Theoretical studies of mononuclear non-heme iron active sites

The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined. The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.

Chemical Bonding of Hydrocarbons to Metal Surfaces

Using x-ray absorption spectroscopy (XAS), x-ray emission spectroscopy (XES) and x-ray photoelectron spectroscopy (XPS) in combination with density functional theory (DFT) the changes in electronic and geometric structure of hydrocarbons upon adsorption are determined. The chemical bonding is analyzed and the results provide new insights in the mechanisms responsible for dehydrogenation in heterogeneous catalysis. In the case of alkanes, n-octane and methane are studied. XAS and XES show significant changes in the electronic structure upon adsorption. XES shows new adsorption induced occupied states and XAS shows quenching of CH*/Rydberg states in n-octane. In methane the symmetry forbidden gas phase lowest unoccupied molecular orbital becomes allowed due to broken symmetry. New adsorption induced unoccupied features with mainly metal character appear just above the Fermi level in XA spectra of both adsorbed methane and n-octane. These changes are not observed in DFT total energy geometry optimizations. Comparison between experimental and computed spectra for different adsorbate geometries reveals that the molecular structures are significantly changed in both molecules. The C-C bonds in n-octane are shortened upon adsorption and the C-H bonds are elongated in both n-octane and methane. In addition ethylene and acetylene are studied as model systems for unsaturated hydrocarbons. The validity of both the Dewar-Chatt-Duncanson chemisorption model and the alternative spin-uncoupling picture is confirmed, as well as C-C bond elongation and upward bending of the C-H bonds. The bonding of ethylene to Cu(110) and Ni(110) are compared and the results show that the main difference is the amount of back-donation into the molecular π* orbital, which allows the molecule to desorb molecularly from the Cu(110) surface, whereas it is dehydrogenated upon heating on the Ni(110) surface. Acetylene is found to adsorb in two different adsorption sites on the Cu(110) surface at liquid nitrogen temperature. Upon heating the molecules move into one of these sites due to attractive adsorbate-adsorbate interaction and only one adsorbed species is present at room temperature, at which point the molecules start reacting to form benzene. The bonding of the two species is very similar in both sites and the carbon atoms are rehybridized essentially to sp2.

Computational chemistry studies of UV induced processes in human skin

This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility. A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum. A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield. Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a SN1 type of mechanism seems the most efficient one.

Local Structure of Hydrogen-Bonded Liquids

Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding. This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified. Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.