Comment on “Roles of Hydration and Magnetism on the Structure of Ferrihydrite from First Principles”

International audienceSassi and Rosso 1 asserted to have rediscovered the akdalaite model of Michel and coworkers 2, 3 for the structure of ferrihydrite having a composition of Fe5O8H·nH2O (0 ≤ n ≤ 2) using ab initio calculations. Here, we show that the predicted polyhedral configuration and magnetic properties of the lowest enthalpy model correspond to those of hydromaghemite, not ferrihydrite. This is demonstrated by compiling results published in eleven uncited articles by seven independent research groups (Table 1). Taken together, the results in these articles validate the model structure of ferrihydrite obtained by X-ray diffraction 4 (Drits model) and do not support the model obtained from pair distribution function (PDF) analysis 2, 3 (Michel model). The results pertain to the chemical composition and structure of ferrihydrite, and are synthesized below in five statements that counter some of the hypotheses, statements, and interpretations in Sassi and Rosso

Crystal structure of Ni-sorbed synthetic vernadite: A powder X-ray diffraction study

International audienceVernadite is a nanocrystalline turbostratic phyllomanganate ubiquitous in the environment, which contains nickel in specific settings such as oceanic sediments. To improve our understanding of nickel uptake in this mineral, two series of synthetic analogs to vernadite (δ-MnO2) were prepared with Ni/Mn atomic ratios ranging from 0.002 to 0.105 at pH 4 and from 0.002 to 0.177 at pH 7, and their structures characterised using X-ray diffraction (XRD). The δ-MnO2 nano-crystals are essentially monolayers with coherent scattering domain sizes of ~10 Å perpendicular to the layer and of ~55 Å in the layer plane. The layers contain an effective proportion of ~18% vacant octahedral sites, regardless of the Ni content. At Ni/Mn ratios <1%, XRD has no sensitivity to Ni, and the layer charge deficit is apparently entirely balanced by interlayer Mn, Na, and protons. At higher Ni/Mn ratios, Ni occupies the same site as interlayer Mn above and/or below layer vacancies together with sites along the borders of the MnO2 layers, but the layer charge is balanced differently at the two pH values. At pH 4, Ni uptake is accompanied by a decrease in structural Na and protons, whereas interlayer Mn remains strongly bound to the layers. At pH 7, interlayer Mn is less strongly bound and partly replaced by Ni. The results also suggest that the number of vacant layer sites and multivalent charge-compensating interlayer species are underestimated in the current structure models for δ-MnO2

Analysis of the Major Fe Bearing Mineral Phases in Recent Lake Sediments by EXAFS Spectroscopy

Extended X-ray absorption fine structure (EXAFS) spectroscopy and chemical analyses were combined to determine the Fe bearing minerals in recent lake sediments from Baldeggersee (Switzerland). The upper section of a laminated sediment core, deposited under eutrophic conditions, was compared to the lower part from an oligotrophic period. Qualitative analysis of FeK EXAFS agreed well with chemical data: In the oligotrophic section Fe(II)-O and Fe(III)-O specieswere present, whereas a significant fraction of Fe(II)-S sulfides was strongly indicated in the eutrophic part. A statistical analysis was performed by least square fitting of normalized reference spectra. The set of reference minerals included Fe(III) oxides and Fe(II) sulfides, carbonates and phosphates. In the oligotrophic regime no satisfying fit was obtained using the set of reference spectra, indicating that siderite (FeCO3) was not present in a significant amount in these carbonate-rich sediments. Simulated EXAFS spectra for a(Cax, Fe1-x)CO3solid solution allowed reconstructing the specificfeatures of the experimental spectra, suggesting that this phase was the dominant Fe carrier in the oligotrophic section of the core. In the eutrophic part, mackinawite was positively identified and represented the dominant Fe(II) sulfide phase. This finding agreed with chemical extraction, which indicated that18-40 mol% of Fe was contained in the acid volatile iron sulfide fraction. EXAFS spectra of the eutrophic section were best fitted by considering the admixture of mackinawite and the Fe-Ca carbonate phase inferred to be predominant in the oligotrophic regim

Structure of heavy metal sorbed birnessite. Part 1: Results from X-ray diffraction

International audienceThe structure of heavy-metal sorbed synthetic birnessites (MeBi) was studied by powder X-ray diffraction (XRD) using a trial-and-error fitting procedure to improve our understanding of the interactions between buserite/birnessite and environmentally important heavy metals (Me) including Pb, Cd, and Zn. MeBi samples were prepared at different surface coverages by equilibrating at pH 4 a Na-rich buserite (NaBu) suspension in the presence of the desired aqueous metal. Two main types of experimental XRD patterns were obtained as a function of the nature of Me cations sorbed from solution which exerts a strong control on layer stacking sequence, as well as on location and coordination of Me: 1) CdBi and PbBi samples correspond to a one-layer hexagonal (1H) structure, AbCb'A' C'b'AbC..., and 2) ZnBi exhibits a one-layer monoclinic (1M) structure in which adjacent layers are shifted by +a/3, AbCb'A'c'BcAc'B'a'CaBa'C'b'AbC. Simulated XRD patterns shows that octahedral layers contain 0.833 Mn cations (Mn 4+ and Mn 3+) and 0.167 vacant octahedra; Mn3+ interlayer and adsorbed Meinterlayer compensate for the layer charge deficit. Mn 3+ interlayer is octahedrally coordinated in all samples and is located above or below vacant layer octahedra sharing three Olayer with neighboring Mnlayer octahedra to form a triple-corner surface complex ( VITC sites). In ZnBi and CdBi samples, Me interlayer is also located in TC sites; all Cd is octahedrally coordinated whereas about 30% of Zn is tetrahedrally coordinated ( IVTC sites). In PbBi samples, all Pb is octahedrally coordinated, most of these cations (~75%) being located in TC sites. Additional Pb is located above or below empty tridentate cavities, sharing three edges with neighboring Mnlayer octahedra ( VITE sites). Structural formulae calculated for each sample show that during the NaBu-to-MeBi structural transformation, interlayer Na + and Mn2+ are replaced by Me and H+ adsorbed from solution, whereas Mn 3+ interlayer resulting from the equilibration of NaBu at low pH is less affected. Sorption of divalent Me above and below vacant layer sites provides optimal conditions for local charge compensation in MeBi

Structure of nanocrystalline phyllomanganates produced by freshwater fungi

International audienceThe crystal structures of biogenic Mn oxides produced by three fungal strains isolated from stream pebbles were determined using chemical analyses, XANES and EXAFS spectroscopy, and powder X-ray diffraction. The fungi-mediated oxidation of aqueous Mn2+ produces layered Mn oxides analogous to vernadite, a natural nanostructured and turbostratic variety of birnessite. The crystallites have domain dimensions of ~10 nm in the layer plane (equivalent to ~35 MnO6 octahedra), and ~1.5-2.2 nm perpendicularly (equivalent to ~2-3 layers), on average. The layers have hexagonal symmetry and from 22 to 30% vacant octahedral sites. This proportion likely includes edge sites, given the extremely small lateral size of the layers. The layer charge deficit, resulting from the missing layer Mn4+ cations, is balanced mainly by interlayer Mn3+ cations in triple-corner sharing position above and/or below vacant layer octahedra. The high surface area, defective crystal structure, and mixed Mn valence confer to these bio-minerals an extremely high chemical reactivity. They serve in the environment as sorption substrate for trace elements and possess catalytic redox properties

Structural model for the biogenic Mn oxide produced by Pseudomonas putida

International audienceX-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 18 Mn oxide) 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 edge-sharing Mn 4+O 6 26 octahedra and cation vacancies, but no layer Mn 3+O 6 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 Ä in the c* direction, and 60-85 Ä in the ab 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

Structure of the Synthetic K-rich Phyllomanganate Birnessite Obtained by High-Temperature Decomposition of KMnO4. Substructures of K-rich Birnessite from 1000°C Experiment

International audienceThe structure of a synthetic potassium-rich birnessite prepared from the thermal decomposition of KMnO4 at 1000°C in air has been refined by Rietveld analysis of the powder X-ray diffraction (XRD) data, and the structure model shown to be consistent with extended X-ray absorption fine structure data. K-rich birnessite structure is a two-layer orthorhombic polytype (2O) with unit-cell parameters a = 5.1554(3) Ä, b = 2.8460(1) Ä, c = 14.088(1) Ä, α = β = γ = 90°, a/b = √3.281, and was refined in the Ccmm space group. The structure is characterized by the regular alternation of octahedral layers rotated with respect to each other by 180°. Octahedral layers are essentially devoid of vacant sites, the presence of 0.25 Mn 3+ layer cations within these layers being the main source of their deficit of charge, which is compensated for by interlayer K + cations. Mn3+ octahedra, which are distorted by the Jahn-Teller effect, are systematically elongated along the a axis (cooperative Jahn-Teller effect) to minimize steric strains, thus yielding an orthogonal layer symmetry. In addition, Mn 3+ octahedra are segregated in Mn3+-rich rows parallel to the b axis that alternate with two Mn 4+ rows according to the sequence ...-Mn3+-Mn4+-Mn4+-Mn3+-... along the a direction, thus leading to a A = 3a super-periodicity. At 350°C, the structure partially collapses due to the departure of interlayer H2O molecules and undergoes a reversible 2O-to-2H phase transition. This transition results from the relaxation of the cooperative Jahn-Teller effect, that is from the random orientation of elongated Mn 3+ octahedra

Structure of heavy-metal sorbed birnessite. Part 2: Results from electron diffraction

International audienceSelected-area electron diffraction (SAED) and energy dispersive analysis were used to study the structure of synthetic heavy-metal sorbed birnessites (MeBi). Samples were prepared by equilibrating a suspension of Na-rich buserite (NaBu) at pH4 in the presence of various heavy metal cations (Me), including Pb, Cd, Zn, and Cu. Five main types of SAED patterns were observed. Types I and II were observed only for ZnBi micro-crystals, and they both consist of two super-cell reflection networks related by a mirror plane parallel to the a *c* plane. In direct space, these twinned networks correspond to the hexagonal supercells with AH = BH = 7b/ 3, and AH = BH = 7b, for ZnBi type I and II, respectively. In the two varieties, the supercells result from an ordered distribution of vacant layer octahedra capped by interlayer Zn in ZnBi layers. This distribution is described by a hexagonal cell with AH = 7b. In ZnBi micro-crystals of type I, interstratified twinned right- and left-handed fragments are similar to chalcophanite (ZnMn3O7-3H2O - Wadsley 1955; Post and Appleman 1988), and distributions of vacant layer octahedra from adjacent layers are regularly shifted with respect to each other by 1/3 of the long diagonal of the hexagonal layer unit cell. In ZnBi micro-crystals of type II, distributions of vacant layer octahedra are not regularly shifted from one layer to the adjacent one. SAED patterns of types III and IV occur for PbBi, ZnBi, and CdBi micro-crystals and contain super-cell reflections distributed parallel to [100] * with a periodicity which is not commensurate with that of the MeBi sub-structure (a */2.15 and a*/5.25, respectively). The super-cell reflections result from the ordered distribution within MeBi layers of vacant layer sites capped by Me as pairs along the a axis. Within each pair, vacant sites are separated by 2a for type III, and by 5a for type IV. In one-layer monoclinic structures, the apparent incommensurability arises from the +a/3 shift between adjacent layers having a similar one-dimensional periodic distribution of interlayer Me located above and below vacant octahedra sharing three corners with Mnlayer octahedra (TC sites). Tetrahedral coordination of these Me cations in TC sites, as in ZnBi, leads to the formation of strong H-bonds between adjacent layers. A similar incommensurate effect occurs in one layer hexagonal MeBi if octahedrally coordinated Me cations periodically distributed along the a axis are located above and/or below empty tridentate cavities sharing three edges with Mnlayer octahedra ( VITE sites, PbBi). SAED patterns of type V contain only sub-cell reflections and were observed mostly for PbBi and CuBi micro-crystals. Three different conditions can lead to the absence of supercell reflections: (1) a low amount of sorbed Me (PbBi); (2) the presence of Me having a similar scattering power as that of Mn on a single side of vacant layer sites (CuBi); or (3) a random distribution of interlayer species

Localization and speciation of Zn in mycorrihizd roots by μSXRF and μEXAFS.

Mycorrhizae are symbiotic associations between soil fungi and plant roots, which enhance mineral nutrition for the plant, and might play an important role in metals acquisition and accumulation. The processes allowing metals mobilization in the soil, absorption by the root and/or the fungus, transfer or bioaccumulation are still poorly understood. However, the properties of mycorrhizal fungi could be used for phytoremediation, a soft technique using plants for the clean-up of metal polluted soils. In this work, mycorrhized roots of tomato plants grown in a Zn-contaminated soil were investigated. The distribution of metals and the speciation of Zn were studied at the micron scale using micro synchrotron-based X-ray fluorescence (μSXRF) and micro X-ray absorption spectroscopy (μEXAFS). Zn associated to the root was Zn malate and/or Zn citrate, and Zn associated to the fungus was Zn phyllosilicate. This study illustrates the great potential of X-ray microbeams for the study of biological samples containing various amounts of metals