The work described herein is related to gas-phase ion-molecule reactions studied by using mass spectrometry. Chapter 2 describes density functional theory, a method used in chapters 4 and 5 to propose reaction mechanisms for reactions previously observed by others by using mass spectrometry. Chapter 3 describes a study that demonstrates that the fragmentation of saturated hydrocarbons occurs due to proton-transfer reactions that occur between these species and protonated molecules generated from molecules present in air such as nitrogen and water. Saturated hydrocarbons are studied in a wide variety of fields, and better methods to analyze complex mixtures of these compounds would facilitate their analysis. Chapter 4 discusses mechanisms of reactions for previously studied ion-molecule reactions of pyridynes studied by others by using mass spectrometry. Reactions of pyridynes are important to study arynes have been previously used in organic synthesis, and pyridine moieties are particularly common in biological compounds. Chapter 5 discusses density functional theory calculations used to determine why some organic polyradical undergo hydride abstractions from cyclohexane while others do not. The study discusses reactions taking place between both singlet and triplets states of the 2,5-didehydropyridinium cation and cyclohexane as a model, which are compared to reactions of the 2-pyridyl cation and 2-dehydropyridinium cation with cyclohexane. These studies may help improve our understanding of the reactivity-controlling factors of organic polyradicals, which may help improve toxic drug candidates like cytostatic enediynes.

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Ce travail vise à comprendre l’effet de la chiralité sur la structure et la photoréactivité de biomolécules, isolées en phase gazeuse. Pour cela, nous combinons des méthodes de spectroscopie laser couplées à la spectrométrie de masse avec des calculs de chimie quantique. La comparaison entre spectres expérimentaux et simulés permet de déterminer la structure des espèces étudiées et de comprendre leur photoréactivité. La première partie étudie la différence de structure entre les deux diastéréoisomères d’un dipeptide cyclique (cyclo Tyr-Tyr). Une seule forme est observée quand les deux résidus tyrosine n’ont pas la même chiralité. Dans cette structure, un des cycles aromatiques est replié sur le cycle peptidique et l’autre est étendu à l’extérieur. Dans le stéréoisomère où les deux résidus ont la même chiralité, cette forme coexiste avec une autre, dans laquelle les deux cycles aromatiques interagissent par une liaison hydrogène. La deuxième partie concerne la structure et la nature des états excités de complexes d’alcaloïdes dérivés de la quinine avec l’acide sulfurique. Les complexes sont formés par l’ajout de l’ion bisulfate sur l’alcaloïde doublement protoné. L’ion bisulfate protège l’alcaloïde de la photodissociation UV grâce à un effet de cage, qui est identique pour la quinine et son pseudoénantiomère la quinidine. / This thesis aims at understanding chirality effects on the structure and photoreactivity of biomolecules in the gas phase by combining laser spectroscopy coupled to mass spectrometry and quantum chemical calculations. Comparison between experimental and simulated spectra allows determining the structure of the species under study and understanding their photoreactivity. The first part of this work focuses on the structural differences between the two diastereoisomers of a cyclic dipeptide, cyclo Tyr-Tyr. Only one form is observed when the two residues have different chirality. In this form, one of the aromatic rings is folded over the dipeptide ring and the other one is extended outwards. For the diastereomer with residues of identical chirality, this form coexists with a structure in which the two aromatic rings are in a stacked position, stabilized by hydrogen bond formation. The second part of this thesis deals with the structure and the nature of the excited states of complexes of cinchona alkaloids with sulfuric acid. An important finding is that the complexes are formed by adding the bisulfate ions to doubly-protonated alkaloid. The presence of the bisulfate ion has a protective effect towards photodissociation thanks to the cage effect, which is identical for quinine and its pseudo enantiomer quinidine.

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This dissertation describes the implementation of the molecular electronic structure calculations with an implicit solvent model using coupled-cluster theory. The theory for and the implementation of the solvent reaction field method (SCRF) and the reference interaction site model (RISM) at the coupled-cluster singles and doubles (CCSD) are presented. In the SCRF model a solute molecule is placed in a spherical cavity, and the outer solvent is represented by a dielectric continuum, which is characterized by the dielectric constant of the solvent. The reaction field is introduced to the system by using the multipole moment expansion of the electronic structure of the solute molecule and the dielectric constant. The SCRF method has been used to calculate the conformational equilibrium and the rotational barriers of 1,2-dichloroethane in vacuum and in different solvents. The calculated results are compared with experimental values. In addition, the solvent effects on the energetics of the mechanism of nitration of benzene are reported using the implemented CCSD-SCRF model. The idea of RISM is to replace the reaction field in continuum models by a microscopic expression in terms of the site-site radial distribution functions between solute and solvent, which can be calculated from the RISM integral equations. The statistical solvent distribution around the solute is determined based on the electronic structure of the solute, while the electronic structure of solute is influenced by the surrounding solvent distribution. Therefore, the wave function and the RISM equations are solved self-consistently with CCSD. Pair correlation functions, partial atomic charges, and solvation free energies of water and N-methylacetamide are calculated in liquid water using proposed theory. Both the CC-SCRF and CC-RISM methods have been implemented in a developmental version of the Q-Chem 3.2 quantum chemistry package.

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In this thesis, a method to calculate eigenpairs is implemented for the Multipsi library. While the standard implemtentations use the Davidson method with Rayleigh-Ritz extraction to calculate the eigenpairs with the lowest eigenvalues, the new method uses the harmonic Davidson method with the harmonic Rayleigh-Ritz extraction to calculate eigenpairs with eigenvalues near a chosen target. This is done for Configuration Interaction calculations and for Multiconfigurational methods. From calculations, it seems the new addition to the Multipsi library is worth investigating further as convergence for difficult systems with a lot of near-degeneracy was improved. / I denna avhandling implementeras en metod för att beräkna egenpar för Multipsi-biblioteket. Medan standardimplementeringarna använder Davidson-metoden med Rayleigh-Ritz-extraktion för att beräkna egenparen med de lägsta egenvärdena, använder den nya metoden den harmoniska Davidson-metoden med den harmoniska Rayleigh-Ritz-extraktionen för att beräkna egenparen med egenvärden nära ett valt mål. Detta görs för konfigurationsinteraktionsberäkningar och för multikonfigurationsmetoder. Utifrån beräkningarna verkar det nya tillskottet till Multipsi-biblioteket vara värt att undersöka vidare eftersom konvergensen för svåra system med mycket nära degenerering förbättrades.