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Crystal Structure of Potassium Permanganate1,2

You will use the program APEX2 to determine the structure of potassium permanganate.3 These
data, in the file KMnOs.hkl, consist of the x-ray intensities observed for reflections from many
planes, identified by three Miller index numbers, h, k, and l. The diffractometer automatically
orients the crystal and the detector to pick up reflections from each plane, and records the
number of counts per second as the intensity.
These instructions assume that you have previously completed the Single Crystal X-Ray
Crystallography project on the ylid data. These instructions highlight the changes necessary to
solve the structure of a molecule that exhibits a high symmetry. In KMnO4 only the coordinates
for three of the O atoms are defined in the unit cell. The coordinates for the fourth O are
determined from the crystal symmetry. This issue doesnt arise in the less symmetrical ylid
structure.
Use the Single Crystal X-ray Crystallography instructions to work through the integration,
unit cell refinement, and structure solutions phases. The file names and expected space group
parameters are given below.
Data directory: Ko4mn
Unit cell: orthorhombic P

Initial P4P file: Kmn01.P4P

Formula KO4Mn

First data file: kmn01.001

Space Group: Pnma

The differences between the ylid structure procedue and the KMnO4 procedure begin in the
structure refinement in XShell. These differences are discussed below. After completing the XS
structure solution, open the XShell structure refinement program.
XShell Instruction Changes
Orient the molecule by dragging with the left mouse button. The Mn-O distances should be
around 1.6 0.2 . Check the approximate bond lengths to the Mn. The XS program does an
excellent job of finding the optimal structure solution and atom assignments. Record the distance
between the K+ ion and the nearest O-atom. Sketch the orientation of the K+ ion relative to the
closest MnO bond, in case you need to locate this K+ ion later on. To save time, we will accept
the automatic atom assignments. We next need to add the symmetry related fourth O-atom.
Delete the bonds that are drawn to the K+ ion. To do this: move the cursor over a bond that is
drawn to the K+ ion. Click right and choose Delete. Remove any additional bonds to the K+ ion.
We can temporarily remove the K from the display by moving the cursor over the Mn atom (or
one of the O atoms) clicking right and choosing Hide. The K+ ion should be temporarily
removed from the screen. Now pull down the Atoms menu and choose Grow. The symmetry
related O atom should now be added. The results should be a tetrahedral arrangement of O atoms
around the Mn. Symmetry related K+ ions will also be added. The proper K+ position should lay
in one of the OMnO planes and bisect the OMnO angle. Delete the newly added symmetry
related K+ ions, leaving just one K+ ion.
Final Refinement: All atoms have now been located and labeled. So you can now refine all
atomic parameters, including the anisotropic atomic displacement (or temperature) parameters.
Click on the Refine icon. The temperature factors are a measure of how much the atom moves as
the molecule vibrates. This process generates thermal ellipsoids that show graphically the
extent of the motion of the atom. The bigger the thermal ellipsoid the greater the motion.
Therefore, this time make sure to set the Refine All Non-H atoms Anisotropically, Use

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Suggested Weights, and Generate ACTA[CIF] information file checkboxes. You can also set the
Number of Residual (Q) Peaks to a smaller number, since all atoms should now be located. The
extinction parameter applies corrections that depend on the shape of the crystal (e.g. needle, flat
plate, or cube). Check the Refine extinction parameter checkbox and enter a value of 0.0001, so
that this parameter will be optimized (This crystal was a needle).

The final R1 value should now be much smaller than before. You should be able to get a value
less than 0.05. Click right on the background and choose Thermal Ellipsoid. If any of the thermal
ellipsoids are unusually small or large, you may have assigned the atom type incorrectly.
To see the final structure we need to add back the symmetry related fourth O atom in the
following way. Delete any bonds to the K+ if any remain. Hide the K+ ion. Click right on the blue
screen and choose Grow. Delete any added symmetry related K+ ions, leaving just one, as you
did before. Delete any bonds to the remaining K+. Measure and record the Mn-O distances.
Switch to Thermal Ellipsoids by clicking right on the black background and choosing the desired
mode. Check the sizes of the ellipsoids. Switch back to wireframe before proceeding. Remove
the atom labels by clicking on the blue screen and choosing Labels. Report the average MnO
bond length.
To see how the molecule packs into the unit cell, pull down the Atoms menu and choose Pack.
To see the four molecules that constitute the unit cell, use the default X: 0 to 1, Y: 0 to 1, and Z:
0 to 1 setting. To return to a single molecule, pull down the Atoms menu and choose Trim. To
see several complete unit cells, pull down the Atoms menu and choose Pack again. This time
choose X: 0 to 2.0, Y: 0 to 2.0, and Z: 0 to 2.0
Literature Cited
1. Much of this writeup is taken from Patrick E. Hoggard, X-Ray Crystallography, Chem 6H Lab
Santa Clara University.
2. Some parts of the XSHELL section are taken from "XSHELL User Guide: Tutorial," Bruker
AXS, Bellerica, MA.
3. G. J. Palenik, "Structure of Potassium Permanganate," Inorg. Chem., 1967, 6(3), 503-7.