Structure validation in chemical crystallography

Abstract

Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

Figure 1

The asymmetric unit of a structure that was originally reported in the orthorhombic space group Pbca. The molecular threefold axis is obvious from this projection. The real space group, Pa , has the molecular threefold axis coinciding with a crystallographic threefold axis.

Figure 2

(a) Displacement-ellipsoid illustration for a praseodymium complex that was wrongly refined with Z′ = 2 in space group P1. Note that the largest components of the ellipsoids of ‘inversion’-related atom pairs are perpendicular. (b) Displacement-ellipsoid illustration of the same complex refined with Z′ = 1 in space group P . Note in (a) the inversion centre in the centre of the figure that relates the two molecules.

Figure 3

The reported structure with missing H atoms. Atoms C4 and C5 are clearly out of the plane of the five-membered ring and suggest sp ³ hybridization. In fact, H atoms need to be added at atoms C4 and C5.

Figure 4

Example of a misoriented hydroxyl moiety with no hydrogen-bond contacts. (a) Isolated molecule. The H atom on atom O1 is incorrectly positioned. (b) The original hydrogen-bond network with the ‘zombie’ H atom. (c) The correct hydrogen-bond network.

Figure 5

A misinterpreted and retracted structure that turned out to be that of the mineral borax. The atoms labelled N should be oxygen and those marked C should be boron. Figure taken from Fang et al. (2008 ▶).

Figure 6

Erroneous network structure with a charge-balance problem. The displacement ellipsoid of N atom N1 is relatively large. The nitrate anion was reinterpreted as a carbonate anion.

Figure 7

Example of a P structure at 120 K that has approximate C2/m space-group symmetry with the molecule on a mirror plane.