A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model

Abstract

This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis(diphenylphosphanyl)ethylene, namely, 1,2-(ethene-1,2-diyl)bis(diphenylphoshpine sulfide/selenide), C26H22P2S1.13Se0.87. A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between Fobs2 and Fcalc2, plots of |Fobs| vs |Fcalc|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of interatomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures.

Keywords

• checkcif alerts
• f2obs vs f2calc
• omit command
• outliers
• displacement ellipsoids
• solid solution
• disordered electron density
• standard interatomic distances
• crystal structure