Structural model for the biogenic Mn oxide produced by Pseudomonas putida
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Mario Villalobos
,
Bruno Lanson
Abstract
X-ray diffraction (XRD) and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy were combined to elaborate a structural model for phyllomanganates (layer-type Mn oxides) lacking 3D ordering (turbostratic stacking). These techniques were applied to a sample produced by a common soil and freshwater bacterium (Pseudomonas putida), and to two synthetic analogs, δ-MnO2 and acid birnessite, obtained by the reduction of potassium permanganate with MnCl2 and HCl, respectively. To interpret the diffraction and spectroscopic data, we applied an XRD simulation technique utilized previously for well-crystallized birnessite varieties, complementing this approach with single-scattering-path simulations of the Mn K-edge EXAFS spectra. Our structural analyses revealed that all three Mn oxides have an hexagonal layer symmetry with layers comprising edgesharing Mn4+O6 octahedra and cation vacancies, but no layer Mn3+O6 octahedra. The proportion of cation vacancies in the layers ranged from 6 to 17%, these vacancies being charge-compensated in the interlayer by protons, alkali metals, and Mn atoms, in amounts that vary with the phyllomanganate species and synthesis medium. Both vacancies and interlayer Mn were most abundant in the biogenic oxide. The diffracting crystallites contained three to six randomly stacked layers and have coherent scattering domains of 19.42 Å in the c* direction, and of 60.85 Å in the a-b plane. Thus, the Mn oxides investigated here are nanoparticles that bear significant permanent structural charge resulting from cation layer vacancies and variable surface charge from unsaturated O atoms at layer edges.
© 2015 by Walter de Gruyter Berlin/Boston
Articles in the same Issue
- Structural model for the biogenic Mn oxide produced by Pseudomonas putida
- Electron-beam (5–10 keV) damage in triplite-group phosphates: Consequences for electron-microprobe analysis of fluorine
- Vacancy defects in MgO at high pressure
- Plastic flow of pyrope at mantle pressure and temperature
- Parvo-mangano-edenite, parvo-manganotremolite, and the solid solution between Ca and Mn2+ at the M4 site in amphiboles
- Reinvestigation of the MgSiO3 perovskite structure at high pressure
- The mechanism and kinetics of α-NiS oxidation in the temperature range 670–700°C
- Influence of charge location on 29Si NMR chemical shift of 2:1 phyllosilicates
- The size distribution of exsolution lamellae in iron-free clinopyroxene
- The high-pressure phase transformation and breakdown of MgFe2O4
- Elastic behavior, phase transition, and pressure induced structural evolution of analcime
- A new chemical etching technique for peridotites using molten anhydrous borax
- Poppiite, the V3+ end-member of the pumpellyite group: Description and crystal structure
- Cation redistribution in the octahedral sheet during diagenesis of illite-smectites from Jurassic and Cambrian oil source rock shales
- A shock-induced polymorph of anatase and rutile from the Chesapeake Bay impact structure, Virginia, U.S.A.
- Water in the interlayer region of birnessite: Importance in cation exchange and structural stability
- In situ HAFM study of the thermal dehydration on gypsum (010) surfaces
- Influence of dehydration kinetics on T-O-T bridge breaking in zeolites with framework type STI: The case of stellerite
- Estimation of volume fractions of liquid and vapor phases in fluid inclusions, and definition of inclusion shapes
- Thermodynamics of uranyl minerals: Enthalpies of formation of uranyl oxide hydrates
- SIMS investigation of electron-beam damage to hydrous, rhyolitic glasses: Implications for melt inclusion analysis
- Synthetic Ag-rich tourmaline: Structure and chemistry
- Genesis and compositional heterogeneity of smectites. Part III: Alteration of basic pyroclastic rocksA case study from the Troodos Ophiolite Complex, Cyprus
- Ganterite, the barium mica Ba0.5K0.5Al2(Al1.5Si2.5)O10(OH)2, from Oreana, Nevada
- Letter. Transformation of pentlandite to violarite under mild hydrothermal conditions
Articles in the same Issue
- Structural model for the biogenic Mn oxide produced by Pseudomonas putida
- Electron-beam (5–10 keV) damage in triplite-group phosphates: Consequences for electron-microprobe analysis of fluorine
- Vacancy defects in MgO at high pressure
- Plastic flow of pyrope at mantle pressure and temperature
- Parvo-mangano-edenite, parvo-manganotremolite, and the solid solution between Ca and Mn2+ at the M4 site in amphiboles
- Reinvestigation of the MgSiO3 perovskite structure at high pressure
- The mechanism and kinetics of α-NiS oxidation in the temperature range 670–700°C
- Influence of charge location on 29Si NMR chemical shift of 2:1 phyllosilicates
- The size distribution of exsolution lamellae in iron-free clinopyroxene
- The high-pressure phase transformation and breakdown of MgFe2O4
- Elastic behavior, phase transition, and pressure induced structural evolution of analcime
- A new chemical etching technique for peridotites using molten anhydrous borax
- Poppiite, the V3+ end-member of the pumpellyite group: Description and crystal structure
- Cation redistribution in the octahedral sheet during diagenesis of illite-smectites from Jurassic and Cambrian oil source rock shales
- A shock-induced polymorph of anatase and rutile from the Chesapeake Bay impact structure, Virginia, U.S.A.
- Water in the interlayer region of birnessite: Importance in cation exchange and structural stability
- In situ HAFM study of the thermal dehydration on gypsum (010) surfaces
- Influence of dehydration kinetics on T-O-T bridge breaking in zeolites with framework type STI: The case of stellerite
- Estimation of volume fractions of liquid and vapor phases in fluid inclusions, and definition of inclusion shapes
- Thermodynamics of uranyl minerals: Enthalpies of formation of uranyl oxide hydrates
- SIMS investigation of electron-beam damage to hydrous, rhyolitic glasses: Implications for melt inclusion analysis
- Synthetic Ag-rich tourmaline: Structure and chemistry
- Genesis and compositional heterogeneity of smectites. Part III: Alteration of basic pyroclastic rocksA case study from the Troodos Ophiolite Complex, Cyprus
- Ganterite, the barium mica Ba0.5K0.5Al2(Al1.5Si2.5)O10(OH)2, from Oreana, Nevada
- Letter. Transformation of pentlandite to violarite under mild hydrothermal conditions
