The structure of schwertmannite, a nanocrystalline iron oxyhydroxysulfate 

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Selenium bioavailability in volcanic soils: relevance of imogolite nanotubes

Selenium has been identified during long time as a dangerous substance because of its toxicity and it has been only in the recent past that its physiological importance as a trace element fundamental to health has been assessed. (Schwarz and Foltz, 1957), linked the existence of liver, muscle and heart diseases with selenium deficit. The Kashin-Beck disease, an articulation disease found in children from the north of China, north of Korea and Siberia, was shown to be related to selenium deficit in soils (Stone, 2009). Selenium is thus known as a ‘double-edged sword’ element, having one of the narrowest ranges between dietary deficiency (< 40 µg day-1) and toxic levels (> 400 µg day-1) (Levander and Burk, 2006). Therefore, it is essential to understand the physico-chemical and biological processes that govern its bioavailability in the environment.
The bioavailability of a trace element is related to the factors that make it available to an organism, that is, in a form that can be transported across the organism’s biological membrane (Reeder et al., 2006). However, this concept is not very precise, as, for instance, a substance could be adsorbed on a colloidal particle small enough to pass through this membrane. This has motivated the use of the term “bioaccessibility”, representing “the fraction of a substance that becomes soluble within the gut or lungs and therefore available for absorption through a membrane” (Reeder et al., 2006; Ruby et al., 1996; Ruby et al., 1999). Bioavailability and bioaccessibility rely then on a variety of entangled physico-chemical factors affecting mainly solubility of the substances, like speciation, ionic strength, pH or redox potential.

Selenium speciation: its role on selenium bioavailability

An example emphasizing the relevance of selenium bioavailability against high selenium concentrations has been provided by (Amweg et al., 2003). The authors have studied the effects of an algae-bacterial selenium-reduction system applied to irrigation waters of the San Joaquin Valley (California, USA). The system helped to reduce 80% of the influent selenium in waters, but the concentration of selenite and organic selenium suffered an 8-fold increase. As a result of the water treatment, selenium concentrations in organisms increased 2-4 times due to the presence of these two forms of selenium, which are more bioavailable to biota than the original species. Speciation is thus a key factor in the fate of selenium species in the environment and in their availability to organisms. Usually, Se(0) is considered to have little toxicological significance to most organisms (Combs et al., 1996; Schlekat et al., 2000), although biological activity has been reported for elemental selenium nanoparticles (Zhang et al., 2005). Selenite and selenate are both water soluble inorganic species typically found in aerobic water sources. Selenite is both more bioavailable and approximately 5 to 10 times more toxic than selenate (Lemly, 1993). Organic selenium, in the form of selenide, Se(-II), is the most bioavailable form, and it is taken up by algae 1000 times more readily than inorganic forms (Lemly, 1993; Maier et al., 1993). Another example showing the importance of selenium speciation in soils on bioavailability is the case of selenium deficiency in the Zhangjiakou District of the Hebei province in China (Johnson et al., 2000). Soils from the Zhangjiakou District present an average of 0.15 mg of selenium kg-1, which can be considered a low concentration, but not a critically low level. In this area, the Keshan disease, a heart disease, affects some part of the population. This disease had been usually attributed to a lack of selenium in diet. However, (Johnson et al., 2000) demonstrated that the prevalence of the disease is not correlated with a lack of selenium in the soil as might be expected. The cause for the selenium deficiency is rather a result of the fact that the soil-bound selenium is not in a form available for plants. These soils are rich in organic matter, which can be the responsible of the selenium immobilization, either through direct adsorption or through redox processes: reduction of selenate to selenite would favor the adsorption of the latter onto iron and aluminum oxyhydroxides.

Role of adsorption processes on selenium bioavailability

Apart from speciation, other factors have influence on selenium bioavailability, like the sorption properties of soils, sediments and aquifer substrates, the mobility of the different species and their solubility with respect to solid phases. Different processes at the mineral/water interface can be considered responsible for the selenium associations with mineralogical soil components: adsorption, co-precipitation and surface precipitation processes, the two latter depending on solubility of the target solid phases. Adsorption is defined as ‘the process through which a chemical substance accumulates at the common boundary of two contiguous phases’ (Sposito, 2004). It highly depends on factors like ionic strength of the medium, which can reduce the adsorption properties of some minerals through the reduction of the size of Stern layer of adsorption (Sposito, 2004). Competition effects are also an important factor which may reduce selenium adsorption, e.g., when fertilizers are applied on soils, like phosphates or nitrates. For instance, selenite sorption in Indian soils have been studied by (Dhillon and Dhillon, 2000), showing that selenite adsorption is reduced by a 50% when phosphate anions are present as competitors.
Selenium species can be adsorbed through two different mechanisms at the mineral/water interface (Balistrieri and Chao, 1987; Hansmann and Anderson, 1985; Neal et al., 1987a; Neal et al., 1987b): outer-sphere and inner-sphere complexation. Formation of outer-sphere complexes is an electrostatic-driven sorption mechanism, strongly dependent on surface charge and thus on solution ionic strength (Sposito, 2004). Inner-sphere complexes form when an ion is adsorbed “specifically” on a “crystallographic site”, i.e., when covalent or ionic bonds are created with functional sites present on the mineral faces. These bonds have a stronger degree of covalence and are more stable than outer-sphere complex formation (Sposito, 2004). They are responsible in much cases of the long-term immobilization of ions at the mineral/water interface (Duc et al., 2003).
Soils from volcanic regions, volcanic-ashes produced simultaneously to volcanic gases, and sediments developed from these ashes are usually rich in selenium (Byers et al., 1938; Davidson and Powers, 1959; Ihnat, 1989; Lakin, 1972). But, paradoxically, diseases related to selenium deficiency (i.e., ‘white muscle disease’) have been reported in regions of the world dominated by selenium-rich volcanic soils such as andosols (Rayman, 2000). In fact, andosols are the soils with higher selenium distribution coefficients (Nakamaru et al., 2005). The particle / solution distribution coefficient (Kd) of selenium in Japanese agricultural andosols are as high as 600-800 L kg-1. The origin in this apparent discrepancy is two folded: on one hand, it has been reported that the specific mineralogical characteristics of volcanic soils lead to the immobilization of large quantities of organic matter (Wang and Chen, 2003); selenium associates with organic matter being immobilized and thus becomes unavailable to the biota (Wang and Gao, 2001). As stated above, clear difference should be made then between low bioavailability and deficiency, terms that have been used in a confusing way by some authors (Rayman, 2000; Reilly, 1997; Sirichakwal et al., 2005). On the other hand, little is known about the specific interactions of selenium oxyanions (predominant species of inorganic selenium in volcanic soils) and the mineralogical components specific to these soils (imogolite and allophane), which could be responsible of the low selenium bioavailability. Some studies have highlighted this possibility: sequential extractions performed on andosol samples have shown high correlation coefficients between occurrence of short-range-ordered aluminosilicates such as allophane, imogolite and active aluminum, and selenium Kd values (Nakamaru et al., 2005). Selenium bioavailability in these soils may be thus controlled by the adsorption of selenite and selenate, the two predominant species in those oxic soils, on mineral surfaces and organic matter.
In Chapter 3 of this thesis a study of the adsorption mechanisms of selenite, SeO32-, and selenate, SeO42-, the two oxyanions present in aerated soils like andosols, on two different specimens of imogolite (synthetic and biogenic) will be presented.

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Diffraction techniques for structural studies of environmental nanoparticles

Nanosize minerals present structural features that difficult their study by classical diffraction analysis methods. Atoms in their surfaces are exposed to interactions with solvents and ionic species, which cause relaxation effects and so deviations from the bulk periodic structure. Moreover, the ratio of surface atoms vs. bulk atoms scales with 1/R, being R the radius of the mineral nanoparticle (assuming spherical shape). This implies that for very small nanoparticle sizes relaxation effects will be very relevant to the average structure. On the other hand, reduced number of atoms in the bulk implies that only few atomic planes will be participating coherently in the diffraction. This translates into ill-defined Bragg peaks in the diffraction patterns, and a non-negligible diffuse scattering.
Classical diffraction analysis methods are limited under these conditions, as they rely on the Bragg peaks’ positions and intensity. This kind of analyses are performed usually in the reciprocal space, through the use of convolution methods as Rietveld refinement (Rietveld, 1969), pattern reconstruction through microstructural analyses (Lanson, 1997), or following de-convolution strategies, as the Warren-Averbach method (Warren, 1969). These methods have been applied to the study of environmental nanoparticles during the last 30 years. However, in most cases present in the literature, their use has been restricted to identification purposes. This is especially true in the cases of imogolite and schwertmannite. The diffraction patterns of these two environmental nanoparticles present very broad oscillations, which prevent the use of any convolution or de-convolution technique (Barham, 1997; Bigham et al., 1994; Farmer et al., 1983; Vandergaast et al., 1985; Wada, 1989).
In some cases, the use of these techniques has led to incorrect or incomplete results, generating debates that are still open today. It is the case of the structures of the mackinawite and ferrihydrite nanoparticles (Michel et al., 2005; Michel et al., 2007a; Michel et al., 2007b; Wolthers et al., 2003). The first analysis of fresh precipitates of mackinawite presented by Wolthers et al. (2003) proposed a structure composed by two different tetragonal phases with different lattice parameters, one of them corresponding to the lattice planes closer to the surface of the nanoparticle. However, the analysis relied on peak fitting of very broad reflections. Recently, a paper by Michel et al. (2007) showed using real-space analysis of PDF functions that only one phase was necessary to describe its local atomic ordering. Interestingly, the resulting lattice parameters from the PDF analysis coincided with the lattice parameters of bulk mackinawite (Lennie et al., 1995) meaning that, in this system, relaxation effects at the surface and structural strains do not affect the nanoparticle structure. The structure of ferrihydrite has been a subject of debate over the last 20 years. The most widely accepted idea is that it is formed by three different phases: major defect-free crystallites, minor defective crystallites and ultradisperse hematite (Manceau and Gates, 1997). In a recent paper, Michel et al. (1997) have proposed a structure with the Baker-Figgis δ-isomer of the Al13-Keggin structure as its structural motif. The PDF analyses reported in this paper show a perfect match between the real space structures of the experimental and the proposed Al13-Keggin structure for ferrihydrite. However, some authors have reported that, although the short-range structure is well reproduced, there is a lack of agreement in the diffraction pattern, with one diffraction peak absent, indicative of a different long-range  ordering (Rancourt and Meunier, 2008). This result highlights the complementarity of short-range real-space studies with long-range diffraction pattern analyses.
This complementarity is highlighted in the Chapter 5 of this thesis, devoted to the study of the structure of schwertmannite, a nanocrystalline iron oxyhydroxysulfate. While the presence of sulfate cannot be discerned from PDF measurements due to the dominant signal of Fe-Fe and Fe-O correlations, variations in sulfate concentration in the samples are responsible of strong variations in the intensity of the (101) reflection in the X-ray diffraction pattern of schwertmannite. This result indicates that, although schwertmannite has a small coherent domain size, there is an underlying long range order in the structure.
The use of PDF analysis (presented in Chapter 2), in combination with other techniques, has revealed thus as a powerful technique to the study of mineral nanoparticles, with diffraction patterns dominated by diffuse scattering that are very difficult to analyze by reciprocal-space methods.

Table of contents :

1.- Introduction
1 1.1.- Mineral nanoparticles
1 1.1.1.- Imogolite nanotubes
1.2.- Selenium bioavailability in volcanic soils: relevance of imogolite nanotubes
1.3.- Diffraction techniques for structural studies of environmental nanoparticles
2.- Experimental and theoretical methods 
2.1.- Pair Distribution Function technique
2.2.- X-ray Absorption Spectroscopy
2.3.- Simulations
2.3.1.- Ab-initio DFT calculations
2.3.2.- Classical Molecular Dynamics and Monte Carlo simulations Molecular Dynamics method Monte Carlo method
3.- Selenite and selenate adsorption mechanisms at the synthetic and biogenic imogolite – water interface 
3.1.- Introduction
3.2.- Selenite and selenate adsorption mechanisms at the imogolite – water interface
4.- Molecular dynamics investigation of the structure of water at the imogolite and gibbsite – water interfaces: effect of the curvature on the hydrophilicity and surface acidity 
4.1.- Introduction
4.2.- Water structure and hydration properties of imogolite: ‘The nanotube effect’
5.- The structure of schwertmannite, a nanocrystalline iron oxyhydroxysulfate 
5.1.- Introduction
5.2.- The structure of schwertmannite, a nanocrystalline iron oxyhydroxysulfate
6.- Conclusions 
Annex I. Multi-scale characterization of synthetic imogolite
Annex II. Other publications


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