Crystallographic disorder

Crystallographic disorder is variation in atomic positions, orientations or chemical occupation that is represented by an average crystal structure rather than one perfectly repeated local arrangement. A split-site disorder model can describe alternative positions with fractional crystallographic site occupancies. The IUCr disorder-group convention distinguishes atoms present together in one configuration from mutually alternative configurations.^[ref]

For an original single-atom model, suppose an atom occupies position0 along an axis with probability0.6 and position $d$ with probability0.4. ThenAt $d=1\mathring{\mathrm{A}}$, the mean is $0.4\mathring{\mathrm{A}}$ and the variance is $0.24{\mathring{\mathrm{A}}}^2$. There need be no atom at the mean position in any individual configuration. Fitting only an average position with a large atomic displacement parameter can conceal this distinction.

The same average occupation could arise from different unit cells adopting different configurations, from motion among configurations during measurement, or from a mixture of these effects. A static average alone does not determine an interchange rate.

Experimental interpretation therefore combines the electron density map, the allowed chemical geometry, occupation constraints and other evidence. Weak or broadened density should not automatically be assigned one specific dynamic mechanism.

A split-site disorder model represents alternative atomic positions explicitly within an average crystal structure. Each alternative has its own coordinate and crystallographic site occupancy. For one atom distributed between exactly two alternatives, with no vacancy, the occupancies sum to1. Correlated alternative arrangements can be collected into disorder groups: atoms within one group occur together, while different groups in the same assembly represent alternatives.^[ref]

For an original scattering example, put the alternatives at fractional coordinates $(0,0,0)$ and $(1/2,0,0)$ with occupancies0.7 and0.3. Give both the same real atomic scattering amplitude $f$, and omit all other atoms and displacement attenuation. The coherent average contribution to a reflection $(h00)$ isFor an even integer $h$, this equals $f$; for an odd integer $h$, it equals $0.4f$. The corresponding squared amplitudes are $f^2$ and $0.16f^2$. Treating both alternatives as fully occupied would predict a different structure factor. This calculation concerns the periodic average contribution, not a complete description of diffuse scattering from local fluctuations.

A split-site disorder model is useful when an electron density map supports distinct alternative locations instead of one broad peak. An anisotropic atomic displacement parameter can describe directional broadening, but does not by itself encode two mutually exclusive chemical arrangements.

Occupancy constraints depend on the physical model: alternatives for a fully present atom sum to1, whereas a model admitting vacancies need not. An average crystal structure alone also cannot establish whether the alternatives exchange during the measurement, occur in different cells, or have particular local correlations.