Free Dioxygen Research Articles

Materials and pathways of the organic carbon cycle through time

The cycle of organic carbon through the atmosphere, oceans, continents and mantle reservoirs is a hallmark of Earth. Over geological time, chemical exchanges between those reservoirs have produced a diversity of reduced carbon materials that differ in their molecular structures and reactivity. This reactive complexity challenges the canonical dichotomy between the surface and deep, short-term and long-term organic carbon cycle. Old and refractory carbon materials are not confined to the lithosphere but are ubiquitous in the surface environment, and the lithosphere hosts various forms of reduced carbon that can be very reactive. The biological and geological pathways that drive the organic carbon cycle have changed through time; from a synthesis of these changes, it emerges that although a biosphere is required to produce organic carbon, mortality is required to ensure its export to the lithosphere, and graphitization is essential for its long-term stabilization in the solid Earth. Among the by-products of the organic carbon cycle are the accumulation of a massive lithospheric reservoir of organic carbon, the accumulation of dioxygen in the atmosphere and the rise of a terrestrial biosphere. Besides driving surface weathering reactions, free dioxygen has allowed the evolution of new metabolic pathways to produce and respire organic carbon. From the evolution of photosynthesis until the expansion of biomineralization in the Phanerozoic, inorganic controls on the organic carbon cycle have diversified, tightening the connection between the biosphere and geosphere. A review of the organic carbon cycle explores the interactions between the Earth’s surface and deeper reservoirs, the expanding inorganic controls on the organic carbon cycle, and how these links have strengthened through geological time.

On the Dynamical Behavior of the Cysteine Dioxygenase-l-Cysteine Complex in the Presence of Free Dioxygen and l-Cysteine.

In this work, viable models of cysteine dioxygenase (CDO) and its complex with l-cysteine dianion were built for the first time, under strict adherence to the crystal structure from X-ray diffraction studies, for all atom molecular dynamics (MD). Based on the CHARMM36 FF, the active site, featuring an octahedral dummy Fe(II) model, allowed us observing water exchange, which would have escaped attention with the more popular bonded models. Free dioxygen (O2 ) and l-cysteine, added at the active site, could be observed being expelled toward the solvating medium under Random Accelerated Molecular Dynamics (RAMD) along major and minor pathways. Correspondingly, free dioxygen (O2 ), added to the solvating medium, could be observed to follow the same above pathways in getting to the active site under unbiased MD. For the bulky l-cysteine, 600 ns of trajectory were insufficient for protein penetration, and the molecule was stuck at the protein borders. These models pave the way to free energy studies of ligand associations, devised to better clarify how this cardinal enzyme behaves in human metabolism.

Flower-like Cobalt Hydroxide/Oxide on Graphitic Carbon Nitride for Visible-Light-Driven Water Oxidation

Direct water oxidation via photocatalysis is a four-electron and multiple-proton process which requires high extra energy input to produce free dioxygen gas, making it exacting, especially under visible light irradiation. To improve the oxygen evolution reaction rates (OERs) and utilize more visible light, flower-like cobalt hydroxide/oxide (Fw-Co(OH)2/Fw-Co3O4) photocatalysts were prepared and loaded onto graphitic carbon nitride (g-C3N4) by a facile coating method in this work. Influenced by the unique three-dimensional morphologies, the synthesized Fw-Co(OH)2 or Fw-Co3O4/g-C3N4 hybrids reveal favorable combination and synergism reflected by the modified photoelectric activities and the improved OER performances. Attributed to its prominent hydrotalcite structure, Fw-Co(OH)2 shows better cocatalytic activity for g-C3N4 modification compared with that of Fw-Co3O4. Specifically, 7 wt % Fw-Co(OH)2/g-C3N4 photocatalyst exhibits photocurrent density 4 times higher and OER performance 5 times better than pristine g-C3N4. This work unambiguously promotes the application of sustainable g-C3N4 in water oxidation.

Fixation of Zinc(II) Ion to Dioxygen in a Highly Deformed Porphyrin: Implications for the Oxygen Carrier Mechanism of Distorted Heme.

Three saddle-type nonplanar zinc porphyrins strapped by two short alkyl linkers have been synthesized. The deformation induced by the linkers can cause a spectral red shift of >30 nm compared with the absorption maxima of regular porphyrins and can also regulate the electronic structure of the central zinc(II) ion. The zinc(II) ion then complexes and activates a free dioxygen to form a superoxide group ligand by enlarging the splitting of energy levels of d orbitals under strong core deformation. The fixation of dioxygen can be reasonably explained by the Dewar-Chatt-Duncanson model. These results indicate that this type of saddle porphyrin has the potential to be used as a new model system of heme.

Spin Transition during H2O2 Formation in the Oxidative Half-Reaction of Copper Amine Oxidases

Dioxygen reduction in the oxidative half-reaction of copper amine oxidases (CAOs) has been studied quantum chemically using the hybrid density functional theory (B3LYP). The reductive activation of dioxygen is a spin-forbidden process for which substantial kinetic O-18 (but no deuterium) isotope effects have been found experimentally. The proposed mechanism was divided into three steps, and the last step was studied for two different potential energy surfaces: the quartet and the doublet surfaces. It is suggested that dioxygen reduction occurs through a spin transition that is induced by the exchange interaction between the unpaired spins of the Cu(II) ion and the O2- anion. The step involving this spin transition is suggested to be rate-limiting, which gives a rationalization for the puzzling experimental results when copper is substituted for other metals. The spin transition is triggered by the calculated vibronic perturbation of 5.4 (kcal/mol) Å-1, which leads to a very fast rate of 8 × 1010 s-1 for the spin transition. However, since the spin transition occurs at a calculated energy that is 18−20 kcal/mol higher than that of the reactant, this step could still be rate-limiting. The difference in the O−O bond distance between the resting state (free dioxygen) and the point of the spin transition provides an explanation for the oxygen isotope effect.

Inorganic Geobiochemical Implications of the Oxic-Anoxic Transition in Ancient Earth Oceans

The development of free dioxygen in the Earth's atmosphere around 2.2Ga led to considerable biological changes. In particular, the early Earth biota was dominated by anaerobic prokaryotes including archaebacteria, possibly the most primitive life forms. Subsequent to the development of an oxic environment, aerobic bacteria and eventually prokaryotes developed. The inorganic biochemistry of the two groups are characterized in part by the relative dominance of nickel and cobalt proteins in the primitive anoxic group and the appearance of copper proteins in aerobic bacteria and multicellular organisms (Frausto di Silva and Williams 1996). Nickel and cobalt proteins are less important in aerobic organisms and copper is insignificant in the primitive anaerobes. Iron and zinc appear equally important throughout, although their dominant biochemical functions change. It is well established that base metal concentrations constitute limiting growth factors for present-day aerobic and anaerobic communities. For example, increasing oceanic iron concentrations enhances the growth of planktonic algae (Martin et al 1991). Iron has long been known as a limiting factor for the development of anaerobic sulphate reducing bacteria because of its importance to cytochrome c 3. (Postgate 1965). The present paper presents the results of a study of thermodynamic of oxic and anoxic ocean models based on the recent definition and discovery of a large number of base metal sulphide and polysulphide complexes (Luther et al. 1996; Chadwell et al. in prep). I assume that biological availability potentially embraces any soluble metal species and not only free metal aquo ions. The chemica l models were made using Geochemists Workbench | version 3.4 (GWB). The GWB seawater model has been discussed by Bethke (1996). The input thermodynamic database is a modified selection of the Lawrence Livermore National Labora tory thermodynamic dataset THERMO.COM.V8.R6.FULL. based on a compilation by Thomas Wolery and co-workers which is in turn largely based on Helgeson et al.(1978). The composition of early Earth oceans is not rigorously constrained and both acid and alkaline oceans have been proposed. I take a conservative view in this study, assuming that ocean composition is currently buffered by reaction with oceanic lithosphere and that this effect is likely to have been enhanced in the higher heat flow regimes of the ancient Earth. As a starting point, I therefore take the composition of the modem oxic oceans, which is fairly well defined. I then reduce it through the GWB reaction progress algorithm, basically by titrating electrons. During this process, the total major element concentration (excluding dioxygen) of the oceans remains constant. The pH remains around 8.0. In oxic oceans, inorganic base metal chemistry is dominated by free metal aquo ions, hydroxide, oxyhydroxide and chloride complexes. The database includes a number of simple base metal organic complexes, but these do not appear to affect the model and their stability constants may not be wellconstrained. In a n o x i c oceans , base metal speciation is simplified and their chemistry is largely controlled by sulphide and bisulphide complexes. The introduction of base metals (bi)sulphide complexes into the anoxic ocean model increases the relative dissolved concentrations of all base metals except Mn. The enhancement is approximately 2 magnitudes or more. This relative enhancement is independent of the sulphide mineral substrate. The total dissolved metal concentrations decrease markedly with peak concentrations around -200mV. The concentrations increase from around -300mV through -400mV. A feature of the anoxic ocean is the diminution of the free metal aquo ion concentrations. I took a computed dissolved metal concentration of 10 -15 M as being a limiting value for the presence of the metal in solution. The absolute concentrations of base metals in anoxic systems is not well constrained because of the lack of information about the nature of the metastable mineral sulphides. The increase in solubility of metastable compared with stable iron sulphides is better known. The first precipitated FeS

Electrochemical evidence for weak interaction between oxovanadium(IV) complexes and the dioxygen molecule

We have observed that the presence of some oxovanadium(IV) complexes has a considerable effect on the electrochemical behaviour (O 2 → O − 2) of the dioxygen molecule, and concluded that there is a weak interaction between the dioxygen molecule and the oxovanadium(IV) ion in the solution. This interaction leads to the shift of reduction potential of the dioxygen molecule to a more positive region than that of the free dioxygen molecule.

Calorimetric studies of oxyhemoglobin dissociation. II. Erythrocytic oxygen depletion by sodium dithionite

Dithionite causes the depletion of dioxygen from suspensions of erythrocytes by reduction of the external dioxygen and not by diffusion into the cell. The molar enthalpy for the reduction shows a small difference with respect to the values found for free hemoglobin; and the normal stoichiometry of 2 moles dithionite/mole dioxygen found there is not observed with erythrocytes. At low hematocrit, the stoichiometry is 2.6:1 and decreases to 1.5:1 at high hematocrit. The change is not due to differences in the hemoglobin saturation or to an inability of dithionite to reduce all oxygen all dioxygen present at the higher hematocrit. Neither catalase nor peroxidase added to the extracellular volume significantly alters the stoichiometry or the enthalpy of dioxygen reduction by dithionite. Addition of superoxide dismutase, however, restores the normal stoichiometry at high hematocrit and further increases the stoichiometry at low hematocrit. The calorimetrical signal of hydrogen peroxide, clearly seen with free dioxygen, is not present with erythrocytes. In all these cases the total heat evolved is the same.