Metal-mediated organometallic reactions are critical for both catalytic and synthetic chemistry. Density functional theory (DFT) potential-energy calculations are routinely used with a transition-state theory type of approach to understand and predict the reaction mechanisms of organometallic reactions. However, these calculations do not include atomic momentum and thus ignore dynamic effects. Molecular dynamics is a powerful tool for elucidating mechanistic details of chemical reactions. In this dissertation, quasiclassical molecular dynamics studies reveal key mechanistic details about several fundamental organometallic reactions. Chapter 1 provides a brief overview of key molecular dynamics details. Chapters 2-4 provide details on for three classic organometallic reactions involving alkane C-H bonds. These Chapters are from previously published works (J. Am. Chem. Soc. 2018, 140, 11039; Organometallics 2019, 38, 2280; Organometallics, 2021, 40, 1454). Chapter 5 provides details about progress toward performing quasiclassical molecular dynamics simulations of organometallic reactions in explicit organic solvent.

Organic reactions are systematically examined experimentally and theoretically to determine the role dynamics plays in the outcome of the reaction. It is shown that trajectory studies are of vital importance in understanding reactions influenced by dynamical motion. This dissertation discusses how a combination of kinetic isotope effects, theoretical calculations, and quasiclassical dynamics trajectories aid in the understanding of the solvolysis of p-tolyldiazonium cation in water, the cycloadditions of cyclopentadiene with diphenylketene and dichloroketene, and the cycloaddition of 2- methyl-2-butene with dichloroketene. In the solvolysis of p-tolyldiazonium cation, significant 13C kinetic isotope effects are qualitatively consistent with a transition state leading to formation of an aryl cation, but on a quantitative basis, the isotope effects are not adequately accounted for by simple SN1 heterolysis to the aryl cation. The best predictions of the 13C isotope effects for the heterolytic process arise from transition structures solvated by clusters of water molecules. Dynamic trajectories starting from these transition structures afford products very slowly. The nucleophilic displacement process for aryldiazonium ions in water is determined to be at the boundary of the SN2Ar and SN1 mechanisms. The reaction of cyclopentadiene with diphenylketene affords both [4 + 2] and [2 + 2] cycloadducts directly. This is surprising. There is only one low-energy transition structure for adduct formation. Investigation of this reaction indicates that quasiclassical trajectories started from a single transition structure afford both [4 + 2] and [2 + 2] products. Overall, an understanding of the products, rates, selectivities, isotope effects, and mechanism in these reactions requires the explicit consideration of dynamic trajectories.

This Thesis is concerned with the quasiclassical theory of meso-scopic superconductivity. The aim of the Thesis is to introduce the boundary conditions for a quasiclassical Green’s function on partially transparent interfaces in mesoscopic superconducting structures and to analyze the range of applicability of the quasiclassical theory. The linear boundary conditions for Andreev amplitudes, factoring the quasiclassical Green’s function, are presented.  The quasiclassical theory on classical trajectories is reviewed and then generalized to include knots with paths intersections.  The main focus of the Thesis is on the range of validity of the quasiclassical theory. This goal is achieved by comparison of quasiclassical and exact Green’s functions.  The exact Gor’kov Greens function cannot be directly used for the comparison because of its strong microscopic variations on the length-scale of λF. It is the coarse-grain averaged exact Green’s function which is appropriate for the comparison. In most of the typical cases the calculations show very good agreement between both theories. Only for certain special situations, where the classical trajectory contains loops, one encounters discrepancies. The numerical and analytical analysis of the role of the loop-like structures and their influence on discrepancies between both exact and quasiclassical approaches is one of the main results of the Thesis. It is shown that the terms missing in the quasiclassical theory can be attributed to the loops formed by the interfering paths.  In typical real samples any imperfection on the scale larger than the Fermi wavelength disconnects the loops and the path is transformed into the tree-like graph. It is concluded that the quasiclassical theory is fully applicable in most of real mesoscopic samples. In the situations where the conventional quasiclassical theory is inapplicable due to contribution of the interfering path, one can use the modification of the quasiclassical technique suggested in the Thesis.

The reparametization of semiempirical Hamiltonians is an emerging method used in direct dynamics studies. The use of semiempirical Hamiltonians in direct dynamics studies diminishes the computational cost of trajectory calculations and negates the need for an analytical potential energy surface when performing reaction dynamics studies. The reparametization of semiempirical Hamiltonians increases the agreement with experiment and high level ab initio theory. We have chosen to create one set of new parameters that apply to two related reactions, F + CH₄ → HF + CH₃ and F + C₂H₆ → HF + C₂H₅. We have performed an electronic structure study for these reactions. The ab initio data obtained from the electronic structure study is then used as the reference for a reparametization of the PM3 Hamiltonian. The reparametization has improved the ab initio and PM3 reaction energy and potential energy surface scan agreement. This new set of parameters for PM3 (SRP-PM3) is used to perform a direct quasiclassical trajectory study of the reactions. The vibrational and rotational HF distributions calculated using SRP-PM3 are compared with experiments. We have observed an improvement in the agreement with experimental vibrational distributions but have seen no change in the rotational distributions. / Master of Science

Les processus élémentaires hétérogènes à l’interface gaz-solide présentent un intérêt fondamental dans de nombreux domaines tels que la catalyse hétérogène, la chimie atmosphérique et des milieux interstellaires, la rentrée atmosphérique de véhicules spatiaux ou encore la description des interactions plama-paroi. Cette thèse a pour objet l’étude de la dynamique des processus de collision non réactive de l’azote N2 sur une surface de tungstène W(100) et des processus de recombinaison moléculaire de l’hydrogène H2 sur des surfaces de tungstène W(100) et W(110). Leur dynamique quasi classique est simulée au moyen de surfaces d’énergie potentielle préalablement construites à partir de calculs de théorie de la fonctionnelle de la densité. Un potentiel multi-adsorbats est notamment développé pour tenir compte du taux de couverture de surface afin d’étudier la compétition entre la recombinaison directe, de type Eley-Rideal et la recombinaison par « atomes chauds » après diffusion hyperthermique d’un atome sur la surface. / Heterogeneous elementary processes at the gas-solid interface are ofgreat interest in many domains such as heterogeneous catalysis, atmospheric and interstellar media chemistry, spacecraft atmospheric re-entry and plasma-wall interactions description. This thesis focus on the dynamics of nitrogen, N2, non reactive scattering on a tungsten W(100) surface and hydrogen, H2, recombination processes on tungsten surfaces W(100) and W(110). The quasiclassical dynamics of these processes is simulated using potential energy surfaces based on density functional theory calculations. In particular, a multi-adsorbate potential is developed to include surface coverage in the dynamics simulation in order to scrutinize the interplay between both direct abstraction, the so-called Eley-Rideal recombination,and the Hot-Atom recombination process after hyperthermal diffusion on the surface

La rationalisation des processus chimiques élémentaires aux surfacesest d'intérêt primordial pour de nombreux phénomènes naturels ou d'intérêttechnologique. D'un point de vue fondamental, la façon dont l'énergie, concomitanteà toute réaction chimique, est distribuée parmi les degrés de liberté des moléculesformées et/ou transférée à la surface est loin d'être systématisée. Dans ce travail,des simulations, reposant sur la méthode des trajectoires quasi-classiques (QCT),sont réalisées pour examiner cette problématique lors de recombinaisons demolécules d'hydrogène (H2) et d'azote (N2) résultant de l'abstraction d'atomesadsorbés via collision par un atome provenant de la phase gazeuse sur des surfacesde Tungstène - W(100) et W(110) - à taux de couverture non nul. Ces processussont ici étudiés pour leur intérêt en physique des interactions plasma-paroi. Dessurfaces d'énergie potentielle, construites à partir de calculs de structure électroniquebasés sur la théorie de la fonctionnelle densité (DFT), sont utilisées pour simuler,dans le cadre de la mécanique classique - incluant les corrections semi-classiquespertinentes - les processus ultrarapides dit de "Eley-Rideal" et par "atomes-chauds"(sub-picoseconde). La mise en place de modèle effectifs, pour tenir compte de ladissipation de l'énergie aux phonons de la surface et aux excitations électroniques(paires électron-trou), permet de rationaliser la dynamique non-adiabatique del'abstraction atomique aux surfaces métalliques. / The rationalization of elementary processes at surfaces is of prime importance for numerous natural and technological areas. From a fundamental pointof view, the way the energy concomitant to any chemical reaction is distributed among the desorbing molecules degrees-of-freedom and the surface is far frombeing fully pictured. In this work, quasiclassical molecular dynamics (QCT)simulations have been carried out to investigate this issue for the recombination ofH2 and N2 resulting from atomic adsorbate abstraction by atom scattering off theW(100) and W(110) covered surfaces, these processes being of relevance inplasma-wall interactions. Potential energy surfaces, built from density functional(DFT) theory calculations, have been used to simulate, within the framework ofclassical dynamics (including semi-classical corrections), the subpicosecond Eley-Rideal and Hot-Atom processes. The implementation of effective models to accountfor energy dissipation to surface phonons and electron-hole pair excitations, have allowed to rationalize the non-adidabatic dynamics of atom abstraction at metalsurfaces.