Bulk mineral quantification using XRD refinement on randomly oriented powders 

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The unit cell of clay minerals

As with every crystallized mineral, clay structures are described through their unit cell, the smallest part of the mineral’s crystal with all its symmetry elements. Thus, the crystals can be reproduced by repeating the unit cell in the entire 3D space. Depending on the mineral type, the unit cell is formed from a single or several layers. Details on the crystallography and symmetry in clay minerals can be found elsewhere; Moore and Reynolds, (1997); Velde and Meunier, (2008); Waseda et al., (2011). Here, we focus on the general definitions in relation to this work.
The unit cell for clay minerals is defined by its three-axis (a, b, and c) and the angles between them (α, β, and γ) (Fig. I.1). The length of this three-axis can be calculated using atom to atom bonds length and basic geometry rules. However, since clay minerals have uniaxial symmetry (i.e., clay particles for which their c axis is the only symmetry axis (Wenk et al., 2010, and references therein), we are interested in the c-axis value. In this work, the c-axis value is denoted as the basal spacing (d001 or c*) in Å, this value corresponds to the layer-to-layer distance in one clay particle or the distance between 001 planes in the reciprocal space. The basal spacing is derived from the c-axis value in the real space by the relation c=c*/sin β.

Linkage and deformation of the tetrahedral and octahedral sheets

The tetrahedral sheet is linked to the octahedral through its apical oxygens. Yet, in one unit cell of clay mineral, the dimensions of the tetrahedra and octahedral sheets don’t match. For instance, the calculated b value for the tetrahedral sheet is 9.27Å, and 8.99 and 8.19Å for the tri- and di-octahedral sheets, respectively. The same case for a parameter, which is calculated from the b value. To achieve the linkage between the two sheets, a deformation in their structure must occur. Hence, each tetrahedron in the tetrahedral ring will rotate by an angle « a˚ », as illustrated in Fig. I.4a.
Consequently, the tetrahedral sheet loses its hexagonal symmetry to a ditrigonal one. Because of the repulsion forces between basal oxygens of each adjacent tetrahedrons, a˚ will not exceed 30˚. In addition, the occupied octahedrons become asymmetric in the di-octahedral sheet (Fig. I.4b). However, this is not the case for tri-octahedral sheets, which « theoretically » don’t undergo any deformation. Furthermore, additional rotation and deformation may occur to achieve the linkage between the deformed sheets (Fig. I.4c).

The classification of the clay minerals

Based on their layer composition, the clay minerals are classified into three families (Table I.1):
I. The 1:1 family layer comprises one octahedral sheet and one tetrahedral sheet denoted as 1:1 or TO layer Fig. I.5a. Clay minerals from this family include kaolin and serpentine groups.
II. The 2:1 family layer comprises one octahedral sheet sandwiched between two tetrahedral sheets Fig. I.5b. Such arrangement is denoted as 2:1 or TOT layer. If no isomorphic substitutions in the TOT layer (e.g., Talc and Pyrophyllite), Hydrogen bonds link every two consecutive layers together, and the space between the layers is the interlayer space/porosity. Suppose some isomorphic substitutions exist in the tetrahedral and/or octahedral sheets. In that case, a permanent charge is created in the layer, and cations are adsorbed in the interlayer space to neutralize the charge (more information is given below). In this family’s swelling (expandable) clays, such as smectites and vermiculites, the interlayer space can be accessible for water, and cations are generally exchangeable. In the non-swelling clays such as illite and micas, the interlayer space is none-accessible for water, and the cations are theoretically none-exchangeable.
III. The 2:1:1 family: the clay layer has the same structure as the 2:1 family, but the interlayer cations are bonded with oxygen or hydroxyl to form a brucite or gibbsite-like octahedral sheet (Fig. I.5c).

Clay particles, aggregates, and porosity types

The stacking of clay layers leads to the formation of clay particles (Fig. I.8a). Particles size ranges from single sheets (≈1nm) to centimetric single crystals (i.e., Santa Olalla vermiculite). Different rotations and translations may occur during the stacking of the various layers to form a clay particle, resulting in the polytypes of the same mineral. On the one hand, the polytypes have the same chemical composition and layer structure but differ by their stacking mode. The stacking modes can be ordered, semi-ordered, or turbostratic (Fig. I.8b). Each corresponds to a polytype of the same mineral. The ordered and semi-ordered stacking are very common in micas, illite, and kaolinite. In contrast, turbostratic stacking is commonly found in the smectite family, particularly montmorillonite.
On the other hand, the stacking sequence of layers with different chemical compositions (interstratification) leads to mixed-layer minerals (MLM). MLMs are characterized by; the proportion of the various layers, layer compositions, and the ordering degree of the layers stacking sequence (Meunier, 2005; Moore and Reynolds, 1997). Examples of MLMs are smectite/ illite, kaolinite/smectite, and chlorite/saponite.
In a rock or an artificial porous medium, clay particles stack together to form « aggregates » (Bergaya and Lagaly, 2013), as illustrated in (Fig. I.8c). The spatial distribution of clay particles and their aggregates defines the interparticle porosity (εinterp.), the voids between clay particles (Fig. I.8c). If these particles belong to swelling clay minerals (section I.5), an additional volume of interlayer porosity (εinterl.) is present (Fig. I.8c). In this work the terms clay porous media and clay sample are used interchangeably to refer to compressed sample made from clay particles.

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Conditioning and preparation of the different size fractions

IDP raw material was washed with hydrochloric acid (pH 1, room temperature) to remove carbonate and sparingly soluble minerals. Carbonate dissolution was considered completed when the pH of the clay/acid suspension was between 5 to 5.5 after a few hours of contact (typically two hours). Carbonate removal was further confirmed by recording X-Ray Diffraction (XRD) pattern (not shown) from an oriented mount. Next, the materials were washed by centrifugation with distilled water, and the <50 µm of the was retrieved by wet sieving. For SO vermiculite, the centimetric mono-crystals were broken by sonication in wet conditions, as described in Reinholdt et al. (2013). Finally, pretreatment before saturation was made for KGa-2.
All three clay minerals were transformed into homoiconic form (e.g., Na-vermiculite, Na-IDP) through three cycles of saturation with high purity NaCl salt. In each cycle, the Na+ concentration was 100 times that of the cations released by the clay materials during the exchange process. The latter was estimated based on the mineral’s cationic exchange capacity (CEC) and solid mass. After the third cycle, the excess of salt was removed by dialysis, using a 6-8 KD membrane until the test with silver nitrate was negative.
From the dispersion of the conditioned clays, different size fractions were obtained using sequential separation by centrifugation protocol adapted from the one developed by Reinholdt et al. (2013). For IDP, the < 2 µm fraction was first separated by Thermo Scientific legend XFR centrifuge from Fisher scientific®. Then, 5g of < 2 µm material were divided between 6 centrifuging tubes (38.5mL polypropylene tubes) and dispersed in Milli-Q® (MQ) pure water by sonication, centrifuged using Avanti J 301 centrifuge (swinging bucket rotor JS-24.38) from Beckman Coulter®. The extraction process for IDP started with the finest fraction (<0.05 µm) through 5 centrifugation cycles until the supernatant became clear. Followed by the coarser size fraction (0.05-0.1 µm), and then the 0.1-0.2 µm until the materials remained in the tubes are the 0.2-2 µm fraction. The extraction started with the <0.1 µm for SO-vermiculite, then the 0.1-0.2 µm fraction. Finally, three aliquots (1 mL each) from the dispersion of each fraction were dried at ambient humidity and weighted to calculate the conversion yields. Centrifugation parameters and mass contributions of each fraction are reported in Table II.1.

Table of contents :

Chapter I Clay minerals and clay porous clay media
I.1. Clay structure and classification
I.1.1. The definition of clay minerals
I.1.2. The unit cell of clay minerals
I.1.3. The structure of the clay sheet
I.1.4. Linkage and deformation of the tetrahedral and octahedral sheets
I.1.5. The classification of the clay minerals
I.1.6. The chemical formula of the clay minerals used in this work
I.1.7. External surface properties and structural charge in clay minerals
I.1.8. The Electrical Double Layer (EDL)
I.2. Clay porous media
I.2.1. Clay particles, aggregates, and porosity types
I.2.2. Definition and main properties of a clayey medium
I.2.3 Diffusion of water and solutes in a clayey medium
Chapter II Material and Methods
II.1. Materials
II.1.1. Santa Olalla vermiculite
II.1.2. Illite du Puy
II.1.3. KGa-2 kaolinite
II.2. Conditioning and preparation of the different size fractions
II.3. Building the clay porous media
II.3.1 Building clay media with variable anisotropy in particles organization
II.3.2. Induration and slicing of the clay porous media
II.4. Analyzing the preferred orientation of clay particles
II.4.1. The Orientation Distribution Function (ODF)
II.4.2. Two-dimensional X-ray Scattering (2D-XRS) measurements
II.4.3. Treatment of 2D-XRS patterns
II.4.4. Calculating the 〈P2〉 order parameter
II.5. Experimental techniques used to measure diffusion in the clay porous media
II.5.1. Through-Diffusion (TD) experiment
II.5.2. 1H NMR pulsed Gradient Spin Echo experiments
Chapter III Mineralogical and morphological characterization of different size fractions of Illite du Puy
III.1. Materials and Methods
III.1.1. Illite du Puy materials
III.1.2. Bulk mineral quantification using XRD refinement on randomly oriented powders
III.1.3. Quantification of clay mineralogy using profile modelling of XRD 00ℓ reflections
III.1.4. Microchemical analysis by electron microscopy
III.1.5. Low-pressure nitrogen and argon adsorption at 77 K
III.2. Results and discussion
III.2.1. Mineralogy comparison between V-IDP and E-IDP raw materials
III.2.2. Crystal-chemistry and geometrical characterization of sub-fractions from E-IDP sample
III.3. Concluding remarks and perspectives
III.4. Acknowledgements
III.5. References
III.6. Supplementary Data (S.D.)
Chapter IV Water diffusion in Na-vermiculite, illite and kaolinite
IV.1. Water diffusion in Na-saturated illite du Puy (Na-IDP)
IV.1.1. Particle organization measurements in IDP
IV.1.2. Experimental challenges and modification of the diffusion cell
IV.1.3. Results and discussion
IV.2. Water diffusion in Na-Santa Olalla (SO) vermiculite
IV.2.1. Article; Role of interlayer porosity and particle organization in the diffusion of water in swelling clays
IV.2.1. Supplementary data for “Role of interlayer porosity and particle organization in the diffusion of water in swelling clays”
IV.3. A comparison of HDO diffusion in Na-IDP, Na-vermiculite, and Na-kaolinite
IV.4. Summary of Chapter IV
Chapter V: Na+ and Cl- diffusion in Na-vermiculite and Na-illite
V.I. Generalities
V.2 Summary of the TD experiments
V.3. Na+ and Cl- diffusion in Na-saturated Illite du Puy (Na-IDP)
V.4. Na+ and Cl- diffusion in Na-Santa Olalla (SO) vermiculite
V.5. Summary and conclusions
General conclusions and perspectives


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