Korean Journal of Mineralogy and Petrology (광물과 암석)

The Petrological Society of Korea & The Mineralogical Society of Korea (한국암석학회 & 한국광물학회)
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A Molecular Dynamics Simulation Study of Na- and K-birnessite Interlayer Structures

Na-, K-버네사이트 층간 구조에 대한 분자동역학 시뮬레이션 연구

  • Park, Sujeong (Department of Geology of Kangwon National University) ;
  • Kwon, Kideok D. (Department of Geology of Kangwon National University)
  • 박수정 (강원대학교 자연과학대학 지질학과) ;
  • 권기덕 (강원대학교 자연과학대학 지질학과)
  • Received : 2020.09.10
  • Accepted : 2020.09.23
  • Published : 2020.09.30
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Abstract

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.

버네사이트(birnessite)는 약 7Å의 d-spacing을 가지는 대표적인 층상형 산화망간광물로 높은 양이온 교환능력을 가지기 때문에 지하수나 퇴적물 공극 유체의 화학조성을 결정짓는 중요한 역할을 한다. 버네사이트의 양이온 교환 반응 기작을 규명하기 위해서는 층간 내 양이온의 배위 환경과 결정구조에 대한 원자 수준의 이해가 매우 중요하다. 이번 연구에서는 원자 수준의 계산광물학 방법인 고전 분자동역학(classical molecular dynamics; MD) 시뮬레이션을 이용하여 기존 실험에서 보고된 화학조성을 가지는 삼사정계 Na-와 K-버네사이트의 결정구조, 층간 양이온의 배위 환경 및 적층 구조를 계산하였다. 계산 결과는 기존 X-선 실험에서 보고된 격자 상수와 층간 배위 환경을 잘 재현하여 시뮬레이션 방법의 신뢰성을 보여주었으며, X-선 실험만으로는 구분하기 어려운 층간의 양이온과 물 분자 위치를 구별한 원자 수준의 정보를 제공하였다. 망간 팔면체 층의 적층 순서는 동일하지만 층간 내 Na+와 K+의 위치가 서로 상이하고, 층간 양이온의 배위 환경과 결정구조 간의 상관관계를 보인다. 원자 수준의 분자동역학 시뮬레이션은 버네사이트의 양이온 교환 반응 기작 규명에 크게 기여할 것으로 기대한다.

Keywords

References

  1. Aldi, K.A., Cabana, J., Sideris, P.J. and Grey, C.P., 2012, Investigation of cation ordering in triclinic sodium birnessite via 23Na MAS NMR spectroscopy. American Mineralogist, 97(5-6), 883-889. https://doi.org/10.2138/am.2012.3933
  2. BIOVIA, Dassault systemes, 2020, BIOVIA Materials Studio, BIOVIA Materials Studio 2020, San Diego: Dassault Systemes.
  3. Birkner, N. and Navrotsky, A., 2017, Thermodynamics of manganese oxides: Sodium, potassium, and calcium birnessite and cryptomelane. Proceedings of the National Academy of Sciences, 114(7), E1046-E1053. https://doi.org/10.1073/pnas.1620427114
  4. Chitrakar, R., Makita, Y., and Sonoda, A., 2011, Cesium ion exchange on synthetic birnessite ($Na_{0.35}MnO_{2}{\cdot}0.6H_{2}O$). Chemistry Letters, 40(10), 1118-1120. https://doi.org/10.1246/cl.2011.1118
  5. 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. The Journal of Physical Chemistry B, 108(4), 1255-1266. https://doi.org/10.1021/jp0363287
  6. Cygan, R.T., Post, J.E., Heaney, P.J., and Kubicki, J.D., 2012, Molecular models of birnessite and related hydrated layered minerals. American Mineralogist, 97(8-9), 1505-1514. https://doi.org/10.2138/am.2012.3957
  7. Drits, V.A., Lanson, B., and Gaillot, A.C., 2007, Birnessite polytype systematics and identification by powder X-ray diffraction. American mineralogist, 92, 771-788. https://doi.org/10.2138/am.2007.2207
  8. Drits, V.A., Silvester, E., Gorshkov, A.I., and Manceau, A., 1997, Structure of synthetic monoclinic Na-rich birnessite and hexagonal birnessite: I. Results from X-ray diffraction and selected-area electron diffraction. American Mineralogist, 82, 946-961. https://doi.org/10.2138/am-1997-9-1012
  9. Ewald, P.P., 1921, The computation of optical and electrostatic lattice potentials. Annalen der Physik, 64, 253-287. https://doi.org/10.1002/andp.19213690304
  10. Feng, Q., Yanagisawa, K., and Yamasaki, N., 1997, Synthesis of birnessite-type potassium manganese oxide. Journal of materials science letters, 16(2), 110-112. https://doi.org/10.1023/A:1018577523676
  11. Golden, D.C., Dixon, J.B., and Chen, C.C., 1986, Ion exchange, thermal transformations, and oxidizing properties of birnessite. Clays and Clay Minerals, 34, 511-520. https://doi.org/10.1346/CCMN.1986.0340503
  12. Hou, J., Li, Y., Mao, M., Ren, L., and Zhao, X,. 2014, Tremendous effect of the morphology of birnessite-type manganese oxide nanostructures on catalytic activity. ACS applied materials & interfaces, 6(17), 14981-14987. https://doi.org/10.1021/am5027743
  13. Iyer, A., Del-Pilar, J., King'ondu, C.K., Kissel, E., Garces, H.F., Huang, H., El-Sawy, A.M., Dutta, P.K. and Suib, S.L., 2012, Water oxidation catalysis using amorphous manganese oxides, octahedral molecular sieves (OMS-2), and octahedral layered (OL-1) manganese oxide structures. The Journal of Physical Chemistry C, 116(10), 6474-6483. https://doi.org/10.1021/jp2120737
  14. Jo, M.R., Kim, Y., Yang, J., Jeong, M., Song, K., Kim, Y.I., Lim, J.M., Cho, M., Shim, J.H., Kim, Y.M., Yoon, W.S., and Kang, Y.M., 2019, Triggered reversible phase transformation between layered and spinel structure in manganese-based layered compounds. Nature communications, 10(1), 1-9. https://doi.org/10.1038/s41467-018-07882-8
  15. Johnson, E.A., and Post, J.E., 2006, Water in the interlayer region of birnessite: Importance in cation exchange and structural stability. American Mineralogist, 91, 609-618. https://doi.org/10.2138/am.2006.2090
  16. Julien, C., Massot, M., Baddour-Hadjean, R., Franger, S., Bach, S. and Pereira-Ramos, J.P., 2003, Raman spectra of birnessite manganese dioxides. Solid State Ionics, 159(3-4), 345-356. https://doi.org/10.1016/S0167-2738(03)00035-3
  17. Kuma, K., Usui, A., Paplawsky, W., Gedulin, B., and Arrhenius, G., 1994, Crystal structures of synthetic 7 A and 10 A manganates substituted by mono-and divalent cations. Mineralogical Magazine, 58, 425-447. https://doi.org/10.1180/minmag.1994.058.392.08
  18. Lanson, B., Drits, V.A., Feng, Q., and Manceau, A., 2002, Structure of synthetic Na-birnessite: Evidence for a triclinic one-layer unit cell. American Mineralogist, 87, 1662-1671. https://doi.org/10.2138/am-2002-11-1215
  19. Lanson, B., Drits, V.A., Silvester, E. and Manceau A., 2000, Structure of H-exchanged hexagonal birnessite and its mechanism of formation from Na-rich monoclinic buserite at low pH. American Mineralogist, 85, 826-838. https://doi.org/10.2138/am-2000-5-625
  20. Le G off, P., B affier, N ., B ach, S. a nd Pereira-Ramos, J .P., 1996, Synthesis, ion exchange and electrochemical properties of lamellar phyllomanganates of the birnessite group. Materials Research Bulletin, 31(1), 63-75. https://doi.org/10.1016/0025-5408(95)00170-0
  21. Lopano, C.L., Heaney, P.J., Post, J.E., Hanson, J., and Komarneni, S., 2007, Time-resolved structural analysis of K-and Ba-exchange reactions with synthetic Na-birnessite using synchrotron X-ray diffraction. American Mineralogist, 92, 380-387. https://doi.org/10.2138/am.2007.2242
  22. Lopano, C.L., Heaney, P.J., Bandstra, J.Z., Post, J.E., and Brantley, S.L., 2011, Kinetic analysis of cation exchange in birnessite using time-resolved synchrotron X-ray diffraction. Geochimica et Cosmochimica Acta, 75(14), 3973-3981. https://doi.org/10.1016/j.gca.2011.04.021
  23. Newton, A.G., and Kwon, K.D., 2018, Molecular simulations of hydrated phyllomanganates. Geochimica et Cosmochimica Acta, 235, 208-223. https://doi.org/10.1016/j.gca.2018.05.021
  24. Newton, A.G., and Kwon, K.D., 2020, Classical mechanical simulations of layer-and tunnel-structured manganese oxide minerals. Geochimica et Cosmochimica Acta.
  25. Nose, S., 1984, A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52, 255-268. https://doi.org/10.1080/00268978400101201
  26. Madison, A.S., Tebo, B.M., Mucci, A., Sundby, B. and Luther, G.W., 2013, Abundant porewater Mn (III) is a major component of the sedimentary redox system. science, 341(6148), 875-878. https://doi.org/10.1126/science.1241396
  27. Manceau, A., Silvester, E., Bartoli, C., Lanson, B., and Drits, V.A, 1997, Structural mechanism of Co2+ oxidation by the phyllomanganate buserite. American mineralogist, 82(11-12), 1150-1175. https://doi.org/10.2138/am-1997-11-1213
  28. McKeown, D.A. and Post, J.E., 2001, Characterization of manganese oxide mineralogy in rock varnish and dendrites using X-ray absorption spectroscopy. American Mineralogist, 86(5-6), 701-713. https://doi.org/10.2138/am-2001-5-611
  29. Owocki K., Kremer B., Wrzosek B., Krolikowska A., and Kazmierczak J., 2016, Fungal ferromanganese mineralisation in Cretaceous dinosaur bones from the Gobi desert, Mongolia. PLOS ONE 11, e0146293. https://doi.org/10.1371/journal.pone.0146293
  30. Parrinello, M., and Rahman, A., 1981, Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied physics, 52, 7182-7190. https://doi.org/10.1063/1.328693
  31. Post, J.E., 1999, Manganese oxide minerals: Crystal structures and economic and environmental significance. Proceedings of the National Academy of Sciences of the USA, 96, 3447-3454. https://doi.org/10.1073/pnas.96.7.3447
  32. Post, J.E., and Veblen, D.R., 1990, Crystal structure determinations of synthetic sodium, magnesium, and potassium birnessite using TEM and the Rietveld method. American Mineralogist, 75, 477-489.
  33. Post, J.E., Heaney, P.J., and Cho, Y., 2011, Neutron diffraction study of hydrogen in birnessite structures. American Mineralogist, 96, 534-540. https://doi.org/10.2138/am.2011.3629
  34. Post, J.E., Heaney, P.J., and Hanson, J., 2002, Rietveld refinement of a triclinic structure for synthetic Na-birnessite using synchrotron powder diffraction data. Powder Diffraction, 17, 218-221. https://doi.org/10.1154/1.1498279
  35. Shan, X., Guo, F., Charles, D.S., Lebens-Higgins, Z., Razek, S.A., Wu, J., Xu, W., Yang, W. Page, K.L., Neuefeind, J.C., Feygenson, M., Piper L.F.J. and Teng, X., 2019, Structural water and disordered structure promote aqueous sodium-ion energy storage in sodium-birnessite. Nature communications, 10(1), 1-11. https://doi.org/10.1038/s41467-018-07882-8
  36. Tebo, B.M., Bargar, J.R., Clement, B.G., Dick, G.J., Murray, K.J., Parker, D., Verity, R. and Webb, S.M., 2004, Biogenic manganese oxides: properties and mechanisms of formation. Annu. Rev. Earth Planet. Sci., 32, 287-328. https://doi.org/10.1146/annurev.earth.32.101802.120213
  37. Trouwborst, R.E., Clement, B.G., Tebo, B.M., Glazer, B.T., and Luther, G.W., 2006, Soluble Mn (III) in suboxic zones. science, 313(5795), 1955-1957. https://doi.org/10.1126/science.1132876
  38. Verlet, L., 1967, Computer "Experiments" on classical fluids. I. Thermodynamical properties of Lannard-Jones molecules. Physical Review, 159, 98-103. https://doi.org/10.1103/PhysRev.159.98