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Reexamination of the structure of nanomineral opal-CT using synchrotron X-ray diffraction, transmission electron microscopy, X-ray scattering structure factor, and pair distribution function analyses

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Published/Copyright: July 7, 2025
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American Mineralogist
From the journal American Mineralogist Volume 110 Issue 5

Abstract

Nanomineral opal-CT is a natural precursor to quartz formed by various geological processes, including weathering, biological precipitation, hydrothermal alteration, and shock metamorphism. These processes play a crucial role in the formation of siliceous rocks as well as abiotic and biogenic interactions in natural systems. Hydrous opal-CT was recently found on the surfaces of Mars and the Moon by microanalyses and remote sensing, which has led to further investigation into the characteristics of opal-CT. In this work, we have investigated the local structures of natural opal-CT samples with various degrees of crystallinity using a combination of synchrotron X-ray diffraction (XRD), X-ray scattering structure factor S(Q) analysis, transmission electron microscopy (TEM), and pair distribution function (PDF) analysis. The combined results indicate that opal-CT is mainly composed of interstratified tridymite and cristobalite nanodomains with twins and stacking faults. S(Q) patterns are used to delineate the XRD data of opal-CT samples, which provide more precise peak profiles, allowing for better determination of the degree of ordering. TEM images and selected-area electron diffraction (SAED) patterns directly show nanodomain structures with planar defects. X-ray PDF analysis is a powerful characterization tool that can further unveil local structures, defects, and crystallinity in opal-CT. The rise in ordered domain size and two peaks at 10.01 and 11.16 Å in G(r) plot reflect the increase in the amount of cristobalite units and crystallinity. Both four- and eight-membered [SiO4] rings are created by twinning and stacking faults of the tridymite and cristobalite domains. X-ray PDF analysis provides unique insights into the local structures, crystalline sizes, and ordering degree of opal-CT. Quantifying the crystallinity of natural opals is important to understanding the diagenetic processes of opals and the associated diatomaceous clays in sedimentary formations.

Keywords: Opal-CT; nanomineral; mineraloid; synchrotron X-ray diffraction; X-ray scattering structure factor; transmission electron microscopy; pair distribution function analysis

Acknowledgments and Funding

We thank Yifeng Wang of Sandia National Laboratories for providing the opal-CT (2) sample. Synchrotron X-ray scattering experiments were performed at beamline 17-BM, Advanced Photon Source (APS), Argonne National Laboratory. APS is a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. S.L. was also supported by the National Research Foundation of Korea (NRF) grant from the Korean government (MSIT) (RS202400342773).

References Cited

Adams, S.J., Hawkes, G.E., and Curzon, E.H. (1991) A solid state 29Si nuclear magnetic resonance study of opal and other hydrous silicas. American Mineralogist, 76, 1863–1871.Search in Google Scholar

Barnard, A.S. and Xu, H. (2008) An environmentally sensitive phase map of titania nanocrystals. ACS Nano, 2, 2237–2242, https://doi.org/10.1021/nn800446w.Search in Google Scholar

Cady, S.L., Wenk, H.R., and Downing, K.H. (1996) HRTEM of microcrystalline opal in chert and porcelanite from the Monterey Formation, California. American Mineralogist, 81, 1380–1395, https://doi.org/10.2138/am-1996-11-1211.Search in Google Scholar

Clarke, J. (2003) The occurrence and significance of biogenic opal in the regolith. Earth-Science Reviews, 60, 175–194, https://doi.org/10.1016/S0012-8252(02)00092-2.Search in Google Scholar

Curtis, N.J., Gascooke, J.R., Johnston, M.R., and Pring, A. (2019) A review of the classification of opal with reference to recent new localities. Minerals, 9, 299, https://doi.org/10.3390/min9050299.Search in Google Scholar

Curtis, N.J., Gascooke, J.R., Johnston, M.R., and Pring, A. (2022) 29Si solid-state NMR analysis of opal-AG, opal-AN and opal-CT: Single pulse spectroscopy and spin-lattice T1 relaxometry. Minerals, 12, 323, https://doi.org/10.3390/min12030323.Search in Google Scholar

Damby, D.E., Llewellin, E.W., Horwell, C.J., Williamson, B.J., Najorka, J., Cressey, G., and Carpenter, M. (2014) The a–ß phase transition in volcanic cristobalite. Applied Crystallography, 47, 1205–1215, https://doi.org/10.1107/S160057671401070X.Search in Google Scholar

de Jong, B.H.W.S., van Hoek, J., Veeman, W.S., and Manson, D.V. (1987) X-ray diffraction and 29Si magic-angle-spinning NMR of opals; incoherent long-and short-range order in opal-CT. American Mineralogist, 72, 1195–1203.Search in Google Scholar

Elzea, J.M. and Rice, S.B. (1996) Tem and X-ray diffraction evidence for cristobalite and tridymite stacking sequences in opal. Clays and Clay Minerals, 44, 492–500, https://doi.org/10.1346/CCMN.1996.0440407.Search in Google Scholar

Farfan, G.A., McKeown, D.A., and Post, J.E. (2023) Mineralogical characterization of biosilicas versus geological analogs. Geobiology, 21, 520–533, https://doi.org/10.1111/gbi.12553.Search in Google Scholar

Farrow, C.L., Juhas, P., Liu, J.W., Bryndin, D., Božin, E.S., Bloch, J., Proffen, T., and Billinge, S.J.L. (2007) PDFfit2 and PDFgui: Computer programs for studying nanostructure in crystals. Journal of Physics Condensed Matter, 19, 335219, https://doi.org/10.1088/0953-8984/19/33/335219.Search in Google Scholar

Flörke, O.W. (1955) Strukturanomalien bei Tridymit und Cristobalit. Berichte der Deutschen Keramischen Gesellschaft, 32, 369–381.Search in Google Scholar

Fröhlich, F. (2020) The opal-CT nanostructure. Journal of Non-Crystalline Solids, 533, 119938, https://doi.org/10.1016/j.jnoncrysol.2020.119938.Search in Google Scholar

Ghisoli, C., Caucia, F., and Marinoni, L. (2010) XRPD patterns of opals: A brief review and new results from recent studies. Powder Diffraction, 25, 274–282, https://doi.org/10.1154/1.3478554.Search in Google Scholar

Graetsch, H., Gies, H., and Topalović, I. (1994) NMR, XRD and IR study on microcrystalline opals. Physics and Chemistry of Minerals, 21, 166–175, https://doi.org/10.1007/BF00203147.Search in Google Scholar

Guthrie, G.D., Bish, D.L., and Reynolds, R.C. (1995) Modeling the X-ray diffraction pattern of opal-CT. American Mineralogist, 80, 869–872, https://doi.org/10.2138/am-1995-7-823.Search in Google Scholar

Hatch, D.M. and Ghose, S. (1991) The α-β phase transition in cristobalite, SiO2 Symmetry analysis, domain structure, and the dynamical nature of the β-phase. Physics and Chemistry of Minerals, 17, 554–562, https://doi.org/10.1007/BF00202234.Search in Google Scholar

Hill, T.R., Konishi, H., Hobbs, F., Lee, S., and Xu, H. (2019) Precipitates of α-cristobalite and silicate glass in UHP clinopyroxene from a Bohemian Massif eclogite. American Mineralogist, 104, 1402–1415, https://doi.org/10.2138/am-2019-6773.Search in Google Scholar

Hinman, N.W. (1990) Chemical factors influencing the rates and sequences of silica phase transitions: Effects of organic constituents. Geochimica et Cosmochimica Acta, 54, 1563–1574, https://doi.org/10.1016/0016-7037(90)90391-W.Search in Google Scholar

Isaacs, C.M. (1982) Influence of rock composition on kinetics of silica phase changes in the Monterey Formation, Santa Barbara area. Geology, 10, 304–308, https://doi.org/10.1130/0091-7613(1982)10<304:IORCOK>2.0.CO;2.Search in Google Scholar

Jones, J.B. and Segnit, E.R. (1971) The nature of opal I. nomenclature and constituent phases. Journal of the Geological Society of Australia, 18, 57–68, https://doi.org/10.1080/00167617108728743.Search in Google Scholar

Jones, J.B., Sanders, J.V., and Segnit, E.R. (1964) Structure of opal. Nature, 204, 990–991, https://doi.org/10.1038/204990a0.Search in Google Scholar

Jones, J.B., Biddle, J., and Segnit, E.R. (1966) Opal genesis. Nature, 210, 1353–1354, https://doi.org/10.1038/2101353a0.Search in Google Scholar

Juhás, P., Davis, T., Farrow, C.L., and Billinge, S.J.L. (2013) PDFgetX3: A rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions. Journal of Applied Crystallography, 46, 560–566, https://doi.org/10.1107/S0021889813005190.Search in Google Scholar

Kano, K. (1983) Ordering of opal-CT in diagenesis. Geochemical Journal, 17, 87–93, https://doi.org/10.2343/geochemj.17.87.Search in Google Scholar

Kastner, M., Keene, J.B., and Gieskes, J.M. (1977) Diagenesis of siliceous oozes —I. Chemical controls on the rate of opal-A to opal-CT transformation—an experimental study. Geochimica et Cosmochimica Acta, 41, 1041–1059, https://doi.org/10.1016/0016-7037(77)90099-0.Search in Google Scholar

Kayama, M., Nagaoka, H., and Niihara, T. (2018) Lunar and martian silica. Minerals, 8, 267, https://doi.org/10.3390/min8070267.Search in Google Scholar

Kryshtal, A., Mielczarek, M., and Pawlak, J. (2022) Effect of electron beam irradiation on the temperature of single AuGe nanoparticles in a TEM. Ultramicroscopy, 233, 113459, https://doi.org/10.1016/j.ultramic.2021.113459.Search in Google Scholar

Lee, S. and Xu, H. (2016) Size-dependent phase map and phase transformation kinetics for nanometric iron (III) oxides (γ→ε→α pathway). The Journal of Physical Chemistry C, 120, 13316–13322, https://doi.org/10.1021/acs.jpcc.6b05287.Search in Google Scholar

Lee, S. and Xu, H. (2019) Using powder XRD and pair distribution function to determine anisotropic atomic displacement parameters of orthorhombic tridymite and tetragonal cristobalite. Acta Crystallographica Section B, 75, 160–167, https://doi.org/10.1107/S2052520619000933.Search in Google Scholar

Lee, S. and Xu, H. (2020) Using complementary methods of synchrotron radiation powder diffraction and pair distribution function to refine crystal structures with high quality parameters—A review. Minerals, 10, 124, https://doi.org/10.3390/min10020124.Search in Google Scholar

Lee, S., Xu, H., Xu, W., and Sun, X. (2019) The structure and crystal chemistry of vernadite in ferromanganese crusts. Acta Crystallographica Section B, 75, 591–598, https://doi.org/10.1107/S2052520619006528.Search in Google Scholar

Lee, S., Cai, J., Jin, S., Zhang, D., Thevamaran, R., and Xu, H. (2020) Coesite formation at low pressure during supersonic microprojectile impact of opal. ACS Earth & Space Chemistry, 4, 1291–1297, https://doi.org/10.1021/acsearthspacechem.0c00090.Search in Google Scholar

Lee, S., Xu, H., and Xu, H. (2022) Reexamination of the structure of opal-A: A combined study of synchrotron X-ray diffraction and pair distribution function analysis. American Mineralogist, 107, 1353–1360, https://doi.org/10.2138/am-2022-8017.Search in Google Scholar

Levien, L. and Prewitt, C.T. (1981) High-pressure crystal structure and compressibility of coesite. American Mineralogist, 66, 324–333.Search in Google Scholar

Levien, L., Prewitt, C.T., and Weidner, D.J. (1980) Structure and elastic properties of quartz at pressure. American Mineralogist, 65, 920–930.Search in Google Scholar

Levin, I. and Ott, E. (1933) X-Ray Study of Opals, Silica Glass and Silica Gel. Zeitschrift für Kristallographie. Crystalline Materials, 85, 305–318, https://doi.org/10.1524/zkri.1933.85.1.305.Search in Google Scholar

Meral, C. (2012) The study of disorder in amorphous silica, alkali-silica reaction gel and fly ash, 172 p. Ph.D. thesis, UC Berkeley.Search in Google Scholar

Mitchell, R.S. and Tufts, S. (1973) Wood opal—A tridymite-like mineral. American Mineralogist, 58, 717–720.Search in Google Scholar

Nagase, T. and Akizuki, M. (1997) Texture and structure of opal-CT and opal-C in volcanic rocks. Canadian Mineralogist, 35, 947–958.Search in Google Scholar

Nakagawa, T., Kihara, K., and Harada, K. (2001) The crystal structure of low melanophlogite. American Mineralogist, 86, 1506–1512, https://doi.org/10.2138/am-2001-11-1219.Search in Google Scholar

Nyfeler, D. and Armbruster, T. (1998) Silanol groups in minerals and inorganic compounds. American Mineralogist, 83, 119–125, https://doi.org/10.2138/am-1998-1-211.Search in Google Scholar

Patterson, A.L. (1939) The Scherrer formula for X-ray particle size determination. Physical Review, 56, 978–982, https://doi.org/10.1103/PhysRev.56.978.Search in Google Scholar

Ragueneau, O., Tréguer, P., Leynaert, A., Anderson, R.F., Brzezinski, M.A., DeMaster, D.J., Dugdale, R.C., Dymond, J., Fischer, G., François, R., and others. (2000) A review of the Si cycle in the modern ocean: Recent progress and missing gaps in the application of biogenic opal as a paleoproductivity proxy. Global and Planetary Change, 26, 317–365, https://doi.org/10.1016/S0921-8181(00)00052-7.Search in Google Scholar

Rapin, W., Chauviré, B., Gabriel, T.S.J., McAdam, A.C., Ehlmann, B.L., Hard-grove, C., Meslin, P.-Y., Rondeau, B., Dehouck, E., Franz, H.B., and others (2018) In situ analysis of opal in Gale Crater, Mars. Journal of Geophysical Research. JGR Planets, 123, 1955–1972.Search in Google Scholar

Sanders, J.V. (1980) Close-packed structures of spheres of two different sizes I. Observations on natural opal. Philosophical Magazine, 42, 705–720, https://doi.org/10.1080/01418618008239379.Search in Google Scholar

Smith, D.K. (1998) Opal, cristobalite, and tridymite: Noncrystallinity versus crystallinity, nomenclature of the silica minerals and bibliography. Powder Diffraction, 13, 2–19, https://doi.org/10.1017/S0885715600009696.Search in Google Scholar

Struyf, E. and Conley, D.J. (2009) Silica: An essential nutrient in wetland biogeochemistry. Frontiers in Ecology and the Environment, 7, 88–94, https://doi.org/10.1890/070126.Search in Google Scholar

Sun, V.Z. and Milliken, R.E. (2018) Distinct geologic settings of opal-A and more crystalline hydrated silica on Mars. Geophysical Research Letters, 45, 10 221– 10 228, https://doi.org/10.1029/2018GL078494.Search in Google Scholar

Tarnas, J.D., Mustard, J.F., Lin, H., Goudge, T.A., Amador, E.S., Bramble, M.S., Kremer, C.H., Zhang, X., Itoh, Y., and Parente, M. (2019) Orbital identification of hydrated silica in Jezero Crater, Mars. Geophysical Research Letters, 46, 12771–12782, https://doi.org/10.1029/2019GL085584.Search in Google Scholar

Toby, B.H. and Egami, T. (1992) Accuracy of pair distribution function analysis applied to crystalline and non-crystalline materials. Acta Crystallographica Section A, 48, 336–346, https://doi.org/10.1107/S0108767391011327.Search in Google Scholar

Toby, B.H. and Von Dreele, R.B. (2013) GSAS-II: The genesis of a modern open-source all purpose crystallography software package. Journal of Applied Crystallography, 46, 544–549, https://doi.org/10.1107/S0021889813003531.Search in Google Scholar

Wallmann, K., Aloisi, G., Haeckel, M., Tishchenko, P., Pavlova, G., Greinert, J., Kutterolf, S., and Eisenhauer, A. (2008) Silicate weathering in anoxic marine sediments. Geochimica et Cosmochimica Acta, 72, 2895–2918, https://doi.org/10.1016/j.gca.2008.03.026.Search in Google Scholar

Wang, H.W., Page, K., Neder, R.B., Stack, A.G., and Bish, D.L. (2023) Multilevel atomic structural model for interstratified opal materials. Journal of Applied Crystallography, 56, 1813–1823, https://doi.org/10.1107/S1600576723009913.Search in Google Scholar

Williams, L.A. and Crerar, D.A. (1985) Silica diagenesis; II, General mechanisms. Journal of Sedimentary Research, 55, 312–321.Search in Google Scholar

Wilson, M.J. (2014) The structure of opal-CT revisited. Journal of Non-Crystalline Solids, 405, 68–75, https://doi.org/10.1016/j.jnoncrysol.2014.08.052.Search in Google Scholar

Wright, A.F. and Leadbetter, A.J. (1975) The structures of the β-cristobalite phases of SiO2 and AlPO4. Philosophical Magazine, 31, 1391–1401, https://doi.org/10.1080/00318087508228690.Search in Google Scholar

Yarnell, J.L., Katz, M.J., Wenzel, R.G., and Koenig, S.H. (1973) Structure factor and radial distribution function for liquid argon at 85 K. Physical Review A: General Physics, 7, 2130–2144, https://doi.org/10.1103/PhysRevA.7.2130.Search in Google Scholar
Received: 2023-01-25
Accepted: 2024-09-04
Published Online: 2025-07-07
Published in Print: 2025-05-26

© 2025 Mineralogical Society of America

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https://doi.org/10.2138/am-2024-9333
Keywords for this article
Opal-CT; nanomineral; mineraloid; synchrotron X-ray diffraction; X-ray scattering structure factor; transmission electron microscopy; pair distribution function analysis

Articles in the same Issue

  1. Atomic-scale visualization and quantification of lithium in lepidolite by AC-TEM-EELS: Implications for pegmatite genesis and advancing lithium extraction techniques
  2. The use of X-ray micro-computed tomography to visualize and quantify lithium-bearing silicate minerals in pegmatites: Examples from the Tanco Pegmatite, Manitoba, Canada
  3. Single- and multi-mineral classification using dual-band Raman spectroscopy for planetary surface missions
  4. Magnesite formation during nesquehonite decomposition in the presence and absence of retained self-generated gases and the role of X-ray amorphous materials as essential stores for CO2
  5. Formation of bonanza Au-Ag-telluride ores in epithermal systems: Constraints from Cu-O isotopes and modeling
  6. Reexamination of the structure of nanomineral opal-CT using synchrotron X-ray diffraction, transmission electron microscopy, X-ray scattering structure factor, and pair distribution function analyses
  7. Titanium substitutions in garnet at magmatic, granulite facies, and high-pressure granulite facies conditions
  8. Mechanistic understanding of the dehydroxylation reaction of smectites: Insights from reactive force field (ReaxFF) molecular dynamics simulation
  9. Estimating the iron oxidation state of serpentinite using X-ray absorption fine structure spectroscopy
  10. Episodic magmatism contributes to sub-seafloor copper mineralization: Insights from textures and geochemistry of zoned pyrite in the Ashele VMS deposit
  11. Development of oxy-symplectites in a slow-spreading lower oceanic crust: Insights from the Atlantis Bank Gabbro Massif, Southwest Indian Ridge
  12. Heterogeneous distribution of Al-hematite regulated by hydrologic regime in a basaltic laterite of Hainan Island, South China: Implications for the aqueous history of Mars
  13. Allanite-(Sm), CaSm(Al2Fe2+)(Si2O7)(SiO4)O(OH), the third samarium mineral from Jordanów Śląski, Lower Silesia, Poland
  14. Letter
  15. The “breathing” Earth at Solfatara-Pisciarelli, Campi Flegrei, southern Italy (2005–2024): Nature’s attenuation of the effects of bradyseism
  16. New Mineral Names
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