible présence dans le milieu interstellaire qui expliquerait l'observation des bandes d'émission IR encore non attribuées. Dans ce travail de thèse, la dynamique de refroidissement du cation naphtalène C10H8+, la plus petite molécule de la famille des PAH, est étudiée dans un anneau de stockage électrostatique, le Mini-Ring. La distribution en énergie interne des ions stockés est sondée en induisant la photo dissociation d'une fraction des ions par une excitation laser à la longueur d'onde 532 nm. La dynamique de refroidissement des cations photo-excités est observée en mesurant en fonction du temps le nombre de neutres émis par dissociation. La courbe de déclin du signal de neutres est directement reliée à la distribution en énergie interne des ions à l'instant de l'excitation laser. Cette distribution en énergie interne peut alors être déterminée à différents temps de stockage en analysant les courbes de déclin à l'aide d'un programme numérique développé pendant la thèse. L'évolution temporelle de la distribution met en évidence un processus de refroidissement rapide caractérisé par un taux de refroidissement compris entre 70 et 90 s−1 pour des énergies internes de 5.9 et 6.8 eV. Ce refroidissement rapide ne peut être expliqué par l'émission de photons infrarouges. Il est attribué à la "fluorescence de Poincaré" caractérisée par un processus de conversion interne inverse suivie de l'émission d'un photon dans le domaine du visible. Cette fluorescence de Poincaré ou fluorescence récurrente a été prédite il y a plus de 20 ans mais n'a jamais été mesurée directement à ce jour. Les taux de refroidissement mesurés lors de ce travail de thèse apportent une évidence indirecte de ce processus / The study of Polycyclic Aromatic Hydrocarbons (PAH) has been of increasing interest during the last thirty years: their possible presence in the interstellar medium is commonly invoked to explain the observation of still unassigned IR emission bands. In this thesis, the cooling dynamics of the naphthalene cations C10H8 +, the smallest molecule of the PAH family, is studied in an electrostatic storage ring, the Mini-Ring. Particularly, we consider the two main cooling processes for naphthalene cation, the dissociation and photon emission. Naphthalene molecules are ionized in an electron cyclotron resonance source (ECR), accelerated to 12 keV and then injected and stored in the Mini-Ring for several milliseconds. The internal energy distribution of the stored ions is probed by laser induced dissociation using an excitation wavelength at 532 nm. The cooling dynamics of the photo-excited cations is observed by measuring the number of emitted neutrals as a function of time. The decay curve of the neutral signal is directly related to the internal energy distribution of the ions at the excitation time. This internal energy distribution can then be determined at various storage times by analyzing the decay curves using a code developed during this thesis. The time evolution of the internal energy distribution shows a fast cooling process characterized by a cooling rate increasing from 70 to 90 s−1 for internal energies from 5.9 to 6.8 eV. This fast cooling process can’t be explained by infrared photons emission. It is attributed to the "Poincaré fluorescence " which involves an inverse internal conversion process followed by the emission of a visible photon. This fluorescence from thermally excited electron or recurrent fluorescence was predicted more than 20 years ago, but has never been measured directly up to now. The measured cooling rates in this thesis provide indirect evidence of this process

A l'aide de la spectroscopie par Résonance Paramagnétique Électronique (RPE), la détection des certaines espèces radicalaires à très faible durée de vie se fait par la méthode du spin-trapping. Cette technique permet de caractériser ces radicaux “libres” en les piégeant à l'aide d'une molécule diamagnétique (nitrone) pour donner naissance à une espèce paramagnétique persistante (adduit de spin), ayant un spectre RPE caractéristique du radical piégé. Le temps de demi-vie d'un adduit du spin est fortement corrélé à la nature de la nitrone et du radical piégé (alkyle, alcoxyle, alkylperoxyle, ...). Cependant, le lien entre la structure de l'adduit et sa durée de vie n'est toujours pas clairement établi. De ce fait, nous avons entrepris une étude théorique des réactions mises en jeu dans la disparition de l'adduit de spin résultant du piégeage de radicaux alkylperoxyle par des nitrones de type N-oxy-pyrroline. Plus précisément nous avons postulé un mécanisme de dégradation unimoléculaire en deux étapes. Étant donné la complexité des états de spin dans les composés considérés dans le profil réactionnel, nous avons effectué cette étude par l'approche ab initio multidéterminantale (CASSCF). Les calculs ab initio CASSCF en phase gazeuse sur une série d'adduits de spin nous ont permis de valider ce mécanisme de décomposition dans les solvants organiques et de mieux comprendre le lien entre la structure de l'adduit et sa durée de vie. / In the field of electron paramagnetic resonance (EPR) spectroscopy, the detection of some radical species with a very short half-life time is possible using the spin-trapping method. This technique allows us to characterize transient radicals by trapping them with a diamagnetic molecule (nitrone for example) to give rise to a persistent paramagnetic species (spin-adduct), whose EPR spectrum is characteristic of the trapped radical. Half-life times are strongly correlated to the nature of the nitrone and the trapped radical (alkyl, alkoxyl, alkylperoxyl, ...). However, the link between the structure of the adduct and its half-life time is still not clear. Therefore, we carried out a theoretical study of the reactions involved in the decay of spin-adducts resulting from the trapping of alkylperoxyl radicals by pyrroline-N-oxide nitrones. More precisely, we were interested in the mechanism of the two-step unimolecular degradation. Given the difficulty to discribe the spin states in the considered compounds, we chose to rationalize this study by means of ab initio multireference approach (CASSCF). The ab initio CASSCF calculations of a series of nitroxides allowed to validate this mechanism in organic solvents and to better understand the relationship between the structure of the spin-adduct and its half-life time.

Proteomic studies aim to identify, quantify and characterise the full complement of proteins in a cell or organism under a defined set of conditions, and are important to our understanding of cellular mechanisms. However, such studies represent a major analytical challenge. A typical proteome analysis involves enzyme-mediated digestion of complex protein mixtures to yield an even more complex mixture of peptides. Combined reverse-phase liquid chromatography and tandem mass spectrometry is then traditionally utilised to ascertain sequence information from the characteristic peptide sequences. Analytical data derived for the peptides are employed as search terms in database searching of protein sequences derived from gene sequences. The extreme complexity of the peptide mixtures analysed means that additional novel approaches are required to fully interrogate the vast number of tandem mass spectra generated, assigning peptide identity and thereby helping to address demanding biological questions. The research reported here aims to further our understanding of both gas phase peptide/peptide fragment ion structure and peptide fragmentation behaviour using a combination of tandem mass spectrometry and ion mobility measurement.To facilitate the determination of peptide ion collision cross section, a novel standard, QCAL-IM, produced using the QconCAT strategy, has been developed to enable calibration of drift time in Travelling Wave Ion Mobility instruments. The standard facilitates empirical determination of the rotationally averaged collision cross section of any peptide/peptide fragment ion that lies within the calibration range encompassed. QCAL-IM was subsequently utilised to determine the collision cross section of a range of peptide ions produced by Lys-C and Lys-N proteolysis of ‘standard’ proteins. Data produced allowed the effect upon gas phase ion conformation through changing the location of the basic residue lysine within a peptide sequence to be assessed.The fragmentation behaviour of peptide ions produced by a variety of digestion regimes during both collision-induced dissociation (CID) and electron transfer dissociation (ETD) has also been extensively studied. The proteases trypsin and Lys-C are those typically utilised during proteomic studies and peptides produced by each have either the basic residues arginine or lysine at their carboxy-terminus. Secondary enzymatic treatment with the exoprotease carboxypeptidase B cleaves these basic residues from the C-terminus. Tandem mass spectrometric analysis of both tryptic/Lys-C peptides and their CBPB truncated analogue highlights that the dominant fragment ion series observed during both CID and ETD is determined, at least in part, by the location of such basic residues.Finally, studies were undertaken to investigate the factors which may promote/inhibit scrambling of peptide fragment ion sequence, which has recently been shown to take place during CID. The effect of modifying the gas phase basicity of the N-terminal amino acid residue is studied through a combination of derivatisation and synthesis of alternative peptide sequences. Increasing the gas phase basicity is shown to inhibit the observed sequence scrambling while promoting concomitant rearrangement/retention of a carboxyl oxygen at the C-terminus to give enhanced formation of bn+H2O product ion species.

Mass spectrometry (MS) has become a widely used technique for the characterization of a wide range of substances in diverse fields. The selection of appropriate ionization techniques, source parameters, charge carriers based on the analyte’s polarity is essential in MS as only the ions are detected. When using a soft ionization technique, single stage-MS at best provides only chemical composition; thus, tandem MS is needed to determine structural information and dissociation pathways. This dissertation focuses on the characterization of various small molecules and ions using different ionization techniques, charge carriers, and collision-induced dissociation (CID). In Chapter II, commercially available ionic liquid (IL) cations, specifically imidazolium-based IL cations with different side-chain chemistries, were characterized by CID-MS. The imidazolium-based IL cations have diverse dissociations pathways depending on the nature of the side chain (aliphatic or aromatic) or the functional groups (allyl, vinyl, alcohol, methoxy, nitro) present on the side chain. Additionally, it was observed that some IL cations undergo thermal degradation under normal operating temperatures of electrospray ~275 °C. A variety of experimental and complementary computational chemistry results are presented. In Chapter III, cis-3-hydroxyproline (c3hPro) and cis-4-hydroxyproline (c4hPro) isomers were differentiated upon lithiation using CID-MS. The CID-MS of [c4hPro+Li]+ produces three primary fragmentation pathways, namely the neutral losses of H2O, CO, and CO2; whereas CID-MS of [c3hPro+Li]+ produces only loss of CO2 in this same region. These observations may have analytical utility, and in this work, the experimental observations were explored with thermodynamic and transition state calculations to better understand the processes. In Chapter IV, the accurate mass of synthetic monomers including PAH perfluorocycloalkene monomers and their precursors were measured and reported with a publication-quality mass accuracy using atmospheric pressure chemical ionization (APCI)-MS. Additionally, the effect of solution flow rate, ionization mode, source parameters (such as vaporization temperature, dry gas temperature and dry gas flow rate, nebulizer gas pressure), acidification, and different solvent systems on APCI-MS signal intensity were studied.

No description available.

The relation between dissociative symptoms and posttraumatic stress disorder (PTSD) was investigated in women who had experienced trauma or sexual assault. Subjects were administered the Dissociative Experiences Scale (DES), the Sexual Experiences Scale (SES), and the PTSD Interview (PTSD-I). Subjects were grouped according to their scores on the SES and the PTSD-I. Analysis of variance revealed a relation between DES scores and PTSD symptom severity scores. Correlational analyses showed a relation between dissociative symptoms and PTSD symptom severity but not recency of trauma. Three factors from a previously published factor analysis of the DES were found to contribute to the DES scores of PTSD subjects.

Doctor of Philosophy / Department of Physics / Itzhak Ben-Itzhak / Lasers are being used widely for the study and manipulation of the dynamics of atomic and molecular targets, and advances in laser technology makes it possible to explore new areas of research — for example attosecond physics. In order to probe the fragmentation dynamics of molecular ions, we have developed a coincidence three-dimensional momentum imaging method that allows the kinematically complete study of all fragments except electrons. Recent upgrades to this method allow the measurement of slow dissociation fragments, down to nearly zero velocity, in intense ultrafast laser fields. Evidences for the low energy breakup are presented using the benchmark molecules diatomic H[subscript]2[superscript]+ and polyatomic H[subscript]3[superscript]+ . The low energy fragments in H[subscript]2[superscript]+ dissociation are due to the intriguing zero-photon dissociation phenomenon. This first experimental evidence for the zero-photon dissociation is further supported by sophisticated theoretical treatment. We have explored the laser pulse length, intensity, wavelength, and chirp dependence of zero-photon dissociation of H[subscript]2[superscript]+, and the results are well described by a two-photon process based on stimulated Raman scattering. Similar studies of the slow dissociation of H[subscript]3[superscript]+ reveal that two-body dissociation is dominant over three-body dissociation. The most likely pathways leading to low-energy breakup into H[superscript]++H[subscript]2, in contradiction to the assessments of the channels in at least one previous study, are explored by varying the laser pulse duration and the wavelength. In addition, we have investigated the dissociation and single ionization of N[subscript]2[superscript]+ , and an interesting high energy feature in addition to the low energy has been observed at higher intensities. Such high energy results from the breakup of molecules in excited states are accessible at higher intensities where their potential energy is changing rapidly with the internuclear distance. We have extended the intense field ionization studies to other molecular ions N[subscript]2[superscript]+ , CO[superscript]+, NO[superscript]+, and O[subscript]2[superscript]+ . The dissociative ionization of these molecules follow a general mechanism, a stairstep ionization mechanism. Utilizing the capability of the upgraded experimental method we have measured the non-dissociative and dissociative ionization of CO[superscript]+ using different pulse lengths. The results suggest that dissociative ionization can be manipulated by suppressing some ionization paths.

Master of Science / Department of Physics / Itzhak Ben-Itzhak / Imaging the interaction of molecular ion beams with ultrafast intense laser fields is a very powerful method to understand the fragmentation dynamics of molecules. Femtosecond laser pulses with different wavelengths and intensities are applied to dissociate and ionize molecular ions, and each resulting fragmentation channel can be studied separately by implementing a coincidence three-dimensional (3D) momentum imaging method. The work presented in this master’s report can be separated into two parts. First, the interaction between molecular ion beams and femtosecond laser pulses, in particular, the dissociation of CO[superscript]+ into C[superscript]++O, is studied. For that purpose, measurements are conducted at different laser intensities and wavelengths to investigate the possible pathways of dissociation into C[superscript]++O. The study reveals that CO[superscript]+ starts to dissociate from the quartet electronic state at low laser intensities. Higher laser intensity measurements, in which a larger number of photons can be absorbed by the molecule, show that the doublet electronic states with deeper potential wells, e.g. A [superscript]2Π, contribute to the dissociation of the molecule. In addition, the three-body fragmentation of CO[subscript]2[superscript]+ into C[superscript]++O[superscript]++O[superscript]+ is studied, and two breakup scenarios are separated using the angle between the sum and difference of the momentum vectors of two O[superscript]+ fragments. In the second part, improvements in experimental techniques are discussed. Development of a reflective telescope setup intended to increase the conversion efficiency of ultraviolet (UV) laser pulse generation is described, and the setup is used in the studies of CO[superscript]+ dissociation described in this report. The other technical study presented here is the measurement of the position dependence of timing signals picked off of a microchannel plate (MCP) surface. The experimental method is presented and significant time spread over the surface of the MCP detector is reported [1].

No description available.