Abstract Interpretation of lateral variations in upper mantle seismic wave speeds requires constraints on the relationship between elasticity and water concentration at high pressure for all major mantle minerals, including the garnet component. We have calculated the structure and energetics of charge-balanced hydrogen substitution into tetragonal MgSiO3 majorite up to P = 25 GPa using both classical atomistic simulations and complementary first-principles calculations. At the pressure conditions of Earth’s transition zone, hydroxyl groups are predicted to be bound to Si vacancies (□) as the hydrogarnet defect, [□Si+4OHO]X, at the Si2 tetrahedral site or as the [□Mg+2OHO]X defect at the octahedral Mg3 site. The hydrogarnet defect is more favorable than the [□Mg+2OHO]X defect by 0.8-1.4 eV/H at 20 GPa. The presence of 0.4 wt% Al2O3 substituted into the octahedral sites further increases the likelihood of the hydrogarnet defect by 2.2-2.4 eV/H relative to the [□Mg+2OHO]X defect at the Mg3 site. OH defects affect the seismic ratio, R = dlnvs/dlnvp, in MgSiO3 majorite (ΔR = 0.9-1.2 at 20 GPa for 1400 ppm wt H2O) differently than ringwoodite at high pressure, yet may be indistinguishable from the thermal dlnvs/dlnvp for ringwoodite. The incorporation of 3.2 wt% Al2O3 also decreases R(H2O) by ~0.2-0.4. Therefore, to accurately estimate transition zone compositional and thermal anomalies, hydrous majorite needs to be considered when interpreting seismic body wave anomalies in the transition zone.

Abstract Yttrium and the rare-earth elements (Y+REEs) are incorporated into aluminosilicate garnet as trivalent ions replacing divalent Mg, Fe, Mn, or Ca (“M2+”) in dodecahedral sites, which requires some form of coupled substitution to maintain electroneutrality. We compare the energetic costs of competing coupled-substitution schemes, using lattice dynamics calculations to assess defect energies and exchange energies for each scheme. Substitutions with relatively low energetic costs introduce menzerite-like components via the exchange vector [YM-1·(Mg,Fe)Al-1], or alkali components via the exchange vector [Y(Na,Li)M-2]. Substitutions with substantially higher energetic costs introduce a vacancy component via the exchange vector [Y2□M-3], or the yttrogarnet (YAG) component via the exchange vector [YM-1·AlSi-1], or a component with octahedral Li via the exchange vector [Y2M-2·LiAl-1]. Energetic costs decrease significantly as the host-garnet unit-cell dimension expands, decrease very modestly as temperature rises or pressure falls, and decrease substantially with the contraction in ionic radius across the lanthanide series. These results, combined with critical re-examination of arguments cited in favor of each substitution scheme in natural occurrences, suggest that Y+REE incorporation in natural garnet is dominated by coupled substitutions that introduce menzerite and alkali components, that the YAG substitution plays only a subsidiary role, and that the other schemes are likely to be of very minor importance.

Lithium is an important geochemical tracer used to infer the thermal and chemical evolution of minerals in the Earth’s upper mantle. Knowledge of point defect chemistry and diffusion is critical for the interpretation of Li distribution in minerals. Using quantum mechanical methods we show that in forsterite Li will be incorporated as bound interstitial–substitutional pairs. Furthermore, there will be temperature dependent fractionation of its two isotopes between the different sites. The fractionation decreases dramatically from 87.1‰ at 300 K to 1.0‰ at 3000 K. Diffusion is predicted to occur via two inter-related mechanisms: Mg–Li exchange, and a second, vacancy assisted interstitial mechanism. This behaviour is complex, facilitates migration of the heavier isotope and offers insights into observations of Li mobility and zoning in olivine, the most volumetrically important upper mantle mineral.

Jarosites are produced during metallurgical processing, on oxidized sulfide deposits, and in acid mine drainage environments. Despite the environmental relevance of jarosites, few studies have examined their biogeochemical stability. This study demonstrates the simultaneous reduction of structural Fe(III) and aqueous As(V) during the dissolution of synthetic Pb-As jarosite (PbFe(3)(SO(4),AsO(4))(2)(OH)(6)) by Shewanella putrefaciens using batch experiments under anaerobic circumneutral conditions. Fe(III) reduction occurred immediately in inoculated samples while As(V) reduction was observed after 72 h. XANES spectra showed As(III) (14.7%) in the solid phase at 168 h coincident with decreased aqueous As(V). At 336 h, XANES spectra and aqueous speciation analysis demonstrated 20.2% and 3.0% of total As was present as As(III) in the solid and aqueous phase, respectively. In contrast, 12.4% of total Fe was present as aqueous Fe(II) and was below the detection limits of XANES in the solid phase. TEM-EDS analysis at 336 h showed secondary precipitates enriched in Fe and O with minor amounts of As and Pb. Based on experimental data and thermodynamic modeling, we suggest that structural Fe(III) reduction was thermodynamically driven while aqueous As(V) reduction was triggered by detoxification induced to offset the high As(V) (328 μM) concentrations released during dissolution.

Atomistic computer simulations methods are used to examine the influence of Li and Al impurities on the uptake of hydrogen in forsterite. We find that Li-Mg+OHo is more stable at the Mg1 site than at the Mg2 site and that Li+ increases the ability of forsterite to incorporate hydrogen associated with magnesium sites. When both Al and Li are present, then a complex comprising a bound Al-Mg2-Li-Mg1 defect is highly stable. When all three impurity components are mixed together, then hydrogen will strongly partition to Si vacancies forming the hydrogamet defect. Thus the ability of forsterite to incorporate water is likely to be intimately linked to the nuances of defect chemistry, and to concentrations of impurity elements such as Li+ and Al3+.

The thermally induced transformation of kaolinite to metakaolin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal of structural water through dehydroxylation produces a distortion or buckling effect in the 1 : 1 Al-Si layers, which is due to the migration of the aluminium into vacant sites provided by the inter-layer spacing. The structural change is characterized by a loss of crystallinity and a concomitant change in aluminium coordination from octahedral to tetrahedral, with this study confirming the presence of 5-fold aluminium within the metakaolin structure. The degree and probability of Al migration are proportional to the amount of local disorder within the structure, which is governed by the degree of local hydroxyl group loss. This results in the formation of aluminium clusters within the layers. This study proposes that instead of a uniform structure, metakaolin exhibits regions of differing aluminium concentrations, which can have major effects in the reaction chemistry at those sites.

The performance of density functional theory has been widely examined with regard to its ability to predict the properties of minerals, though less attention has been given to the correct determination of the relative stability of structurally similar polymorphs. Here a detailed examination is performed of the numerical and theoretical factors that may influence the structure and relative energetics of two such polymorphs of iron disulfide, namely, pyrite and marcasite, within density functional theory. Both the local-density approximation and commonly used generalized gradient approximation exchange-correlation functionals, such as Perdew, Burke and Ernzerhof (PBE), are found to predict that marcasite is more stable than pyrite, at variance with experiment. Allowing for the zero-point energy of vibration fails to remedy this discrepancy. While inclusion of a sufficiently large Hubbard $U$ parameter for iron is found to reverse the stability, this comes at the expense of a very poor description of other properties. Examination of three generalized gradient approximations developed specifically for the solid state, namely, AM05, Wu-Cohen and PBEsol, demonstrates that all of these functionals offer a superior description of the structures and relative energies of pyrite and marcasite through correctly predicting that the former is the ground-state phase at ambient conditions.

Coupled substitutions involving hydrogen plus trivalent elements (Al, Eu, Fe, Ga, Gd, Lu, Mn, Nd, Pu, Sc, Y and Yb) in forsterite (Mg2SiO4) are studied using atomistic simulation methods. Incorporation of hydrogen is energetically favourable when included in the forsterite lattice as hydroxyl groups (OH−) at O3 sites while the trivalent cations replace either magnesium or silicon. Our calculations show a strong dependence on the ionic radius of the impurity species and some variation with pressure. There are also significant structural distortions around the impurity defects. At low pressure (0GPa), the smaller trivalent cations, (e.g. Al, Fe, Mn and Ga) substitute into forsterite by replacing Si as: MSi′+OHO3•. The larger trivalent cations (e.g. Eu, Gd, Lu, Nd, Pu, Y and Yb) however, replace Mg at the M2 site coupled with an Mg1 vacancy as described by VMg1″+MMg2•+OHO3•. At 12GPa, the large cations are more stable at Mg1 relative to Mg2, but both are predicted to be less stable than configurations associated with Si vacancies. The trivalent ionic radius has a significant effect on the H incorporation mechanism, however, the high formation energy of Si vacancies suggests that the presence of H in forsterite could inhibit incorporation of these elements, particularly at high pressure.

Quantum mechanical techniques, based on density functional theory, have been used to study the distribution of iron impurities in sphalerite (ZnS) at compositions ranging from 3.125 to 12.5mol% FeS. Our results show that iron is most easily incorporated by direct substitution onto the zinc site and that energies for solution reactions involving FeS are exothermic when the system is zinc deficient. Furthermore, there appears to be a small driving force for the formation of bound Fe–Fe pairs at low iron concentrations, though there is no particular preference found for larger clusters of iron. The influence of iron on the sphalerite cell parameter is shown to be sensitive to the presence of Fe–Fe pairs and to the degree of sample non-stoichiometry.

The movement of impurities and point defects in materials plays a key role in determining their rheological properties, both by permitting diffusional creep and by allowing recovery by dislocation climb. Impurity and point defect diffusion can also control the kinetics of phase transitions and grain growth, and can determine the rate of chemical equilibration between phases. Thus the study of point defects and their migration has been of considerable interest. So far, studies using computer simulation methods have concentrated on point defects moving through otherwise perfect crystals. Here, we report calculations on the behavior of the isovalent substitutional cation impurities, Ca and Sr, close to the core of an edge dislocation in MgO. By mapping the distribution of energies for impurities and point defects around the dislocation line, we reveal that the impurities are segregated towards and trapped inside the MgO edge dislocation core. In addition, Mg vacancies will strongly partition to the impurity bearing dislocation. We also find that the presence of impurities slightly increases the Mg migration activation energy. However, impurity migration in the dislocation core is substantially enhanced compared to migration through the dislocation-free crystal structure. Activation energies are 0.76-0.86 of the barrier in the perfect crystal, demonstrating the importance of pipe diffusion along extended defects for low temperature mobility in ionic materials.

Jarosite is an important mineral on Earth, and possibly on Mars, where it controls the mobility of iron, sulfate and potentially toxic metals. Atomistic simulations have been used to study the incorporation of Al3+, and the M2+ impurities Cd, Cu and Zn, in the (012) and (001) surfaces of jarosite. The calculations show that the incorporation of Al on an Fe site is favorable on all surfaces in which terminal Fe ions are exposed, and especially on the (001) [Fe3(OH)3]6+ surface. Incorporation of Cd, Cu or Zn on a K site balanced by a K vacancy is predicted to stabilize the surfaces, but calculated endothermic solution energies and the high degree of distortion of the surfaces following incorporation suggest that these substitutions will be limited. The calculations also suggest that incorporation of Cd, Cu and Zn on an Fe site balanced by an OH vacancy, or by coupled substitution on both K and Fe sites, is unfavorable, although this might be compensated for by growth of a new layer of jarosite or goethite, as predicted for bulk jarosite. The results of the simulations show that surface structure will exert an influence on uptake of impurities in the order Cu>Cd>Zn, with the most favorable surfaces for incorporation being (012) [KFe(OH)4]0 and (001) [Fe3(OH)3]6+.

Dislocations are known to influence the formation and migration of point defects in crystalline materials. We use a recently developed method for the simulation of the cores of dislocations in ionic materials to study the energy associated with the formation of point defects close to the core of a 1/2 < 110 >{1 (1) over bar0} edge dislocation in MgO. These are then compared with the energies for the same point defects in otherwise perfect MgO. It is found that all of the defect species are bound to the dislocation core, with binding energies of between 1.5 and 2.0 eV. Vacancies are found to be most stable when they remove under-coordinated ions at the tip of the extra half plane, while the impurities are most stable within the dilatational stress field below the glide plane. By mapping the distribution of energies for point defects around the dislocation line we reveal the coupling between the effective point defect size and the stress field associated with the dislocation. We also examine the energy barrier to diffusion of vacancies along the dislocation line and find that vacancy migration along the dislocation line will be substantially enhanced compared to migration through the dislocation-free crystal structure. Activation energies are 0.85-0.92 of the barrier in the perfect crystal, demonstrating the importance of pipe diffusion along extended defects for low temperature mobility in ionic materials.

The existence or otherwise of the hydronium cation within the mineral alunite has proved difficult to verify based on experimental data alone. In the present study, we employ first-principles quantum mechanical techniques to determine the nature of the structure of hydronium alunite. A new model for the hydrogen atom disorder is predicted that differs from a proposed arrangement in the case of the analogous stoichiometric hydronium jarosite. Instead of occupying one of two orientations that respect the threefold symmetry axis passing through the oxygen, the cation is found to occupy a tilted orientation leading to a greater degree of disorder. Dynamical simulations indicate that the reorientation of the hydronium ions is rapid and exhibits no correlation between the cation sites. The higher level of disorder in the hydrogen positions offers an explanation as to why their location has proved elusive thus far

Research Article| January 01, 2010 Lattice Dynamics from Force-Fields as a Technique for Mineral Physics Julian D. Gale; Julian D. Gale Department of Chemistry/Nanochemistry Research Institute, Curtin University of Technology, P.O. Box U1987, Perth, WA 6845, Australia Search for other works by this author on: GSW Google Scholar Kate Wright Kate Wright Department of Chemistry/Nanochemistry Research Institute, Curtin University of Technology, P.O. Box U1987, Perth, WA 6845, Australia Search for other works by this author on: GSW Google Scholar Author and Article Information Julian D. Gale Department of Chemistry/Nanochemistry Research Institute, Curtin University of Technology, P.O. Box U1987, Perth, WA 6845, Australia Kate Wright Department of Chemistry/Nanochemistry Research Institute, Curtin University of Technology, P.O. Box U1987, Perth, WA 6845, Australia Publisher: Mineralogical Society of America First Online: 09 Mar 2017 © The Mineralogical Society Of America Reviews in Mineralogy and Geochemistry (2010) 71 (1): 391–411. https://doi.org/10.2138/rmg.2010.71.18 Article history First Online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Julian D. Gale, Kate Wright; Lattice Dynamics from Force-Fields as a Technique for Mineral Physics. Reviews in Mineralogy and Geochemistry 2010;; 71 (1): 391–411. doi: https://doi.org/10.2138/rmg.2010.71.18 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyReviews in Mineralogy and Geochemistry Search Advanced Search Theory and computation play an increasingly important role in the field of mineral physics by allowing the scientist to probe environments, such as the deep Earth, that are challenging or impossible to access extensively by experiment. Quantum mechanical methods are often the technique of choice, usually based on Kohn-Sham density functional theory as the computationally most practical approach for solids. Although calculations at this level can already be performed on thousands of atoms (Soler et al. 2002; Cankurtaran et al. 2008), the ability to sample nuclear configuration space is often restricted. While density functional theory is typically... You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Techniques of atomistic simulation have been used to study the incorporation of the M 2+ impurities iron, manganese and cadmium into sphalerite. The calculations show that bulk impurity ions are most easily incorporated by direct substitution at the Zn site, and that the substitution energies exhibit a linear relationship with ionic radii. Furthermore, there appears to be no driving force for the creation of clusters, or any barrier to their formation. However, the formation of iron pairs leads to deviations from Vegard’s Law. Simulations of pure ZnS surfaces have identified a new reconstruction for the zinc-terminated (111), which has the lowest energy of all {111}-type surfaces. Furthermore, impurities can exchange with zinc more easily on (111) than on any of the other surfaces studied. The results of the simulations show that crystal morphology and surface structure will exert an influence on uptake of impurities, with the effect being most noticeable for cadmium and least important for iron.

We have studied the formation and migration of point defects within the magnesium sub-lattice in forsterite using a combination of empirical and quantum mechanical modelling methodologies. Empirical models based on a parameterised force field coupled to a high throughput grid computing infrastructure allow rapid evaluation of a very large number of possible defect configurations. An embedded cluster approach reveals more accurate estimates of defect energetics for the most important defect configurations. Considering all defects in their minimum energy, equilibrium positions, we find that the lowest energy intrinsic defect is the magnesium Frenkel type, where a magnesium atom moves from the M1 site to form a split interstitial defect. This defect has 2 four-co-ordinated magnesium atoms located outside opposite triangular faces of an otherwise vacant M1 octahedron. The split interstitial defect is more stable than regular interstitials where magnesium is located in either of the two structurally vacant octahedral sites in the hexagonally close packed oxygen lattice. M1 vacancies are also found to form when iron(II) oxidises to iron(III). The energy of the defects away from the equilibrium positions allows the energy barrier to diffusion to be calculated. We have considered the migration of both magnesium vacancies and interstitials and find that vacancies are more mobile. When the contribution from the formation energy of the defects is included we arrive at activation energies for vacancy diffusion that are in agreement with experiment.