• Journal of the Mineralogical Society of Korea
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• v.27 no.4
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• pp.271-281
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• 2014

The physicochemical properties of clay minerals have been investigated at the atomistic to nano scale. The microscopic studies are often challenging to perform by using experimental approaches alone. In particular, hydroxyl groups of octahedral sheets in 2:1 clay minerals have been hypothesized to impact the sorption process of metal cations; however, X-ray based techniques alone, a common tool for mineral structure examination, cannot properly test the hypothesis. The current study has examined whether computational mineralogy techniques can be applied to examine the hydroxyl structures of clay minerals. Based on quantum-mechanics and molecular-mechanics computational methods, geometry optimizations were carried out for representative dioctahedral and trioctahedral phyllosilicate minerals. Both methods well reproduced the experimental lattice parameters; however, for structural distortion occurring in the tetrahedral or octahedral sheets, molecular mechanics showed significant deviations from experimental data. The orientation angle of the hydroxyl with respect to (001) basal plane is determined by the balance of repulsion between the hydroxyl proton and Si cations of tetrahedral sites; the quantum-mechanics method predicted $25-26^{\circ}$ for the angle, whereas the angle predicted by the molecular-mechanics method was much higher by $10^{\circ}$ (i.e., $35^{\circ}$). These results demonstrate that computational mineralogy techniques are a reliable tool for clay mineral studies and can be used to further elucidate the roles of hydroxyls in metal sorption process.

• Journal of the Mineralogical Society of Korea
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• v.31 no.1
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• pp.13-22
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• 2018

Aluminum silicates ($Al_2SiO_5$) undergo phase transitions among kyanite, andalusite, and sillimanite depending on temperature and pressure conditions. The minerals are often used as an important indicator of the degree of metamorphism for certain metamorphic rocks. In this study, we have applied classical molecular dynamics (MD) simulations and density functional theory (DFT) to the aluminum silicates. We examined the crystal structures as a function of applied pressure and the corresponding stabilities based on calculated enthalpies at each pressure. In terms of the lattice parameters, both methods showed that the volume decreases as the pressure increases as observed in the experiment. In particular, DFT results differed from experimental results by much less than 1%. As to the relative stability, however, both methods showed different levels of accuracy. In the MD simulations, a transition pressure at which the relative stability between two minerals reverse could not be determined because the enthalpies were insensitive to the applied pressure. On the other hand, in DFT calculations, the relative stability relation among the three minerals was consistent with experiment, although the transition pressure was strongly dependent on the choice of the electronic exchange-correlation functional.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.3
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• pp.143-152
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• 2020

Birnessite is a layered manganese oxide mineral with ~7 Å of d-spacing. Because of its high cation exchange capacity, birnessite greatly impacts the chemical compositions of ground water and fluids in sediment pores. Understanding the cation exchange mechanisms requires atomistic investigations of the crystal structures and coordination environments of hydrated cations in the interlayer. In this study, we conducted classical molecular dynamics (MD) simulations, an atomistic simulation method of computational mineralogy, for triclinic Na-birnessite and K-birnessite whose chemical formula are from previous experiments. We report our MD simulation results of the crystal structures, coordination environments of Na⁺ and K⁺, and the polytypes of birnessite and compare them with available experimental results. The simulation results well reproduced experimental lattice parameters and provided atomic level information for the interlayer cation and water molecule sites that are difficult to distinguish in X-ray experiments. We also report that the polytype of the Mn octahedral sheets is identical between Na- and K-birnessite, but the cation positions differ from each other, demonstrating a correlation between the coordination environment of the interlayer cations and the crystal lattice parameters. This study shows that MD simulations are very promising in elucidating ion exchange reactions of birnessite.