Models of the Oxygen-Evolving Complex of Photosystem II

In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn₄CaO₅ cluster with a distorted Mn₃CaO₄ cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn₃CaO₄ heterometallic cubane complexes.

In Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes’ structures, magnetic behavior, and redox properties are discussed.

Chapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from Mn^II₄ to Mn^IIIMn^IV₃ were observed, with 1-4 O^2– ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.

As Ca²⁺ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn₃CaO₄ cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn₃CaO₄ heterometallic cubane complex— and comparison to an all-Mn Mn₄O₄ analog—suggests a role for Ca²⁺ in the OEC. Modification of the Mn₃CaO₄ system by ligand substitution affords low symmetry Mn₃CaO₄ complexes that are the most accurate models of the OEC to date.

Finally, in Chapter 5 the reactivity of the Mn₃CaO₄ cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn₄O₄ and Mn₄O₃ clusters, respectively, are studied through computation and ¹⁸O-labeling studies. The μ3-oxos of the Mn₄O₄ system prove fluxional, lending support for proposals of O^2– fluxionality within the OEC.

Observations of nitrogen and oxygen isotopes in the low energy cosmic rays

The isotopic composition of the enhanced low energy nitrogen and oxygen cosmic rays can provide information regarding the source of these particles. Using the Caltech Electron/Isotope Spectrometer aboard the IMP-7 satellite, a measurement of this isotopic composition was made. To determine the isotope response of the instrument, a calibration was performed, and it was determined that the standard range-energy tables were inadequate to calculate the isotope response. From the calibration, corrections to the standard range-energy tables were obtained which can be used to calculate the isotope response of this and similar instruments.

The low energy nitrogen and oxygen cosmic rays were determined to be primarily ^(14)N and ^(16)O. Upper limits were obtained for the abundances of the other stable nitrogen and oxygen isotopes. To the 84% confidence level the isotopic abundances are: ^(15)N/N ≤ 0.26 (5.6- 12.7 MeV/nucleon), ^(17)0/0 ≤ 0.13 (7.0- 11.8 MeV/nucleon), (18)0/0 ≤ 0.12 (7.0 - 11.2 MeV/nucleon). The nitrogen composition differs from higher energy measurements which indicate that ^(15)N, which is thought to be secondary, is the dominant isotope. This implies that the low energy enhanced cosmic rays are not part of the same population as the higher energy cosmic rays and that they have not passed through enough material to produce a large fraction of ^(15)N. The isotopic composition of the low energy enhanced nitrogen and oxygen is consistent with the local acceleration theory of Fisk, Kozlovsky, and Ramaty, in which interstellar material is accelerated to several MeV/nucleon. If, on the other hand, the low energy nitrogen and oxygen result from nucleosynthesis in a galactic source, then the nucleosynthesis processes which produce an enhancement of nitrogen and oxygen and a depletion of carbon are restricted to producing predominantly ^(14)N and ^(16)O.

Oxygen isotope ratios in coexisting minerals of regionally metamorphosed rocks

The O¹⁸/O¹⁶ ratios of coexisting minerals from a number of regionally metamorphosed rocks have been measured, using a bromine pentafluoride extraction-technique. Listed in order of their increasing tendency to concentrate O¹⁸, the minerals analyzed are magnetite, ilmenite, chlorite, biotite, garnet, hornblende, kyanite, muscovite, feldspar, and quartz. The only anomalous sequence detected occurs in a xenolith of schist, in which quartz, muscovite, biotite, and ilmenite, but not garnet, have undergone isotopic exchange with surrounding trondjemite.

With few exceptions, quartz-magnetite and quartz-ilmenite fractionations decrease with increasing metamorphic grade determined by mineral paragenesis and spatial distribution. This consistency does not apply to quartz-magnetite and quartz-ilmenite fractionations obtained from rocks in which petrographic evidence of retrogradation is present.

Whereas measured isotopic fractionations among quartz, garnet, ilmenite, and magnetite are approximately related to metamorphic grade, fractionations between these minerals and biotite or muscovite show poor correlation with grade. Variations in muscovite-biotite fractionations are relatively small. These observations are interpreted to mean that muscovite and biotite are affected by retrograde re-equilibration to a greater extent than the anhydrous minerals analyzed.

Measured quartz-ilmenite fractionations range from 12 permil in the biotite zone of central Vermont to 6.5 permil in the sillimanite-orthoclase zone of southeastern Connecticut. Analyses of natural assemblages from the kyanite and sillimanite zones suggest that equilibrium quartz-ilmenite fractionations are approximately 8 percent smaller than corresponding quartz-magnetite fractionations. Employing the quartz-magnetite geothermometer calibrated by O'Neil and Clayton (1964), a temperature of 560°C was obtained for kyanite-bearing schists from Addison County, Vermont. Extending the calibration to quartz-ilmenite fractionations, a temperature of 600°C was obtained for kyanite-schists from Shoshone County, Idaho. At these temperatures kyanite is stable only at pressures exceeding 11 kbars (Bell, 1963), corresponding to lithostatic loads of over 40 km.

Determination of dissolved oxygen in water with leukoberbelin-blue I. A quick Winkler method. [Translation from: Z.analyt.Chem. 262 97-99, 1972.]

The reaction of Mn(II) with water-dissolved oxygen, to a higher manganese hydroxide in an alkaline medium, as with the longstanding classic Winkler method, is the first step in the method described here. The assumption for faultless results by the conventional and modified Winkler method is clean water, which contains no organic substances by Mn(III) or Mn(IV). In many cases, however, eg. in river and lake-water tests, it can be seen with the naked eye that after some time the originally brown-coloured precipitate of manganese hydroxide becomes more and more colourless. Oxygen content was analysed in the water samples and evaluated by raising the amount of the leuko-base and giving the corresponding dilution of the colouring matter solution formed still higher oxygen contents can be measured.

The periodicity in the consumption of oxygen in Asellus aquaticus [Translation from: Vestnik ceskoslovenske zoologicke Spolecnosti, 15, 1, 89-97, 1951]

The consumption of oxygen in Asellus aquaticus was measured to find if there existed a periodicity in the consumption of oxygen and how this showed itself during the course of the day, year and in various experimental conditions. From the figures obtained comparative values were calculated and from these curves were plotted of the changes in the consumption of oxygen during the day and year.

The effect of oxygen concentration in water on the growth and nitrogen metabolism in the fry of rainbow trout [Translation from: Rybnoe Khoziaistvo,V.33, 74-75, 1957]

To ascertain the effect of various concentrations of oxygen in water on the fry of rainbow trout experiments were made with aquaria at various concentrations of oxygen. The food supplied was chironomid larvae (Chironomus plumosus). A surplus of food was supplied to the fry. Indices are given of the reaction of the fry to different temperatures.

Design of an oxygen flow meter for hospital application

A general description of the need for hospital flow meters is given along with an analysis of some common flow measurement methods.

The design criteria, establishment of the basic configuration of the instrument, and the evolution of the final design are presented in detail. The ability of the magnetic crossover mechanism to extract the square root of an input is explained, and design curves are presented. The action of the flow totalizer is described in relation to the rest of the instrument. A complete set of manufacturing drawings for the instrument and its tooling is included in the thesis.

In conclusion, an evaluation of the completed instrument is made, and improvements and modifications are indicated. Mention is made of the adaptability of the magnetic crossover mechanism to other instrumentation.

Oxygen relationships in intermittent sand filtration of wastewaters

A model for some of the many physical-chemical and biological processes in intermittent sand filtration of wastewaters is described and an expression for oxygen transfer is formulated.

The model assumes that aerobic bacterial activity within the sand or soil matrix is limited, mostly by oxygen deficiency, while the surface is ponded with wastewater. Atmospheric oxygen reenters into the soil after infiltration ends. Aerobic activity is resumed, but the extent of penetration of oxygen is limited and some depths may be always anaerobic. These assumptions lead to the conclusion that the percolate shows large variations with respect to the concentration of certain contaminants, with some portions showing little change in a specific contaminant. Analyses of soil moisture in field studies and of effluent from laboratory sand columns substantiated the model.

The oxygen content of the system at sufficiently long times after addition of wastes can be described by a quasi-steady-state diffusion equation including a term for an oxygen sink. Measurements of oxygen content during laboratory and field studies show that the oxygen profile changes only slightly up to two days after the quasi-steady state is attained.

Results of these hypotheses and experimental verification can be applied in the operation of existing facilities and in the interpretation of data from pilot plant-studies.

Oxygen flux through salmonid spawning gravels

Laboratory and field studies have shown that the survival of salmonid fish eggs and alevins is dependent upon the supply rate or flux of dissolved oxygen through gravel beds used for spawning. Although there have been a number of studies concerned with North American species there are few data for Atlantic salmon (Salmo salar) and the brown trout (S. trutta). For this study intragravel seepage velocities and dissolved oxygen concentrations have been measured throughout the incubation period in spawning gravels utilized by brown trout (Salmo trutta). Variation in the hatching success of batches of trout and salmon (Salmo salar) can, in part, be attributed to a critical threshold of oxygen flux through the gravels.

I. Phosphorescence and the true lifetime of triplet states in fluid solutions. II. Why is condensed oxygen blue?

I. PHOSPHORESCENCE AND THE TRUE LIFETIME OF TRIPLET STATES IN FLUID SOLUTIONS

Phosphorescence has been observed in a highly purified fluid solution of naphthalene in 3-methylpentane (3-MP). The phosphorescence lifetime of C₁₀H₈ in 3-MP at -45 °C was found to be 0.49 ± 0.07 sec, while that of C₁₀D₈ under identical conditions is 0.64 ± 0.07 sec. At this temperature 3-MP has the same viscosity (0.65 centipoise) as that of benzene at room temperature. It is believed that even these long lifetimes are dominated by impurity quenching mechanisms. Therefore it seems that the radiationless decay times of the lowest triplet states of simple aromatic hydrocarbons in liquid solutions are sensibly the same as those in the solid phase. A slight dependence of the phosphorescence lifetime on solvent viscosity was observed in the temperature region, -60° to -18°C. This has been attributed to the diffusion-controlled quenching of the triplet state by residual impurity, perhaps oxygen. Bimolecular depopulation of the triplet state was found to be of major importance over a large part of the triplet decay.

The lifetime of triplet C₁₀H₈ at room temperature was also measured in highly purified benzene by means of both phosphorescence and triplet-triplet absorption. The lifetime was estimated to be at least ten times shorter than that in 3-MP. This is believed to be due not only to residual impurities in the solvent but also to small amounts of impurities produced through unavoidable irradiation by the excitation source. In agreement with this idea, lifetime shortening caused by intense flashes of light is readily observed. This latter result suggests that experiments employing flash lamp techniques are not suitable for these kinds of studies.

The theory of radiationless transitions, based on Robinson's theory, is briefly outlined. A simple theoretical model which is derived from Fano's autoionization gives identical result.

Il. WHY IS CONDENSED OXYGEN BLUE?

The blue color of oxygen is mostly derived from double transitions. This paper presents a theoretical calculation of the intensity of the double transition (a ¹Δ_g) (a ¹Δ_g)←(X ³Σ_g^-) (X ³Σ_g^-), using a model based on a pair of oxygen molecules at a fixed separation of 3.81 Å. The intensity enhancement is assumed to be derived from the mixing (a ¹Δ_g) (a ¹Δ_g) _~~~ (X ³Σ_g^-) (X ³Σ_u^-) and (a ¹Δ_g) (¹Δ_u) _~~~ (X ³Σ_g^-) (X ³Σ_g^-). Matrix elements for these interactions are calculated using a π-electron approximation for the pair system. Good molecular wavefunctions are used for all but the perturbing (B ³Σ_u^-) state, which is approximated in terms of ground state orbitals. The largest contribution to the matrix elements arises from large intramolecular terms multiplied by intermolecular overlap integrals. The strength of interaction depends not only on the intermolecular separation of the two oxygen molecules, but also as expected on the relative orientation. Matrix elements are calculated for different orientations, and the angular dependence is fit to an analytical expression. The theory therefore not only predicts an intensity dependence on density but also one on phase at constant density. Agreement between theory and available experimental results is satisfactory considering the nature of the approximation, and indicates the essential validity of the overall approach to this interesting intensity enhancement problem.

Characterization of a dissolved oxygen sensor made of plastic optical fiber coated with ruthenium-incorporated solgel

A dissolved oxygen sensor made of plastic optical fiber as the substrate and dichlorotris (1, 10-phenanthroline) ruthenium as a fluorescence indicator is studied. Oxygen quenching characteristics of both intensity and phase were measured; the obtained characteristics showed deviation from the linear relation described by the Stern-Volmer equation. A two-layer model is proposed to explain the deviation, and main parameters can be deduced with the model. (C) 2009 Optical Society of America