- Research article
- Open Access
Cryptomelane formation from nanocrystalline vernadite precursor: a high energy X-ray scattering and transmission electron microscopy perspective on reaction mechanisms
Geochemical Transactionsvolume 16, Article number: 12 (2015)
Vernadite is a nanocrystalline and turbostratic phyllomanganate which is ubiquitous in the environment. Its layers are built of (MnO6)8− octahedra connected through their edges and frequently contain vacancies and (or) isomorphic substitutions. Both create a layer charge deficit that can exceed 1 valence unit per layer octahedron and thus induces a strong chemical reactivity. In addition, vernadite has a high affinity for many trace elements (e.g., Co, Ni, and Zn) and possesses a redox potential that allows for the oxidation of redox-sensitive elements (e.g., As, Cr, Tl). As a result, vernadite acts as a sink for many trace metal elements. In the environment, vernadite is often found associated with tectomanganates (e.g., todorokite and cryptomelane) of which it is thought to be the precursor. The transformation mechanism is not yet fully understood however and the fate of metals initially contained in vernadite structure during this transformation is still debated. In the present work, the transformation of synthetic vernadite (δ-MnO2) to synthetic cryptomelane under conditions analogous to those prevailing in soils (dry state, room temperature and ambient pressure, in the dark) and over a time scale of ~10 years was monitored using high-energy X-ray scattering (with both Bragg-rod and pair distribution function formalisms) and transmission electron microscopy.
Migration of Mn3+ from layer to interlayer to release strains and their subsequent sorption above newly formed vacancy in a triple-corner sharing configuration initiate the reaction. Reaction proceeds with preferential growth to form needle-like crystals that subsequently aggregate. Finally, the resulting lath-shaped crystals stack, with n × 120° (n = 1 or 2) rotations between crystals. Resulting cryptomelane crystal sizes are ~50–150 nm in the ab plane and ~10–50 nm along c*, that is a tenfold increase compared to fresh samples.
The presently observed transformation mechanism is analogous to that observed in other studies that used higher temperatures and (or) pressure, and resulting tectomanganate crystals have a number of morphological characteristics similar to natural ones. This pleads for the relevance of the proposed mechanism to environmental conditions.
Vernadite (and δ-MnO2, its synthetic analogue) is a nanocrystalline turbostratic birnessite, a phyllomanganate whose layers are built of (MnO6)8− octahedra connected through their edges and separated by hydrated interlayer cations. Vernadite is ubiquitous in the environment, and probably results mainly from the aqueous oxidation of Mn2+ by bacteria [1–3], fungi [4–6], and higher living forms , as abiotic oxidation catalyzed by mineral surfaces is about two orders of magnitude slower [8–11]. Vernadite layers frequently contain vacancies and (or) isomorphic substitutions (substitution of layer Mn4+ by a foreign cation, e.g., Co3+, Mn3+, or Ni2+ [12–14]), both types of defects inducing a layer charge deficit. For example, layer charge was 0.86–1.22 and 1.58 valence unit (v.u.) per layer octahedron for samples produced by fungal strains  and by grass roots , respectively. Layer charge induces a high chemical reactivity, which is reinforced by the nanometric size of vernadite (typically 5–50 nm in the layer plane—[1, 15, 16]) and the induced proportion of reactive edge sites [3, 17, 18]. Vernadite also presents a high affinity for many trace elements such as transition metals (e.g., Co, Ni, Zn), actinides and rare earth elements [14, 19–36]. For example, vernadite is the main sink for Ni in mixed mineral/biotic systems (vernadite and Pseudomonas Putida biofilm [37, 38]). Vernadite can also oxidize organic pollutants and redox-sensitive elements such as arsenic [39–42], chromium [39–43], and thallium [34, 44], possibly because of the common coexistence of heterovalent Mn cations in its structure. Specifically, Mn3+ cations can be present both within octahedral layers and (or) adsorbed above layer vacancies, forming triple-corner-sharing complexes (TCMn3+; Fig. 1 in ).
Additional interest in understanding vernadite structure arises from its frequent association with tectomanganates (i.e., tunnel structures) in the environment. Tectomanganates include a variety of minerals with [n × m] tunnel sizes, where n stands for the number of octahedra connected to form the “walls” of the tunnels, whereas m stands for the number of octahedra forming the “ceiling” and the “floor”. For example, vernadite is frequently found with todorokite and cryptomelane, [3 × 3] and [2 × 2] tunnel structures, respectively [26, 46–48]. Tectomanganates can form from phyllomanganate precursors [46, 49, 50] provided that they possess a particular crystal-chemistry, for example possess Mn3+ [51, 52]. Phyllomanganate-to-tectomanganate reaction mechanisms have been widely investigated owing to the tectomanganate potential as octahedral molecular sieves. Reaction products must have homogenous tunnel size for this purpose to achieve optimal efficiency and the relation between the layered precursor and the resulting tunnel structure is studied with special care (e.g.,  and references therein and [53, 54]). Relations between layer and tunnel structures is also of interest in natural settings, mainly because defective todorokite (i.e., having mainly [3 × 3] tunnel size, together with [3 × m] size, m varying from 2 to 5) is found associated with vernadite in oceanic ferromanganese nodules. These nodules consist of alternating layers of iron and manganese oxides [31, 34, 55], the latter containing typically over 1 wt% of Ni [56–58], and are increasingly considered for their potential as a source of strategic trace metals including rare-earth elements. A comprehensive understanding of phyllomanganate to tectomanganate transformation, at the atomic scale, thus appears key to an improved prediction and modeling of the impact of structure defects (layer vacancies and isomorphic substitutions) on the fate of trace elements.
Observations of vernadite-to-todorokite transformation in natural samples are scarce, but suggest a topotactic reaction . It was first reported by Golden and coworkers  for synthetic analogues and has since been repeatedly described for a variety of hydrothermal protocols. Recently, these protocols were reviewed by Atkins and coworkers , who also characterized the structural mechanisms of the δ-MnO2 to todorokite transformation at 100 °C and atmospheric pressure. These authors described the transformation as a four-stage process, starting with the formation of todorokite tunnel walls via layer kinking, followed by the growth of the particles along the  direction (i.e., along the tunnel direction) during a dissolution–recrystallization step and subsequent oriented attachment of the resulting particles along the  direction to form todorokite laths which then stack. A last step is described as the growth of todorokite crystals by Ostwald ripening. These authors mentioned also that the density of structural Mn3+ has to be “significant” to allow for a complete transformation and linked this condition to the ability of Mn3+ to induce layer kinking, owing to its Jahn–Teller distorted environment. Another important parameter appears to be the presence of an interlayer cation enforcing a ~10 Å layer-to-layer distance (e.g., Mg2+).
Similar to todorokite, cryptomelane formation in environmental conditions is little documented. A recent study  focused on δ-MnO2 samples equilibrated at pH values ranging from 3 to 10. Initially, all samples had a similar number of layer Mn3+ per octahedron (0.10 ± 0.02–0.14 ± 0.02), whereas the number of interlayer TCMn3+ increased with decreasing equilibration pH. Although such evolution might seem counter-intuitive because, by analogy with clay minerals, decreasing pH should increase proton competition for sorption [61–63], it is made possible by the fact that pH decrease is accompanied by partial layer dissolution and thus by an increase of Mn concentration in the equilibrium solution, making it possible for dissolved Mn to adsorb above vacancies . Structural formulae from samples initially equilibrated at pH 3 and 10 were Na 0.06 + (H2O)0.30Mn 0.185 3+ [Mn 0.12 3+ Mn 0.71 4+ Vac0.17O2] and Na 0.27 + (H2O)0.30Mn 0.095 3+ [Mn 0.10 3+ Mn 0.76 4+ Vac0.14O2], respectively. In these formulae, species within brackets form the layer, those to the left the interlayer, Vac stands for layer vacancies, and all interlayer Mn sites (TC and triple-edge sharing  configurations) are summed. Samples were then dried, and aged in the dark. With time, it was observed that layer Mn3+ leaves the layer to form TCMn3+ above the newly generated vacancy. Partial transformation to cryptomelane was observed only for pH 3 sample that had the highest initial number of Mn3+ (layer plus interlayer). Samples initially equilibrated at pH 4–10 did not show evidence for transformation to cryptomelane, but had contrasting crystal chemistry (Na+ 0.12(H2O)0.30Mn 0.315 3+ [Mn 0.74 4+ Vac0.26O2] and Na+ 0.27(H2O)0.30Mn 0.205 3+ [Mn 0.79 4+ Vac0.21O2], respectively) after 8 years of ageing. The structure of pH 3 sample was not precisely determined, but crystals that transformed certainly had ~1/3 of TCMn3+ per layer octahedron . Still, many questions remain open as to the transformation mechanisms. In particular, it was unclear if the transformation was homogeneous at the crystal scale (if some crystals transformed to cryptomelane while others remained lamellar) or if it only affected portions of the crystals (topotactic transformation). Finally, tectomanganates observed in natural environments are larger than typical vernadite [65, 66]. The mechanisms leading to crystal growth during or following vernadite to cryptomelane transformation (e.g., dissolution/recrystallization, aggregation, oriented attachment, Ostwald ripening) could not be elucidated.
The present study focuses further on the structure of aged δ-MnO2 samples studied by Grangeon and coworkers . Samples that were initially equilibrated at pH values of 3, 4, 8, and 10, and then left ageing in the dark in the dry state for 10 years are hereafter referred to as MndBiXX_10y, where XX stands for the equilibration pH. These samples were selected because of their contrasting structures after 8 years of ageing (i.e., 2 years before the present study). MndBi3_10y and MndBi10_10y respectively represent the highest degree of transformation and an aged δ-MnO2 that retained its original lamellar structure. In the present study, synchrotron X-ray diffraction data is analyzed with both Bragg-rod and pair distribution function (PDF) methods to determine the sample structure as a function of pH, after two more years of ageing. Bragg-rod formalism is used to determine whether samples were partially transformed to cryptomelane, and to determine the size of coherent scattering domains (CSD) and the number of TCMn3+. PDF analysis is used to determine if layer vacancies are ordered and to cross-check the number of TCMn3+. In addition, transmission electron microscopy (TEM) will be used to determine actual crystal sizes and to provide textural and structural constraints on the vernadite-to-cryptomelane transformation mechanisms. Scanning TEM will be used to reveal structural heterogeneities at the atomic scale.
Analysis of X-ray diffraction patterns and Bragg-rod modeling
X-ray diffraction (XRD) patterns can be divided in two groups (Fig. 1). Patterns of MndBi8_10y and MndBi10_10y are typical for δ-MnO2, exhibiting reflections at 25.9 nm−1 (2.43 Å), 44.3 nm−1 (1.42 Å), and 51.3 nm−1 (1.22 Å) that can be assigned to [11, 20], [31, 02], and [22, 40] bands, using a C-centered unit cell with γ = 90° [67, 68]. Compared to MndBi10_10y, the hump at 30–33 nm−1 (2.1–1.9 Å) is better defined in MndBi8_10y (Fig. 1), likely as the result of a higher density of heavy interlayer species at TC sites. The symmetry and position of their [31, 02] bands suggest that MndBi10_10y and MndBi8_10y both have hexagonal layer symmetry  and similar a and b unit-cell parameters . CSD sizes along the c* axis and layer-to-layer distance could not be determined owing to present experimental conditions that prevented modeling of low-angle 00l reflections.
Compared to MndBi8_10y and MndBi10_10y, additional reflections are observed at 29.0 nm−1 (2.17 Å), 34.4 nm−1 (1.83 Å), and 40.6 nm−1 (1.55 Å) in MndBi3_10y and MndBi4_10y. These reflections are more intense in MndBi3_10y than in MndBi4_10y (Fig. 1) and can be attributed to a cryptomelane-like structure. MndBi3_10y and MndBi4_10y are thus well-suited to study initial stages of the phyllomanganate-to-tectomanganate transformation, with part of MndBi3_10y and, to a lesser extent, of MndBi4_10y crystals having a cryptomelane-like structure.
Quantitative modeling of hk bands from MndBi8_10y and MndBi10_10y XRD patterns is shown in Fig. 2. Modeling of MndBi3_10y and MndBi4_10y patterns was not undertaken owing to the presence of cryptomelane, whose most intense reflections overlap δ-MnO2 [11, 20] band (Fig. 1). Relative intensity ratios calculated for cryptomelane and δ-MnO2 having similar CSD sizes (~6 nm) indicate that cryptomelane represent <5 % of the crystalline phases in the sample. MndBi10_10y has a CSD size in the ab plane of 5.8 nm and contains 0.11(1) TCMn3+ per layer octahedron (Table 1), lower than the value obtained 2 years sooner [0.165(10) per layer octahedron]. Similar decrease of TCMn3+ with time was previously observed  and attributed to TCMn3+ to Mn4+ oxidation with time, followed by migration to the layer. This phenomenon may also be at play in other samples but could not be identified either because the structures were not refined (MndBi3_10y and MndBi4_10y) or because the structure of the same sample was not determined 2 years sooner owing to a restricted amount of sample available for analysis with conventional XRD instruments (MndBi8_10y). Finally, the number of interlayer H2O molecules in MndBi10_10y was refined to 0.12 per interlayer site, slightly more than 2 years sooner (0.10). MndBi8_10y has CSD size in the ab plane of 6.2 nm, contains 0.02 more TCMn3+ and 0.02 more layer vacancies per layer octahedron than MndBi10_10y.
Analysis of PDF data
As PDF analysis will hereafter focus on short-range order, MndBi3_10y and MndBi4_10y, which contain a minor amount of cryptomelane, will be treated as pure δ-MnO2 owing to the structural similarities between the two species. Indeed, Mn–Mn pairs from δ-MnO2 layers are similar to those in cryptomelane walls or floor/ceiling, and pairs formed by layer Mn and TCMn in δ-MnO2 are similar to those formed by Mn atoms from adjacent walls and floor/ceiling in cryptomelane. An implication of this similarity is that PDF data cannot be used, in the present study, to detect a minor amount of cryptomelane in the samples.
From a qualitative examination of the PDF data (Fig. 3), a systematic evolution is observed with sample equilibration pH. From MndBi10_10y to MndBi3_10y, correlations at 2.87, 4.95, 5.72, and 7.56 Å decrease in intensity (although the third appears less affected). These correlations are attributed to atomic pairs involving two layer Mn atoms and forming the first, second, third, and fourth Mn shells around a given layer Mn (Mn–MnL1, Mn–MnL2, Mn–MnL3 and Mn–MnL4 shells—Fig. 4a). Contrastingly, correlations at 3.45 and 5.32 Å increase in intensity. They are attributed to pairs formed by a layer Mn atom and a TCMn (Mn–TCMn pairs—Fig. 4b), with TCMn at vacancies belonging respectively to the first (Mn–TCMn1) and second (Mn–TCMn2) Mn–MnL shells (Fig. 4a, b, c). The number of layer vacancies thus increases from MndBi10_10y to MndBi3_10y, TCMn being sorbed above these vacancies. The first, second and fourth Mn–MnL shells are more affected than the third shell. All these shells contain, in a defect-free δ-MnO2 layer, 6 Mn atoms. Thus, a layer vacancy normally affects equally all of these shells, and the observed behavior can most straightforwardly be explained by an ordered layer vacancy distribution. Finally, the correlation at 7.22 Å increases in intensity from MndBi10_10y to MndBi3_10y. It corresponds to a TCMn–TCMn pair, with TCMn atoms being on opposite sides of layer vacancies separated from each other by one layer Mn atom (TCMn–TCMn1 in Fig. 4c). All these correlations and in particular the TCMn–TCMn one are typical for δ-MnO2 layers having 0.25 layer vacancy per layer octahedron and TCMn as in Fig. 4c. In addition, the correlation at 6.13 Å (Mn–TCMn3 pair, i.e., TCMn above a vacancy belonging to the Mn–MnL3 shell) may indicate the minor presence of domains with 0.33 vacancy per layer octahedron in low pH samples (Fig. 4d). Such domains could correspond to the cryptomelane-like structure or to their precursors.
As discussed hereafter and by Manceau and coworkers , δ-MnO2 PDF data are affected by sample turbostratism, that is by the systematic presence of random translation and/or rotation between successive layers. Turbostratism decreases the intensity of correlations for r values higher than the layer-to-layer distance, because coherency between adjacent layers is lost. In the present samples both ~7.2 and ~10 Å layer-to-layer distances were observed (see below), the former being by far the most frequent. As a consequence, refinement was restricted to the 1.5–7 Å intra-layer interval which is not affected by turbostratism. The model from Manceau and coworkers  was used and no attempt was made to refine atomic coordinates nor layer symmetry. Refined parameters corresponding to the simulations shown in Fig. 5 are reported in Table 1 and Additional file 1: Data S1. With decreasing pH, the abundance of TCMn3+ steadily increased, from 0.09(2) per layer octahedron in MndBi10_10y to 0.28(1) per layer octahedron in MndBi3_10y (Table 1), consistent with previous studies [49, 70, 71]. Layer parameters decreased from b = 2.869(4) Å in MndBi10_10y to b = 2.854(1) Å in MndBi3_10y, certainly as a result of the increase in TCMn3+ . These values are systematically lower [0.013(4)–0.014(4) Å] than those obtained using the Bragg-rod approach (Table 1) possibly as a consequence of layer bending .
Morphological and structural evolution with pH as seen by transmission electron microscopy
Bragg-rod and PDF data analysis allowed probing structure of coherent scattering domains but could not determine their distribution within crystals, and in particular the possible coexistence of δ-MnO2 and cryptomelane domains within crystals. As they are representative of samples undergoing the maximum and minimum degree of structural conversion, MndBi3_10y and MndBi10_10y were investigated by TEM to gain further insights into transformation mechanisms.
MndBi10_10y was composed of crystals having homogenous size and morphology, often found aggregated in a xerogel-like configuration. Selected area electron diffraction (SAED) patterns were typical for δ-MnO2, with two broad diffraction maxima at ~2.42 and ~1.40 Å (Fig. 6) that correspond to [11, 20] and [31, 02] diffraction bands. Crystal sizes in the ab plane range 5–10 nm, consistent with CSD size determined from XRD pattern modeling (5.8 nm). Some crystals exhibited hexagonal shape in the ab plane (Fig. 6a), as observed in other δ-MnO2 samples [45, 70]. Finally, interference fringes having spacing of ~2.8 Å could be observed (Fig. 6b) and are attributed to the b parameter.
Observation of MndBi3_10y samples revealed a much more complex assemblage. The sample contained at least four types of crystals distinguishable on the basis of their morphology and size (Figs. 7, 8). Crystal type 1 had sizes of 5–20 nm, similar to fresh samples (data not shown) and MndBi10_10y. Crystal type 2 had a needle-like morphology, typically 10–30 nm in length. Crystal type 3 had lath-like morphology, with its long distance in the ab plane (20–150 nm) up to ~5–10 times larger than crystal type 2. It was also typically 2–10 times wider, and interference fringes were frequently disrupted, as if it was built of aggregated type 2 crystals (Fig. 9). Aggregation was observed to occur within the ab plane, in agreement with the aggregation mechanism proposed previously [50, 60, 72]. It was also observed along c*, with disruption of interference fringes that had geometrical shapes identical to previous observations [60, 72, 73] and indicate that growth may also take place through stacking along c* of two or more type 2 crystals. Finally, crystal type 4 often had typical sizes of 50–150 nm in the ab plane and 10–50 nm along c*, and was built of stacks of lath-like layers resembling type 3 crystals rotated by n × 120° (n being equal to 1 or 2) relative to each other.
Similar to MndBi10_10y, crystal type 1 in MndBi3_10y exhibited SAED patterns typical for δ-MnO2, with only weak diffraction maxima at 2.42 and 1.40 Å (Fig. 8). Contrastingly, crystal type 4 exhibited additional reflections (e.g., at 2.19, 1.80, and 1.54 Å—Fig. 8) attributed to cryptomelane. Consequently, MndBi3_10y is built of four main types of crystals: crystal type 1 is a phyllomanganate, whereas crystal type 4 locally has a tectomanganate-like structure. We propose that crystals type 2 and 3, that could not be investigated by SAED as no isolated crystal or homogeneous aggregate could be found, have an intermediate structure. When viewed perpendicular to the c* axis, crystal type 4 systematically showed the presence of tunnel-like structures, with sizes of 6.9 Å × 6.9 Å typical for cryptomelane (Fig. 10). The minor presence of heterogeneous tunnel size (dotted arrows in Fig. 10) is likely. Finally, analysis of images collected on type 1, 2 and 3 crystals (Figs. 7a, b, 9) reveal distances of ~6.9–7.1 Å, consistent with layer-to-layer distance of phyllomanganates hosting a single plane of interlayer H2O molecules. 9.5 Å distances expected for phyllomanganates hosting two planes of water molecules  were also observed, although much less frequent. This uncommon persistence of highly hydrated states under TEM vacuum conditions [60, 75] is likely related to sample impregnation in resin prior to analysis.
Additional high-resolution STEM image was obtained at 100 keV (Fig. 11) to minimize structure evolution under the electron beam and to improve resolution in an effort to investigate the possible segregation of heterovalent Mn cations. Consistent with TEM observations (Fig. 10), [2 × 3] tunnels were observed in crystal type 4 together with prevailing [2 × 2] tunnels size, with individual Mn atoms being clearly observed. The latter tunnels have contrasting floor/ceiling and wall dimensions, with their small dimension (supposedly the former phyllomanganate layers) ~5 % smaller than the perpendicular dimension (Fig. 11c). This supports the hypothesis of Mn3+ atoms (that have a larger distorted coordination octahedron) segregation in the walls whereas Mn4+ atoms are mainly present in tunnel floors and ceilings. Finally, the structure was found to suffer from bending (Fig. 11d).
Mechanism of the phyllomanganate to tectomanganate transformation
To our knowledge, this study is the first to document the transformation of vernadite to cryptomelane under conditions that can be considered relevant for soils, i.e. at room temperature, ~105 Pa, under unsaturated conditions, and in the dark. As previously discussed , this structural transformation requires a locally high number of Mn3+ (~0.33 per layer octahedron) in the octahedral layer. This can be obtained experimentally by equilibrating phyllomanganates at low pH values (≤4) that can be observed in forest soils, soils developed on parent granite or gneiss, or organic-rich soils . Such assumption is confirmed by independent laboratory experiments which show that δ-MnO2 to cryptomelane transformation is favored at low pH .
From many viewpoints, the studied transformation is similar to that of δ-MnO2 to todorokite described by Atkins and coworkers . The contrasting reaction products obtained in the two studies are most likely due to the different nature of interlayer cation in the initial phyllomanganate (Na+ in the present study and Mg2+ for Atkins and coworkers). The first reaction step differs however as Atkins and coworkers propose that the presence of layer Mn3+ leads to layer kinking, owing to their Jahn–Teller distorted coordination sphere. In our opinion, reaction first step rather corresponds to the migration of Mn3+ from the layer to the interlayer, which allows also releasing strains related to the Jahn–Teller distortion of Mn3+ octahedra. This interpretation is consistent with the infrared data of Atkins and coworkers that showed an increased density of TCMn during the initial steps of the transformation. The proposed mechanism accounts also for their observation, corroborated by Feng and coworkers , that transformation occurs at constant mean Mn oxidation degree. In contrast to the hypothesis of Atkins and coworkers this initial step is likely not thermally triggered but reaction kinetics is enhanced with increasing temperature. The next steps of the reaction described by Atkins and coworkers are also observed in the present study. Needle-like crystal type 2 results indeed from the crystal growth along tectomanganate tunnels proposed by Atkins and coworkers, whereas lath-like crystal type 3 results from crystal growth perpendicular to tectomanganate tunnels (by coalescence of type 2 crystals along their long dimension). Finally, crystal type 4, built of lath-like units rotated by n × 120° (n being equal to 1 or 2), results from stacking of crystal type 3. The crystallographic axes along which crystal growth/aggregation takes place could not be determined in the present study, as SAED patterns could not be collected on type 2 and 3 crystals, and as instrumental limitations hampered the observations of in-plane lattice fringes. A last transformation step was described by Atkins and coworkers as Ostwald ripening and would involve cryptomelane crystal growth. This final step could not be observed in the present samples as evidence for a cryptomelane-like signal could only be found in crystal type 4 (Fig. 8). To date, only Bodeï and coworkers  have investigated in detail the mechanisms of phyllomanganate (vernadite) to tectomanganate (todorokite) transformation in natural samples. Collation of the present study with that of these authors is hampered however by numerous unknowns inherent to natural systems, such as the density of layer and interlayer Mn3+ in the initial phyllomanganate and the structural variety of natural tectomanganates [77, 78]. However, several clues suggest that the observed transformation is similar to that occurring in natural systems. First, proposed transformation mechanisms are valid both in surface soil conditions (present study) and in saturated conditions [50, 72], making them relevant to a variety of natural systems. Second, naturally occurring tectomanganates frequently exhibit textures similar to those observed in experimental studies (Figs. 7, 8; [51, 53, 60, 79, 80]) with rotations of aggregated crystals by n × 120° [46, 66, 79]. Third, transformations occur via topotactic transformation in both experimental and natural systems and are heterogeneous at the crystal scale. In particular, transformation systematically affects only part of the crystals and the transformed parts show heterogeneous tunnel sizes. This latter point is certainly related to an imperfect distribution of Mn3+ atoms (TCMn3+ + layer Mn3+) in the initial phyllomanganate structure.
The phyllomanganate-to-tectomanganate transformation (Fig. 12) was studied using a combination of high-energy X-ray scattering and transmission electron microscopy. It was confirmed that this transformation is triggered when the number of TCMn3+ locally reaches ~0.33 per layer octahedron. The possible influence of Mn4+ to Mn3+ photo-reduction  on the transformation remains to be investigated. Part of TCMn3+ cations result from the migration of layer Mn3+ to the interlayer, which demonstrates that prediction of vernadite to tectomanganate transformation requires a sound understanding of vernadite structure, including quantification of both TCMn3+ and layer Mn3+ in starting material. In addition, the nature of the tectomanganate that will be formed is dependent on the nature of the interlayer cation: if the cation is capable of enforcing a 10 Å layer-to-layer distance, todorokite will be formed; otherwise, the product of reaction will be cryptomelane.
Growth mechanisms proposed from previous experimental studies performed at higher temperatures were confirmed for conditions relevant to surface soil. The four-stage transformation begins with the migration of Mn3+ from layer to the interlayer to form TCMn3+ that further connect to hydration spheres belonging to TCMn3+ from adjacent layers. Crystals then grow first along the “tunnel” direction to form needle-like crystals. These crystals coalesce along their long dimension to form lath-like crystals which, in a final step, stack along c* with rotation by n × 120° between adjacent laths. Cryptomelane structure was observed only in these latter crystals (type 4), but is certainly present also in crystals type 2 and 3.
Samples used for the present study are those studied by Grangeon and coworkers  and Manceau and coworkers . They were synthesized using the redox method  and were left for equilibration at pH values ranging from 3 to 10 immediately after synthesis. They were then left to age for 10 years in the dark and in the dry state. For consistency with Grangeon and coworkers , samples are labeled MndBiXX_10y, where XX is the equilibrium pH and “10y” stands for “10 years of ageing”.
X-ray diffraction pattern (XRD) analysis and modeling
XRD patterns were modeled using the software developed by Plançon , based on the formalism developed by Drits and Tchoubar . This specific routine allows for the simulation of (lamellar) structures affected by various nature and density of layer defects (e.g., layer vacancies, isomorphic substitutions) and stacking defects (e.g., well-defined or random stacking faults, interstratification). It has been previously applied to the study of nanocrystalline manganese or iron oxides [69, 84, 85], nanocrystalline calcium silicate hydrates [86–88] and phyllosilicates [89, 90]. As discussed by Manceau and coworkers  the simulation of the [11, 20], [31, 02] and [22, 40] bands (using a C-centered hexagonal unit-cell, with γ = 90°) is sufficient to accurately determine the structure of synthetic phyllomanganates, and only these bands were modeled here. All structure parameters but crystallite size, a and b lattice parameters, abundance of TCMn3+, layer vacancies and of interlayer water molecules were kept identical to those determined by Grangeon and coworkers . An example of the sensitivity of calculated XRD patterns to the number of TCMn3+ is available in the Additional File 2: Data S2. The cryptomelane pattern was calculated using the structure model from Vicat and coworkers , assuming a CSD size of 6 nm.
High energy X-ray scattering coupled with pair distribution function (PDF) analysis and modeling
X-ray diffraction patterns were collected at ID15B high-energy beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France), using energy of 87 keV and a PerkinElmer flat panel detector. Data were acquired on randomly-oriented powders packed in polyimide capillaries having a diameter of 1 mm and on empty capillary used for background subtraction. 40 frames of 5 s, corrected for detector’s dark current, were collected for each sample. After instrumental calibration using a NIST certified CeO2 powder sample, frames were integrated to one dimensional patterns  and averaged. Data were then transformed to PDF patterns using PdfGetX3 , and fit using PDFGui . The model from Manceau and coworkers  was used to refine the patterns. The only modification was that TCMn3+ was allowed to sorb on both sides of a layer vacancy. The refined parameters were the abundance of TCMn3+, layer vacancies, lattice parameters and Debye–Waller factors. q broadening and q dampening factors were retrieved from simulation of a CeO2 pattern and found to be equal to, respectively, 0.044 and 0.048.
Transmission electron microscopy (TEM)
TEM was performed using a Philips CM20 operated at 200 kV. Samples were deposited on a copper grid prior to observation. When samples were first dispersed in ethanol or in water, and deposited on the grid from the suspension, they were rapidly altered under the beam, with amorphous products occurring within a few seconds. To circumvent this problem, samples were first embedded in epoxy resin and left in the dark for 48 h until full polymerization. Cutting was performed using an ultramicrotome Reichert-Jung Ultra-cut E. Five to ten thin sections having thicknesses of about 100 nm were collected on the surface of the water contained in the boated knife and picked up on a lacey carbon film loaded on copper grids.
Scanning transmission electron microscopy (STEM)
STEM experiments were performed using a Nion Ultra-STEM 200 operated at 100 kV. Sample preparation was identical to that applied for TEM measurements, except that the thickness of the slices containing the sample embedded in epoxy resin was reduced to ~50 nm. Image presented in the present study was acquired in high-angular annular dark-field (HAADF) mode. In order to ease visualization of the structural features, the raw image was Fourier-transformed and filtered using a band pass with a window set for spatial frequencies between 1.6 and 40 nm−1, and a color threshold was then applied to reduce the contribution from pixels having a grey color lower than half of the mean image grey value.
Jürgensen A, Widmeyer JR, Gordon RA, Bendell-Young LI, Moore MM, Crozier ED (2004) The structure of the manganese oxide on the sheath of the bacterium Leptothrix discophora: an XAFS study. Am Miner 89:1110–1118
Villalobos M, Toner B, Bargar J, Sposito G (2003) Characterization of the manganese oxide produced by Pseudomonas putida strain MnB1. Geochim Cosmochim Acta 67:2649–2662
Webb SM, Tebo BM, Bargar JR (2005) Structural characterization of biogenic Mn oxides produced in seawater by the marine Bacillus sp. strain SG-1. Am Miner 90:1342–1357
Grangeon S, Lanson B, Miyata N, Tani Y, Manceau A (2010) Structure of nanocrystalline phyllomanganates produced by freshwater fungi. Am Miner 95:1608–1616
Miyata N, Maruo K, Tani Y, Tsuno H, Seyama H, Soma M, Iwahori K (2006) Production of biogenic manganese oxides by anamorphic ascomycete fungi isolated from streambed pebbles. Geomicrobiol J 23:63–73
Tani Y, Miyata N, Iwahori K, Soma M, Tokuda S-I, Seyama H, Theng BKG (2003) Biogeochemistry of manganese oxide coatings on pebble surfaces in the Kikukawa River System, Shizuoka, Japan. Appl Geochem 18:1541–1554
Lanson B, Marcus MA, Fakra S, Panfili F, Geoffroy N, Manceau A (2008) Formation of Zn–Ca phyllomanganate nanoparticles in grass roots. Geochim Cosmochim Acta 72:2478–2490
Crerar DA, Barnes HL (1974) Deposition of deep-sea manganese nodules. Geochim Cosmochim Acta 38:279–300
Morgan JJ (2005) Kinetics of reaction between O2 and Mn(II) species in aqueous solutions. Geochim Cosmochim Acta 69:35–48
Tebo BM, Bargar JR, Clement BG, Dick GJ, Murray KJ, Parker D, Verity R, Webb SM (2004) Biogenic manganese oxides: properties and mechanisms of formation. Annu Rev Earth Planet Sci 32:287–328
Tebo BM, Johnson HA, McCarthy JK, Templeton AS (2005) Geomicrobiology of Manganese(II) oxidation. Trends Microbiol 13:421–428
Lanson B, Drits VA, Silvester E, Manceau A (2000) Structure of H-exchange hexagonal birnessite and its mechanism of formation from Na-rich monoclinic buserite at low pH. Am Miner 85:826–838
Manceau A, Drits VA, Silvester E, Bartoli C, Lanson B (1997) Structural mechanism of Co2+ oxidation by the phyllomanganate buserite. Am Miner 82:1150–1175
Manceau A, Lanson M, Geoffroy N (2007) Natural speciation of Ni, Zn, Ba, and As in ferromanganese coatings on quartz using X-ray fluorescence, absorption, and diffraction. Geochim Cosmochim Acta 71:95–128
Bargar JR, Fuller CC, Marcus MA, Brearley AJ, Perez De la Rosa M, Webb SM, Caldwell WA (2009) Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ. Geochim Cosmochim Acta 73:889–910
Hochella MF Jr, Kasama T, Putnis A, Putnis CV, Moore JN (2005) Environmentally important, poorly crystalline Fe/Mn hydrous oxides: Ferrihydrite and a possibly new vernadite-like mineral from the Clark Fork River Superfund Complex. Am Miner 90:718–724
Peña J, Bargar JR, Sposito G (2015) Copper sorption by the edge surfaces of synthetic birnessite nanoparticles. Chem Geol 396:196–207
Simanova AA, Kwon KD, Bone SE, Bargar JR, Refson K, Sposito G, Peña J (2015) Probing the sorption reactivity of the edge surfaces in birnessite nanoparticles using Nickel(II). Geochim Cosmochim Acta 164:191–204
Aplin AC, Cronan DS (1985) Ferromanganese oxide deposits from the Central Pacific Ocean, I. Encrustations from the Line Islands Archipelago. Geochim Cosmochim Acta 49:427–436
Chukhrov FV, Sakharov BA, Gorshkov AI, Drits VA, Dikov YP (1985) Crystal structure of birnessite from the Pacific ocean. Int Geol Rev 27:1082–1088
Duff MC, Hunter DB, Triay IR, Bertsch PM, Reed DT, Sutton SR, Shea-McCarthy G, Kitten J, Eng P, Chipera SJ, Vaniman DT (1999) Mineral associations and average oxidation states of sorbed Pu on Tuff. Environ Sci Technol 33:2163–2169
Exon NF, Raven MD, De Carlo EH (2002) Ferromanganese nodules and crusts from the Christmas Island Region, Indian Ocean. Mar Georesour Geotechnol 20:275–297
Friedl G, Wehrli B, Manceau A (1997) Solid phases in the cycling of manganese in eutrophic lakes: new insights from EXAFS spectroscopy. Geochim Cosmochim Acta 61:275–290
Isaure M-P, Manceau A, Geoffroy N, Laboudigue A, Tamura N, Marcus MA (2005) Zinc mobility and speciation in soil covered by contaminated dredged sediment using micrometer-scale and bulk-averaging X-ray fluorescence, absorption and diffraction techniques. Geochim Cosmochim Acta 69:1173–1198
Koschinsky A, Halbach P (1995) Sequential leaching of marine ferromanganese precipitates: Genetic implications. Geochim Cosmochim Acta 59:5113–5132
Koschinsky A, Hein JR (2003) Uptake of elements from seawater by ferromanganese crusts: solid-phase associations and seawater speciation. Mar Geol 198:331–351
Lienemann C-P, Taillefert M, Perret D, Gaillard J-F (1997) Association of cobalt and manganese in aquatic systems: chemical and microscopic evidence. Geochim Cosmochim Acta 61:1437–1446
Manceau A, Lanson B, Schlegel ML, Harge JC, Musso M, Eybert-Berard L, Hazemann J-L, Chateigner D, Lamble GM (2000) Quantitative Zn speciation in smelter-contaminated soils by EXAFS spectroscopy. Am J Sci 300:289–343
Manceau A, Tamura N, Celestre RS, MacDowell AA, Geoffroy N, Sposito G, Padmore HA (2003) Molecular-scale speciation of Zn and Ni in soil ferromanganese nodules from loess soils of the Mississippi Basin. Environ Sci Technol 37:75–80
Manceau A, Tommaseo C, Rihs S, Geoffroy N, Chateigner D, Schlegel M, Tisserand D, Marcus MA, Tamura N, Chen Z-S (2005) Natural speciation of Mn, Ni, and Zn at the micrometer scale in a clayey paddy soil using X-ray fluorescence, absorption, and diffraction. Geochim Cosmochim Acta 69:4007–4034
Marcus MA, Manceau A, Kersten M (2004) Mn, Fe, Zn and As speciation in a fast-growing ferromanganese marine nodule. Geochim Cosmochim Acta 68:3125–3136
McKenzie RM (1980) The adsorption of lead and other heavy metals on oxides of manganese and iron. Aust J Soil Res 18:61–73
Ostwald J, Frazer FW (1973) Chemical and mineralogical investigations on deep sea manganese nodules from the Southern Ocean. Miner Deposita 8:303–311
Peacock CL, Moon EM (2012) Oxidative scavenging of thallium by birnessite: explanation for thallium enrichment and stable isotope fractionation in marine ferromanganese precipitates. Geochim Cosmochim Acta 84:297–313
Peacock CL, Sherman DM (2007) Crystal-chemistry of Ni in marine ferromanganese crusts and nodules. Am Miner 92:1087–1092
Takahashi Y, Manceau A, Geoffroy N, Marcus MA, Usui A (2007) Chemical and structural control of the partitioning of Co, Ce, and Pb in marine ferromanganese oxides. Geochim Cosmochim Acta 71:984–1008
Peña J, Bargar JR, Sposito G (2011) Role of bacterial biomass in the sorption of Ni by biomass-birnessite assemblages. Environ Sci Technol 45:7338–7344
Peña J, Kwon KD, Refson K, Bargar JR, Sposito G (2010) Mechanisms of nickel sorption by a bacteriogenic birnessite. Geochim Cosmochim Acta 74:3076–3089
Lafferty BJ, Ginder-Vogel M, Sparks DL (2011) Arsenite oxidation by a poorly-crystalline manganese oxide. 3. Arsenic and manganese desorption. Environ Sci Technol 45:9218–9223
Lafferty BJ, Ginder-Vogel M, Zhu M, Livi KJT, Sparks DL (2010) Arsenite oxidation by a poorly crystalline manganese-oxide. 2. Results from X-ray absorption spectroscopy and X-ray diffraction. Environ Sci Technol 44:8467–8472
Manning BA, Fendorf SE, Bostick B, Suarez DL (2002) Arsenic(III) oxidation and arsenic(V) adsorption reactions on synthetic birnessite. Environ Sci Technol 36:976–981
Tournassat C, Charlet L, Bosbach D, Manceau A (2002) Arsenic(III) oxidation by birnessite and precipitation of Manganese(II) arsenate. Environ Sci Technol 36:493–500
Ying SC, Kocar BD, Fendorf S (2012) Oxidation and competitive retention of arsenic between iron- and manganese oxides. Geochim Cosmochim Acta 96:294–303
Bidoglio G, Gibson PN, O’Gorman M, Roberts KJ (1993) X-ray absorption spectroscopy investigation of surface redox transformations of thallium and chromium on colloidal mineral oxides. Geochim Cosmochim Acta 57:2389–2394
Grangeon S, Manceau A, Guilhermet J, Gaillot A-C, Lanson M, Lanson B (2012) Zn sorption modifies dynamically the layer and interlayer structure of vernadite. Geochim Cosmochim Acta 85:302–313
Bodeï S, Manceau A, Geoffroy N, Baronnet A, Buatier M (2007) Formation of todorokite from vernadite in Ni-rich hemipelagic sediments. Geochim Cosmochim Acta 71:5698–5716
Chukhrov FV (1980) Structural varieties of todorokite. Int Geol Rev 22:75–83
Ostwald J (1984) Two varieties of lithiophorite in some Australian deposits. Miner Mag 48:383–388
Grangeon S, Lanson B, Lanson M (2014) Solid-state transformation of nanocrystalline phyllomanganate into tectomanganate: influence of initial layer and interlayer structure. Acta Crystallogr Sect B Struct Sci Cryst Eng Mater 70:828–838
Portehault D, Cassaignon S, Baudrin E, Jolivet J-P (2009) Structural and morphological control of manganese oxide nanoparticles upon soft aqueous precipitation through MnO4 −/Mn2+ reaction. J Mater Chem 19:2407–2416
Cui H, Feng X, Tan W, He J, Hu R, Liu F (2009) Synthesis of todorokite-type manganese oxide from Cu-buserite by controlling the pH at atmospheric pressure. Microporous Mesoporous Mater 117:41–47
Cui H, Liu X, Tan W, Feng X, Liu F, Ruan HD (2008) Influence of Mn(III) availability on the phase transformation from layered buserite to tunnel-structured todorokite. Clays Clay Miner 56:397–403
Feng XH, Zhu MQ, Ginder-Vogel M, Ni CY, Parikh SJ, Sparks DL (2010) Formation of nano-crystalline todorokite from biogenic Mn oxides. Geochim Cosmochim Acta 74:3232–3245
Zhang Q, Xiao Z, Feng X, Tan W, Qiu G, Liu F (2011) α-MnO2 nanowires transformed from precursor δ-MnO2 by refluxing under ambient pressure: the key role of pH and growth mechanism. Mater Chem Phys 125:678–685
Manceau A, Lanson M, Takahashi Y (2014) Mineralogy and crystal chemistry of Mn, Fe Co, Ni, and Cu in a deep-sea Pacific polymetallic nodule. Am Miner 99:2068–2083
Aplin AC, Cronan DS (1985) Ferromanganese oxide deposits from the Central Pacific Ocean, II. Nodules and associated sediments. Geochim Cosmochim Acta 49:437–451
Dutta RK, Sideras-Haddad E, Connell SH (2001) Distribution of various components in a hydrogeneous ferromanganese nodule and an Afanasiy Nikitin Seamount crust from Indian Ocean: a geochemical study using micro-PIXE. Nucl Instrum Methods Phys Res Sect B 181:545–550
Wegorzewski AV, Kuhn T (2014) The influence of suboxic diagenesis on the formation of manganese nodules in the Clarion Clipperton nodule belt of the Pacific Ocean. Mar Geol 357:123–138
Golden DC, Chen CC, Dixon JB (1986) Synthesis of Todorokite. Science 231:717–719
Atkins AL, Shaw S, Peacock CL (2014) Nucleation and growth of todorokite from birnessite: implications for trace-metal cycling in marine sediments. Geochim Cosmochim Acta 144:109–125
Baeyens B, Bradbury MH (1997) A mechanistic description of Ni and Zn sorption on Na-montmorillonite.1. Titration and sorption measurements. J Contam Hydrol 27:199–222
Bradbury MH, Baeyens B (1997) A mechanistic description of Ni and Zn sorption on Na-montmorillonite. 2. Modelling. J Contam Hydrol 27:223–248
Tournassat C, Grangeon S, Leroy P, Giffaut E (2013) Modeling specific pH dependent sorption of divalent metals on montmorillonite surfaces. A review of pitfalls, recent achievements and current challenges. Am J Sci 313:395–451
Silvester E, Manceau A, Drits VA (1997) Structure of synthetic monoclinic Na-rich birnessite and hexagonal birnessite; II, Results from chemical studies and EXAFS spectroscopy. Am Miner 82:962–978
Buatier MD, Guillaume D, Wheat CG, Herve L, Adatte T (2004) Mineralogical characterization and genesis of hydrothermal Mn oxides from the flank of the Juan the Fuca Ridge. Am Miner 89:1807–1815
Xu H, Chen T, Konishi H (2010) HRTEM investigation of trilling todorokite and nano-phase Mn-oxides in manganese dendrites. Am Miner 95:556–562
Drits VA, Lanson B, Gaillot A-C (2007) Birnessite polytype systematics and identification by powder X-ray diffraction. Am Miner 92:771–788
Giovanoli R (1980) Vernadite is random-stacked birnessite. Miner Deposita 15:251–253
Grangeon S, Lanson B, Lanson M, Manceau A (2008) Crystal structure of Ni-sorbed synthetic vernadite: a powder X-ray diffraction study. Miner Mag 72:1197–1209
Manceau A, Marcus MA, Grangeon S, Lanson M, Lanson B, Gaillot AC, Skanthakumar S, Soderholm L (2013) Short-range and long-range order of phyllomanganate nanoparticles determined using high-energy X-ray scattering. J Appl Crystallogr 46:193–209
Zhu M, Ginder-Vogel M, Parikh SJ, Feng X-H, Sparks DL (2010) Cation effects on the layer structure of biogenic Mn-oxides. Environ Sci Technol 44:4465–4471
Portehault D, Cassaignon S, Baudrin E, Jolivet J-P (2007) Morphology control of cryptomelane type MnO2 nanowires by soft chemistry. Growth mechanisms in aqueous medium. Chem Mater 19:5410–5417
Galindo HM, Carvajal Y, Njagi E, Ristau RA, Suib SL (2010) Facile one-step template-free synthesis of uniform hollow microstructures of cryptomelane-type manganese oxide K-OMS-2. Langmuir 26:13677–13683
Usui A, Mita N (1995) Geochemistry and mineralogy of a modern buserite deposit from a hot spring in Hokkaido, Japan. Clays Clay Miner 43:116–127
Post JE, Veblen DR (1990) Crystal structure determinations of synthetic sodium, magnesium, and potassium birnessite using TEM and the Rietveld method. Am Miner 75:477–489
Fabian C, Reimann C, Fabian K, Birke M, Baritz R, Haslinger E (2014) GEMAS: Spatial distribution of the pH of European agricultural and grazing land soil. Appl Geochem 48:207–216
Burns RG, Burns VM (1977) Mineralogy of manganese nodules. In: Glasby GP (ed) Marine manganese deposits. Elsevier, New York
Burns RG, Burns VM (1979) Manganese oxides. In: Burns RG (ed) Marine minerals. Mineral Society of America, Washington, D.C
Feng XH, Tan WF, Liu F, Wang JB, Ruan HD (2004) Synthesis of todorokite at atmospheric pressure. Chem Mater 16:4330–4336
Lee J, Ju JB, Cho WI, Cho BW, Oh SH (2013) Todorokite-type MnO2 as a zinc-ion intercalating material. Electrochim Acta 112:138–143
Marafatto FF, Strader ML, Gonzalez-Holguera J, Schwartzberg A, Gilbert B, Peña J (2015) Rate and mechanism of the photoreduction of birnessite (MnO2) nanosheets. Proc Natl Acad Sci 112:4600–4605
Plancon A (2002) CALCIPOW: a program for calculating the diffraction by disordered lamellar structures. J Appl Crystallogr 35:377
Drits VA, Tchoubar C (1990) X-ray diffraction by disordered lamellar structures: theory and applications to microdivided silicates and carbons. Springer, Berlin
Hadi J, Grangeon S, Warmont F, Seron A, Greneche J-M (2014) A novel and easy chemical-clock synthesis of nanocrystalline iron–cobalt bearing layered double hydroxides. J Colloid Interface Sci 434:130–140
Villalobos M, Lanson B, Manceau A, Toner B, Sposito G (2006) Structural model for the biogenic Mn oxide produced by Pseudomonas putida. Am Miner 91:489–502
Grangeon S, Claret F, Lerouge C, Warmont F, Sato T, Anraku S, Numako C, Linard Y, Lanson B (2013) On the nature of structural disorder in calcium silicate hydrates with a calcium/silicon ratio similar to tobermorite. Cem Concr Res 52:31–37
Grangeon S, Claret F, Linard Y, Chiaberge C (2013) X-ray diffraction: a powerful tool to probe and understand the structure of nanocrystalline calcium silicate hydrates. Acta Crystallogr Sect B Struct Sci 69:465–473
Marty NCM, Grangeon S, Warmont F, Lerouge C (2015) Alteration of nanocrystalline calcium silicate hydrate (C–S–H) at pH 9.2 and room temperature: a combined mineralogical and chemical study. Miner Mag 79:437–458
Gates WP, Slade PG, Manceau A, Lanson B (2002) Site occupancies by iron in nontronites. Clays Clay Miner 50:223–239
Roosz C, Grangeon S, Blanc P, Montouillout V, Lothenbach B, Henocq P, Giffaut E, Vieillard P, Gaboreau S (2015) Crystal structure of magnesium silicate hydrates (M–S–H): The relation with 2:1 Mg–Si phyllosilicates. Cem Concr Res 73:228–237
Vicat J, Fanchon E, Strobel P, Tran Qui D (1986) The structure of K1.33Mn8O16 and cation ordering in hollandite-type structures. Acta Crystallogr Sect B 42:162–167
Hammersley A (1997) FIT2D: an introduction and overview. European Synchrotron Radiation Facility Internal Report ESRF97HA02T
Juhas P, Davis T, Farrow CL, Billinge SJL (2013) PDFgetX3: a rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions. J Appl Crystallogr 46:560–566
Farrow C, Juhas P, Liu J, Bryndin D, Božin E, Bloch J, Proffen T, Billinge S (2007) PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals. J Phys Condens Matter 19:335219
AFM, AP, SG and NM participated to high-energy X-ray scattering experiments (HEXS). SG processed HEXS data. FW and SG did TEM experiments. SG and FW processed and analyzed TEM data. AG conducted STEM experiments to which FW and SG participated. AG, FW and SG interpreted STEM data. SG wrote the main parts of the manuscript. AFM, FW, NM, AG and BL participated to manuscript writing. All authors read and approved the final manuscript.
S.G. acknowledges funding from the ANR (NACRE—ANR-14-CE01-0006). AFM was supported by a grant from Labex OSUG@2020 (Investissements d’avenir—ANR10 LABX56). Synchrotron experiments were performed on the ID15B beamline at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. STEM experiments were performed at the LPS (Laboratoire de Physique des Solides, Orsay, France) in the frame of a research project granted to SG and FW by the national network for transmission electron microscopy and atom probe studies in France (METSA). This article benefited from comments and suggestions made by two anonymous reviewers and by Xionghan Feng (associate editor).
Compliance with ethical guidelines
Competing interests The authors declare that they have no competing interests.
About this article
- Pair Distribution Function
- Bragg rod
- High-energy X-ray scattering
- X-ray diffraction
- Transmission electron microscopy