Absolute Structure

Absolute structure determination

Latest news

  • May 2013: Simon Parsons, Howard Flack and Trixie Wagner have published a paper (Acta Cryst. B69, 249-259) that refines a number of structures on Bijvoet differences and on similarly purposed quotients. This procedure can take care of the suspected correlations between the absolute structure and other structural parameters. One of their conclusions is that no difference can be seen: post-refinement determination of absolute structure using Gaussian error distributions in PLATON or CRYSTALS is equally good as their full-matrix refinements.
  • March 2011: A screencast was made to show how to use PLATON to determine the absolute structure using our method.
  • March 2011: We have found a mistake in a formula in our 2009 paper on using the t-distribution in probability plots. See: Erratum
  • February 2011: Our method is now implemented and automatically run in OLEX2
  • August 2010: Our paper entitled Using the t-distribution to improve the absolute structure assignment with likelihood calculations is published as Journal of Applied Crystallography, 2010, Volume 43, pages 665-668.


Since J.M. Bijvoet discovered that X-ray crystallography could be used to determine the absolute structure of molecules, this technique has been refined many times.

Our quest for absolute structures of C/H/N/O crystals

This site concentrates on the discussion about a method described by Rob Hooft, Leo Straver and Anthony Spek that has been published in the Journal of Applied Crystallography in February 2008: J. Appl. Cryst. (2008). 41, 96-103 (pdf). This method gives a more reliable calculation of the absolute structure than other existing methods. Imagine: you can finally determine the absolute structure for a structure containing no atoms heavier than oxygen. Without resorting to exceptional data collection techniques. It is easy with CuKa, but in good cases it can be done even using a MoKa data set.

You do not only get a qualitative assignment of the absolute structure, but also a quantitative estimate of the reliability of that assignment. The paper uses a combination of maximum likelihood estimation and Bayesian statistics to calculate:

  • A value y, comparable to the value of the Flack x parameter, with its standard deviation. This does not assume any prior knowledge about the compound.
  • A pair of values P2(right) and P2(wrong) expressing the likelihood that the given absolute structure is right or wrong, assuming the prior knowledge that the compound is enantiopure.
  • A triplet of values P3(right), P3(twin) and P3(wrong) expressing the likelihood that the given absolute structure is right, that the crystal is a 50%/50% inversion twin, or that the absolute structure should be inverted. This assumes the prior knowledge that the crystal can not be an inversion twin with another ratio.
The method has been implemented at least in PLATON, in OLEX2, and in CRYSTALS

Further reading

Questions or suggestions

If you have any questions on the method or its application, or any suggestion regarding the content of these web pages, feel free to contact us via E-mail.