Tag Archives: crystal structures

Pentagonal Bipyramid vs. Capped Octahedron (Updated)

In a very interesting article by Giese and Seppelt from 1994 [1] the question of the preferred coordination geometry for the coordination number 7 is explored. Until then, it has been shown that the pentagonal bipyramid is preferred for main group elements (for instance in the compound IF7), although this geometry results in an overall slightly higher ligand repulsion than the alternative arrangements according to a capped octahedron or capped tigonal prism, respectively.

In this article they raised the question if this is also valid for transition elements, and the ideal candidate to answer this question would be the homoleptic compound ReF7. Unfortunately, for various reasons it is very difficult to determine the crystal structure of ReF7.

Alternatively, they synthesized several ionic compounds comprising of anions with transition elements with the coordination number 7 and varied the nature of the cation to exclude lattice energy effects that might influence the arrangement of the ligands.

The results were as follows:

The anions in Cs+MoF7 (see Fig. 1), Cs+WF7, NO2+MoF7 ∙ CH3CN, and C11H24N+MoF7 (C11H24N+ = 1,1,3,3,5,5-hexamethylpiperidinium) (all belong to the cubic crystal system) as well as (H3C)4N+MoF7 (tetragonal, space group P4/nmm, ) form a capped octahedron coordination polyhedron. The latter result is of special interest as the 7 fluorine atoms around Tellurium in (H3C)4N+TeF7 (again space group P4/nmm) form a pentagonal bipyramid instead.

Fig. 1: The crystal structure of Cs+MoF7 (space group Pa-3, ICSD deposition number = 78390); Cs = purple, Mo = gray, F = green. (Image made with VESTA [2]).

According to the authors, it can therefore be concluded that neither the lattice type nor the crystal packing have an influence on the different structures of the anions.

Now, what will happen, if one of the 7 fluorine ligands is exchanged with a larger atom? As expected, a pentagonal bipyramid is then realised, as in Cs+ReOF6 (space group P21/a), where the larger ligand occupies one of the two axial positions (see Fig. 2).

Fig. 2: The crystal structure of Cs+ReOF6 (space group P21/a, ICSD deposition number = 78392); Cs = purple, Re = gray, O = red, F = green. (Image made with VESTA [2]).

Update:

I have to admit that I was too lazy to check if the structure of ReF7 is known by now. In fact – thanks to Robert McMeeking (from The Chemical Database Service/CrystalWorks, @cds_daresbury) for the hint – the crystal structure of ReF7 was published in Science only a single(!) day after the publication of the Angewandte paper by Giese & Seppelt: ReF7 builds a (slightly distorted) pentagonal bipyramid [3], see Fig. 3!

Fig. 3: The crystal structure of ReF7 (space group C-1, ICSD deposition number = 78311); Re = gray, F = green. (Image made with VESTA [2]).

References:

[1] S. Giese, K. Seppelt, Angew. Chem. Int. Ed Engl. 1994, 33, 461. http://dx.doi.org/10.1002/anie.199404611

[2] K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr. 2011, 44, 1272-1276).

[3] T. Vogt, A. N. Fitch, J. K. Cockcroft, Science 1994, 263, 1265.
https://doi.org/10.1126/science.263.5151.1265

Despujolsite

Despujolsite

  • Named in honor of Pierre Despujols (1888–1981), the founder of the Moroccan Geologic Survey (“Service de la carte géologique du Maroc”)
  • The mineral was first observed in 1962 in manganese ore samples from Tachgagalt (Anti-Atlas, Morocco).
  • Formula: Ca3Mn(SO4)2(OH)6  · 3 H2O
  • Space group: P-62c
  • Crystal system: hexagonal
  • Crystal class: -6m2
  • Lattice parameters: a = b =  8.5405(5) Å, c = 10.8094(9) Å, α = β = 90°, γ  120°
Despujolsite_0438792001298611550

Picture: Rob Lavinsky, iRocks.com – CC BY-SA 3.0


Crystal structure (click on the pictures to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr., 44, 1272-1276 (2011).)

Despujolsite
  • CaO8 polyhedra (blue)
  • Mn(OH)6 octahedra (purple)
  • SO4 tetrahedra (yellow)
  • Oxygen (red)
  • Hydrogen (white)

For a 3D interactive version, see here:

https://skfb.ly/onvGo

Refs:

[1] M.C. Barkley, H. Yang, S.H. Evans, R.T. Downs, M.J. Origlieri, Acta Cryst E 2011, 67, i47-i48.
DOI: 10.1107/S1600536811030911

Kapellasite

Kapellasite

  • Named after Christo Kapellas (1938-2004), collector and mineral dealer of Kamariza, Lavrion, Greece
  • Kapellasite is isostructural with Haydeeite [Cu3Mg(OH)6Cl2]
  • Kapellasite is a metastable polymorph of Herbertsmithite
  • Formula: Cu3Zn(OH)6Cl2
  • Space group: P-3m1 (No. 164)
  • Crystal system: trigonal
  • Crystal class: -3m
  • Lattice parameters: a = b = 6.300(1) Å, c =  5.733(1) Å, α = β = 90°, γ = 120°

Crystal structure[1] (click on the pictures to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • CuO4 square-planar coordination polygons (blue)
  • ZnO6 distorted octahedra (gray)
  • Oxygen (red)
  • Chlorine (green)

For a 3D interactive version, see here:

https://skfb.ly/6ZNHM

References:

[1] W. Krause, H.-J. Bernhardt, R.S.W. Braithwaite, U. Kolitsch, R. Pritchard
Kapellasite, Cu3Zn(OH)6Cl2, a new mineral from Lavrion, Greece, and its crystal structure
Mineralogical Magazine, 2006, 70, 329-340
DOI: 10.1180/0026461067030336

Bloedite

Blödite (also Bloedite)

  • named after the German mineralogist and chemist Karl August Blöde (1773 – 1820)
  • fun fact: the German adjective “blöd(e)” means “stupid”
  • Formula: Na2Mg(SO4)2  · 4 H2O
  • Space group: P21/a
  • Crystal system: monoclinic
  • Crystal class: 2/m
  • Lattice parameters: a = 11.126(2), b =  8.242(1) Å, c = 5.539(1) Å, α = 90°, β = 100.84(1)°, γ  90°

Crystal structure (click on the pictures to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • SO4 tetrahedra (yellow)
  • (distorted) NaO6 octahedra (purple)
  • MgO6 octahedra (green)
  • Oxygen (red)
  • Hydrogen (white)

For a 3D interactive version, see here:

https://skfb.ly/6ZEPS

Refs:

[1] F. C. Hawthorne, The Canadian Mineralogist 1985, 23, 669-674.
(PDF)

Atacamite and Hibbingite

Atacamite

  • Named after its type locality, the Atacama desert in Chile.
  • Atacamite is isostructural with Hibbingite [Fe2Cl(OH)3], and Kempite [Mn2Cl(OH)3]
  • In 2002 it was found out that the jaws of the marine bloodworm Glycera dibranchiata contain Atacamite.[1]
  • Atacamite is polymorphous with Botallackite and Clinoatacamite (both monoclinic).
  • Formula: Cu2Cl(OH)3
  • Space group: Pnma (No. 62)
  • Crystal system: orthorhombic
  • Crystal class: mmm
  • Lattice parameters: a = 6.030(2) Å, b =  6.865(2) Å, c = 9.120(2) Å, α = βγ = 90°

Picture: By Stefan Schorn – CC BY-SA 3.0
http://www.mineralienatlas.de/lexikon/index.php/Bildanzeige?pict=1081079762,
https://commons.wikimedia.org/w/index.php?curid=399210


Crystal structure[2] (click on the pictures to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • CuO5Cl distorted octahedra (orange)
  • CuO4Cl2 distorted octahedra (blue)
  • Oxygen (red)
  • Chlorine (green)
  • Hydrogen (white)

For a 3D interactive version, see here:

https://skfb.ly/6QpQY

References:

[1] H.C. Lichtenegger, Th. Schöberl, M.H. Bartl, H. Waite, G.D. Stucky
Science 2002, 298, 389-392.
DOI: 10.1126/science.1075433

[2] J.B. Parise, B.G. Hyde
Acta Cryst. C 1986, 42, 1277-1280.
DOI: 10.1107/S0108270186092570


Hibbingite

  • Named after its type locality, the city of Hibbing, which was built on the rich iron ore of the Mesabi Iron Range. At the edge of the town is the largest open-pit iron mine in the world.
  • Hibbingite is isostructural with Atacamite [Cu2Cl(OH)3] and Kempite [Mn2Cl(OH)3]
  • Formula: Fe2Cl(OH)3
  • Space group: Pnma (No. 62)
  • Crystal system: orthorhombic
  • Crystal class: mmm
  • Lattice parameters: a = 6.3373(2) Å, b =  6.9892(2) Å, c = 9.3457(3) Å, α = βγ = 90°

Crystal structure (click on the pictures to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • FeO5Cl distorted octahedra (green)
  • FeO4Cl2 distorted octahedra (brown)
  • Oxygen (red)
  • Chlorine (green)
  • Hydrogen (white)

For a 3D interactive version, see here:

https://skfb.ly/6QpRS

Reference:

N.V. Zubkova, I.V. Pekov, E.V. Sereda, V.O. Yapaskurt, D.Y. Pushcharovsky
Z. Kristallogr. 2019, 234 (6), 379-382.
DOI: 10.1515/zkri-2018-2124


 

Schoenfliesite

Schoenfliesite

  • Named in 1971 by George T. Faust and Waldemar T. Schaller in honor of Arthur Moritz Schoenflies ( 17 April 1853 – 27 May 1928) Professor of Mathematics, University of Frankfurt. Schoenflies’ researches in group theory and topology resulted in his proof of the 230 space groups.
  • Formula: MgSn(OH)
  • Space group: Pn-3 (No. 201)
  • Crystal system: cubic
  • Crystal class: m-3
  • Lattice parameters: a = b = c = 7.7449(4) Å, α = β = γ = 90°

Crystal structure (click on the picture to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,”J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • MgO6 octahedra (orange)
  • SnO6 octahedra (blue-gray)
  • Hydrogen (white)

For a 3D interactive version on sketchfab, see here:

https://skfb.ly/6QpyS

Reference:

Description of Schoenfliesite, MgSn(OH)6, and Roxbyite, Cu1.72S, from a 1375 BC Shipwreck, and Rietveld Neutron-diffraction Refinement of Synthetic Schoenfliesite, Wickmanite, MnSn(OH)6, and Burtite, CaSn(OH)6
L.C. Basciano, R.C. Peterson, P.L. Roeder
The Canadian Mineralogist 1998, 36, 1203-1210.

Spangolite – A Pyroelectric Copper Sulfate Sheet Mineral

Spangolite

  • Named in honour of Norman Spang (1841–1922), a mineral collector from Pennsylvania, USA; for details, see here.
  • Spangolite is pyroelectric
  • Formula: Cu6Al(SO4)(OH)12Cl · 3 H2O
  • Space group: P31(No. 159)
  • Crystal system: trigonal
  • Crystal class: 3m
  • Lattice parameters: a = b = 8.254(4) Å, c = 14.354(8) Å, α = β = 90°, γ = 120°

Picture: Christian Rewitzer, CC BY-SA 3.0
https://commons.wikimedia.org/w/index.php?curid=14865917


Crystal structure (click on the picture to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,”J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • CuO6 distorted octahedra (blue)
  • AlO6 octahedra (orange)
  • SOtetrahedra (yellow)
  • Oxygen (red)
  • Chlorine (green)
  • Hydrogen (white)

For a 3D interactive version on sketchfab, see here:

https://skfb.ly/6Q6U7

References:

[1] Spangolite
H. A. Miers
Mineralogical Magazine 1894, 10, 273-277

DOI: 10.1180/minmag.1894.010.48.02

[2] The Crystal Structure of Spangolite, a Complex Copper Sulfate Sheet Mineral
F.C. Hawthorne, M. Kimata, R.K. Eby
American Mineralogist 1993, 78 (5-6), 649-652.

Suzukiite – polymorphic to Bavsiite

Suzukiite

  • Named in honor of Jun Suzuki, a professor of mineralogy and petrology, at the Hokkaido University, Sapporo (Japan).
  • Suzukiite belongs to the inosilicates (chain silicates) and is polymorphic to Bavsiite, which is tetragonal.
  • Formula: BaVSi2O7
  • Space group: Cmcm (No. 63)
  • Crystal system: orthorhombic
  • Crystal class: mmm
  • Lattice parameters: a = 5.3546(16), b = 15.249(5) Å, c = 7.094(2) Å, α = β = γ = 90°

Picture: D. Nishio-Hamane – CC BY-NC-SA 2.0


Crystal structure (click on the picture to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,”J. Appl. Crystallogr., 44, 1272-1276 (2011).)

 

  • BaO10 polyhedra (not shown as polyhedra, Ba green)
  • SiO4 tetrahedra (yellow)
  • VO5 square pyramids (purple)
  • Oxygen (red)

For a 3D interactive version on sketchfab, see here:

https://skfb.ly/6Q6GC

Reference:
Crystal Structure of Suzukiite from the Mogurazawa Mine, Gunma Prefecture, Japan,
M. Ito, S. Matsubara, K. Yokoyama, K. Momma, R. Miyawaki, I. Nakai, A. Kato
Journal of Mineralogical and Petrological Sciences 2014, 109, 222-227

DOI: 10.2465/jmps.140520

Bavsiite – A mineral containing Ba, V, Si,…

Bavsiite

  • Named for the constituting elements Barium, Vanadium and Silicon.
  • Bavsiite is polymorphic to Suzukiite, BaVSi2O7, which is orthorhombic.
  • Formula: Ba2V2O2[Si4O12]
  • Space group: I4/(No. 87)
  • Crystal system: tetragonal
  • Crystal class: 4/m
  • Lattice parameters: a = b = 7.043(1) Å, c = 11.444(2) Å, α = β = γ = 90°

Crystal structure (click on the picture to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,”J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • BaO12 polyhedra (not shown as polyhedra, Ba green)
  • SiO4 tetraedra (yellow) building single four-rings
  • VO5 square pyramids (blue)
  • Oxygen (red)

For a 3D interactive version on sketchfab, see here:

https://skfb.ly/6PYVA

Reference:
Bavsiite, Ba2V2O2[Si4O12], mineral data and crystal structure
H.-P. Bojar, F. Walter, J. Baumgartner
Mineralogical Magazine 2019, 83, 821-827

DOI: 10.1180/mgm.2019.59

Vanadinite – the most important vanadium source

Vanadinite

  • Named for its vanadium content
  • Vanadinite is the most important source of vanadium and finds application as V2O5 in the famous contact process (production of sulfuric acid) and in alloys for chromium-vanadium steel (typically the content is below 0.2 %)
  • Formula: Pb5(VO4)3Cl
  • Space group: P63/(No. 176)
  • Crystal system: hexagonal
  • Crystal class: 6/m
  • Lattice parameters: a = b = 10.299(2) Å, c = 7.308(1) Å, α = β = 90°, γ = 120°

Picture: Didier Descouens – CC BY-SA 4.0
https://commons.wikimedia.org/w/index.php?curid=12436369


Crystal structure (click on the picture to download the VESTA file):

(K. Momma and F. Izumi, “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,”J. Appl. Crystallogr., 44, 1272-1276 (2011).)

  • PbO9 irregular polyhedra (black)
  • PbO7 capped trigonal prisms (blue)
  • VO4 tetrahedra (purple)
  • Oxygen (red)
  • Chlorine (green)

For a 3D interactive version on sketchfab, see here:

https://skfb.ly/6PT8q

Reference:
Crystal structure of vanadinite: refinement of anisotropic displacement parameters
F. Laufek et al.
J. Czech Geol. Soc. 2006, 51, 271-275

DOI: 10.3190/JCGS.999