<p>Mass spectrometry (MS) is an important tool in analytical chemistry today, particularly in the field of proteomics where identification of proteins is the central activity. The focus in this thesis has been to improve the mass accuracy of MS-analyses in order to improve the possibility for unambiguous identification of proteins.</p><p>In paper I a new peak picking algorithm has been developed for Matrix Assisted Laser Desorption/Ionization - Time of Flight - Mass Spectrometry (MALDI-TOF-MS). The new algorithm is based on the assumption that two sets of ions are formed during the ionisation, and that these two sets have different Gaussian-distributed velocity profiles. The algorithm then deconvolutes the spectral peak into two Gaussian distributions, were the narrower of the two distributions is utilized for peak picking. The two-Gaussian peak picking algorithm proved to be especially useful when dealing with weak, distorted peaks.</p><p>In paper II a novel chip-based target for MALDI analysis is described. The target features pairs of 50x50 μm anchors in close proximity. Each anchor within a pair could be individually addressed with different sample solutions. Each pair could then be irradiated with the MALDI laser, which allowed ionization to take place on separated anchors simultaneously. This made it possible for us to calibrate analytes with calibration standards that where physically separated from the analyte, but ionized simultaneously. The use of new chip-based MALDI target resulted in a 2-fold reduction of relative mass errors. We could also report a significant reduction of ion suppression. The small size of the anchors provided a good platform for efficient utilization of sample. This resulted in a detection limit of ca. 1.5 attomole of angiotensin I at a S/N of 22:1.</p>

Mass spectrometry (MS) is an important tool in analytical chemistry today, particularly in the field of proteomics where identification of proteins is the central activity. The focus in this thesis has been to improve the mass accuracy of MS-analyses in order to improve the possibility for unambiguous identification of proteins. In paper I a new peak picking algorithm has been developed for Matrix Assisted Laser Desorption/Ionization - Time of Flight - Mass Spectrometry (MALDI-TOF-MS). The new algorithm is based on the assumption that two sets of ions are formed during the ionisation, and that these two sets have different Gaussian-distributed velocity profiles. The algorithm then deconvolutes the spectral peak into two Gaussian distributions, were the narrower of the two distributions is utilized for peak picking. The two-Gaussian peak picking algorithm proved to be especially useful when dealing with weak, distorted peaks. In paper II a novel chip-based target for MALDI analysis is described. The target features pairs of 50x50 μm anchors in close proximity. Each anchor within a pair could be individually addressed with different sample solutions. Each pair could then be irradiated with the MALDI laser, which allowed ionization to take place on separated anchors simultaneously. This made it possible for us to calibrate analytes with calibration standards that where physically separated from the analyte, but ionized simultaneously. The use of new chip-based MALDI target resulted in a 2-fold reduction of relative mass errors. We could also report a significant reduction of ion suppression. The small size of the anchors provided a good platform for efficient utilization of sample. This resulted in a detection limit of ca. 1.5 attomole of angiotensin I at a S/N of 22:1. / QC 20101206

Using multiple theoretical methods, comprehensive calculations are performed to create a new and more comprehensive data set for elastic scattering and related transport cross sections for collisions of (H$^+$ + H), (H + H) and (He$^{2+}$ + H) in the center-of-mass energy frame. In proton-atomic hydrogen collisions, we have significantly updated and extended previous work of elastic scattering, charge transfer and related transport integral and differential cross sections in the center-of-mass energy range $10^{-4} - 10^4$ eV where the multi-channel molecular orbital approach (MO3) is used. For atomic hydrogen-hydrogen collisions, similar updates have been made of elastic scattering and spin exchange differential and integral cross sections, also for the H + H collision the ionization and negative ion formation cross sections are provided in energy range (1-20 KeV) by use of the 'hidden crossing' theoretical framework. For collisions of alpha particles with atomic hydrogen we have computed the elastic scattering cross section in the center-of-mass energy range $10^{-4} - 10^8$ eV. In this case, at the lowest energies where elastic scattering greatly dominates other reaction channels, a single-channel quasi-molecular-orbital approach (MO1) is used. With the opening of inelastic channels at higher energies the multi-channel atomic-orbital, close-coupling method is applied, and at the highest energies considered perturbation theory (the Born approximation) is used. The results are compared with other data available in literature.

Le travail de cette thèse porte sur l’étude expérimentale de la diffusion d’atomes d’hydrogène sur des surfaces et sous incidence rasante. L’énergie des atomes et des ions varie de quelques centaines d’eV à quelques keV, tandis que les surfaces étudiées sont des isolants et des semi-métaux. En particulier on a étudié la formation de l’ion H- sur du graphite pyrolytique dit HOPG (highly oriented pyrolytic graphite) et sur une surface de LiF(001). Pour ce dernier système, nous avons étudié en détail la diffraction d’atomes H° et d’ions H+. Ces expériences ont été réalisées sur un montage expérimental utilisant un faisceau pulsé et permettant de détecter en coïncidence les particules diffusées et les électrons secondaires. L’ensemble permet de connaître la charge finale de la particule diffusée, sa perte d’énergie, son angle de diffusion, le tout en corrélation avec la statistique et l’énergie des électrons émis.Le résultat de ce travail a révélé que la diffraction persiste dans le régime inélastique. En effet, nous observons un motif de diffraction après la neutralisation de proton sur la surface de LiF(001). Un modèle est proposé pour expliquer ces résultats qui semblent en contradiction avec ceux publiés par le groupe de H. Winter sur la diffraction d’atomes d’hydrogène sur cette même surface. Concernant la formation d’ion négatif sur HOPG, nous avons mis en évidence un taux de H- (~10%) sur une surface propre. C’est le plus haut taux de H- jamais observé avec ce type d’expérience en incidence rasante. C’est encore plus élevé qu’avec des isolants ioniques, ces derniers donnant un taux déjà 10 fois plus grand que celui observé sur métaux propres. Ces résultats confirment l’efficacité du graphite à convertir des ions et des atomes en ions négatifs. En exploitant les données fournies par la technique des coïncidences, nous avons pu élucider le mécanisme à l’œuvre dans cette conversion. Du fait de la structure électronique particulière de HOPG, avec une bande interdite projetée dans la direction Gamma, seuls les électrons localisés sigma contribuent à la formation de l’ion négatif, donnant au HOPG un caractère isolant du point de vue de la capture électronique. Les électrons pi contribuant de manière efficace à la perte d’énergie par collisions binaires, donnant de ce point de vue au HOPG son caractère métallique. / In this thesis, we have investigated experimentally the scattering of hydrogen atoms and ions on solid surfaces at grazing incidence. The projectile energy ranges from several hundred eV to few keV. The formation of H- ions is studied on highly oriented pyrolytic graphite (HOPG) surface; and surface diffraction is carried out on LiF(001) surface with H° and H+ particle scattering. Both experiments were performed in the same experimental setup (see Figure 1.2 and 2.1)—with grazing scattering geometry and a PSD (position sensitive detector) located downstream to record scattered particles. For charge state analysis a set of electrostatic plates is inserted between sample and PSD. During the experiment, coincident measurement technique is used to identify the energy loss associated to 0, 1, 2…electrons emission. Clear evidence of diffraction with inelastic scattering by proton on LiF(001) has been obtained, which has not been observed before. Indeed, the group of H. Winter reported that no diffraction exists with inelastic scattering of H° on LiF(001). However, according to our result, a coherence scattering factor still exists even though the electron capture by the proton is an inelastic process. For negative ion formation on HOPG surface, we report here the highest fraction of H- (~10%) measured in grazing scattering experiments; it is larger than those obtained on ionic insulators, the latter being typically 10 times larger than those measured on clean metals. These results confirm the high yields of negative hydrogen ions from graphite reported in the literature. Electron emission and energy loss of scattered beam have also been deciphered via coincidence measurement. Due to the special structure of HOPG, two kinds of electron emissions (σ and π-band electron) and energy losses (cycles and metal-like energy loss) have been measured. Furthermore, the total electron emission on HOPG with insulator-like behavior and total energy loss with metal-like are the most representative property of HOPG which have been first presented in this thesis.

<p>This thesis concerns the study of reaction mechanisms by means of kinetic isotope effects (KIEs). Studies of the nucleophilic bimolecular substitution (S_N2) reaction had the dual purpose of improving our fundamental understanding of molecular reactivity and assessing the ability of kinetic isotope effects to serve as mechanistic tools. The transition state of the S_N2 reaction between a cyanide ion and ethyl chloride in tetrahydrofuran was found to be reactant like and only slightly tighter than has been found previously for the same reaction in dimethyl sulphoxide. One conclusion was that the transition-state structure in this reaction was predicted fairly well by the theoretical calculations, even without solvent modelling. The S_N2 reactions between cyanide ions and <i>para</i>-substituted benzyl chlorides were found to have reactant-like transition states, of which the C_α-Cl bond was most influenced by the <i>para</i>-substitution. Theoretical calculations indicated that the chlorine KIEs could be used as probes of the substituent effect on the C_α-Cl bond if bond fission was not too advanced in the transition state. Furthermore, the nucleophile carbon ¹¹C/¹⁴C KIEs were determined for the reactions between cyanide ions and various ethyl substrates in dimethyl sulphoxide.</p><p>Precision conductometry was employed to estimate the aggregation status of tetrabutylammonium cyanide in tetrahydrofuran and in dimethyl sulphoxide, which is of interest as tetrabutylammonium cyanide is frequently used as the nucleophilic reagent in mechanistic investigations and synthetic reactions. The tendency for ion-pair formation was found to be very slight, significant, and very strong in dimethyl sulphoxide, water, and tetrahydrofuran, respectively. </p><p>The nitrogen kinetic isotope effect on monoamine oxidase B catalysed deamination of benzylamine was determined in an attempt to obtain conclusive evidence regarding the mechanism of the oxidation. Monoamine oxidase is an important drug target in connection with the treatment of, for example, depression and Parkinson’s disease, and knowledge on how the enzyme effects catalysis would facilitate the design of highly selective and efficient inhibitors.</p>

This thesis concerns the study of reaction mechanisms by means of kinetic isotope effects (KIEs). Studies of the nucleophilic bimolecular substitution (SN2) reaction had the dual purpose of improving our fundamental understanding of molecular reactivity and assessing the ability of kinetic isotope effects to serve as mechanistic tools. The transition state of the SN2 reaction between a cyanide ion and ethyl chloride in tetrahydrofuran was found to be reactant like and only slightly tighter than has been found previously for the same reaction in dimethyl sulphoxide. One conclusion was that the transition-state structure in this reaction was predicted fairly well by the theoretical calculations, even without solvent modelling. The SN2 reactions between cyanide ions and para-substituted benzyl chlorides were found to have reactant-like transition states, of which the Cα-Cl bond was most influenced by the para-substitution. Theoretical calculations indicated that the chlorine KIEs could be used as probes of the substituent effect on the Cα-Cl bond if bond fission was not too advanced in the transition state. Furthermore, the nucleophile carbon 11C/14C KIEs were determined for the reactions between cyanide ions and various ethyl substrates in dimethyl sulphoxide. Precision conductometry was employed to estimate the aggregation status of tetrabutylammonium cyanide in tetrahydrofuran and in dimethyl sulphoxide, which is of interest as tetrabutylammonium cyanide is frequently used as the nucleophilic reagent in mechanistic investigations and synthetic reactions. The tendency for ion-pair formation was found to be very slight, significant, and very strong in dimethyl sulphoxide, water, and tetrahydrofuran, respectively. The nitrogen kinetic isotope effect on monoamine oxidase B catalysed deamination of benzylamine was determined in an attempt to obtain conclusive evidence regarding the mechanism of the oxidation. Monoamine oxidase is an important drug target in connection with the treatment of, for example, depression and Parkinson’s disease, and knowledge on how the enzyme effects catalysis would facilitate the design of highly selective and efficient inhibitors.

Title from second page of PDF document. Includes bibliographical references (p. 144-152).

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