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http://dx.doi.org/10.9727/jmsk.2017.30.4.161

A Molecular Dynamics Simulation Study of Trioctahedral Clay Minerals  

Lee, Jiyeon (Critical zone Frontier Research Laboratory, Kangwon National University)
Lee, Jin-Yong (Critical zone Frontier Research Laboratory, Kangwon National University)
Kwon, Kideok D. (Critical zone Frontier Research Laboratory, Kangwon National University)
Publication Information
Journal of the Mineralogical Society of Korea / v.30, no.4, 2017 , pp. 161-172 More about this Journal
Abstract
Clay minerals play a major role in the geochemical cycles of metals in the Critical Zone, the Earth surface-layer ranging from the groundwater bottom to the tree tops. Atomistic scale research of the very fine particles can help understand the fundamental mechanisms of the important geochemical processes and possibly apply to development of hybrid nanomaterials. Molecular dynamics (MD) simulations can provide atomistic level insights into the crystal structures of clay minerals and the chemical reactivity. Classical MD simulations use a force field which is a parameter set of interatomic pair potentials. The ClayFF force field has been widely used in the MD simulations of dioctahedral clay minerals as the force field was developed mainly based on dioctahedral phyllosilicates. The ClayFF is often used also for trioctahedral mineral simulations, but disagreement exits in selection of the interatomic potential parameters, particularly for Mg atom-types of the octahedral sheet. In this study, MD simulations were performed for trioctahedral clay minerals such as brucite, lizardite, and talc, to test how the two different Mg atom types (i.e., 'mgo' or 'mgh') affect the simulation results. The structural parameters such as lattice parameters and interatomic distances were relatively insensitive to the choice of the parameter, but the vibrational power spectra of hydroxyls were more sensitive to the choice of the parameter particularly for lizardite.
Keywords
Trioctahedral clay minerals; Molecular dynamics simulations; ClayFF; Magnesium; vibrational power spectra; lizardite;
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1 Gregorkiewitz, M., Lebech, B., Mellini, M., and Viti, C. (1996) Hydrogen positions and thermal expansion in lizardite-1T from Elba: A low-temperature study using Rietveld refinement of neutron diffraction data. American Mineralogist, 81, 1111-1116.   DOI
2 Grim, R. E. (1968) Clay Mineralogy. McGraw-Hill, New York, 596p.
3 Hansen, J. P. and McDonald, I. R. (1990) Theory of simple liquids (2nd ed.). Academic Press, San Diego, 104p.
4 Jones, J. E. (1924) On the determination of molecular fields. II. From the equation of state of a gas. Proceedings of the Royal Society, 106, 463-477.   DOI
5 Komadel, P., Bujdak, J., Madejova, J., Sucha, V., and Elsass, F. (1996) Effect of non-swelling layers on the dissolution of reduced-charge montmorillonite in hydrochloric acid. Clay Minerals, 31, 333-345.   DOI
6 Kwon, K. D. and Newton, A. G. (2016) Structure and stability of pyrophyllite edge surfaces: Effect of temperature and water chemical potential. Geochimica et Cosmochimica Acta, 190, 100-114.   DOI
7 Larentzos, J. P., Greathouse, J. A., and Cygan, R. T. (2007) An ab initio and classical molecular dynamics investigation of the structural and vibrational properties of talc and pyrophyllite. Journal of Physical Chemistry C, 111, 12752-12759.   DOI
8 Lee, J. G. (2006) Computational Materials Science: Introduction, Young, Uiwang, 179p.
9 Lien, R. H. and Kramer, D. A. (1985) Recovery of Lithium from a Montmorillonite-type Clay. US Department of the Interior, Bureau of Mines.
10 Mellini, M. (1982) The crystal structure of lizardite 1T: hydrogen bonds and polytypism. American Mineralogist, 67, 587-598.
11 Mellini, M. and Viti, C. (1994). Crystal structure of lizardite-1T from Elba, Italy. American Mineralogist, 79, 1194-1198.
12 Moore, D. M. and Reynolds, R. C. (1989) X-ray Diffraction and the Identification and Analysis of Clay Minerals. Oxford university press, Oxford, 332p.
13 Newton, A. G., Kwon, K. D., and Cheong, D. K. (2016) Edge structure of montmorillonite from atomistic simulations. Minerals, 6, 25.   DOI
14 Nose, S. (1984a) A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52, 255-268.   DOI
15 Nose, S. (1984b) A unified formulation of the constant temperature molecular dynamics methods. Journal of Chemical Physics, 81, 511-519.   DOI
16 Nose, S. (1991) Constant temperature molecular dynamics methods. Progress of Theoretical Physics Supplement, 103, 1-46.   DOI
17 U.S. Geological Survey (2017) Mineral Commodity Summaries 2017. National Minerals Information Center available on the World Wide Wep, accessed October 17, 2017, at URL https://minerals.usgs.gov/minerals/pubs/mcs/.
18 Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182-7190.   DOI
19 Perdikatsis, B. and Burzlaff, H. (1981) Strukturverfeinerung am Talk $Mg_3[(OH)_2Si_4O_{10}]$. Zeitschrift fur Kristallographie-Crystalline Materials, 156, 177-186.
20 Redfern, S. A. T. and Wood, B. J. (1992) Thermal expansion of brucite, $Mg(OH)_2$. American mineralogist, 77, 1129-1132.
21 Sainz-Diaz, C. I., Hernandez-Laguna, A., and Dove, M. T. (2001) Modeling of dioctahedral 2 : 1 phyllosilicates by means of transferable empirical potentials. Physics and Chemistry of Minerals, 28, 130-141.   DOI
22 Wang, J., Kalinichev, A. G., and Kirkpatrick, R. J. (2004) Molecular modeling of water structure in nano-pores between brucite (001) surfaces. Geochimica et Cosmochimica Acta, 68, 3351-3365.   DOI
23 Savage, D. (ed.) (1995) The scientific and regulatory basis for the geological disposal of radioactive waste. Wiley, 454p.
24 Soma, Y. and Soma, M. (1989) Chemical reactions of organic compounds on clay surfaces. Environmental Health Perspectives, 83, 205.   DOI
25 Teppen, B. J., Rasmussen, K., Bertsch, P. M., Miller, D. M., and Schafer, L. (1997) Molecular dynamics modeling of clay minerals. 1. Gibbsite, kaolinite, pyrophyllite, and beidellite. Journal of Physical Chemistry B, 101, 1579-1587.   DOI
26 Tucker, M. R. (1999) Soil Fertility Notes 13; Clay minerals: their importance and function in soils. NCDA and CS Agronomic Division available on the Wep, accessed October 17, 2017, at URL http://www.ncagr.gov/agronomi/uyrst.htm.
27 Velde, B. (1992) Introduction to clay minerals: chemistry, origins, uses and environmental significance. Chapman and Hall Ltd., 198p.
28 Wang, J., Kalinichev, A. G., and Kirkpatrick, R. J. (2006) Effects of substrate structure and composition on the structure, dynamics, and energetics of water at mineral surfaces: A molecular dynamics modeling study. Geochimica et Cosmochimica Acta, 70, 562-582.   DOI
29 Zeitler, T. R., Greathouse, J. A., Gale, J. D., and Cygan, R. T. (2014) Vibrational analysis of brucite surfaces and the development of an improved force field for molecular simulation of interfaces. Journal of Physical Chemistry C, 118, 7946-7953.
30 Allen, M. P. (2004) Introduction to molecular dynamics simulation. In Attig, N., Binder, K., Grubmuller, H., Kremer, K. (eds.), Computational Soft Matter: From Synthetic Polymers to Proteins, John von Neumann Institute for Computing, Julich, NIC Series 23, 1-28.
31 Allen, M. P. and Tildesley, D. J. (2017) Computer simulation of liquids (2nd ed.). Oxford university press. 626p.
32 Braterman, P. S. and Cygan, R. T. (2006) Vibrational spectroscopy of brucite: A molecular simulation investigation. American Mineralogist, 91, 1188-1196.   DOI
33 Bailey, S. W. (1980) Summary of recommendations of AIPEA nomenclature committee on clay minerals. American Mineralogist, 65, 1-7.
34 Balan, E., Saitta, A., Mauri, F., Lemaire, C., and Guyot, F. (2015). First-principles calculation of the infrared spectrum of lizardite. American Mineralogist, 87, 1286-1290.
35 Bougeard, D., Smirnov, K. S., and Geidel, E. (2000) Vibrational spectra and structure of kaolinite: A computer simulation study. Journal of Physical Chemistry B, 104, 9210-9217.   DOI
36 Catti, M., Ferraris, G., Hull, S., and Pavese, A. (1995) Static compression and H disorder in brucite, Mg (OH) 2, to 11 GPa: a powder neutron diffraction study. Physics and Chemistry of Minerals, 22, 200-206.
37 Costanzo, P. M. (2001) Baseline studies of the clay minerals society source clays: Introduction. Clays and Clay Minerals, 49, 372-373.   DOI
38 Cygan, R. T. (2001) Molecular modeling in mineralogy and geochemistry. Reviews in Mineralogy and Geochemistry, 42, 1-35.   DOI
39 Du, H. and Miller, J. D. (2007) A molecular dynamics simulation study of water structure and adsorption states at talc surfaces. International Journal of Mineral Processing, 84, 172-184.   DOI
40 Cygan, R. T., Liang, J. J., and Kalinichev, A. G. (2004) Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. Journal of Physical Chemistry B, 108, 1255-1266.   DOI
41 Frost, R. L. and Kloprogge, J. T. (1999). Infrared emission spectroscopic study of brucite. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 55, 2195-2205.   DOI
42 Dube, A., Zbytniewski, R., Kowalkowski, T., Cukrowska, E., and Buszewski, B. (2001) Adsorption and migration of heavy metals in soil. Polish journal of environmental studies, 10, 1-10.
43 Ewald, P. P. (1921) Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen der Physik, 369, 253-287.   DOI
44 Farmer, V. C. (1958) The infrared spectra of talc, saponite and hectorite. Mineralogical Magazine, 31, 829-845.   DOI
45 Fuchs, Y., Linares, J., and Mellini, M. (1998). Mossbauer and infrared spectrometry of lizardite-1T from Monte Fico, Elba. Physics and Chemistry of Minerals, 26, 111-115.   DOI
46 Gonzalez, M. A. (2011) Force fields and molecular dynamics simulations. Ecole thematique de la Societe Francaise de la Neutronique, 12, 169-200.
47 Greathouse, J. A. and Cygan, R. T. (2005) Molecular dynamics simulation of uranyl (VI) adsorption equilibria onto an external montmorillonite surface. Physical Chemistry Chemical Physics, 7, 3580-3586.   DOI
48 Greathouse, J. A., Durkin, J. S., Larentzos, J. P., and Cygan, R. T. (2009) Implementation of a Morse potential to model hydroxyl behavior in phyllosilicates. Journal of Chemical Physics, 130, 134713.   DOI