Iron (Fe) exerts strong control over environmental biogeochemistry. As the fourth most abundant element, Fe is present in nearly all earth environments, where it plays important roles in governing the transformation and movement of organic and inorganic constituents, and in microbial respiration. Consequently, the body of work on Fe biogeochemistry is vast. This study is specifically concerned with the dynamic changes in the oxidation state of Fe (i.e., redox cycling) and their impact on the inorganic, organic and microbial components in soil. I constructed a special apparatus to fluctuate redox potential on soil slurries while concurrently sampling a wide range of biogeochemical variables (pH, redox potential, major and trace elements, CO2 release, DNA community composition charges, etc.). Previous research has documented redox fluctuations along a climate gradient in Hawaii and a primary goal of this dissertation was to reconstruct these redox fluctuations, subjected to experimental constraints afforded by a laboratory setting, with minimal disruption to the biogeochemical processes controlling Fe redox cycling. By recasting the spatial and temporal characteristics of in situ Fe redox cycling in the laboratory, I was able to form testable hypotheses regarding the importance of Fe redox oscillations to soil mineral transformations, colloid composition/dynamics and microbial community structure. A second goal of this dissertation was to explore the utility of Fe isotopic composition for providing information on soil weathering processes along age and climate gradients at the field scale in Hawaii. This portion of the study tested emerging theories of Fe isotope fractionation during mineral dissolution using well-characterized sequences in soil weathering intensity.The principal findings of the laboratory redox fluctuation experiments are that Fe redox oscillations: (1) trigger an increase in the crystallinity of Fe-oxides; (2) mobilize colloids containing refractory elements (e.g., Zr, Nb, U, etc.); (3) reveal redox sensitive rare earth element (REE) anomalies in the aqueous phase; and (4) induce changes in the microbial community favoring microbes capable of growth under both oxic and anoxic conditions. The principal finding of the Fe isotope measurements is that isotopic composition is directly related to weathering intensity in the field, consistent with theoretical predictions.

El objeto principal de mi tesis es el desarrollo de nuevos complejos polipiridílicos de rutenio, mas concretamente complejos Ru-aguo. Una de las propediades mas interesantes que presentan este tipo de complejos es su capacidad para llevar a cabo un proceso de ”Proton Coupled Electron Transfer”. Este proceso le permite acceder a estados de oxidación elevados. Este es un requisito para ejecutar catálisis redox. Como interesante aplicaciones podemos nombrar la transformación de sulfitos a sulfoxidos (sulfoxidación) y la oxidación de agua a oxígeno molecular. Al principio del manuscrito se presentan complejos mononucleares de rutenio que contienen el ligando DMSO. Los resultados obtenidos respecto la isomerización de enlace están conectados con los resultados obtenidos durante la sulfoxidación utilizando los correspondientes complejos Ru(H2O). El segundo campo de interés esta basado en la oxidación de agua a oxigeno molecular. Una variedad de complejos Ru(H2O) mono- y dinucleares son presentados. Estos se distinguen entre si en sus propiedades estéricas y electrónicas. Estas propiedades están realizadas con su reactividad respeto la oxidación de agua a oxígeno molecular. Los resultados obtenidos permiten tener un mayor conocimiento sobre el mecanismo, formando una base para el futuro desarrollo de nuevos catalizadores para la oxidación de agua. Un punto culminante de esta tesis es la presentación de un sistema capaz de oxidar agua a oxigeno utilizando la irradiación con luz visible. Este sistema consiste en uno de los complejos Ru(H2O) anteriormente descritos, un “photosensitizer” ([Ru(bpy)3]2+) y un aceptor de electrones ([CoCl(NH3)5]2+). Este tipo de reacción juega un papel importante como reacción en el ánodo / The main topic of my thesis is the development of new Ruthenium based polypyridyl complexes, with the focus on Ru-aquo compounds. These Ru-aquo compounds present the interesting property of undergoing proton coupled electron processes. This allows such compounds to reach high oxidation states, which is a requirement in redox catalysis. Applications of interest involve the transformation of sulfites into sulfoxides (sulfoxidation) and the oxidation of water to molecular oxygen (water oxidation). At first different mononuclear ruthenium compounds containing one or two DMSO ligands are presented. The obtained findings concerning S- to O-linkage isomerization are transferred and connected to results from catalysis using Ru(H2O)-compounds as catalysts. The second field of interest concerns water oxidation. A variety of mono- and dinuclear Ru(H2O)-compounds differing in electronic and steric properties are described. These differences are connected to the catalytic activity towards water oxidation reaction. New insights in the underlying reaction mechanisms are provided, which constitute a strong basis for the development of future water oxidation catalysts. One highlight of this thesis is the introduction of mononuclear Ru(H2O)-compounds combined with a [Ru(bpy)3]2+ and a CoIII sacrificial electron acceptor, which successfully produce molecular oxygen upon light irradiation. Light driven water oxidation as anode reaction and the recombination of the electrons and protons from the oxidation process at the cathode form a device called solar fuel cell, that once fully mature may play an important role in a future renewable energy system.

Constraint-based models of metabolism seldom incorporate capacity constraints on intracellular fluxes due to the lack of experimental data. This can sometimes lead to inaccurate growth phenotype predictions. Meanwhile, other forms of data such as fitness profiling data from growth competition experiments have been demonstrated to contain valuable information for elucidating key aspects of the underlying metabolic network. Hence, the optimal capacity constraint identification (OCCI) algorithm is developed to reconcile constraint-based models of metabolism with fitness profiling data by identifying a set of flux capacity constraints that optimally fits a wide array of strains. OCCI is able to identify capacity constraints with considerable accuracy by matching 1,155 in silico-generated growth rates using a simplified model of Escherichia coli central carbon metabolism. Capacity constraints identified using experimental fitness profiles with OCCI generated novel hypotheses, while integrating thermodynamics-based metabolic flux analysis allowed prediction of metabolite concentrations.

Remediation of trace element-contaminated sites must consider both the nature of the contaminants and environmental surroundings. This thesis examined treatments for two contamination scenarios. The first study characterized chromium dynamics during the redox-sorption treatment of aqueous hexavalent chromium with the reducing agent sodium dithionite and two iron oxides. Results showed that chromium was successfully removed from solution by precipitation and sorption. The iron oxide derived from ferric chloride had a greater sorption capacity for hexavalent chromium than the oxide derived from ferrous chloride. The second study examined the phytoextraction treatment of soils contaminated with multiple trace elements. Deschampsia caespitosa plants had better early growth in the contaminated high-organic matter soil than three Brassica species. However, D. caespitosa plants did not take up sufficient amounts of trace elements during the study to be considered useful for short-term phytoextraction. These findings are applicable to the development of effective trace element remediation methods.

Constraint-based models of metabolism seldom incorporate capacity constraints on intracellular fluxes due to the lack of experimental data. This can sometimes lead to inaccurate growth phenotype predictions. Meanwhile, other forms of data such as fitness profiling data from growth competition experiments have been demonstrated to contain valuable information for elucidating key aspects of the underlying metabolic network. Hence, the optimal capacity constraint identification (OCCI) algorithm is developed to reconcile constraint-based models of metabolism with fitness profiling data by identifying a set of flux capacity constraints that optimally fits a wide array of strains. OCCI is able to identify capacity constraints with considerable accuracy by matching 1,155 in silico-generated growth rates using a simplified model of Escherichia coli central carbon metabolism. Capacity constraints identified using experimental fitness profiles with OCCI generated novel hypotheses, while integrating thermodynamics-based metabolic flux analysis allowed prediction of metabolite concentrations.

The tumor suppressor p53 has a close relation with reactive oxygen species (ROS). As an indispensable component of the cellular redox system, ROS not only have been established to be involved in p53-dependent apoptosis, but also regulate p53 activity. Recent studies revealed several novel actions of p53, such as transactivation of antioxidative proteins, mitochondria translocation and inhibition of glycolysis. The fate of cells where p53 signaling pathways are initiated is either survival or death. In this review, we examine the hypothesis that ROS regulate cell fate through p53, in a way that physiological ROS levels trigger the protective pathways, while p53 behaves more like a cell killer under cytotoxic oxidative stress.

In cellular respiration, electron transfer from the breakdown of foodstuff is coupled to the formation of an electrochemical proton gradient. This is accomplished through proton translocation by respiratory complexes, and the proton gradient is subsequently used e.g. to drive ATP production. Consequently, proton- and electron-transfer reactions through the hydrophobic interior of membrane proteins are central to cellular respiration. In this thesis, proton- and electron transfer through an aa3-type terminal oxidase, cytochrome c oxidase (CytcO) from Rhodobacter sphaeroides, have been studied with the aim of understanding the molecular proton-transfer machinery of this proton pump. In the catalytic site of CytcO the electrons combine with protons and the terminal electron acceptor O2 to form water in an exergonic reaction that drives proton pumping. Therefore, CytcO must transfer both protons that are pumped and protons for the oxygen chemistry through its interior. This is done through its two proton-transfer pathways, termed the D pathway and the K pathway. Our studies have shown that the protons pumped during oxidation of CytcO are taken through the D pathway, and that this process does not require a functional K pathway. Furthermore, our data suggests that the K pathway is used for charge compensation of electron transfer to the catalytic site, but only in the A2 → P3 state transition. Our data also show that the water molecules identified in the crystal structures of CytcO play an important role in proton transfer through the D pathway. Finally, the effects of liposome reconstitution of CytcO on D-pathway proton transfer were investigated. The results suggest that the membrane modulates the rates of proton transfer through the D pathway, and also influences the extent of electron transfer between redox-active sites CuA and heme a.

Remediation of trace element-contaminated sites must consider both the nature of the contaminants and environmental surroundings. This thesis examined treatments for two contamination scenarios. The first study characterized chromium dynamics during the redox-sorption treatment of aqueous hexavalent chromium with the reducing agent sodium dithionite and two iron oxides. Results showed that chromium was successfully removed from solution by precipitation and sorption. The iron oxide derived from ferric chloride had a greater sorption capacity for hexavalent chromium than the oxide derived from ferrous chloride. The second study examined the phytoextraction treatment of soils contaminated with multiple trace elements. Deschampsia caespitosa plants had better early growth in the contaminated high-organic matter soil than three Brassica species. However, D. caespitosa plants did not take up sufficient amounts of trace elements during the study to be considered useful for short-term phytoextraction. These findings are applicable to the development of effective trace element remediation methods.

Ligand design plays an important role in the development and control of new coordination compounds. A new ligand architecture, Nindigo, has previously been reported and this study represents an expansion of that research to gain better insights into the attributes of this multifunctional ligand family. Mono- and bis-palladium chelates of Nindigo have been synthesized with resulting electrochemical measurements allowing for the reversible redox-active nature of the ligand set to be identified. The electronic absorption properties of these complexes were also studied. The presence of the palladium centre was found to drastically perturb the ligand centered π-π* transition resulting in significant red shifts in the absorption spectra with respect to free Nindigo. The main group coordination chemistry of Nindigo was explored by generating mono- and bis-BF2 Nindigo chelates. The electrochemical and spectral properties of these compounds were investigated with both families displaying weak emission in the NIR region. The bis-BF2 chelates were found to be sensitive in nature and decompose to the mono-BF2 chelates. In addition, heteroleptic complexes of mono-BF2 Nindigo chelates with palladium were also synthesized. The redox chemistry as well as the electronic absorption characteristics of these compounds provides a conceptual bridge between the two homologues. Homoleptic zinc and copper complexes of mono-BF2 Nindigo chelates have been synthesized. The zinc derivative serves as an “innocent” system where all redox and spectral properties are ligand centered and the oxidation states of both the metal and surrounding ligands can be assigned. The copper complexes exhibit more diverse chemistry with the redox and electronic absorption properties differing dramatically from the zinc system. A combination of EPR, XPS and computational analysis suggests the copper systems to be non-innocent in nature. In addition to the bis-bidentate anionic Nindigo ligand system, the fully oxidized neutral analogue has also been synthesized. DehydroNindigo exhibits significantly different chemical behaviour from Nindigo. Bridged ruthenium dimers have been synthesized that are obtained as two isomers, cis and trans (with respect to the bridging ligand). Both isomers exhibit rich electrochemical behaviour. The mixed valence states of both species are found, electrochemically, to be extremely stable with respect to disproportionation. / Graduate / 0485 / 0488 / gnawn@uvic.ca

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