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Article

Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite

by
Sergey V. Krivovichev
1,2,*,
Taras L. Panikorovskii
2,3,
Andrey A. Zolotarev
2,
Vladimir N. Bocharov
4,
Anatoly V. Kasatkin
5 and
Radek Škoda
6
1
Nanomaterials Research Centre, Kola Science Centre, Russian Academy of Sciences, Fersmana 14, 184209 Apatity, Russia
2
Department of Crystallography, Institute of Earth Sciences, St. Petersburg State University, University Emb. 7/9, 199034 St. Petersburg, Russia
3
Laboratory of Nature-Inspired Technologies and Environmental Safety of the Arctic, Kola Science Centre, Russian Academy of Sciences, Fersmana 14, 184209 Apatity, Russia
4
Geo Environmental Centre “Geomodel”, Saint-Petersburg State University, Ul’yanovskaya Str. 1, 198504 St. Petersburg, Russia
5
Fersman Mineralogical Museum, Russian Academy of Sciences, Leninsky Prospekt 18-2, 119071 Moscow, Russia
6
Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
*
Author to whom correspondence should be addressed.
Minerals 2019, 9(6), 370; https://doi.org/10.3390/min9060370
Submission received: 23 May 2019 / Revised: 16 June 2019 / Accepted: 18 June 2019 / Published: 20 June 2019
(This article belongs to the Special Issue Selected Papers from the XIX International Meeting on Crystal Chemistry, X-ray Diffraction and Spectroscopy of Minerals)
Browse Figures
Versions Notes

Abstract

:
The crystal structure of paratooite-(La) has been solved using crystals from the type locality, Paratoo copper mine, near Yunta, Olary Province, South Australia, Australia. The mineral is orthorhombic, Pbam, a = 7.2250(3) Å, b = 12.7626(5) Å, c = 10.0559(4) Å, V = 927.25(6) Å3, and R1 = 0.063 for 1299 unique observed reflections. The crystal structure contains eight symmetrically independent cation sites. The La site, which accommodates rare earth elements (REEs), but also contains Sr and Ca, has a tenfold coordination by seven carbonate groups. The Ca, Na1, and Na2 sites are coordinated by eight, eight, and six O atoms, respectively, forming distorted CaO8 and Na1O8 cubes, and Na2O6 octahedra. The Cu site is occupied solely by copper and possess a distorted octahedral coordination with four short (1.941 Å) and two longer (2.676 Å) apical Cu–O bonds. There are three symmetrically independent carbonate groups (CO3)2− with the average <C–O> bond lengths equal to 1.279, 1.280, and 1.279 Å for the C1, C2, and C3 sites, respectively. The crystal structure of paratooite-(La) can be described as a strongly distorted body-centered lattice formed by metal cations with (CO3)2− groups filling its interstices. According to the chemical and crystal-structure data, the crystal-chemical formula of paratooite-(La) can be described as (La0.74Ca0.11Sr0.07)4CuCa(Na0.75Ca0.15)(Na0.63)(CO3)8 or REE2.96Ca1.59Na1.38CuSr0.28(CO3)8. The idealized formula can be written as (La,Sr,Ca)4CuCa(Na,Ca)2(CO3)8. The structure of paratooite is a 1 × 2 × 2 superstructure of carbocernaite, CaSr(CO3)2. The superstructure arises due to the ordering of the chemically different Cu2+ cations, on one hand, and Na+ and Ca2+ cations, on the other hand. The formation of a superstructure due to the cation ordering in paratooite-(La) compared to carbocernaite results in the multiple increase of structural complexity per unit cell. Therefore, paratooite-(La) versus carbocernaite represents a good example of structural complexity increasing due to the increasing chemical complexity controlled by different electronic properties of mineral-forming chemical elements (transitional versus alkali and alkaline earth metals).

1. Introduction

Rare earth elements (REE)-bearing carbonates belong to one of the most widespread group of REE minerals and are the major form of the REE occurrence at the largest world mineral deposits such as Bayan Obo, China [1,2]. REE carbonate minerals also show a large range of chemical and structural variations, which is reflected in the recent discoveries and investigations [3,4,5,6,7,8,9,10,11,12]. In addition, inorganic REE carbonates are important from the material science point of view, showing interesting physical and chemical properties [13,14,15,16,17].
There are very few natural REE carbonates containing transitional metals such as copper. Only four Cu-REE carbonate minerals are known to date: schuilingite-(Nd), CuPbNd(CO3)3(OH)·1.5H2O [18,19,20], astrocyanite-(Ce), Cu2Ce2(UO2)(CO3)5(OH)2·1.5H2O [21], decrespignyite-(Y), Y4Cu(CO3)4Cl(OH)5·2H2O [22], and paratooite-(La), (La,REE,Ca,Na,Sr)6Cu(CO3)8 or REE3(Ca,Sr)2NaCu(CO3)8 (according to the original description [23], see below). Both decrespignyite-(Y) and paratooite-(La) have been found in the Paratoo copper deposit near Yunta, South Australia, Australia. The assemblage of rare earth minerals at this locality is associated with the weathered base metal and magnetite ores. The origin of paratooite-(La) is due to the secondary hydrothermal reworking of primary ores, where REEs and copper were introduced by hydrothermal fluids [24]. Paratooite-(La) forms tiny crystals, thin and flexible, which prevented the structural characterization of the species up to date. Pring et al. [23] tried to solve the crystal structure from the high-resolution synchrotron powder data, but their attempts were unsuccessful.
The aim of the present paper is to report on crystal structure of paratooite-(La) solved using single crystal from the type locality, and to describe its structural correlations with related phases.

2. Materials and Methods

2.1. Materials

The specimen of paratooite-(La) studied herein originates from its type locality, Paratoo copper mine, near Yunta, Olary Province, South Australia, Australia. It comes from the collection of one of us (A.V.K.) and was obtained in 2007 from the senior author of the original description of the species Dr. Allan Pring (South Australian Museum, Adelaide, Australia). Paratooite-(La) occurs as pale blue radiating aggregates on matrix and associates with bastnäsite-(La), donnayite-(Y), kamphaugite-(Y), malachite, and nontronite. Individual crystals are tabular and reach up to 60 × 40 × 10 μm3 in size.

2.2. Chemical Composition

The chemical composition of the mineral was studied by scanning electron microscopy and electron-probe microanalysis using both ED and WD spectrometers. Preliminary semi-quantitative chemical analysis was made in the laboratory of the Fersman Mineralogical Museum (Moscow, Russia) using a CamScan 4D SEM equipped with an ED spectrometer and INCA Energy microanalyzer (conditions of analysis: Accelerating voltage 20 kV, beam current 5 nA on metallic cobalt, and beam diameter 5 μm).
Quantitative chemical composition of paratooite-(La) was conducted in the laboratory of electron microscopy and microanalysis at the department of geological sciences, Masaryk University (Brno, Czech Republic), using a Cameca SX 100 electron probe at WDS mode (conditions of analysis: Accelerating voltage 15 kV, beam current 10 nA, beam diameter 5 μm, and impulses time acquisition at peak—10 s for main elements and 20–120 s for minor elements). The following standards were used: NaKα—albite A; CaKα—wollastonite; SrLα—SrSO4; BaLα—baryte; CuKα—lammerite; YLα—YAG; LaLα—LaPO4; PrLβ—PrPO4; NdLβ—NdPO4; SmLβ—SmPO4; GdLβ—GdPO4; and SiKα—andalusite.
The average chemical composition was as follows (in wt. %): Na2O 4.33, CaO 8.35, SrO 2.51, BaO 0.03, CuO 5.86, Y2O3 0.57, La2O3 24.85, Pr2O3 2.18, Nd2O3 7.65, Sm2O3 0.63, Gd2O3 0.50, SiO2 0.46, CO2 (calc.) 28.30, and total 86.22. Paratooite forms porous aggregates composed of very thin crystals. Due to the sensitivity of the mineral to an electron beam, the mineral was analyzed under defocused conditions (10 μm in diameter) to reduce the electron-beam flux density, which resulted in the low analytical total. The empirical chemical formula calculated on the basis of C + Si = 8 and O = 24 (as in the original study [23]) can be written as Na1.72Sr0.30Ca1.84Cu0.91La1.88Nd0.56Pr0.16Y0.06Sm0.04Gd0.03C7.91Si0.09O24. This agrees generally well with the chemical formula defined in [23] as Na1.16Sr0.33Ca1.47Cu0.79La1.77Nd0.53Pr0.57Y0.07Sm0.04Gd0.05C7.92N0.27- O23.87F0.12, taking into account the difficulties associated with the rapid deterioration of crystals under the electron beam. Both chemical formulae are also in general agreement with the results of crystal-structure study (see below).

2.3. Single-Crystal X-ray Diffraction Study

A single-crystal X-ray diffraction study of paratooite-(La) was performed at the Resource Center “X-ray Diffraction Methods” of St. Petersburg State University using a Bruker Kappa APEX DUO diffractometer operated at 45 kV and 0.6 mA and equipped with a CCD area detector. The study was done by means of a monochromatic MoKα X-radiation (λ = 0.71073 Å), frame widths of 0.5° in ω, and 100 s counting time for each frame. The intensity data were reduced and corrected for Lorentz, polarization, and background effects using the Bruker software APEX2 [25]. A semiempirical absorption-correction based upon the intensities of equivalent reflections was applied (SADABS [26]). The unit cell parameters obtained in this study (Table 1) are in agreement with those reported in the original study [23] (a = 7.2360 Å, b = 12.8088 Å, and c = 10.0862 Å), taking into account the interchange of crystallographic axes for a standard setting. The structure was solved and refined in the space group Pbam to R1 = 0.063 (wR2 = 0.170) for 1299 unique observed reflections using the ShelX program package [27]. During the refinement, 93 reflections were noticed that violated the absence conditions for the space group Pbam. However, all attempts to refine the structure in the lower-symmetry groups resulted in physically unrealistic displacement parameters for C and O atoms and instability of the refinement. In our opinion, the appearance of the “forbidden” reflections may be due to the presence in the crystal studied of ordered domains with lower symmetry, since the structure contains several sites with mixed occupancies and defects (see below). The assignment of cations to the mixed-occupied sites was done on the basis of crystal-chemical considerations and chemical data. Crystal data, data collection, and structure refinement details are given in Table 1; atom coordinates and bond-valence sums (calculated using bond-valence parameters taken from [28]) in Table 2; observed and theoretical site-scattering factors for cation sites in Table 3; anisotropic displacement parameters in Table 4; and selected interatomic distances in Table 5. Supplementary crystallographic data have been deposited as the crystallographic information file (CIF) available at the journal website.

2.4. Raman Spectroscopy

The Raman spectrum of paratooite-(La) single plate crystal was measured using a Jobin–Yvon LabRam HR 800 spectrometer (Horiba, Kyoto, Japan) with a 514 nm laser. The laser beam (2 μm in diameter) was oriented along the c axis. The power at the sample surface was 5–6 mW.

3. Results

3.1. Raman Spectroscopy

The Raman spectrum of paratooite-(La) (Figure 1) agrees well with the previously reported data [23], except for the presence of weak bands in the range from 3200 to 3700 cm−1. These bands are assignable to O–H stretching vibrations, but it is highly unlikely that the crystal structure of paratooite-(La) contains hydroxyl groups as structural elements. There are no sites that could accommodate OH-groups, except for the O sites of the carbonate groups. However, the Raman spectrum does not contain any other bands that could be explained by the presence of bicarbonate groups, (HCO3)−. It seems most probable that the bands observed at 3460 and 3572 cm−1 are artefacts appearing due to the admixture of other minerals or the presence of defects (probably, on the surface of the mineral grain) associated with irregularly distributed protonated O sites.
The most intense band at 1095 and two weak bands at 1369 and 1434 cm−1 (Table 6) can be assigned to the C–O symmetric and asymmetric modes of stretching vibrations of the (CO3)2− groups. The weak bands observed in the range of 900–600 cm−1 can be related to the asymmetric and symmetric bending vibrations of the same bonds [29,30]. Only one peak was observed in the region of v1 vibrations in the (CO3)2− groups instead of two observed previously (at 1095 and 1075 cm−1), most probably due to the absence of polarization of carbonate groups along the c direction [23]. The bands at 386, 343, and 261 cm−1 correspond to the bending/stretching vibrations of the Cu–O bonds of the CuO6 distorted polyhedra [31]. The bands below 150 cm−1 can be assigned to the lattice vibrations.

3.2. Cation Coordination

The crystal structure of paratooite-(La) contains eight symmetrically independent cation sites (Figure 2). The La site, which accommodates REEs, but also contains Sr and Ca, has a tenfold coordination from seven carbonate groups. The Ca, Na1, and Na2 sites are coordinated by eight, eight, and six O atoms, respectively, forming distorted CaO8 and Na1O8 cubes, and Na2O6 octahedra. The Cu site is occupied solely by copper and possesses a distorted octahedral coordination with four short (1.941 Å) and two longer (2.676 Å) apical Cu–O bonds. This type of distortion is typical for octahedrally coordinated Cu2+ ions, according to the well-known Jahn–Teller theorem [32,33]. The crystal structure contains three symmetrically independent C sites that form carbonate groups (CO3)2− with the average <C–O> bond lengths equal to 1.279, 1.280, and 1.279 Å for the C1, C2, and C3 sites, respectively.

3.3. Structure Description

The crystal structure of paratooite-(La) is shown in Figure 3a. It can conveniently be described in terms of packing of cations with (CO3)2− groups filling its interstices. The Ca, Cu, Na1, and Na2 sites locate exactly in the corners of a primitive orthorhombic cell with all unit-cell parameters twice as small as the original cell. The La sites are located in each of the eight subcells that constitute the unit cell, shifting from the centers of the subcells in the ab plane along the b axis. Therefore, the whole cation array in paratooite-(La) may be considered as a strongly distorted cation-ordered body-centered lattice.
Figure 3 compares the crystal structure of paratooite-(La) (Figure 3a) with that of carbocernaite, ideally CaSr(CO3)2 [34,35,36,37,38]. It is obvious that the two crystal structures are very similar, with that of paratooite being the superstructure of carbocernaite. The relations between the two structures can be described using the following equations (crb = carbocernaite; prt = paratooite-(La)):
aprt = ccrb
bprt = 2bcrb,
cprt = 2acrb
Thus, the structure of paratooite-(La) is a 1 × 2 × 2 superstructure of that of carbocernaite. Figure 4 shows the cation packing in paratooite-(La) (a) and its sections at the z = ½ (b) and z = 0 (c) levels. This clearly shows that the superstructure arises due to the ordering of the chemically different Cu2+ cations, on one hand, and Na+ and Ca2+ cations, on the other hand. The chemical difference arises due to the Jahn–Teller distortion of the Cu2+ coordination geometry in contrast to the relatively uniform (in terms of bond lengths) Na+ and Ca2+ coordinations. Thus, one may speculate that the superstructure formation is governed by different electronic properties of cations constituting the crystal structure of paratooite-(La).

3.4. Crystal-Chemical Formula

According to the chemical and crystal-structure data, the crystal-chemical formula of paratooite-(La) can be described as (La0.74Ca0.11Sr0.07)4CuCa(Na0.75Ca0.15)(Na0.63)(CO3)8 or REE2.96Ca1.59Na1.38CuSr0.28(CO3)8. The idealized formula can be written as (La,Sr,Ca)4CuCa(Na,Ca)2(CO3)8. This formula is in general agreement with the results of chemical analyses reported in the original study [23] and in our work, taking into account the difficulties related with the instability of the mineral under the electron beam.

4. Discussion

Carbocernaite, ideally CaSr(CO3)2, was discovered by Bulakh et al. [34] at the Vuoriyarvi complex, Northern Karelia, Russia. Recently, Chakhmouradian et al. [38] investigated carbocernaite from Bear Lodge, Wyoming, USA, and demonstrated that the mineral can be described as a solid solution between CaSr(CO3)2 and NaREE(CO3)2. The crystal structure of carbocernaite was originally solved by Voronkov and Pyatenko [36] in the space group Pb21m, which was confirmed in [37]. However, the recent study of carbocernaite from Wyoming [38] revealed the presence of reflections that violated the above-mentioned space group, very similar to our observations concerning paratooite-(La) (see above). Therefore, the alternative space group was chosen as P11m (Table 6). Our attempts to refine the crystal structure of paratooite-(La) in this space group were unsuccessful, due to the high number of correlations between the displacement parameters of symmetry-related sites. The additional reflections may appear due to the presence of domains with different symmetries or incommensurate modulations induced by complex substitution mechanisms.
The information-based structural complexity parameters have been calculated by means of the TOPOS software [39] using techniques proposed in [40,41] and are listed in Table 7. The formation of a superstructure due to the cation ordering in paratooite-(La) compared to carbocernaite results in the essential increase of structural complexity per unit cell. Therefore, paratooite-(La) versus carbocernaite represents a good example of structural complexity increasing due to the increasing chemical complexity controlled by different electronic properties of mineral-forming chemical elements (transitional versus alkali and alkaline earth metals).
Our study may also have interesting implications with regard to the propensity of the carbocernaite structure type to incorporate chemical elements with drastically different electronic properties. For instance, paratooite-(La) incorporates REE and copper simultaneously, which may be of interest from the viewpoint of its physical properties and, in particular, of its magnetism. However, the experimental study of magnetic and other properties of paratooite-(La) is currently impossible due to the tiny amount of available material. Therefore, it is of interest to reproduce the mineral under laboratory conditions, which would allow to investigate its structure and properties in more details.

Supplementary Materials

The following are available online at https://www.mdpi.com/2075-163X/9/6/370/s1, Crystallographic Information File (CIF).

Author Contributions

Conceptualization, T.L.P. and S.V.K.; methodology, T.L.P., V.N.B. and A.V.K.; investigation, T.L.P., A.A.Z., V.N.B., A.V.K. and R.Š.; writing—original draft preparation, S.V.K., T.L.P. and A.V.K.; writing—review and editing, S.V.K., T.L.P. and A.V.K.; and visualization, S.V.K. and T.L.P.

Funding

This research was funded by the Russian Science Foundation (grant 19-17-00038 to S.V.K.).

Acknowledgments

We are grateful to Nikita V. Chukanov for useful comments on the interpretation of the Raman spectrum of paratooite-(La).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Zhang, P.; Tao, K.; Yang, Z.; Yang, X.; Song, R. Rare earth, niobium and tantalum minerals in Bayan Obo ore deposit and discussion on their genesis. J. Rare Earths 2002, 20, 81–86. [Google Scholar]
  2. Deng, M.; Xu, C.; Song, W.; Tang, H.; Liu, Y.; Zhang, Q.; Zhou, Y.; Feng, M.; Wei, C. REE mineralization in the Bayan Obo deposit, China: Evidence from mineral paragenesis. Ore Geol. Rev. 2017, 91, 100–109. [Google Scholar] [CrossRef]
  3. Srinivasan, S.G.; Shivaramaiah, R.; Kent, P.R.C.; Stack, A.G.; Navrotsky, A.; Riman, R.; Anderko, A.; Bryantsev, V.S. Crystal structures, surface stability, and water adsorption energies of La-Bastnäsite via density functional theory and experimental studies. J. Phys. Chem. C 2016, 120, 16767–16781. [Google Scholar] [CrossRef]
  4. Plášil, J.; Škoda, R. Crystal structure of the (REE)–uranyl carbonate mineral shabaite-(Nd). J. Geosci. 2017, 62, 97–105. [Google Scholar] [CrossRef]
  5. Ciobanu, C.L.; Kontonikas-Charos, A.; Slattery, A.; Cook, N.J.; Wade, B.P.; Ehrig, K. Short-Range Stacking Disorder in Mixed-Layer Compounds: A HAADF STEM Study of Bastnäsite-Parisite Intergrowths. Minerals 2017, 7, 227. [Google Scholar] [CrossRef]
  6. Plášil, J.; Petříček, V. Crystal structure of the (REE)-uranyl carbonate mineral kamotoite-(Y). Mineral. Mag. 2017, 81, 653–660. [Google Scholar] [CrossRef]
  7. Schmandt, D.S.; Cook, N.J.; Ciobanu, C.L.; Ehrig, K.; Wade, B.P.; Gilbert, S.; Kamenetsky, V.S. Rare Earth Element Fluorocarbonate Minerals from the Olympic Dam Cu-U-Au-Ag Deposit, South Australia. Minerals 2017, 7, 202. [Google Scholar] [CrossRef]
  8. Panikorovskii, T.L.; Kalashnikova, G.O.; Zhitova, E.S.; Pakhomovsky, Y.A.; Bocharov, V.N.; Yakovenchuk, V.N.; Zolotarev, A.A.; Krivovichev, S.V. Crystal chemistry of Na-rich kihlmanite-(Ce) from arfvedsonite-aegirine-microcline pegmatite at the Kihlman Mt. (Khibiny massif, Kola Peninsula, Russia). Zap. Ross. Mineral. Obshch. 2017, 146, 113–124. (In Russian) [Google Scholar]
  9. Kalatha, S.; Perraki, M.; Economou-Eliopoulos, M.; Mitsis, I. On the Origin of Bastnaesite-(La,Nd,Y) in the Nissi (Patitira) Bauxite Laterite Deposit, Lokris, Greece. Minerals 2017, 7, 45. [Google Scholar] [CrossRef]
  10. Kim, P.; Anderko, A.; Navrotsky, A.; Riman, R.E. Trends in Structure and Thermodynamic Properties of Normal Rare Earth Carbonates and Rare Earth Hydroxycarbonates. Minerals 2018, 8, 106. [Google Scholar] [CrossRef]
  11. Škoda, R.; Plášil, J.; Čopjaková, R.; Novák, M.; Jonsson, E.; Galiová, M.V.; Holtstam, D. Gadolinite-(Nd), a new member of the gadolinite supergroup from Fe-REE deposits of Bastnäs-type, Sweden. Mineral. Mag. 2018, 82, 133–145. [Google Scholar] [CrossRef]
  12. Menezes Filho, L.A.D.; Chaves, M.L.S.C.; Chukanov, N.V.; Atencio, D.; Scholz, R.; Pekov, I.; Da Costa, G.M.; Morrison, S.M.; Andrade, M.B.; Freitas, E.T.F.; et al. Parisite-(La), ideally CaLa2(CO3)3F2, a new mineral from Novo Horizonte, Bahia, Brazil. Mineral. Mag. 2018, 82, 133–144. [Google Scholar] [CrossRef]
  13. Luo, M.; Ye, N.; Zou, G.; Lin, C.; Cheng, W. Na8Lu2(CO3)6F2 and Na3Lu(CO3)2F2: Rare earth fluoride carbonates as deep-UV nonlinear optical materials. Chem. Mater. 2013, 25, 3147–3153. [Google Scholar] [CrossRef]
  14. Wang, Y.; Han, T.; Ding, Y.-S.; Zheng, Z.; Zheng, Y.-Z. Sodalite-like rare-earth carbonates: A study of structural transformation and diluted magnetism. Dalton Trans. 2016, 45, 1103–1110. [Google Scholar] [CrossRef] [PubMed]
  15. Zhang, R.-H.; Zhao, D.; Huang, M.; Yang, R.-J.; Ma, F.-X.; Fan, Y.-C. Synthesis, crystal structure and photoluminescence properties of a new rare-earth carbonate Na3Eu(CO3)3·6H2O. J. Chil. Chem. Soc. 2017, 62, 3403–3406. [Google Scholar] [CrossRef]
  16. Hämmer, M.; Höppe, H.A. Crystalline orthorhombic Ln[CO3][OH] (Ln = La, Pr, Nd, Sm, Eu, Gd) compounds hydrothermally synthesised with CO2 from air as carbonate source. Z. Naturforsch. 2019, 74b, 59–70. [Google Scholar] [CrossRef]
  17. Cao, L.; Song, Y.; Peng, G.; Luo, M.; Yang, Y.; Lin, C.-S.; Zhao, D.; Xu, F.; Lin, Z.; Ye, N. Refractive index modulates second-harmonic responses in RE8O(CO3)3(OH)15X (RE = Y, Lu; X = Cl, Br): Rare-earth halide carbonates as ultraviolet nonlinear optical materials. Chem. Mater. 2019, 31, 2130–2137. [Google Scholar] [CrossRef]
  18. Piret, P.; Deliens, M. Nouvelles données sur la schuilingite, carbonate hydrate de terres rares, de plomb et de cuivre. Bull. Mineral. 1982, 105, 225–228. [Google Scholar]
  19. Sarp, H.; Bertrand, J.; Deferne, J. Données nouvelles sur la schuilingite de Shinkolobwe (Shaba, Zaire), carbonate hydrate de plomb, cuivre et de terres rares. Schweiz. Mineral. Petrogr. Mitt. 1983, 63, 1–6. [Google Scholar]
  20. Schindler, M.; Hawthorne, F.C. The crystal structure of schuilingite-(Nd). Can. Mineral. 1999, 37, 1463–1470. [Google Scholar]
  21. Deliens, M.; Piret, P. L’astrocyanite-(Ce), Cu2(TR)2(UO2)(CO3)5(OH)2·1,5 H2O, nouvelle espèce minérale de Kamoto, Shaba, Zaïre. Eur. J. Mineral. 1990, 2, 407–411. [Google Scholar] [CrossRef]
  22. Wallwork, K.; Kolitsch, U.; Pring, A.; Nasdala, L. Decrespignyite-(Y), a new copper yttrium rare earth carbonate chloride hydrate from Paratoo, South Australia. Mineral. Mag. 2002, 66, 181–188. [Google Scholar] [CrossRef] [Green Version]
  23. Pring, A.; Wallwork, K.; Brugger, J.; Kolitsch, U. Paratooite-(La), a new lanthanum-dominant rare-earth copper carbonate from Paratoo, South Australia. Mineral. Mag. 2006, 70, 131–138. [Google Scholar] [CrossRef]
  24. Brugger, J.; Ogierman, J.; Pring, A.; Waldron, H.; Kolitsch, U. Origin of the secondary REE-minerals at the Paratoo copper deposit near Yunta, South Australia. Mineral. Mag. 2006, 70, 609–627. [Google Scholar] [CrossRef]
  25. Bruker-AXS. APEX2, Version 2014.11-0; Bruker-AXS: Madison, WI, USA, 2014.
  26. Sheldrick, G.M. SADABS; University of Goettingen: Goettingen, Germany, 2007. [Google Scholar]
  27. Sheldrick, G.M. Crystal structure refinement with SHELXL. Acta Crystallogr. 2015, C71, 3–8. [Google Scholar]
  28. Gagné, O.C.; Hawthorne, F.C. Comprehensive derivation of bond-valence parameters for ion pairs involving oxygen. Acta Crystallogr. 2015, B71, 562–578. [Google Scholar] [CrossRef] [PubMed]
  29. Frost, R.L.; Martens, W.N.; Rintoul, L.; Mahmutagic, E.; Kloprogge, J.T. Raman spectroscopic study of azurite and malachite at 298 and 77 K. J. Raman Spectrosc. 2002, 33, 252–259. [Google Scholar] [CrossRef] [Green Version]
  30. Michiba, K.; Miyawaki, R.; Minakawa, T.; Terad, Y.; Nakai, I.; Matsubara, S. Crystal structure of hydroxylbastnäsite-(Ce) from Kamihouri, Miyazaki Prefecture, Japan. J. Miner. Petrol. Sci. 2013, 108, 326–334. [Google Scholar] [CrossRef]
  31. Buzgar, N.; Apopei, A.I. The Raman study of certain carbonates. Geologie Tomul L 2009, 55, 97–112. [Google Scholar]
  32. Jahn, H.A.; Teller, E. Stability of polyatomic molecules in degenerate electronic states. I. Orbital degeneracy. Proc. R. Soc. 1937, A161, 220–235. [Google Scholar]
  33. Hathaway, B.J. Copper. In Comprehensive Coordination Chemistry; Wilkinson, G., Ed.; Pergamon: Oxford, UK, 1987; Volume 5, pp. 533–774. [Google Scholar]
  34. Bulakh, A.G.; Kondrateva, V.V.; Baranova, E.N. Carbocernaite—a new rare-earth carbonate. Zap. Vses. Mineral. Obsh. 1961, 90, 42–49. (In Russian) [Google Scholar]
  35. Bulakh, A.G.; Izokh, E.P. New data on carbocernaite. Dokl. Akad. Nauk SSSR 1967, 175, 175–177. (In Russian) [Google Scholar]
  36. Voronkov, A.A.; Pyatenko, Y.A. Crystal structure of carbocernaite (Na,Ca)(TR,Sr,Ca,Ba)(CO3)2. J. Struct. Chem. 1967, 8, 835–840. [Google Scholar] [CrossRef]
  37. Shi, N.; Ma, Z.; Peng, Z. The crystal structure of carbocernaite. Kexue Tongbao 1982, 27, 76–80. (In Chinese) [Google Scholar]
  38. Chakhmouradian, A.R.; Cooper, M.A.; Reguir, E.P.; Moore, M.A. Carbocernaite from Bear Lodge, Wyoming: Crystal chemistry, paragenesis, and rare-earth fractionation on a microscale. Am. Mineral. 2017, 102, 1340–1352. [Google Scholar] [CrossRef]
  39. Blatov, V.A.; Shevchenko, A.P.; Proserpio, D.M. Applied topological analysis of crystal structures with the program package ToposPro. Cryst. Growth. Des. 2014, 14, 3576–3586. [Google Scholar] [CrossRef]
  40. Krivovichev, S.V. Structural complexity of minerals: Information storage and processing in the mineral world. Miner Mag. 2013, 77, 275–326. [Google Scholar] [CrossRef]
  41. Krivovichev, S.V. Which inorganic structures are the most complex? Angew. Chem. Int. Ed. 2014, 53, 654–661. [Google Scholar] [CrossRef]
Minerals 09 00370 g001 550
Figure 1. Raman spectrum of paratooite-(La).
Figure 1. Raman spectrum of paratooite-(La).
Minerals 09 00370 g001
Minerals 09 00370 g002 550
Figure 2. Coordination environments of the La, Ca, Cu, Na1, and Na2 sites in the crystal structure of paratooite-(La). Legend: La, Ca, Na, C, and O atoms are shown as orange, blue, greenish-yellow, gray, and red spheres, respectively.
Figure 2. Coordination environments of the La, Ca, Cu, Na1, and Na2 sites in the crystal structure of paratooite-(La). Legend: La, Ca, Na, C, and O atoms are shown as orange, blue, greenish-yellow, gray, and red spheres, respectively.
Minerals 09 00370 g002
Minerals 09 00370 g003 550
Figure 3. The crystal structures of paratooite-(La) (a) and carbocernaite (b). Legend is as in Figure 1; Sr atoms are shown as yellow spheres, and carbonate triangles are shaded in gray.
Figure 3. The crystal structures of paratooite-(La) (a) and carbocernaite (b). Legend is as in Figure 1; Sr atoms are shown as yellow spheres, and carbonate triangles are shaded in gray.
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Minerals 09 00370 g004 550
Figure 4. The cation arrangement in the unit cell of the crystal structure of paratooite-(La) (a) and its sections on the levels z = ½ (b) and 0 (c).
Figure 4. The cation arrangement in the unit cell of the crystal structure of paratooite-(La) (a) and its sections on the levels z = ½ (b) and 0 (c).
Minerals 09 00370 g004
Table
Table 1. Crystal data and structure refinement for paratooite-(La).
Table 1. Crystal data and structure refinement for paratooite-(La).
Crystal SystemOrthorhombic
Space groupPbam
a, Å7.2250(3)
b, Å12.7626(5)
c, Å10.0559(4)
V, Å3927.25(6)
Z1
ρcalc, g/cm33.690
μ, mm−17.837
Crystal dimensions, mm 0.06 × 0.04 × 0.01
λ, Å0.71073
2θ range, deg.4.05–57.92
Index ranges−9 ≤ h ≤ 7, −17 ≤ k ≤ 16, −13 ≤ l ≤ 13
Reflections collected9442
Independent reflections1299 [Rint = 0.061]
Data/restraints/parameters1299/0/111
GOF (goodness-of-fit)1.103
Final R indexes [I ≥ 2σ(I)]R1 = 0.063, wR2 = 0.170
Final R indexes (all data)R1 = 0.076, wR2 = 0.195
Table
Table 2. Atomic coordinates, isotropic displacement parameters (Å2), and bond-valence sums (BVS, in valence units (v.u.)) for paratooite-(La).
Table 2. Atomic coordinates, isotropic displacement parameters (Å2), and bond-valence sums (BVS, in valence units (v.u.)) for paratooite-(La).
AtomxYzUeq.BVS
La0.71419(8)0.69022(5)0.74855(4)0.0161(3)3.31
Cu½ ½ ½ 0.0222(6)2.08
Ca½ 000.0237(8)2.07
Na10½ ½ 0.025(2)1.09
Na2½ ½ 00.017(4)0.98
C10.3107(12)0.5452(7)0.7449(6)0.0159(16)4.05
C20.5435(15)0.7731(9)00.016(2)4.04
C3Vladimir N. Bocharov 0.0438(16)0.7177(9)½ 0.017(2)4.05
O10.3047(9)0.4929(5)0.6323(6)0.0233(13)2.14
O20.6306(16)0.6864(7)00.028(2)2.11
O30.0059(9)0.6741(5)0.6122(6)0.0208(12)2.11
O40.5057(10)0.8179(4)0.8891(6)0.0215(13)2.18
O50.3789(9)0.6359(5)0.7497(5)0.0210(13)2.19
O60.1304(15)0.8036(7)½ 0.026(2)2.14
O70.2460(10)0.4974(6)0.8447(6)0.0282(14)2.22
Table
Table 3. Observed (exp.) and theoretical (theor.) site-scattering factors (SSF, e−) and assigned occupancies for selected atom sites in the crystal structure of paratooite-(La).
Table 3. Observed (exp.) and theoretical (theor.) site-scattering factors (SSF, e−) and assigned occupancies for selected atom sites in the crystal structure of paratooite-(La).
AtomSSFexp.SSFtheorOccupancy
La46.6446.07La0.71Sr0.10□0.10Ca0.09
Cu29.0029.00Cu
Ca20.0020.00Ca
Na111.0010.62Na0.82□0.10Ca0.08
Na26.386.38Na0.58□0.42
Table
Table 4. Anisotropic displacement atom parameters for paratooite-(La) (Å2).
Table 4. Anisotropic displacement atom parameters for paratooite-(La) (Å2).
AtomU11U22U33U23U13U12
La0.0247(5)0.0146(4)0.0090(4)−0.00037(18)−0.00006(19)−0.00050(19)
Cu0.0247(5)0.0146(4)0.0090(4)−0.00037(18)−0.00006(19)−0.00050(19)
Ca0.0318(11)0.0265(12)0.0083(9)000.0026(10)
Na10.0347(18)0.0234(17)0.0131(14)000.0008(16)
Na20.038(4)0.020(4)0.015(3)00−0.005(3)
C10.016(5)0.021(6)0.014(6)000.002(5)
C20.026(4)0.014(4)0.008(4)−0.003(2)0.004(3)0.002(3)
C30.024(6)0.016(5)0.008(4)000.000(4)
O10.026(6)0.018(5)0.006(4)000.001(4)
O20.040(3)0.019(3)0.011(3)−0.003(2)−0.002(2)0.001(3)
O30.045(6)0.025(5)0.014(4)000.013(4)
O40.026(3)0.020(3)0.016(3)0.006(2)0.003(3)0.001(3)
O50.028(3)0.019(3)0.017(3)0.007(2)0.000(3)0.000(2)
O60.026(3)0.017(3)0.019(3)0.001(2)−0.002(2)−0.005(2)
O70.040(5)0.022(5)0.015(4)00−0.010(4)
Table
Table 5. Selected bond lengths (Å) in the crystal structure of paratooite-(La).
Table 5. Selected bond lengths (Å) in the crystal structure of paratooite-(La).
La–O52.518(7)Cu–O11.941(6) 4×C1–O51.259(11)
La–O52.520(7)Cu–O62.676(6) 2×C1–O71.264(9)
La–O32.523(6)<Cu–O>2.186C1–O11.315(9)
La–O42.539(7) <C1–O>1.279
La–O62.573(3)Ca–O72.367(7) 4x
La–O72.598(7)Ca–O42.578(6) 4xC2–O21.273(14)
La–O22.600(3)<Ca–O>2.473C2–O41.283(8)
La–O12.617(7) C2–O41.283(8)
La–O42.631(6)Na1–O32.492(6) 4x<C2–O>1.280
La–O32.673(6)Na1–O12.573(6) 4x
<La–O>2.579<Na1–O>2.533C3–O61.262(14)
C3–O31.287(8)
Na2–O72.410(7) 4xC3–O31.287(8)
Na2–O22.560(10) 2x<C3–O>1.279
<Na2–O>2.460
Table
Table 6. Raman bands in the paratooite-(La) spectrum and their interpretation.
Table 6. Raman bands in the paratooite-(La) spectrum and their interpretation.
Raman Shift, cm−1AssignmentType
1369 w, 1434 w CO3v3
1095 s, 988 w *, 922 w *CO3v1
870 w CO3v2
733, 686 w, 665 wCO3v4
386 sh, 343CuO6v1, v2
261 sCuO6v3, v4
166, 119 lattice vibrations
sh = shoulder; s = strong intensity; w = weak; * these can also be assigned to a small admixture of silicate anions.
Table
Table 7. Unit-cell parameters, space groups, and structural complexity parameters for paratooite-(La) and carbocernaite.
Table 7. Unit-cell parameters, space groups, and structural complexity parameters for paratooite-(La) and carbocernaite.
MineralSpace Groupa (Å)b (Å)c (Å)/γ (deg.)IG (bits/atom)IG,total (bits/cell)
paratooite-(La)Pbam7.22512.76310.0563.722297.754this work
carbocernaiteP21am *7.306.415.232.92258.439[36]
carbocernaiteP21am *7.3016.4305.2142.92258.439[37]
carbocernaiteP11m *7.2666.4345.220/89.983.92278.439[38]
* Crystallographic axes interchanged for the ease of comparison.

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Krivovichev, S.V.; Panikorovskii, T.L.; Zolotarev, A.A.; Bocharov, V.N.; Kasatkin, A.V.; Škoda, R. Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite. Minerals 2019, 9, 370. https://doi.org/10.3390/min9060370

AMA Style

Krivovichev SV, Panikorovskii TL, Zolotarev AA, Bocharov VN, Kasatkin AV, Škoda R. Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite. Minerals. 2019; 9(6):370. https://doi.org/10.3390/min9060370

Chicago/Turabian Style

Krivovichev, Sergey V., Taras L. Panikorovskii, Andrey A. Zolotarev, Vladimir N. Bocharov, Anatoly V. Kasatkin, and Radek Škoda. 2019. "Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite" Minerals 9, no. 6: 370. https://doi.org/10.3390/min9060370

APA Style

Krivovichev, S. V., Panikorovskii, T. L., Zolotarev, A. A., Bocharov, V. N., Kasatkin, A. V., & Škoda, R. (2019). Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite. Minerals, 9(6), 370. https://doi.org/10.3390/min9060370

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