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1 Dipartimento di Scienze Geologiche e Geotecnologie, Università di Milano Bicocca, Piazza della Scienza 4, 20126 Milano, Italy
2 Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, U.K.
3 Dipartimento di Scienze della Terra, Università di Siena, Via Laterina 8, 53100 Siena, Italy
Correspondence: * E-mail: giancarlo.capitani{at}unimib.it
| ABSTRACT |
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As an additional benefit, we also compare the total energies of two competing models for the m = 17 antigorite structure, the one refined by Capitani and Mellini (2004) and that proposed by Dódony et al. (2002). We found the former more stable, both as published (
E = 1.1 kJ/mol·atom–1) and after full cell relaxation at constant volume (
E = 0.5 kJ/mol·atom–1).
Key Words: Antigorite DFT LDA GGA
| INTRODUCTION |
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The structure of natural and synthetic antigorite is difficult to determine in the lab. Antigorite specimens, when imaged with a transmission electron microscope, appear highly faulted, thus preventing or highly complicating any further structural analysis. Even in the most fortunate cases, crystal disorder (mainly as b/3 stacking disorder or polysomatic disorder) must be taken into account and modeled to achieve reliable structural data (Capitani and Mellini 2004, 2006). This is a general problem not limited to serpentine, and typical of many poorly crystalline, fine-grained materials. Whenever the samples are not ordered at a scale suitable for single-crystal structural analysis, one typically uses X-ray powder diffraction and/or electron crystallography. Unfortunately, these methods also have limitations, since the former suffers from an unfavorable ratio of the number of data to the number of structural parameters to be determined, and the latter from problems related to dynamical scattering.
In part because of these difficulties, two competing and mutually exclusive models have been proposed by Capitani and Mellini (2004, 2006) and Dódony et al. (2002, 2006). To further discriminate between these two models, we now take an entirely different approach based on density functional theory. We use first-principles calculations to further explore the crystal chemistry of these two models and to test their relative energetic favorability. A similar approach was taken by Stixrude and Peacor (2002) in an investigation of competing structure models of illite-smectite. We further show how density functional theory can be used systematically to improve proposed structures based on experimental data, an approach that has been used in other systems (e.g., Weirich 2003).
| STRUCTURAL MODELS |
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| COMPUTATIONAL METHOD |
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To make the solution tractable, one other essential approximation is the pseudopotential approximation (Heine 1970). This approximation is physically motivated by the argument that the core electrons participate little in bonding and structural changes. The nucleus and core electrons are replaced by a simpler object, the pseudopotential, which has the same scattering properties. We used ultrasoft Vanderbilt (Vanderbilt 1990; Kresse et al. 1992) pseudopotentials, which limit the size of the plane-wave basis set required to accurately represent charge density and potential.
All computations were performed with the plane-wave pseudopotential method in the Vienna ab initio simulation package (VASP) (Kresse and Hafner 1993; Kresse and Furthmüller 1996a, 1996b). Calculated forces and stresses are used to perform complete structural relaxations at constant volume via a conjugate gradient scheme that systematically modifies the structure until net forces and deviatoric stresses fall below a tolerance threshold. The relaxation scheme is based on the method of Wentzcovitch (1991) and Wentzcovitch et al. (1993), which conserves the space group symmetry.
Total static energy calculations were performed either in the absence of relaxation or allowing relaxation. The crystal structures of the m = 17 polysome by Capitani and Mellini (2004) and by Dódony et al. (2002), expressed in their respective primitive P1 unit cells [291 atoms for a Mg48Si34O85(OH)62 unit formula]1, were used, as published in the absence of relaxation, and as an initial guess in the presence of relaxation. We used an energy cutoff of 500 eV, and a Monkhorst-Pack (Monkhorst and Pack 1976) 1 x 2 x 2 k point mesh, yielding a value of the energy difference between the two structures that is converged to better than 0.1 meV/unit cell.
| RESULTS |
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Theoretical structural relaxations yield structures that are more sensible crystal-chemically relative to those originally determined experimentally (Table 1
). Whereas the octahedral sheet is not significantly affected by relaxation, especially using LDA, the tetrahedral sheet appears modified. The Si-O bonds are less dispersed after relaxation and no longer show the anomalous long and short distances present in the experimental tetrahedral sheet. Capitani and Mellini (2004) interpreted these sporadic anomalous distances, located at tetrahedral reversals, as biased due to polysomatic disorder. Because of disorder, electron density at reversals is delocalized over several sites and the scattering power affected consequently, which in turn yields poorly constrained bond geometry. In contrast, the octahedral sheet is basically unaffected by polysomatic (and stacking) disorder, and this explains why the relaxed octahedral sheet closely matches the refined one.
The fine structural details of antigorite are well reproduced: apical Si-OA bonds are shorter than basal Si-OB bonds (LDA: 1.596 vs. 1.637 Å; GGA: 1.603 vs. 1.647 Å); external Mg-Oext distances are shorter than internal Mg-Oint distances (LDA: 2.038 vs. 2.127 Å; GGA: 2.049 vs. 2.142 Å).
Also the O-H bonds are less dispersed in the relaxed structure. However, in this case, comparison is difficult because of the very limited scattering power of H atoms. During X-ray refinement, the x and y hydrogen coordinates were assumed to be identical to those of the bonded O atoms and the O-H distances were restrained to a fixed value. Therefore, the present simulations most probably represent the best estimate of hydrogen distributions within antigorite (Fig. 2
). The theoretically relaxed structure reveals a significant difference between the lengths of internal O-Hint distances (LDA: 0.976 Å; GGA: 0.970 Å) and external O-Hext distances (LDA: 0.980 Å; GGA: 0.973 Å), a distinction that is not resolvable with XRD data alone.2
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The mean atomic displacements during relaxation are ~0.06 Å along x, ~0.02 Å along y, and ~0.04 Å along z (Table 2
). In terms of fractional coordinates, the major displacement occurs along z (~0.5%), then along y (~0.2%), and along x (~0.1%). The largest readjustments involve, in most cases, the basal O atoms, and in particular the B17 oxygen, located at the 6-reversal (Fig. 1
) and affected by polysomatic disorder. Finally (and not surprisingly), the Mg atoms move on average less than Si atoms; the latter, in turn, move less than O atoms, which move less than H atoms. This feature in part reflects the relative scattering power of these elements, and in part the fact that magnesium atoms in the octahedral sheet of antigorite are almost insensitive to stacking and polysomatic disorder, and thus much more constrained than any other atom.
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E(VX) at the experimental volume VX that we have computed is very similar to the difference in Gibbs free energy at zero pressure,
G(0)
E(VX) + VX
(PX2)/(2K), where PX is the DFT pressure at VX and K is the bulk modulus, which we take from the static results of Mookherjee and Stixrude (2009). The magnitude of the correction term is 0.7 meV·atom–1, a small fraction of
E(VX).
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| CONCLUDING REMARKS |
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Single-crystal X-ray diffraction structure refinements unequivocally support the model of Capitani and Mellini (2004). These data were collected on the most ordered antigorite sample known to date, and the quality of the inversion is high (R4
= 0.0577). We believe that disagreement in the interpretation of HRTEM and SAED images arises fundamentally because, unlike single-crystal X-ray diffraction, there is no reliable procedure for the formal inversion of intensities (Capitani and Mellini 2008). Electron diffraction can be a powerful tool to rule out structural models, but its ability to uniquely solve structures is limited. We have demonstrated the limitations caused by multiple scattering of the reciprocal lattice sectioning method used by Dódony et al. (2006) and shown that the structure of Capitani and Mellini (2004) is in fact consistent with HRTEM and SAED images (Capitani and Mellini 2008).
The theoretical results presented here fully support the structural model of Capitani and Mellini (2004). The energy difference between the two models is large before (11.5 meV/atom or 1.1 kJ/mol·atom–1) and after relaxation (5.4 meV/atom or 0.5 kJ/mol·atom–1). For comparison, the difference in enthalpy of formation at ambient conditions from quartz and cristobalite is 1.0 kJ/mol·atom–1, and that from andalusite and sillimanite is 0.4 kJ/mol·atom–1 (Waldbraum 1965).
The energy difference between the two structural models can be attributed primarily to the presence of highly unfavorable MgO6 ditrigonal prisms in the model of Dódony et al. (2002). Such Mg-coordination environments are not known in other silicates. The DFT relaxations modify the geometry of these coordination environments substantially, but within the constraints of the bond geometry of the Dódony et al. (2002) model still yield a highly distorted octahedron. In contrast, the 4- and 8-membered rings of the structure of Capitani and Mellini (2004) are common in a wide variety of silicates (Stixrude and Bukowinski 1990). DFT relaxations alter the X-ray refined structure only slightly and yield bond geometries and coordination environments that lie well within the range known from other silicates. We find that the computed powder X-ray diffraction patterns of the LDA and GGA relaxed structures are almost indistinguishable from that of the experimentally refined structure, whereas the structure of Dódony et al. (2002) differs substantially (Fig. 5
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| ACKNOWLEDGMENTS |
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| Footnotes |
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1 Dódony et al. (2002) did not give hydrogen coordinates in their published tables. For the sake of consistency, H atoms were added in calculated positions with the same x and y coordinates as the linked oxygen atoms, and 1 Å distant along z from the latter. ![]()
2 Deposit item AM-09-041, LDA relaxed atomic coordinates of all the atomic specie. Deposit items are available two ways: For a paper copy contact the Business Office of the Mineralogical Society of America (see inside front cover of recent issue) for price information. For an electronic copy visit the MSA web site at http://www.minsocam.org, go to the American Mineralogist Contents, find the table of contents for the specific volume/issue wanted, and then click on the deposit link there. ![]()
MANUSCRIPT RECEIVED February 11, 2009; MANUSCRIPT ACCEPTED May 5, 2009
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