Oxygen atoms missing in VESTA visualisation

[Lee Jay]

Hello,

I am trying to visualise the structure of MgMn2O4, taken from ICSD collection code 290600 and imported as a cif file. The settings look all correct, but the oxygen atoms do not show up on the 3D structure. I checked that the visualisation setting for oxygen atoms is checked in the 'Objects' panel, so it's not a problem involving the setting. I also tried downloading a fresh version of VESTA online and opened the cif file, but the problem persists. Finally, generating a new file and manually constructing the cell with the crystal data also does not show oxygen. Could anyone help me on this matter please?

The cell data is:

I41 /a m d (141), origin choice 2
a=5.6478, c=9.1355
Mg (0, 0.25, 0.375)
Mn (0, 0, 0)
O (0, 0.2735, 0.3664)

Many thanks

Jay

[Philip Howie]

Dear Jay,

The reason the O atoms do not appear is that they're located 'inside' the larger Mg atoms!  You can see them by clicking the 'Properties...' button at the bottom left, selecting the 'Atoms' tab and reducing the radius of each species by a factor of 10.

I strongly suspect there is an error in the data you've obtained from ICSD.  As further evidence, looking at record 290600, the Wyckhoff symbols for Mg, Mn and O are given as 4b, 8c and 16h; this would reproduce the 1:2:4 stoichiometry of the compound with 4 formula units per cell.  In fact, the atom positions listed generate 16, 4 and 16 positions in space group 141, which is incompatible with the stoichiometry.  Indeed, the card comes with the warning that, "Coordinates are those given in the paper but are obviously wrong."

There are several other ICSD records for MgMn2O4 that have the correct atom positions.  I suggest you use one of these, and in future pay attention to the source of your crystallographic data!

Best,

Philip

[Lee Jay]

Dear Philip,

Thanks so much for the help! I actually haven't checked the ICSD data itself, guess this gives me a big lesson.

Cheers,

Jay