Disorder in the para substituents, and disorder in the halides
SUMP
Me
to tie three p-Cl to 2 site occupancy, along with distance restraints.
Ph Cl Sn O P Ph
1
Disorder of 15-crown-5: an odd number of atoms packing in a over a center-of-inversion
O O O O O
1 2 3
Use a ‘PART –1’ command to suppress the calculation of bonds/angles. Assign ½ occupancies to all atoms. DFIX C–C = 1.50, C–O = 1.41, C…O = C…C = 2.37 Å.
The vibration of some atoms 2 - 3 times those of other atoms
of the same molecular fragment.
Peaks in the difference map that are too close to existing
OH O O O O H O O O HO O
H constrained by symmetry (C2/c, Z = 4) O…H = 1.25 Å
H N N H
H restrained by DFIX (P21/c, Z = 4) O–H = 0.85 Å
OH O O
O
O
H
O O O HO
O
H N N H
Because total charge is 8, there are should be 1 Cu(II) and 2 Fe(III) for the 3 sites. Refine each site as ⅓Cu⅔Fe.
THF
F 3C O O O
CF3
O
THF M M O O

Or, use SUMP to tie the 3 Cu atoms to unit occupancy (0.73, 0.15, 0.12). The 0.12 occupancy M atom is coordinated by water.
F
F
F
F
O O Sn O
O
Sn
A phenylene ring disordered along the C1–C4 axis
O O O O O O
As the anion lies on a center-of-inversion, ‘AFIX 66’ cannot be used. DFIX pairs of distances, and FLAT some atoms.
and 4,5 carbon atoms.
Asymmetric unit has 2 aromatic and 1 carboxyl carbon atoms, and 1 oxygen atom only. High R, which is an artifact of the disorder and not because the data are bad.
Point group 2
Point group mmm
Twinning Case 2: Monoclinic with nearly equal a(12.479 Å) and c- (12.597 Å) axes
Look for water near the ion.
Disorder over a center-ofinversion
O O O O O O O O O O
Use a ‘PART –1’ command to suppress symmetry. 2 Refine the ring with ‘AFIX 66’. 3 Some atoms to have full and other half occupancy.
Which SHELX commands to use depend on the disorder. And it is very messy to treat disorder.
The energy barrier to rotation of CO2CH2CH3 radical is of the order of kT – there is nothing you can do about the data.
separated by more than 0.5 Å. Pyridyl rings can also be fitted as hexagons.
‘AFIX 66’ for phenyl rings
Can be used for noncentric space groups because there are fewer reflections, or if there is a spread of C—C distances.
Twinning Case 1: Monoclinic emulating orthorhombic Br = 90.05(1)° Im Im
Im Cu Im
TWIN 1 0 0 0 -1 0 0 0 -1 BASF 0.47 The diffraction pattern emulates orthorhombic but is not because the intensities cannot be averaged in orthorhombic (Rint is large).
Disorder in a cyclopentyl ring
DFIX the C—C to 1.50 Å and the C…C…C distance to 2.45 Å so that the angle is 109.5°.
M
Perchlorate ions are usually disordered: any molecular fragment that is spherical will be disordered.
HO H CH3
O
O
Disorder in the heavy atom only
Ag is 3-coordinate in major component and 4-coordinate in minor component in centric structure. Complicated as two N atoms are disordered with two C–H units. The correctly refined structure should not have any Ag…H interactions.
O O
respect to the C6H6 ring.
Sn
The entire anion is disordered but the [Ph2P(CH2)3PPh2]2Ag cation is ordered.
O
O
F
F F
Refinement of more than two atoms sharing the same site: The SUMP command
Some Strategies for the Refinement of Disordered Crystal Structures
Ng Seik Weng
Department of Chemistry University of Malaya Kuala Lumpur Malaysia
The assumption of perfect periodicity is a basic assumption of crytallography. However, real crystals are not perfect.
atoms to form plausible bonds.
Atoms that are too close to symmetry elements in the space
group to produce chemically-reasonable bonding.
Anyway, the data are mothballed because the structures cannot be published.
Br
A simple idea of twinning
A brick with top and bottom indentations, embossed with ‘London Brick’ on the top only.
Turning brick upside down uses an operation of mmm.
H N H O N H O
H N H O N H O
Disorder in four-atom, pyramidal fragments, e.g., CHCl3 and CH3CH(OH)CO2
H C Cl Cl Cl
The methine –CH fragments are above and below the carboxyl plane.
Disorder imposed by mm2 symmetry
DMF =
H
N O
N
H
O
Disorder imposed by mm2 symmetry
O O O O
Mirror plane passing through ring. Mirror plane perpendicular to ring. Rotation axis through the mid-points of the 1,2