research papers The structure of denisovite, a fibrous IUCrJ nanocrystalline polytypic disordered ‘very complex’ ISSN 2052-2525 silicate, studied by a synergistic multi-disciplinary MATERIALSjCOMPUTATION approach employing methods of electron crystallography and X-ray powder diffraction Received 20 October 2016 Ira V. Rozhdestvenskaya,a Enrico Mugnaioli,b,c* Marco Schowalter,d Martin U. Accepted 14 February 2017 Schmidt,e Michael Czank,f Wulf Depmeierf* and Andreas Rosenauerd a Edited by A. Fitch, ESRF, France Department of Crystallography, Institute of Earth Science, Saint Petersburg State University, University emb. 7/9, St Petersburg 199034, Russian Federation, bDepartment of Physical Sciences, Earth and Environment, University of Siena, Via Laterino 8, Siena 53100, Italy, cCenter for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza Keywords: denisovite; minerals; fibrous San Silvestro 12, Pisa 56127, Italy, dInstitute of Solid State Physics, University of Bremen, Otto-Hahn-Allee 1, Bremen materials; nanocrystalline materials; electron D-28359, Germany, eInstitut fu¨r Anorganische und Analytische Chemie, Goethe-Universita¨t, Max-von-Laue-Strasse 7, crystallography; electron diffraction Frankfurt am Main D-60438, Germany, and fInstitute of Geosciences, Kiel University, Olshausenstrasse 40, Kiel tomography; X-ray powder diffraction; D-24098, Germany. *Correspondence e-mail: [email protected], [email protected] modularity; disorder; polytypism; OD approach; complexity; framework-structured solids; inorganic materials; nanostructure; Denisovite is a rare mineral occurring as aggregates of fibres typically 200– nanoscience. 500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have CCDC references: 1532655; 1532656 remained incompletely known since then. Recently obtained results from Supporting information: this article has studies using microprobe analysis, X-ray powder diffraction (XRPD), electron supporting information at www.iucrj.org crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark- field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) A˚ , = 95.99 (3), V = 4310.1 (5) A˚ 3 and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double 10À 12À chains, [Si6O17] , and a tubular loop-branched dreier triple chain, [Si12O30] . The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K+ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Áz = c/4 or Àc/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nanolamellae separated by stacking faults and twin boundaries. The structure can be described according to the order–disorder (OD) theory as a stacking of layers parallel to (100). 1. Introduction For some chemists, physicists, biologists or even crystal- lographers, the knowledge of minerals is possibly limited to IUCrJ (2017). 4, 223–242 https://doi.org/10.1107/S2052252517002585 223 research papers what they have learned during their early undergraduate independent positions with almost identical occupancies. studies, and therefore they might have developed the idea that When the components in a solid solution differ more strongly minerals are easy objects having high symmetry, small unit in their chemical character they may develop a preference for cells and simple chemistry. Typical examples would then certain positions on the basis of more suitable site symmetry, include diamond (C), halite (NaCl), sphalerite and wurtzite size or neighbourhood. An example from the mineral (ZnS) or fluorite (CaF2). However, most of the more than kingdom is once more olivine. When the mineral also contains 5000 mineral species known to date are much more compli- Ca2+, this will barely mix with Mg2+ and Fe2+ because of its cated: many have low symmetry or large unit cells, or show significantly larger size, and it will occupy preferentially or intricate and variable chemical compositions. One of these even completely either crystallographically independent more complicated minerals is denisovite. In order to aid less- position. Elements occurring in different valence states, such experienced readers in appreciating the present investigation, as Fe2+ and Fe3+, may also coexist in the same crystal structure. 2+ 3+ some significant particularities of minerals in general, and of A prominent example is magnetite, Fe Fe 2O4. Water is denisovite in particular, will be summarized first. often part of an extended network of hydrogen bonds, or it In contrast with the majority of objects studied by ‘small- occupies as virtually isolated species void spaces in an other- molecule’ or ‘macromolecular’ crystallography, most minerals wise extended framework structure. This is also the case for are not composed of molecules as building blocks. Addition- denisovite. Altogether these effects may result in sometimes ally, unlike typical molecules which are composed of integer rather awesome formulae, as e.g. in that of the mineral numbers of atoms and thus have well defined stoichiometry, steenstrupine which, according to Krivovichev (2013), reads different chemical species may be randomly distributed over (Th0.42Zr0.41Ti0.1Al0.07)(Mn1.49Ca0.51)(Fe1.69Mn0.31)(Na1.47- equivalent positions throughout the structure of many Ca0.53)(La19.9Ce2.89Pr0.23Nd0.71Y0.19)Na12((P0.77Si0.23)O4)6- minerals. By averaging over all these positions, a typical (Si6O18)2(PO4)0.88(OH)2(H2O)2.19. diffraction experiment will reveal virtual species in the unit From these remarks, some readers might perhaps get the cell which represent a weighted average over the elemental impression that minerals are in fact ‘dirty’ chemicals and it species involved. Therefore, such mixed crystals, or solid would be more reasonable to deal with pure chemicals solutions, often have non-integer stoichiometry. A certain purchased from a renowned company. Indeed, this might be prerequisite for this isomorphous replacement is that the true for certain fields, but surely not for others. As a species involved have similar sizes. A prominent example is counterexample we mention that it is just the trace amounts of 2+ 2+ olivine, (Mg,Fe)2SiO4, where Fe and Mg share the same ‘impurities’ like chromium or iron and titanium, respectively, crystallographically independent sites in the unit cell. This is which give ruby or sapphire their specific red or blue colour indicated in the formula by grouping their chemical symbols in and thus turn ordinary corundum into valuable highly parentheses. One important objective of a structure determi- appreciated gemstones. Perhaps even more important for our nation is to quantify the ratio of these elements expressed as daily life is the fact that doping with ‘impurities’, including occupancies, e.g. (MgxFe1Àx)2SiO4. vacancies, enables materials scientists to tune the properties of It is a notable feature of many minerals that even differently many solid-state materials, thus making them useful or even charged but similarly sized species can substitute for each indispensable utilities of our modern civilization. other, e.g. Ca2+ and Na+,orOHÀ and O2À, and both of these The ‘mixing’ of the various species in a crystal does not mechanisms act in denisovite. In order to maintain overall necessarily happen at random, but obeys crystal-chemical charge balance, coupled substitution mechanisms may then rules which may allow only certain combinations. Miscibility become necessary. A well known example is Ca2+ ! Na+ gaps have already been mentioned. It is not uncommon to find coupled with Al3+ ! Si4+, as in the case of plagioclase feld- mixed crystals, including minerals, in which, under certain spars, the most common minerals of the Earth’s crust. conditions of temperature and pressure, or as a function of Vacancies and oxidation/reduction of suitable species may also time, their components segregate into separate more or less contribute to maintaining charge balance. ordered areas. Often only partial or short-range order In some cases the mixing of species is ideal, or nearly so, as develops, giving rise to various types of diffuse scattering. In in olivine