Should we remediate small molecule structures? If so, who should do it?

摘要

Problems can arise in crystallographic databases with errors and omissions in the representation of data that impede searches, and with errors in the actual data. While the Cambridge Crystallographic Data Centre with its Improvement Projects has solved many of the first category of problems, errors in atomic coordinates and other crystallographic data are surprisingly common. Although modern software warns of many types of error, such errors appear even in recently deposited Crystallographic Information Files. Richard Marsh found many examples of missed symmetry in assignment of the space group; such errors are now waning. Hydrogen atoms are commonly placed in calculated positions. Particularly for OH and NH groups involved in hydrogen bonds, occupancy factors may need to be reduced to 0.5 or the hydrogen atom positions may require amendment. Examples of acids and imidazole derivatives are provided, showing that sometimes only consideration of bond distances and angles at the heteroatom can distinguish between OH or NH and unprotonated O or N. Significant work by other researchers correcting mis-positioned hydrogen atoms in dihydrogen phosphates and water aggregates as well as mis-identified elements is also summarized. This review concludes with some suggestions for more comprehensive detection and correction of errors in deposited data.