Compound 9854 (Whole Molecule Disorder)

When the model is refined isotropically (click “Iso1”), Molecule 1 has thermal parameters that are all smaller than those for Molecule 2. Generally, all the thermal parameters in the molecule should be similar because all the atoms are in similar chemical environments and should have similar thermal vibrations. These smaller thermal parameters indicate that the atoms have more electron densities than they have been assigned - the thermal motion is artificially decreased in order to concentrate the electron density. To correct this, the occupancies of the atoms in Molecule 1 should be increased and the occupancies of the atoms in Molecule 2 should be decreased. These adjustments lead to similar thermal parameters for the two molecules (click “Iso2”). In this case, Molecule 1 has occupancies of 0.62 and Molecule 2 has occupancies of 0.38.


The results of the final refinement (after converting to anisotropic thermal parameters and adding hydrogens) can be seen by clicking “Final”.
There are two other views of the disordered molecules (“Molecule 1” and “Molecule 2”) plus a red/blue representation.


In order to investigate why this molecule might be disordered, it is instructive to represent Molecule 1 with van der Waal's radii (click “VDW”). It is this “space filling” aspect of the structure that determines how molecules will pack in the unit cell. It is not difficult to convince oneself that there is little difference between, e.g., the “left side” and the “right side” of the molecule. A look at the unit cell packing seems to substantiate this point (click “Cell”; the Cl is colored yellow to distinguish the asymmetric unit from the surrounding molecules). Click “Cell+Mol2” to display the packing diagram with one Molecule 2 substituted for Molecule 1.


When asymmetric unit 1 is displayed, the Me₂N group is on the right; when asymmetric unit 2 is displayed, the Me₂N group is on the left. Molecule 2 “fits” as well as Molecule 1.