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This thesis discusses Kaplan, a free conformer searching package, available at github.com/PeaWagon/Kaplan / Conformer searching algorithms find minima in the Potential Energy Surface (PES) of a molecule, usually by following a torsion-driven approach. The minima represent conformers, which are interchangeable via free rotation around bonds. Conformers can be used as input to computational analyses, such as drug design, that can convey molecular reactivity, structure, and function. With an increasing number of rotatable bonds, finding optima in the PES becomes more complicated, as the dimensionality explodes. Kaplan is a new, free and open-source software package written by the author that uses a ring-based Evolutionary Algorithm (EA) to find conformers. The ring, which contains population members (or pmems), is designed to allow initial PES exploration, followed by exploitation of individual energy wells, such that the most energetically-favourable structures are returned. The strengths and weaknesses of existing publicly available conformer searchers are discussed, including Balloon, RDKit, Openbabel, Confab, Frog2, and Kaplan. Since RDKit is usually considered to be the best free package for conformer searching, its conformers for the amino acids were optimised using the MMFF94 forcefield and compared to the conformers generated by Kaplan. Amino acid conformers are well characterised, and provide insight for protein substructure. Of the 20 molecules, Kaplan found a lower energy minima for 12 of the structures and tied for 5 of them. Kaplan allows the user to specify which dihedrals (by atom indices) to optimise and angles to use, a feature that is not offered by other programs. The results from Kaplan were compared to a known dataset of amino acid conformers. Kaplan identified all 57 conformers of methionine to within 1.2Å, and found identical conformers for the 5 lowest-energy structures (i.e. within 0.083Å), following forcefield optimisation. / Thesis / Master of Science (MSc) / A conformer search affords the low-energy arrangements of atoms that can be obtained via rotation around bonds. Conformers provide insight about the chemical reactivity and physical properties of a molecule. With increasing molecule size, the number of possible conformers increases exponentially. To search the space of possible conformers, this thesis presents Kaplan, which is a software package that implements a novel directed, stochastic, sampling technique based on an Evolutionary Algorithm (EA). Kaplan uses a special type of EA that stores sets of conformers in a ring-based structure. Unlike other conformer-specific packages, Kaplan provides the means to analyse and interact with found conformers. Known conformers of amino acids are used to verify Kaplan. Other tools for generating conformers are discussed, including a comparison of freely available software. Kaplan effectively finds the conformers of small molecules, but requires additional parametrisation to find the conformers of mid-sized molecules, such as Penta-Alanine.

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

Lors d’une rentrée atmosphérique, les boucliers thermiques des véhicules spatiaux subissent un échauffement considérable dont une fraction significative (~30%) est attribuée aux réactions chimiques à leur surface. Cette thèse contribue à la compréhension de cette réactivité hétérogène, la catalycité, au moyen des outils de la chimie théorique. Une méthode de construction de surface d’énergie potentielle globale est développée et appliquée à l’étude de la dynamique de processus élémentaires (adsorption moléculaire dissociative, absorption atomique, recombinaison Eley-Rideal …) pour les systèmes chimiques N,N2/W(100,110) et O,O2/Cu(100). Ces approches sont ensuite couplées à un modèle cinétique permettant de quantifier la catalycité. / During an atmospheric re-entry, the thermal shields of spacecrafts undergo an important heating, a significant fraction (~30%) of which is due to the chemical reactions at their surface. This thesis is a contribution to the understanding of this heterogeneous reactivity, catalycity, with the tools of theoretical chemistry. A method to build a global potential energy surface is developed and applied to the study of elementary processes dynamics (dissociative molecular adsorption, atomic absorption, Eley-Rideal recombination …) for the N,N2/W(100,110) and O,O2/Cu(100) chemical systems. These approaches are then coupled with a kinetic model quantifying catalycity.

La collision entre l'ion hydroxyle (OH+) et l'atome d'hydrogène (H) joue un rôle majeur en physico-chimie de l'atmosphère et en astrophysique. Pour l'étude de ce système, nous avons générés la surface d'énergie potentielle tridimensionnelle (SEP-3D) globale doublet de la réaction H + OH+ --- H2O+ (X2B1)--- O + H2+. Les calculs électroniques ont été effectués au niveau MRCI avec la base aug-cc-pV5Z en incluant la correction des erreurs de superposition de base (BSSE). Cette SEP couvre la région moléculaire et les régions des longues portées pour les différents canaux : OH+ + H, O + H2+ et la réaction d'échange d'hydrogène. La qualité de la SEP a été validée après une comparaison des constantes spectroscopiques de H2O+ (X2B1) et des fragments diatomiques, des niveaux rovibroniques de H2O+ (X2B1), l'énergie de dissociation et de la barrière à linéarité pour H2O+ (X2B1) aux données expérimentales et théoriques existantes. Un bon accord est trouvé. Après avoir déterminé la SEP, nous avons utilisé les outils de la dynamique quantique indépendante du temps pour calculer les sections efficaces élastiques et inélastiques désexcitation de OH+ (v=0, j=1, 2, 3, 4, 5, 6 et 7) en collision avec l'atome d'hydrogène sur un large domaine d'énergie cinétique. Nous avons ainsi déterminé les taux désexcitation rotationnelle pour des températures allant de 10 à 200K. Nous avons également utilisé la surface quadruplet de Martinez et al. pour déduire ces taux désexcitation. Les résultats montrent que les sections efficaces inélastiques calculées sur la surface doublet sont en moyenne au moins deux à trois fois plus importantes que leurs correspondantes obtenues sur la surface quartet. Les potentiels à longue portée des deux surfaces étant identiques, ce résultat montre qu'un modèle basé sur la seule longue portée du potentiel ne pourrait pas rendre compte de la dynamique inélastique de ce système / The collision between the hydroxyl cation (OH+) and hydrogen atoms (H) plays a major role in physical chemistry of the atmosphere and astrophysics. To study this system, we generated the global three-dimensional potential energy surface (3D-PES) of the reaction H + OH+ ---- H2O+ (X2B1) ---- O + H2+. The electronic calculations were performed at the MRCI level with aug-cc-pV5Z basis including the basis set superposition error (BSSE) correction. This PES covers the molecular region and the long ranges close to the OH+ + H, O + H2+ and the hydrogen exchange channels. The quality of the PES is checked after comparison of the spectroscopic constants of H2O+ (X2B1) and of the diatomic fragments, the rovibronic levels, the dissociation energy, and the barrier to linearity of H2O+ (X2B1) to available experimental and theoretical data. A good agreement is found. Then, we used the tools of time-independent Quantum Dynamics to calculate the elastic and inelastic cross sections for the de-excitation of OH+ in collision with the hydrogen atom over a wide range of kinetic energy. We have thus determined the rotational de-excitation rate coefficients for temperatures ranging from 10 up to 200K. The results show that the inelastic cross sections on the doublet surface are on average at least two to three times larger than their cross section obtained on the previously computed cross sections using the quartet surface. Since, the long range parts of the doublet and the quartet PESs are identical, our work invalidates hence previous cross section determination. When only long range potentials are considered. Therefore, we recommend using fully the global 3D PES for scattering and reactive collision relevant for atmospheric and astrophysical studies

The existence of highest proton numbers at which the nuclear landscape cease to ex- ist, the end of the periodic table of elements and the limits of the existence of the nu- clei are some of the difficult questions to answer. To explore those questions, we in- vestigated hyperheavy nuclei (Z ≥ 126) using covariant density functional theory. We demonstrate the existence of three regions of spherical hyperheavy nuclei centered around (Z ∼ 138, N ∼ 230), (Z ∼ 156, N ∼ 310) and (Z ∼ 174, N ∼ 410). Also, we explored other properties of hyperheavy nuclei such as octupole deformation, alpha decay half lives, chemical potential, etc.

This dissertation focuses on computational study of the geometry and energetics small molecules and nanoclusters involving transition metals (TM). These clusters may be used for various industrial applications including catalysis and photonics. Specifically, in this work we have studied hydrides and carbides of 3d-transition metal systems (Sc through Cu), small nickel and gold clusters. Qualitatively correct description of the bond dissociation is ensured by allowing the spatial and spin symmetry to break. We have tested applicability of new exchange-correlation functional and alternative theoretical descriptions (spin-contamination correction in broken symmetry DFT and ensemble Kohn-Sham (EKS)) as well. We studies TM hydrides and carbides systems to understand the importance of underlying phenomenon of bond breaking in catalytic processes. We have tested several exchange-correlation functionals including explicit dependence on kinetic energy density for the description of hydrides (both neutral and cationic) and carbides formed by 3d-transition metals. We find M05-2x and BMK dissociation energies are in better agreement with experiment (where available) than those obtained with high level wavefunction theory methods, published previously. This agreement with experiment deteriorates quickly for other functionals when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Higher fraction of HF exchange is also essential in EKS formalism, but it does not help when spin-adapted unrestricted approach is employed. We analyze the electron spin densities using Natural Bond Orbital population analysis and find that simple description of 3d electrons as non-bonding in character is rarely correct. Unrestricted formalism results in appreciable spin-contamination for some of the systems at equilibrium, which motivated us to investigate it further in details. In order to correct the spin contamination effect on the energies, we propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). We validate our spin-contamination correction approach by a simple example of H2 and applied to more complex MnH system. Ensemble KS formalism is also applied to investigate the dissociation of C2 molecule. We find that high fraction of HF exchange is essential to reproduce the results of EKS treatment with exact exchange-correlation functional. We analyze the geometry and energetics of small nickel clusters (Ni2-Ni5) for several lowest energy isomers. We also study all possible spin states of small nickel cluster isomers and report observed trends in energetics. Finally we determine the geometry and energetics of ten lowest energy isomers of four small gold clusters (Au2, Au4, Au6, and Au8). We have also investigated the influence of cluster geometry, ligation, solvation and relativistic effects on electronic structure of these gold clusters. The effect of one-by-one ligand attachment in vacuum and solvent environment is also studied. Performance of five DFT functionals are tested as well; Local Spin Density Approximation (SVWN5), Generalized Gradient Approximation (PBE), kinetic energy density-dependent functional (TPSS), hybrid DFT (B3LYP), and CAM-B3LYP which accounts for long-range exchange effects believed to be important in the analysis of metal bonding in gold complexes and clusters. Our results exhibit the ligand induced stability enhancement of otherwise less stable isomers of Au4, Au6 and Au8. Ligands are found to play a crucial role in determining the 2D to 3D transition realized in small gold clusters. In order to select an appropriate theory level to use in this study, we investigate the effect of attachment of four different ligands (NH3, NMe3, PH3, PMe3) on cluster geometry and energetics of Au2 and Au4 in vacuum and in solution. Our results benchmark the applicability of DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We employ five different basis sets with increasing amount of polarization and diffuse functions; LANL2DZ, LANL2DZ-P, def2-SVP, def2-TZVP, and def2-QZVP. We obtain NMe3 = NH3 > PH3 > PMe3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. Our results suggest appropriate quantum-chemical methodologies to model small noble metal clusters in realistic ligand environment to provide reliable theoretical analysis in order to complement experiments.

A full understanding of chemical reaction dynamics at the gas/organic-surface interface requires knowledge of energy-transfer processes that happen during the initial gas/surface collision. We have examined the influence of mass and rovibrational motion on the energy-transfer dynamics of gas-phase species scattering from model organic surfaces using theory and experiment. Molecular-beam scattering techniques were used to investigate the rare gases, Ne, Ar, Kr, and Xe, and the diatomics, N₂ and CO, in collisions with CH₃- and CF₃-terminated self-assembled monolayer (SAM) surfaces. Complementary molecular-dynamics simulations were employed to gain an atomistic view of the collisions and elucidate mechanistic details not observable with our current experimental apparatus. We developed a systematic approach for obtaining highly accurate analytic intermolecular potential-energy surfaces, derived from high-quality ab initio data, for use in our classical-trajectory simulations. Results of rare gas scattering experiments and simulations indicate mass to be the determining factor in the energy-transfer dynamics, while other aspects of the potential-energy surface play only a minor role. Additionally, electronic-structure calculations were used to correlate features of the potential-energy surface with the energy-transfer behavior of atoms and small molecules scattering from polar and non-polar SAM surfaces. Collisions of diatomic molecules with SAMs are seen to be vibrationally adiabatic, however translational energy transfer to and from rotational modes of the gas species, while relatively weak, is readily apparent. Examination of the alignment and orientation of the final rotational angular momentum of the gas species reveals that the collisions induce a stereodynamic preference for the expected "cartwheel" motion, as well as a surprising propensity for "corkscrew" or "propeller" motion. The calculated stereodynamic trends suggest that the CH₃-SAM is effectively more corrugated than the CF₃-SAM. Finally, the feasibility for collisional-energy promoted, direct gas/organic-surface reactions was interrogated using the 1,3-dipolar azide-alkyne cycloaddition reaction. We found that geometrical constraints prevented the reaction from proceeding at the probed conditions. / Ph. D.

Comprehension of reactive chemical dynamics in the gas phase and at the gas/organic-surface interface and non-reactive dynamics at the interface between hydrophobic surfaces and water requires an understanding of the fundamental atomic and molecular interactions that undergird these important phenomena. In an effort to study these regimes of chemical interaction, we have performed computational simulations that probe the dynamics of chemical systems that exemplify each of these domains. To study gas-phase chemical dynamics, we reparametrized semiempirical Hamiltonians so that they can accurately describe the potential energy surfaces for two distinct atom+alkane reactions. In addition to their demonstrated accuracy, these methods possess the attractive quality of being computationally inexpensive enough to afford extensive direct-dynamics trajectory studies. Our results on the dynamics of atom+alkane hydrogen-abstraction reactions have shown good agreement with experimental metrics that are as diverse as product velocity distributions, excitation functions, angular distributions and rovibrational state distributions for diatomic products of the abstraction. We have demonstrated that our reparametrized Hamiltonians are suitable for investigating gas-phase reactions with up to 15 (5 heavy) atoms and that they are appropriate for studying reactions beyond the gas phase, especially gas/surface reactions. By employing our semiempirical methods within a quantum-mechanics/molecular-mechanics hybrid scheme we are able to examine hydrogen-abstraction reactions of fluorine atoms with alkanethiolate self-assembled monolayers. Our simulations reproduce the general trends of experimental results for the cousin F+squalane reaction. Our simulations also probe the role that secondary collisions play in determining the final internal and translational energy of the product HF molecules. For instance, we determined that very few interactions with the SAM surface were required to cool rotational and translational modes of the HF product, while its vibrational energy remains unchanged on the time scale that HF molecules trap on the SAM surface. Moving beyond the gas/organic surface interface, we have also performed molecular-dynamics simulations of thin water films confined between hydrophobic SAM surfaces. These simulations illuminated the structural and dynamics behavior induced in the water films by confinement in hydrophobic environments. While most effects of the surface do not penetrate deep into the water layers we have noted that enhanced lateral diffusion of water molecules can persist in these films with > 1 nm length scales. We have elucidated a possible mechanistic precursor for the attractive forces seen in experimental measurement of the hydrophobic effect. / Ph. D.

D’immenses progrès ont été réalisés ces dernières années dans le champ de production de condensats de Bose-Einstein moléculaires pour l’obtention et le piégeage de molécules ultrafroides ioniques et neutres. Ces échantillons de molécules ultrafroides trouvent des applications dans des domaines très variés tels que les mesures pectroscopiques de haute précision ou bien encore le stockage de l’information quantique. La volonté d’optimiser les procédés de refroidissement et des techniques de piégeage a stimulé un grand nombre d’études théoriques. La plupart de ces études sont dédiées au refroidissement des molécules en collision avec un gaz tampon (3 He). La surface d’énergie potentielle de l’état fondamental du complexe de van der Waals He–MnH(X7Σ+) est présentée, suivie du calcul des états liés correspondant au complexe ainsi que l’étude de la relaxation Zeeman associée au système en fonction du champ magnétique appliqué. Dans le domaine de l’astrochimie, l’étude de la désexcitation rotationnelle de CH+ en collision avec l’hélium est également présentée. / Tremendous progress in experimental production and trapping of ultracold neutral and ionic molecules has been achieved over the past few years which even allowed the production of molecular Bose–Einstein condensates. These ultracold molecules samples have potential applications in many different fields, such as precision spectroscopic measurements or quantum information storage and processing. The optimization of the cooling processes and the trapping techniques also stimulated a great number of theoretical studies. Many of them are dedicated to inelastic scattering of molecules in collisions with 3He atoms (buffer gas cooling method). The potential energy surface of the ground state of the He–MnH(X7Σ+) van der Waals complex is presented, followed by the calculations of the bound states of this system and the Zeeman relaxation in function of the magnetic field. In the field of astrochemistry, a quantum mechanical investigation of rotational energy transfer in cold collisions of CH+ with 4He atoms is presented.