Some Experimental Aspects of Absolute Configuration Determination using Single Crystal X-​Ray Diffraction

Nov 012017
 

Tetrahedron Asymmetry 2017, 28(10), 1330-1336 [doi:10.1016/j.tetasy.2017.08.016]

Students of single crystal X-​ray diffraction are often give advice as to how best to collect their data when attempting absolute configuration determination.  These ‘rules’ often have more grounding in gut-​feeling than evidence.  Thus, in an effort to provide advice and evidence that today’s crystallographers can pass onto to tomorrow’s young scientists, we present a systematic study of 1-​deoxy-​L-​arabinitol, a straight chain sugar which crystallizes well in the space group I41.

 

Arabinitol

HUG and SQUEEZE: using CRYSTALS to incorporate resonant-scattering in the SQUEEZE structure factor contributions to determine absolute structure

Oct 232017
 

Acta Crystallographica, 2017, C73, 845–853. [ doi:10.1107/S2053229617013304 ]

Using an approximate correction to the X-ray scattering from disordered, resonantly scattering regions of crystal structures we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refi nement or other post-re finement determination methods.

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

Sep 192016
 

Acta. Cryst. (2016) B72 661-683 (Feature Article) [ doi:10.1107/S2052520616012890 ]

surfaceDirect 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.

Publisher’s copy

Absolute structure determination using CRYSTALS

Mar 072016
 

Acta. Cryst. (2016) C72, 261-267 [ doi:10.1107/S2053229616003570 ]

snipA 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].

Publisher’s copy

CRYSTALS Enhancements: Absolute Structure Determination

Sep 132011
 

J. Appl. Cryst.  (2011), 44, 1017-1022.    [ doi:10.1107/S0021889811034066 ]

A summary of the features for investigating absolute structure available in the crystallographic refinement program CRYSTALS is presented, together with the results of analyses of 150 light-atom structures collected with molybdenum radiation carried out with these tools. The results confirm that the Flack and Hooft parameters are strongly indicative, even when the standard uncertainties are large compared to the thresholds recommended by Flack & Bernardinelli [J. Appl. Cryst. (2000), 33, 1143–1148].

Electronic reprints

  • Oxford University Research Archive [direct pdf]

Publisher’s copy

Practical Applications of Averages and Differences of Friedel Opposites

Dec 072010
 

Acta Cryst. (2011), A67, 21-34.    [ doi:10.1107/S010876731004287X ]

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

Electronic reprints

Publisher’s copy

ACA Annual Meeting 2010

Jul 292010
 

The ACA was held at the Sheraton Hotel in Chicago, IL.  Contributions from Chem. Cryst. include:

James Haestier, Amber L. Thompson, David J. Watkin, George C. Feast, Jeremy Robertson & Lee Page
Why is P21/n a Standard Non-Standard Space Group? (Poster)

Amber L. Thompson & David J. Watkin
Unpublishable” Data:  Does My R-factor Look Big in This? (Poster)

Amber L. Thompson
Absolute Structure Determination – Interpreting the Flack Parameter  (Presentation)

ECM 25

Aug 212009
 

The 25th European Crystallographic Meeting was held in the Harbiye Museum and Cultural Centre in the beautiful city of Istanbul.  It was a very eventful week, and contributions to the conference made by Chem. Cryst. include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
A Further Improved Structure Matching Algorithm (Poster)

James Haestier
Handling of Cell Errors and their Effect on Derived Parameters (Poster)

Mustapha Sadki
New Modelling for Disordered Atoms in Free-form Based Hybrid Refinement and Visual Representation (Poster)

Mustapha Sadki
The Application of Novel Modelling and Refinement Strategies to Crystallography (Presentation)

Amber L. Thompson & David J. Watkin
Absolute Configuration Determination – Is there More Information in the Data? (Poster)

David J. Watkin, Richard I. Cooper & Amber L. Thompson
CRYSTALS:  Refinement and Validation Tools (Poster)

David Watkin
The Future of Small Molecule Software (Session Chair)

X-ray Crystallography and Chirality: Understanding the Limitations

May 072009
 

Tet. Asym. (2009), 20, 712-717.    [ doi:10.1016/j.tetasy.2009.02.025 ]

Advances in hardware and software have made X-ray crystallography even more attractive as the first-option method for structure analysis. For most organic materials containing up to 100 non-hydrogen atoms, getting from the initial visual examination of the sample to producing publication-ready tables and pictures should usually be achievable in a single morning. Improvements in hardware have also increased reliability of the determination of absolute configuration. A recently published new algorithm may extend the range of applicability of the method.

Le Coup de Roi

Le Coup de Roi: making two chiral pieces from an achiral whole

The Absolute Configuration of 1-Epialexine Hemihydrate

Dec 152008
 

Acta Cryst. (2008), C64, o649-o652.    [ doi:10.1107/S0108270108037086 ]

The absolute and relative configurations of 1-epialexine are established by X-ray crystallographic analysis, giving (1S,2R,3R,7S,7aS)-1,2,7-trihydroxy-3-(hydroxymethyl)pyrrolizidine. The compound crystallizes as the hemihydrate C8H15NO4·0.5H2O, with hydrogen bonds holding the water molecule in a hydrophilic pocket between epialexine bilayers. In addition, a comparison was made between results obtained from examination of the Bijvoet pairs from data sets collected using molybdenum and copper radiation.