Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the measurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing. In this thesis we investigate the switching and conducting properties of photoswitching dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to conducting leads may lead to new device implementations. The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with Density Functional Theory (DFT). The potential energy barrier separating the open and closed isomer is investigated, as well as the nature of the excited states involved in the switching. The conducting properties of the molecule inserted between gold, silver and nickel leads is calculated within the Non Equilibrium Green Function theory (NEGF). The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open in the case of gold contacts, and over 30 times larger in the case of silver contacts. For the Ni leads the current for the closed isomer is almost 40 times larger than that of the open. Importantly, the current-voltage characteristics away from the linear response is largely determined by molecular orbital re-hybridization in an electric field, in close analogy to what happens for Mn12 molecules. However in the case of dithienylethene attached to Au and Ag such a mechanism is effective also in conditions of strong electronic coupling to the electrodes. In reality these molecules are in constant motion, and the dynamical properties has to be considered. In this thesis such a line of work is initiated. In order to facilitate efficient and stable dynamical simulations of molecular systems the extended Lagrangian formulation of Born-Oppenheimer molecular dynamics have been implemented in two different codes. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. In the density functional theory code FreeON, different symplectic integrators up to the 6th order have been adapted and optimized. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements. Geometric integration schemes, including a weak dissipation to remove numerical noise, are developed and implemented in the self-consistent tight-binding code LATTE. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic driftin energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories. / QC 20101202

La propriété d’être réversiblement commutable de certaines protéines fluorescenteshomologues à la GFP ouvre un vaste champ d’applications possibles: notamment le biostockagede données à haute densité et la microscopie à super résolution. Parmi ces protéines,on trouve plusieurs variantes de la GFP, notamment la protéine jaune YFP, et des protéinesfluorescentes issues d'espèces marines Anthozoaires, comme Dronpa ou Padron. Plusieursétudes structurales indiquent que ces protéines fluorescentes photochromiques commutent parisomérisation et protonation couplées du chromophore. Cependant, la synchronisation entreces deux événements, le détail des mécanismes de photo-commutation, et le rôle de ladynamique conformationelle restent incomplètement compris. Par l'utilisation combinée de lacristallographie cinétique et de la spectroscopie optique in cristallo à basse température, nousavons comparé le comportement des protéines YFP, Dronpa et IrisFP, et nous avons étudié endétail le mécanisme photo-physique de commutation chez la protéine Padron. Contrairement àDronpa et IrisFP, la photo-commutation d’YFP est plus efficace à basse température qu’àtempérature ambiante. Nos résultats suggèrent que le mécanisme de commutation d’YFPn'implique pas de changement conformationel majeur, mais plutôt une protonation photoinduitedu chromophore ne nécessitant pas d'isomérisation. Au contraire, les études réaliséessur la protéine Padron nous ont permis de montrer que, dans ce cas, l’isomérisation duchromophore peut se produire indépendamment de sa protonation, et, étonnamment, àtempérature cryogénique. De plus, deux états intermédiaires ont pu être caractérisés au coursdu processus de photo-commutation. La protéine Padron a permis de mettre à jour le premiermarqueur codable génétiquement qui soit efficacement photo-commutable à températurecryogénique. / The property to be reversible switchable of some homologues fluorescents protein ofGFP open a large field for possible applications: such as, high-density data bio-storage andsuper-resolution microscopy. Between these proteins, we find several variants of GFP, such asyellow fluorescent protein, YFP, and fluorescents protein from marine Anthozoary species, asDronpa or Padron. Several structural studies suggest that these fluorescent proteins switch viaisomerization coupled with the protonation of the chromophore. However, thesynchronization between these processes, the detail about the photo-switching mechanism,and the role of conformational dynamics remains unclear. In combination of the kineticcrystallography and the optic spectroscopy in cristallo at low temperature, we have comparedthe YFP behavior, Dronpa and IrisFP, and we have studied in detail the photo-physicmechanism of Padron switching. In contrast to Dronpa and IrisFP, the YFP photoswitching ismore efficient at low temperature than at room temperature. Our results suggest that theYFPswitching is not associated to large structural rearrangements, but mostly a photo-inducedprotonation of the chromophore without isomerization. On the contrary, the studies done withPadron allowed us to show, in this case, the chromophore isomerization can be producedindependently of the protonation, at cryo-temperatures. Moreover, two intermediate stateswere revealed in the photo-pathway. Padron fluorescent protein allows to advance the firstgenetically inserted dye, being photo-switchable at cryogenic temperature