This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open source Python package. Rigorous simulation using this code serves to benchmark this implementation as well as the robust- ness of the path integral Langevin equation as a thermostat [J. Chem. Phys. 133, 124104 (2010)]. PIMD is used to calculate equilibrium properties for clusters of HeN-CO2 at low- temperatures, with comparison to experimental and exact results. We characterize the convergence of structural and energetic properties as a function of path-integral discretiza- tion error. The radial and angular distribution of these clusters is studied as a function of size in the absence of rotation and bosonic exchange. These distributions are subsequently used to calculate vibrational shifts of CO2. This result is compared to high-accuracy path integral Monte Carlo simulations which include rotational and exchange effects. These sim- ulations indicate that the neglect of rotational degrees of freedom leads to an unphysical localization of helium atoms and incorrect vibrational shifts when compared to experiment. Approximate real-time quantum dynamics is presented for doped helium clusters using the ring-polymer molecular dynamics (RPMD) method. The accuracy of RPMD is tested iii for low-temperature simulations and compared to exact results. Preliminary calculation of the dynamics of the helium solvated CO2 dopant with respect to the center of mass of the cluster is presented. The effect of a cartesian integrator versus a normal-mode integrator for quantum dynamics is addressed. The path integral ground-state method is applied in order to calculate T = 0 properties. A convergence study of the ground-state energy of the quantum harmonic oscillator with respect to sampling time and path discretization is shown. As a final application of this implementation, a sugar in a periodic water box is simulated at T = 300K. The calculation of rotamer populations and a dipole autocorrelation indicate negligible change with the inclusion of quantum effects. This work offers a comprehensive foundation from which to base future PIMD centered research.

This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open source Python package. Rigorous simulation using this code serves to benchmark this implementation as well as the robust- ness of the path integral Langevin equation as a thermostat [J. Chem. Phys. 133, 124104 (2010)]. PIMD is used to calculate equilibrium properties for clusters of HeN-CO2 at low- temperatures, with comparison to experimental and exact results. We characterize the convergence of structural and energetic properties as a function of path-integral discretiza- tion error. The radial and angular distribution of these clusters is studied as a function of size in the absence of rotation and bosonic exchange. These distributions are subsequently used to calculate vibrational shifts of CO2. This result is compared to high-accuracy path integral Monte Carlo simulations which include rotational and exchange effects. These sim- ulations indicate that the neglect of rotational degrees of freedom leads to an unphysical localization of helium atoms and incorrect vibrational shifts when compared to experiment. Approximate real-time quantum dynamics is presented for doped helium clusters using the ring-polymer molecular dynamics (RPMD) method. The accuracy of RPMD is tested iii for low-temperature simulations and compared to exact results. Preliminary calculation of the dynamics of the helium solvated CO2 dopant with respect to the center of mass of the cluster is presented. The effect of a cartesian integrator versus a normal-mode integrator for quantum dynamics is addressed. The path integral ground-state method is applied in order to calculate T = 0 properties. A convergence study of the ground-state energy of the quantum harmonic oscillator with respect to sampling time and path discretization is shown. As a final application of this implementation, a sugar in a periodic water box is simulated at T = 300K. The calculation of rotamer populations and a dipole autocorrelation indicate negligible change with the inclusion of quantum effects. This work offers a comprehensive foundation from which to base future PIMD centered research.

Cette thèse présente l'étude de la dynamique d'un atome ou d'une molécule en interaction avec un agrégat en vue d'étudier comment un petit système (l'atome, la molécule) échange de l'énergie électronique, cinétique et vibrationnelle avec un système possédant de très nombreux degrés de liberté (l'agrégat).Le premier système est l'étude, expérimentale et théorique, de la dynamique en temps réel d'un atome de baryum déposé sur agrégat d'argon (BaArn). L'atome de baryum est excité dans des niveaux de Rydberg, il en résulte une dynamique extrêmement riche entre le chromophore et l'agrégat. L'interprétation théorique a nécessité la conception d'une méthode de dynamique originale, permettant de traiter à la fois le grand nombre d'états excités mis en jeu, couplés à de nombreux degrés de libertés atomiques. La mise en commun des informations théoriques et expérimentales a permis d'établir l'ensemble du chemin réactionnel ayant lieu au cours de cette dynamique.Le deuxième système concerne l'étude par fluorescence de la photo-dissociation de Ca2 déposé sur agrégat d'hélium ou sur agrégat mixte hélium-argon (Ca2Hen ou Ca2ArmHen). Ces résultats sont comparés à ceux obtenu sur agrégat d'argon pur (Ca2Hen). Les différences entre ces trois types de solvant montrent que les interactions sont différentes suivant que le solvant est ``quantique'' (l'hélium) ou ``classique'' (l'argon). Plusieurs canaux réactionnels ont été mis en évidence selon que l'atome de calcium excité qui résulte de la photo-dissociation est libre ou reste solvaté par de l'hélium et/ou de l'argon. Les rapports de branchement entre ces différents canaux ont également été mesurés. / The dynamics of the interaction of an atom or a molecule with a large cluster has been studied in this manuscript in view of characterising the exchange of electronic vibrational and kinetic energy between a small system with another having a large number of degrees of freedom, the cluster.We have first studied experimentally and theoretically, the real time dynamicsof a barium atom deposited on argon clusters , (BaArn). The Ba atom was excited in high Rydberg states. A rich dynamics ensues between the chromophore an the cluster. For the theoretical interpretation a new method has been developed. It its designed to take into account the large number of electronically accessed states and their coupling with the numerous nuclear degrees of freedom of the atomic movements. The combination of the experimental and theoretical informations has allowed the characterisation of a reaction path for these dynamics. The second system studied is the photodissociation of the Ca2 molecule deposited on helium clusters pure or doped with argon (Ca2Hen or Ca2ArmHen), fluorescence emission. A comparison is also made with the Ca2Hen system. Important differences appear depending upon the nature of the solvating medium be it quantal (helium) or classical (argon). Several reaction channels have been characterised and measured for the formation of the resulting calcium atom in helium or argon solvating media.