Les méthodes hybrides alliant la mécanique quantique et la mécanique moléculaire (QM/MM) sont des outils adéquats pour traiter des systèmes biologiques. Les phénomènes électroniques souvent étudiés sur des petites molécules ont, dès lors pu être envisagés dans des environnements macromoléculaires. Ce travail explore trois phénomènes électroniques en présence d'un environnement protéique: l'absorption, la capture électronique et les ionisations de coeur. Nous avons employé les derniers développements de la méthode QM/MM {Local Self-Consistent Field} (LSCF) pour traiter la jonction covalente entre la partie QM et la partie MM ainsi que le couplage QM/MM avec le PCM. En premier lieu, nous nous sommes focalisés sur les spectres d'absorption de chromophores présents dans des macromolécules. Nous avons mis au point un couplage entre les méthodes LSCF/MM et PCM pour prendre en compte la polarisation électronique de l'environnement suite à l'absorption d'un photon par le chromophore. Ce modèle, le LSCF/MM\string:ERS, a été testé et validé sur le spectre d'absorption du complexe de squaraine-tétralactame. Une étude plus poussée a ensuite été réalisée sur une protéine fluorescente en décomposant la longueur d'onde d'absorption maximale en trois contributions physiques. Les effets de la substitution du chromophore ont aussi été évalués. Dans une seconde partie, nous avons étudié la capture électronique par un cyclotide contenant trois ponts disulfures, qui, après irradiation, forment des demi-liaisons caractéristiques (2c-3e). La dernière partie est consacrée à la validation de l'approche de la projection asymptotique. Elle a été réalisée dans le cadre d'une étude sur les ionisations de coeur d'un ensemble de molécules pour, par la suite, étudier les ionisations de coeur de la glycine présentes dans des systèmes de plus en plus complexes jusqu'à la Sérum-Albumine Humaine. / Hybrid methods that combine quantum mechanics and molecular mechanics (QM/MM) provide a near-ideal treatment of biological system reactivity and spectroscopy. Many electronic phenomena often studied on small systems can be now forseen in macromolecular surroundings. This work considers the treatment with QM/MM tools of three electronic phenomena in biosystem: absoprtion, electronic attachment and core ionization. Latest developments of the Local Self-Consistent Field formalism (LSCF) have been used to treat delicate covalent junctions between the QM part and the MM part and the coupling of QM/MM and PCM methods. Firstly we have focussed on absorption spectra of chromophores embedded in macromolecules. The combined LSCF/MM and PCM approach have been employed to account for the electronic polarization when the chromophore absorbs one photon. This new method, called LSCF/MM\string:ERS has been tested and validated with the study of the absorption spectra on the squarain-tetralactam complex. Then, we have considered a fluorescent protein and decomposed the maximum absorption wavelength into several physical contributions. We have also analyzed the substitution effect of the chromophore. Secondly, the electronic capture have been studied on a cyclotide containing three disulfide bonds, which forms caracteristic hemi-bond (2c-3e) after irradiation. The last electronic phenomena studied is the core ionization tackled within the framework of the asymptotic projection approach. The latter has been implemented, then tested and validated on a set of molecules. This method have been employed to analyze the specific core ionization of glycine-containing systemes of increasing complexity, up to the Human Serum Albumin

<p>In this thesis we have performed core-electron spectroscopy studies of gas phase molecular systems starting with smaller diatomic, continuing with triatomic and extending our research to more complex polyatomic ones. We can subdivide the results presented here into two categories: the first one focusing on electronic fine structure and effect of the chemical bonds on molecular core-levels and the other one dealing with nuclear dynamics induced by creation of a core hole. In our research we have mostly used synchrotron radiation based techniques such as X-ray Photoelectron (XPS), X-ray Absorption (XAS), normal and Resonant Auger (AES and RAS, respectively) and Energy-Selected Auger Electron PhotoIon COincidence (ES-AEPICO) spectroscopies.</p><p>We have demonstrated that resonant Auger spectroscopy can be used to aid interpretation of the features observed in XAS for Rydberg structures in the case of Cl₂ and C1s⁻¹π*¹ states of allene molecules. The combined use of high-resolution spectroscopy with <i>ab initio</i> calculations can help the interpretation of strongly overlapped spectral features and disentangle their complex profiles. This approach enabled us to determine the differences in the lifetimes for core-hole 2p sublevels of Cl₂ which are caused by the presence of the chemical bond. We have shown that contribution in terms of the Mulliken population of valence molecular orbitals is a determining factor for resonant enhancement of different final states and fragmentation patterns reached after resonant Auger decays in N₂O.</p><p>We have also performed a systematic study of the dependence of the C1s resonant Auger kinetic energies on the presence of different substituents in CH₃X compounds. For the first time we have studied possible isomerization reaction induced by core excitation of acetylacetone. We could observe a new spectral feature in the resonant Auger decay spectra which we interpreted as a signature of core-excitation-induced keto-enol tautomerism.</p>

In this thesis we have performed core-electron spectroscopy studies of gas phase molecular systems starting with smaller diatomic, continuing with triatomic and extending our research to more complex polyatomic ones. We can subdivide the results presented here into two categories: the first one focusing on electronic fine structure and effect of the chemical bonds on molecular core-levels and the other one dealing with nuclear dynamics induced by creation of a core hole. In our research we have mostly used synchrotron radiation based techniques such as X-ray Photoelectron (XPS), X-ray Absorption (XAS), normal and Resonant Auger (AES and RAS, respectively) and Energy-Selected Auger Electron PhotoIon COincidence (ES-AEPICO) spectroscopies. We have demonstrated that resonant Auger spectroscopy can be used to aid interpretation of the features observed in XAS for Rydberg structures in the case of Cl2 and C1s−1π*1 states of allene molecules. The combined use of high-resolution spectroscopy with ab initio calculations can help the interpretation of strongly overlapped spectral features and disentangle their complex profiles. This approach enabled us to determine the differences in the lifetimes for core-hole 2p sublevels of Cl2 which are caused by the presence of the chemical bond. We have shown that contribution in terms of the Mulliken population of valence molecular orbitals is a determining factor for resonant enhancement of different final states and fragmentation patterns reached after resonant Auger decays in N2O. We have also performed a systematic study of the dependence of the C1s resonant Auger kinetic energies on the presence of different substituents in CH3X compounds. For the first time we have studied possible isomerization reaction induced by core excitation of acetylacetone. We could observe a new spectral feature in the resonant Auger decay spectra which we interpreted as a signature of core-excitation-induced keto-enol tautomerism.