The structural, electronic, and superconducting properties of one dimensional materials are calculated from first principles, using the density functional theory. Nanotubes and nanowires are important building blocks in nanotechnology, in particular for nanoelectronics. In this manuscript, the growth of carbon nanotubes is studied through the interaction between carbon and the transition metal atoms used as growth catalysts. The accepted model for a new phase of nanotube-like molybdenum disulfide is critically examined using comparisons of energetic stability and types of chemical bonding in different candidate structures which have similar compositions. The epitaxial growth of diamond carbon on (100) iridium is exceptionally favorable. The differences between various substrates used experimentally are studied, and the specificity of Ir is shown. Finally, the characteristics of the electron-phonon interaction in aluminium nanowires are determined. The structural instabilities and the differences in the electron-phonon coupling are calculated for straight monoatomic wires, zigzag wires, and thicker straight wires. The constrained geometry of the wires generates a coupling which can be very strong or almost vanish, depending on the structural details, but which is concentrated in the longitudinal high-frequency phonons.

A new method for the preparation of seven-membered carbocycles via cobalt-mediated [5+2] cycloaddition methodology is presented. We have demonstrated that Cp*Co(5-pentadienyl)+ systems undergo cycloaddition reactions with alkynes in a diastereocontrolled and high-yielding process. When acetylene is employed as the cycloaddition partner, unprecedented Cp*Co(2,3-cycloheptadienyl)+ complexes were isolated as the cycloaddition product under kinetic control. These allyl/olefin species were further transformed to the thermodynamic Cp*Co(5-cycloheptadienyl)+ complexes. Also described are two methods for the preparation of high-valent Co(III) 5-pentadienyl complexes, a compound class that has been under-reported in the literature. This work fills this void and provides a valuable view of the structural properties of 5-pentadienyl complexes as a function of the substitution pattern. The incorporation of tethered pronucleophiles onto the pentadienyl ligand allowed the preparation of fused bicyclic structures of relevance to natural product synthesis. Both conjugated and unconjugated cycloheptadiene species were prepared, made possible via the differing cycloheptadienyl complex hapticity. The oxidative decomplexation of the organic products is also described. Initial steps towards a divergent pronucleophile-bearing pentadienyl synthesis were also undertaken. The mechanism and structure/reactivity relationships for the [5+2] cycloaddition process were studied via density functional theory calculations. These investigations revealed the existence of several convergent reaction pathways on the potential energy surface, and provided a new rationale for the 2,35 isomerization, thereby explaining the low activation barrier for the isomerization of 2-butyne cycloadducts. Of interest is the elucidation of a radical-type pathway, calculated to be of high energy for the Cp* ligand system, yet energetically competitive in the Cp complex reaction manifold. Further, computations on the Cp system demonstrate a potentially viable pathway on the triplet energy surface, suggesting spin-forbidden transitions may play a role in the mechanism. These observations provide an explanation for the differing cycloaddition efficiencies in these two pentadienyl systems. Calculations also suggest that reaction chemoselectivity is determined during the rate-limiting alkyne complexation step; the energetics of this process being dominated by steric interactions between the pentadienyl substituents and the ancillary ligand.

This Ph.D. dissertation is focused on the investigation the structure of nitrile anion containing molecules and how the structure and reactivity of those molecules are affected by solvation and counter ion. A systematic approach was employed in this investigation, beginning with an evaluation of the accuracy of three commonly used model chemistries (Hartree-Fock (HF), Second-order Møller-Plesset perturbation theory (MP2), the Becke three-parameter exchange functional coupled with the nonlocal correlation functional of Lee, Yang, and Parr (B3LYP), all paired with the 6-31+G(d) basis set). A series of complexes of various cations with a number of explicit molecules of tetrahydrofuran (THF) and dimethyl ether (DME) were studied with these model chemistries and the results were compared, where possible, with experimental results. From this work, it was determined that the B3LYP models gave the most accurate results for the complexes in question. This work was then extended to acetonitrile anion containing complexes of solvent and cation. Based on the results of that extension, it was determined that cation size and charge density on the cation were critical factors in determining the structure of the acetonitrile anion molecule and in determining if the anion was metalated at the nitrogen or alpha-carbon position, with larger cations favoring carbon metalation and more significant deformation of the alpha-carbon from the expected sp2 hybridization. The final aspect of this dissertation was the determination of reaction coordinate energy profiles for a pair of substitution reactions involving nitrile anion containing cycloaliphatic molecules. The results of this study showed that, due to steric and kinetic factors, the axial products and transitions states associated with these reactions were favored, and that the degree of preference was kinetically controlled. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / PhD / Dissertation

No description available.

The structural, electronic, and superconducting properties of one dimensional materials are calculated from first principles, using the density functional theory. Nanotubes and nanowires are important building blocks in nanotechnology, in particular for nanoelectronics. In this manuscript, the growth of carbon nanotubes is studied through the interaction between carbon and the transition metal atoms used as growth catalysts. The accepted model for a new phase of nanotube-like molybdenum disulfide is critically examined using comparisons of energetic stability and types of chemical bonding in different candidate structures which have similar compositions. The epitaxial growth of diamond carbon on (100) iridium is exceptionally favorable. The differences between various substrates used experimentally are studied, and the specificity of Ir is shown. Finally, the characteristics of the electron-phonon interaction in aluminium nanowires are determined. The structural instabilities and the differences in the electron-phonon coupling are calculated for straight monoatomic wires, zigzag wires, and thicker straight wires. The constrained geometry of the wires generates a coupling which can be very strong or almost vanish, depending on the structural details, but which is concentrated in the longitudinal high-frequency phonons.

The Diels-Alder reaction is one of the most powerful synthetic tools in organic chemistry, and asymmetric Diels-Alder catalysis allows for rapid construction of chiral carbon scaffolds. For this reason, considerable effort has been invested in developing efficient and stereoselective organo- and biocatalysts. However, Diels-Alder is a virtually unknown reaction in Nature, and to engineer an enzyme into a Diels-Alderase is therefore a challenging task. Despite several successful designs of catalytic antibodies since the 1980’s, their catalytic activities have remained low, and no true artificial ’Diels-Alderase’ enzyme was reported before 2010. In this thesis, we employ state-of-the-art computational tools to study the mechanism of organocatalyzed Diels-Alder in detail, and to redesign existing enzymes into intermolecular Diels-Alder catalysts. Papers I–IV explore the mechanistic variations when employing increasingly activated reactants and the effect of catalysis. In particular, the relation between the traditionally presumed concerted mechanism and a stepwise pathway, forming one bond at a time, is probed. Papers V–X deal with enzyme design and the computational aspects of predicting catalytic activity. Four novel, computationally designed Diels-Alderase candidates are presented in Papers VI–IX. In Paper X, a new parameterization of the Linear Interaction Energy model for predicting protein-ligand affinities is presented. A general finding in this thesis is that it is difficult to attain large transition state stabilization effects solely by hydrogen bond catalysis. In addition, water (the preferred solvent of enzymes) is well-known for catalyzing Diels- Alder by itself. Therefore, an efficient Diels-Alderase must rely on large binding affinities for the two substrates and preferential binding conformations close to the transition state geometry. In Papers VI–VIII, we co-designed the enzyme active site and substrates in order to achieve the best possible complementarity and maximize binding affinity and pre-organization. Even so, catalysis is limited by the maximum possible stabilization offered by hydrogen bonds, and by the inherently large energy barrier associated with the [4+2] cycloaddition. The stepwise Diels-Alder pathway, proceeding via a zwitterionic intermediate, may offer a productive alternative for enzyme catalysis, since an enzyme active site may be more differentiated towards stabilizing the high-energy states than for the standard mechanism. In Papers I and III, it is demonstrated that a hydrogen bond donor catalyst provides more stabilization of transition states having pronounced charge-transfer character, which shifts the preference towards a stepwise mechanism. Another alternative, explored in Paper IX, is to use an α,β -unsaturated ketone as a ’pro-diene’, and let the enzyme generate the diene in situ by general acid/base catalysis. The results show that the potential reduction in the reaction barrier with such a mechanism is much larger than for conventional Diels-Alder. Moreover, an acid/base-mediated pathway is a better mimic of how natural enzymes function, since remarkably few catalyze their reactions solely by non-covalent interactions. / <p>QC 20120903</p>

No description available.

Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms. The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions. Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.

Computational methods are combined with synchrotron-based techniques to analyze the structure and bonding of water and water plus hydroxyl at metal surfaces under UHV and at near-ambient conditions. Water-metal interaction plays a crucial role in a multitude of cosmic, atmospheric and biological phenomena as well as heterogeneous catalysis, electrochemistry and corrosion. A spotlight of renewed interest has recently been cast on water-metal systems due to their relevance for surface chemical reactions related to the production and utilization of hydrogen as a clean energy carrier. In particular, H2O and OH are essential reaction intermediates in the renewable production of hydrogen from sunlight and water and in fuel cell electrocatalysis. Fuel cells are considered one of the most promising power generation technologies for a sustainable energy future. A mechanistic understanding of the oxygen reduction reaction (ORR) pathway, including the role of electronic and geometric structure of the catalyst, is essential to the design of more efficient fuel cell catalysts. This is intimately connected to fundamental factors that affect the ability to form water-metal bonds as well as the site occupation and orientation of the adsorbed H2O and OH at active metal surfaces. Key relationships related to critical issues in the fuel cell reaction are illuminated by the synergy of theory and experiment in this thesis. We emerge with a detailed understanding of the structure of the water-metal interface and the factors that rule the wettability of a metal surface, including geometric and electronic structure effects and the influence of coadsorbed species. We show that the preferred microscopic orientation of the water monolayer has consequences for macroscopic properties, and reveal the origin of the hydrophobic water layer. Finally, we identify a cooperativity effect that drives the stability of the mixed water/hydroxyl layer at metal surfaces, an important ORR intermediate.

Hydrogen is abundant, uniformly distributed throughout the Earth's surface and its oxidation product (water) is environmentally benign. Owing to these features, it is considered as an ideal synthetic fuel for a new world energetic matrix (renewable, secure and environmentally friendly) that could allow a sustainable future development. However, for this prospect to become a reality, efficient ways to produce, transport and store hydrogen still need to be developed. In the present thesis, theoretical studies of a number of potential hydrogen storage materials have been performed using density functional theory. In NaAlH4 doped with 3d transition metals (TM), the hypothesis of the formation of Ti-Al intermetallic alloy as the main catalytic mechanism for the hydrogen sorption reaction is supported. The gateway hypothesis for the catalysis mechanism in TM-doped MgH2 is confirmed through the investigation of MgH2 nano-clusters. Thermodynamics of Li-Mg-N-H systems are analyzed with good agreement between theory and experiments. Besides chemical hydrides, the metal-organic frameworks (MOFs) have also been investigated. Li-decorated MOF-5 is demonstrated to possess enhanced hydrogen gas uptake properties with a theoretically predicted storage capacity of 2 wt% at 300 K and low pressure. The metal-hydrogen systems undergo many structural and electronic phase transitions induced by changes in pressure and/or temperature and/or H-concentration. It is important both from a fundamental and applied viewpoint to understand the underlying physics of these phenomena. Here, the pressure-induced structural phase transformations of NaBH4 and ErH3 were investigated. In the latter, an electronic transition is shown to accompany the structural modification. The electronic and optical properties of the low and high-pressure phases of crystalline MgH2 were calculated. The temperature-induced order-disorder transition in Li2NH is demonstrated to be triggered by Li sub-lattice melting. This result may contribute to a better understanding of the important solid-solid hydrogen storage reactions that involve this compound.