Threefoil is a small engineered protein of 141 amino acids which is a member of the beta-trefoil superfamily, with three-fold symmetry and high thermal and kinetic stability. Its primary sequence was designed based on a predicted beta-trefoil glycosidase from the halophilic Archaeon Haloarcula marismortui. Threefoil predominantly forms inclusion bodies when over-expressed in Escherichia coli at 37??C, with little to no protein soluble in the cytoplasm. Nevertheless, Threefoil is capable of adopting a native beta-trefoil structure when refolded from solubilized inclusion bodies. The focus of this thesis is on characterization of the folding and stability of Threefoil through thermodynamic and kinetic experiments for wild-type Threefoil, in addition to sugar- and metal-binding studies and characterization of Threefoil inclusion bodies. Various Threefoil mutants, designed to increase protein stability, are also characterized to probe the origins of, as well as to give insight into, the mechanism of inclusion body formation. The thermodynamic and kinetic stability of wild-type Threefoil was studied using spectral probes, mainly fluorescence, circular dichroism (CD) and dynamic light scattering (DLS). The major observed spectral changes in kinetic and thermodynamic experiments can be fit to a 2-state transition between the folded state and a denatured state containing extensive residual secondary structure. At high protein concentrations, the folding of wild-type Threefoil is complicated by protein misfolding and aggregation. As Threefoil is remarkably resistant to denaturation even at high concentrations of urea and guanidine hydrochloride (GuHCl), studies were also conducted in guanidine isothiocyanate (GuSCN), which is a much stronger denaturant than urea and GuHCl. Remarkably, the time that is required for Threefoil samples to reach equilibrium in renaturation curves is approximately 100 days, while equilibrium by denaturation in the stronger denaturant, GuSCN, requires more than two years. The expression levels of Threefoil mutants A62V, Q78I, D85P and D93P were also studied. None of the four mutants studied exhibited any pronounced increase in solubility compared to wild-type when expressed in E. coli.

Les nanoparticules (NPs) sont des matériaux fonctionnels importants du fait de leur taille nanométrique. Cette réduction en taille, associée à la composition, à l'orientation des surfaces et à la morphologie contribue à l'exaltation de nombreuses propriétés importantes telles que les propriétés électroniques, magnétiques, catalytiques, optiques, etc. Pour contrôler la morphologie des NPs, de nombreux efforts ont été consacrés à comprendre leurs mécanismes de formation et l'origine de leur stabilité. Parmi les nanoparticules métalliques, le cobalt, avec sa structure hexagonale compact (hcp), est particulièrement intéressant pour la possibilité d'obtenir des nanocristaux de forme "naturellement" anisotropique. Par synthèse chimique en milieu liquide, des NPs de différentes morphologies telles que des disques, des plaques, des bâtonnets, des fils et des cubes ont été obtenues en contrôlant le type de précurseur, de l'agent réducteur, des ligands stabilisants, ainsi que la concentration de ces ligands, la température ou la vitesse d'injection des précurseurs. Même si ces conditions de synthèse ont été rationalisées, les mécanismes à l'origine de ces différentes morphologies ne sont pas encore bien connus. Dans ce travail, nous avons développé deux modèles quantitatifs pour la prédiction de la morphologie, l'un est basé sur l'équilibre thermodynamique de l'état final, et l'autre sur un contrôle par l'effet cinétique. Pour appliquer ces modèles, il a été nécessaire de calculer dans un premier temps, avec la théorie de la fonctionnelle de la densité (DFT), les comportements d'adsorption des molécules ligands en fonction du taux de recouvrement sur les facettes de différentes orientations du métal. Pour ce faire, l'adsorption des ligands CH 3 NH 2 , CH 3 COO, C 5 H 11 COO et C 11 H 23 COO a été modélisée sur les différentes surfaces de Co et de Ni. La morphologie des NPs de Co prédite par ces deux modèles a été comparée à celles obtenues expérimentalement et à d'autres résultats théoriques de la littérature. La variété des formes obtenues par le modèle cinétique semblerait mieux correspondre aux NPs synthétisées avec les différentes conditions expérimentales. Ceci confirme que la morphologie des NPs est guidée avant tout par un effet cinétique. / Nanoparticles are one of the most important families of functional materials due to their nanometric size. This size reduction, associated to their composition, surfaces orientation and morphology has contributed to the emergence of new important properties such as electronic, magnetic, catalytic, optic, etc. To control the morphology of NPs, many efforts have been devoted to understand their formation mechanism and the origin of their stability. Among metallic nanoparticles, cobalt, with its hexagonal closed-packed (hcp) structure, is particularly interesting because of the possibility to grow "naturally" anisotropic shaped nanocrystals. Using chemical synthesis in liquid environment, various morphologies such as disks, plates, rods, wires and cubes have been obtained by controlling the precursor type, the reducing agent, the stabilizing ligands as well as their concentration, the temperature or the rate of precursor injection. Even if these synthesis conditions have been rationalized, few is known concerning the growth mechanisms at the atomic scale. In this work, we have developed two quantitative morphology prediction models, one based on the final thermodynamic equilibrium state, while another is controlled by the kinetics. These models require the knowledge of the adsorption behaviors of stabilizing molecules as a function of surface coverage on preferential facets of NPs. To this end, density functional theory (DFT) calculations were performed on a series of stabilizing molecules (CH3NH2 , CH3COO C5H11OO and C11H23COO) adsorbed on the different Co and Ni surfaces. The shape of the Co NPs obtained by these two models was compared to experimental morphologies and other theoretical results from the literature. The variety of forms predicted by the kinetic model agrees better with the NPs morphologies obtained under the different synthesis conditions. This confirms that the morphology control of NPs is mostly driven by the kinetics.

The influence of grain boundary and interphase junctions on the thermodynamics and kinetics of grain growth in nanocrystalline materials is considered. The presented results of current experimental measurements of the grain boundary and grain boundary – free surface triple junctions give the opportunity to estimate quantitatively the influence of the junctions on the kinetics of the grain growth and on the evolution and stability of nanocrystalline systems.

Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 219-242). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

This thesis addresses the syntheses towards high quality CdSe and CdTe nanoparticles. Therefore, thermodynamic and kinetic aspects of the hot injection method are investigated. By means of the introduction of a thermodynamically less favored nuclei species the nucleation event of CdSe quantum dot synthesis is affected. Utilizing highly reactive tin or lithium silylamides, primarily formed SnSe or Li2Se nuclei undergo a cation exchange to the demanded CdSe particles. The further growth proceeds without the incorporation of the so called quasi-seed species. In this manner, the mechanism of the cation exchange-mediated nucleation is proven and optimized with respect to the required amount of the quasi-seed species. Furthermore, this protocol is applied to up-scaling attempts to reduce the efforts for optimization to a minimum. Following this, a successful laboratory batch up-scaling is achieved by increasing flask size as well as precursor concentrations by factors of 2 and 10, respectively. A further possibility to thermodynamically influence the hot injection synthesis is the activation of the precursor species. By altering the injection pathway, as compared to the standard synthesis, the precursor species are differently coordinated and hence possess different thermodynamic stabilities. Investigations on the system of CdTe quantum dots lead to the result of a cation activation by the use of the thermodynamically less stable carboxylate ligands instead of phosphonates. Additionally, anion activation is suggested due to a kind of aging of the phosphine ligands via their oxidation by phosphonic acids. Furthermore, it is found that the ratio of Cd-to-Te strongly influences the formation of so called magic-sized clusters. Following the results, the smallest detectable species is determined as a cluster species with a size of 1.8 nm. The role of the magic-sized clusters is not fully resolved, but the initial growth is assumed to occur via monomer deposition onto or the fusion of the observed clusters. On the other hand, cluster dissolution is thermodynamically forced by the decreasing monomer concentration and can simply be explained by the process of Ostwald ripening via the creation of a smaller cluster species. Mechanistically this is explained by the formation of configurational deviations from the ideal closed-shell structure. Finally the inorganic coating of the core quantum dots in investigated. Therefore, homoepitaxial coating is employed to overcome the limit in particle size by introducing additional monomer supply. As a result, following the classical crystallization theory, defined injections of precursor material during the diffusion limited growth regime allow a fine tuning of the final particle size. Nevertheless, homoepitaxial coating inevitably leads to photoluminescence quenching, whereas heteroepitaxial growth usually improves the optical quality. By means of a type I structure, CdSe/CdS/ZnS, the successive ion layer adsoption and reaction mechanism is discussed. Furthermore, alloy structures of CdSe/ZnSe with a radially gradated intermediate shell of CdZnSe are achieved by postsynthetic high temperature treatments. This annealing induces internal diffusion processes and allows exactly adjusting the emission wavelength due to defined shrinkage of the initial core size during the alloying process.

Catalysis is a key area of chemistry. Through catalysis it is possible to achieve better synthetic routes, exploit molecules normally considered to be inactive and also attain novel chemical transformations. The development of new catalysts is crucial to furthering chemistry as a field. Computational chemistry, arising from applying the equations of quantum and classical mechanics to solving chemical problems, offers an essential route to investigating the underlying atomistic detail of catalysis. In this thesis calculations have been applied towards studying a number of different catalytic processes. The processing of renewable chemical sources via homogeneous reactions, specifically cardanol from cashew nuts, is discussed. All routes examined for monoreduction of a diene model by [Ru(H)(iPrOH)(Cl)(C₆H₆)] and [Ru(H)(iPrOH)(C₆H₆)]⁺ are energetically costly and would allow for total reduction of the diene if they were operating. While this accounts for the need of high temperatures, further work is required to elucidate the true mechanism of this small but surprisingly complex system. Gold-mediated protodecarboxylation was examined in tandem with experiment to find the subtle steric and electronic effects that dictate CO₂ extrusion from gold N-heterocyclic carbene activated benzene-derived carboxylic acids. The origin of a switch in the rate limiting step from decarboxylation to protodeauration with less activated substrates was also clearly demonstrated. Studies of gold systems are closed with examinations of 1,2-difluorobenzene C–H activation and CO₂ insertion by [Au(IPr)(OH)]. Calculations highlight that the proposed mechanism for oxazole-derived substrates cannot be extended to 1,2-difluorobenzene and instead a digold complex offers more congruent predicted kinetics. The lens of quantum chemistry was turned upon palladium-mediated methoxycarbonylation reactions. An extensive study was undertaken to attempt to understand the bidentate diphosphine ligand dependency on forming either methylpropanoate (MePro) or copolymers. Mechanisms currently suggested in literature are shown to be incongruous with the formation of MePro by Pd(OAc)₂ and bulky diphosphines. A possible alternative route is proposed in this thesis. Four mechanisms for methoxycarbonylation with Pd(2-PyPPh₂)ₙ are detailed. The most accessible route is found to be congruent with experimental reports of selectivity, acid dependency and slight steric modifications. A modification of 2-PyPPh₂ to 2-(4-NMe₂-6-Me)PyPPh₂ is shown to improve both selectivity and turnover, the latter by four orders of magnitude (highest transition state from 22.9 kcal/mol to 16.7 kcal/mol ∆G), and this new second generation in silico designed ligand is studied for its applicability to wider substrate scope and different solvents. The final chapter of this thesis is a mixed quantum mechanics and molecular mechanics (QM/MM) examination of an enzymatic reaction, discussing the need for certain conditions and the role of particular amino acid residues in an S[sub]N2 hydrolysis reaction.