A first-principles linear scaling real-space method for investigating non-collinear magnetic behaviour of nanostructured materials has been developed. With this method, the magnetic structures of small supported transition metal clusters have been examined. The geometric constraints imposed on the clusters by the underlying surface is found to cause non-collinear behaviour for V, Cr, and Mn clusters on Cu(111). Fe clusters supported on Cu and Ni have been studied and both spin and orbital moments are found to be enhanced for the Fe atoms, which is attributed to the recuced symmetry present at the surface. Atoms in Co clusters have been found to order antiferromagnetically, and some times in a non-collinear fasion, when deposited on a W surface. Small clusters of fcc Fe embedded in Cu have been examined and a new type of ordering, not present in larger fcc Fe systems was found. Several theoretical studies of Fe and Co based nanostructures consisting of multilayers or embedded clusters have been conducted, with the aim of predicting high moment materials for use in data storage applications. In agreement with previous experiments an enhancement of the magnetic moment is found compared to the magnetic moment of bcc Fe. The enhancement has been shown to be caused by increased spin moments for Fe atoms in close proximity with Co atoms, and this enhancement depends on the number of Co neighbours. As a result of these studies, a possible method of increasing the magnetic moment of cluster based materials has been proposed. Fermi surface analysis have been performed both on bulk materials, in order to investigate mechanisms for stabilizing non-collinear magnetic states, and in layered structures where the effect of the Fermi surface on the interlayer exchange coupling has been investigated. In addition to the development of a real-space electronic structure method for non-collinear magnetism, a density matrix purification method has been implemented in the framework of linear muffin-tin orbitals.

La compréhension des enzymes et de leurs mécanismes catalytiques est d'une grande importance dans le développement de médicaments plus efficaces Pour mieux appréhender ces phénomènes, différentes approches théoriques comme les méthodes QM, MM-MD et QM/MM, peuvent être utilisées. L'objectif principal de cette thèse est d'obtenir une meilleure compréhension des mécanismes de réactivité et de la dynamique de l'enzyme GABA-AT (y-aminobutyric acid aminotransferase), un modèle d'enzyme dépendante au phosphate pyridoxal (PLP). Notre travail a consisté en 5 étapes vers une plus grande compréhension de GABA-AT. 1) la réaction et le mode d'attachement du substrat naturel GABA ont été étudié pour différents isomères à l'aide de systèmes modèles et de la DFT. 2) l'enzyme a été simulée par dynamique moléculaire classique dans les cas de l'apoenzyme, l'holoenzyme et l'holoenzyme inactivée. Nos résultats montrent que plusieurs résidus du site actif jouent un rôle important et que leur état de protonation ainsi que celui du PLP sont cruciaux dans l'activité de GABA-AT. 3) l'influence des résidus du site actif sur la réactivité a été étudiée par la modélisation quantique de clusters moléculaires. Le plus gros cluster comprenait 165 atomes entouré d'un solvant implicite. 4) de nouvelles routines de diagonalisation pour SEBOMD ont été incorporées dans la suite AMBER à travers l'utilisation des bibliothèques LAPACK et SCALAPACK. Ces nouvelles routines ont été testées et leur efficacité a été évaluée. 5) des énergies libres de réaction ont été évaluées par dynamiques SEBOMD sur des intermédiaires réactionnels GABA-PLP / Understanding enzymes and their catalytic mechanisms is very important in order to develop more effective drugs having little to no side effects. In order to decipher the catalytic behavior of enzymes, different approaches such as QM, MM-MD, and QM/MM can be used and their results can be correlated. The main aim of this thesis is to get a deeper understanding of the mechanistic insights of the reactivity and of the dynamics of the pyridoxal-5-phosphate (PLP) dependent enzyme y-aminobutyric acid aminotransferase (GABA-AT). Because GABA-AT resembles many other PLP-dependent enzymes, understanding it could be of importance for the broad community of biochemists and computational chemists who study such class of proteins. Our work has consisted of five stages to pursuit the comprehension of GABA-AT. First, the reaction and the preferred binding mode of the natural substrate GABA has been elucidated with different isomers by means of model systems with DFT. Second, the dynamics and the behavior of the enzyme has been studied with MM-MD through the use of apoenzyme, holoenzyme and holoenzyme with an inactivator. Third, the effect of the active site residues in the inactivation mechanism has been investigated with the modelling of clusters at the QM level involving key residues. Fourth, new diagonalization routines for the SEBOMD (SemiEmpirical Born-Oppenheimer Molecular Dynamics) approach implemented in the Amber suite of programs, have been incorporated using LAPACK and SCALAPACK libraries, tested and evaluated to optimize the diagonalization procedure of the Fock matrix. Fifth, reaction free energies of PLP containing systems have been investigated with SEBOMD simulations