Absolute structure determination: pushing the limits.

Abstract

It was the Softenon disaster (see Wikipedia) that made the pharmaceutical industry fully aware of the importance of knowing the enantiomeric purity and chirality of drugs and their metabolites. This disaster involved the chiral drug Thalidomide (Fig. 1) that was sold in the 1950s as a racemate under various brand names such as Contergan and Softenon. It was shown in the early 1960s that only the R-enantiomer has the intended pharmaceutical effect and that the S-enantiomer, when the drug is used by pregnant females, may lead to serious miscarriages. Until the 1950s, the chirality of a compound could only be determined by chemical methods relative to the arbitrarily chosen ‘absolute configuration’ of (+)-R-glyceraldehyde (the Fischer–Rosanoff Convention). For a long time it was thought that X-rays could not be used to distinguish between enantiomeric structures (Friedel’s law). It was J. M. Bijvoet’s organic chemistry colleague, F. Kogl, working on the isolation of natural products and on a chirality-related cancer theory, who inspired Bijvoet to reinvestigate the possibility to directly determine the chirality of molecules such as natural and unnatural amino acids with X-ray diffraction techniques without reference to glyceraldehyde. Inspiration for the latter was gleaned from the largely forgotten paper by Coster et al. (1930) on the association of the two macroscopically distinguishable crystal 111 faces with the microscopic Zn and S layers in crystals of the inorganic compound zinc blende, ZnS, using X-ray techniques. Bijvoet realised that Friedel’s law did not apply when resonant scattering (anomalous dispersion) was taken into account. Not only the stacking polarity in crystals but also the chirality of molecules could be determined using X-ray techniques. The current notion of ‘absolute structure’ covers both polarity and chirality determination. The first absolute structure determination of an organic compound, as proof of the principle, was carried out for sodium rubidium (+)-tartrate in 1950 (Bijvoet et al., 1951). This assignment was based on careful measurement of the difference in intensity of Friedel pairs (i.e. hkl and h k l) of reflections. This was a significant experimental feat at that time in view of the long exposure time required for taking the Weissenberg diffraction images (over 200 h), hampered by unstable X-ray sources. The sign of the difference in intensity of a small number of Friedel pairs showing a large observed intensity difference was compared with the associated sign of the intensity difference calculated from the structure model. A Zr K X-ray source along with Rb as the heavy atom was chosen for a maximum anomalous difference signal. By pure chance, the determined absolute structure turned out to be consistent with the arbitrary choice made by Fischer & Rosanoff, which was good for science (avoiding confusion) but obviously with less impact in showing the power of the X-ray technique than when it would have been otherwise. Half a century later the absolute structure assignment to sodium rubidium (+)-tartrate was reaffirmed using state-of-the-art techniques (Lutz & Schreurs, 2008). With the advancement of the diffraction and computer hardware and the inclusion of anomalous dispersion contributions into the structure refinement software, it became customary to refine both enantiomeric models of a determined structure and keep the one with the lowest R-value as that representing the true absolute structure. Probability tests (e.g. the Hamilton test) to determine the validity of the chosen absolute structure were often problematic; neither were the possibilities of an enantiomerically impure sample or of a racemic mixture addressed. This situation was finally resolved with the introduction of the Flack parameter (Flack, 1983) that is based on the physically meaningful inversion twinning model defined in the range 0.0–1.0, where the limiting ISSN 2052-5206