The lattice parameters of harkerite from Skye (Scotland) are: a = 18.131 A, α = 33,46°, space group R3m, twin plane (211). The crystal structure has been solved by Patterson, Fourier, and difference syntheses, then refined by least-squares procedures to a conventional R = 0.067 for the 1175 reflections with F20 > 3 σ(F20); R = 0.147 for all 2695 measured reflections.

The crystal structure of harkerite is comparable with that of sakhaite. The idealized cell contents derived from the structural studies are:

harkerite  Ca24Mg8[AlSi4(O,OH)16]2 (BO3)8(CO3)8(H2O,Cl)

sakhaite  2{Ca24Mg8[(BO3)8 (BO3)8](CO3)8(H2O)),

the main difference between the structures being the replacement of the aluminosilicate group in harkerite (similar to the tetrahedral pentamer found in zunyite) by 4(BO3) in sakhaite. Both minerals show a very marked pseudo-symmetry in the cubic space group Fd3m (a = 14.7 A).

The crystal structure is based on an arrangement of oxygen and calcium atoms in an incomplete cubic closest packing, with Mg in octahedral sites, Si and Al in tetrahedral sites, and B or C in triangular holes. The Ca-coordination ranges from 8 to 10. Two carbonate groups are statistically placed on one of two inversion-related orientations. Some structural disorder follows from the mutual replacement among aluminosilicate, borate, or possibly other atomic groups (CO3, OH, H2O). Such substitutions would be also responsible for some discrepancies between the idealized and actual chemical composition of harkerite. The different ordering of the replacing groups accounts for possible harkerite polymorphs in the cubic pseudo-cell.

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