Absolute-structure reports

Chirality determination in crystals

This tutorial review article discusses chirality determination in the solid state, both in single crystals and in crystal assemblies, with an emphasis on X-ray diffraction. The main principles of using X-ray diffraction to reliably determine absolute structure are summarized, and the complexity which can be encountered in chiral structures-kryptoracemates, scalemates, and inversion twinning-is illustrated with examples from our laboratories and the literature. We then address the problem of the bulk crystallization and discuss different techniques to determine chirality in a large assembly of crystal structures, with a special prominence given to an X-ray natural circular dichroism mapping technique that we recently reported.

Howard Flack and the Flack Parameter

The Flack Parameter is now almost universally reported for all chiral materials characterized by X-ray crystallography. Its elegant simplicity was an inspired development by Howard Flack, and although the original algorithm for its computation has been strengthened by other workers, it remains an essential outcome for any crystallographic structure determination. As with any one-parameter metric, it needs to be interpreted in the context of its standard uncertainty.

The Publications of Howard Flack (1943–2017)

Howard Flack was a driving force in the development of modern crystallography. Today “the Flack parameter” has entered into the common parlance of crystallography but his influence was far wider. This article provides an overview of his scientific output and a full bibliography.

Why direct and post-refinement determinations of absolute structure may give different results

Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.

Absolute structure determination using CRYSTALS

A study of post-refinement absolute structure determination using previously published data was carried out using the CRYSTALS software package. We show that absolute structure determination may be carried out optimally using the analyses available in CRYSTALS, and that it is not necessary to have the separate procedures absolute structure determination and no interest in absolute structure as proposed by Flack [Chimia (2014), 68, 26-30].

Absolute Configuration and Polymorphism of 2-Phenylbutyramide and α-Methyl-α-phenylsuccinimide

Crystal structures of racemic and homochiral forms of 2-phenylbutyramide (1) and 3-methyl-3-phenylpyrrolidine-2,5-dione (2) were investigated in detail by a single crystal X-ray diffraction study. Absolute configurations of the homochiral forms of 1 and 2, obtained by chromatographic separation of racemates, were determined. It was revealed that racemate and homochiral forms of 1 are very similar in terms of supramolecular organization (H-bonded ribbons) in crystal, infrared (IR) spectral characteristics, and melting points. The presence of two different molecular conformations in homochiral forms of 1 allowed mimicking of crystal packing of the H-bonded ribbons in racemate 1. Two polymorph modifications (monoclinic and orthorhombic) comprising very similar H-bonded zigzag-like chains were found for the homochiral forms of compound 2 that were significantly different in terms of crystal structure, IR spectra, and melting points from the racemic form of 2. Unlike compound 1, homochiral forms of compound 2 have a higher density than the corresponding racemate which contradicts the Wallach rule and indicates that, in this case, homochiral forms are more stable than racemate forms.

Absolute configuration of naturally occurring glabridin

The title compound {systematic name: 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol, commonly named glabridin}, C20H20O4, is a species-specific biomarker from the roots Glycyrrhiza glabra L. (European licorice, Fabaceae). In the present study, this prenylated isoflavan has been purified from an enriched CHCl3 fraction of the extract of the root, using three steps of medium-pressure liquid chromatography (MPLC) by employing HW-40F, Sephadex LH-20 and LiChroCN as adsorbents. Pure glabridin was crystallized from an MeOH-H2O mixture (95:5 v/v) to yield colorless crystals containing one molecule per asymmetric unit (Z' = 1) in the space group P212121. Although the crystal structure has been reported before, the determination of the absolute configuration remained uncertain. Stereochemical analysis, including circular dichroism, NMR data and an X-ray diffraction data set with Bijvoet differences, confirms that glabridin, purified from its natural source, is found only in a C3 R configuration. These results can therefore be used as a reference for the assignment of the configuration and enantiopurity of any isolated or synthetic glabridin sample.

TiGePt--a study of Friedel differences

The X-ray single-crystal diffraction intensities of the intermetallic compound TiGePt were analysed. These showed beyond doubt that the crystal structure is non-centrosymmetric. The analysis revolves around the resonant-scattering contribution to differences in intensity between Friedel opposites hkl and \bar h\bar k\bar l. The following techniques were used: R(merge) factors on the average (A) and difference (D) of Friedel opposites; statistical estimates of the resonant-scattering contribution to Friedel opposites; plots of 2A(obs) against 2A(model) and of D(obs) against D(model); the antisymmetric D-Patterson function. Moreover it was possible to show that a non-standard atomic model was unnecessary to describe TiGePt. Two data sets are compared. That measured with Ag Kα radiation at 295 K to a resolution of 1.25 Å(-1) is less conclusive than the one measured with Mo Kα radiation at 100 K to the lower resolution of 0.93 Å(-1). This result is probably due to the fact that the resonant scattering of Pt is larger for Mo Kα than for AgKα radiation.