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How to ensure, that X-ray crystallography structure analysis was done right to provide correct, non-mirrored atomic coordinates?


Example: Following Wikipedia image,

enter image description here

is generated from data taken from the article Redetermination of (+)-methamphetamine hydro­chloride at 90 K.

However, the structure presented by the CIF file represents (R)-methamphetamine, known to be levomethamphetamine, (–)-methamphetamine,

Fig.2 (R)-methamphetamine

the enantiomer of “native” methamphetamine, dextromethamphetamine, (+)-methamphetamine, identified as (S)-methamphetamine.

Fig.2 (S)-methamphetamine

Also, the article does not claim that the absolute configuration of (dextro)methamphetamine has been for so long mistaken and that they come with revolutionary discovery, rather are just focusing on some inter-atomic distances. (Also the “traditional absolute configuration” has been verified e.g. by synthesis from D-phenylalanine.)


As far as I have known, X-ray structure analysis was unable to provide absolute configuration info. But technology evolves. Can one determine from the experimental data, that it's supposed to be “absolute” or “relative” only (so that the coordinates presented can be mirrored)?

UPDATE: After some comments, I should emphasize that the example is just for an example (of case where the reported coordinates seem to be mirrored; I don’t know how rare or common it is), but can be used as an example in the answer as well, of course (e.g. CIF file analysis, e.g. explaining the Flack parameter value meaning, …)

And a subquestion: When hydrogen positions are provided, does it imply that the configuration is absolute? (I presume that the coordinates can still be mirrored even in such case; I mean “uncertain z-coordinate orientation”.)

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    $\begingroup$ X-ray does provide absolute configuration info. It is just that with Mo radiation and light-atom structure it won't be reliable enough. $\endgroup$ – Ivan Neretin Nov 12 '18 at 13:23
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    $\begingroup$ As Ivan Neretin comments x-ray diffraction is the definitive method to obtain structure. However, x-rays are scattered off the electrons in an atom and this makes it very difficult to detect H atoms, and hence your question. Neutron diffraction could be used instead. $\endgroup$ – porphyrin Nov 13 '18 at 8:38
  • $\begingroup$ @porphyrin Hydrogen positions are irrelevant to the configuration determination, as the other substituents are carbon and nitrogen based. (Also in the formula there are no hydrogens, yet it’s stereochemically unambiguous ;) ) $\endgroup$ – mykhal Nov 13 '18 at 8:42
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    $\begingroup$ Ah yes, I mis-read the last two line structures. In that case as long as you have pure crystalline substances x-ray diffraction should be the technique to use. $\endgroup$ – porphyrin Nov 13 '18 at 13:59
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    $\begingroup$ In the linked crystal structure all atom positions (including hydrogen) have been refined, there is no doubt that the measured compound is (R)-N-methyl-1-phenylpropan-2-amine.What they were sold for measuring the compound is another question; "The material for this work was purchased from Sigma-Aldrich and was used without any further purification." They did not specify they how they assigned (+), so I'd guess that was on the label. I don't really understand what the question is; obviously you cannot ensure that the people did their jobs right without checking the raw data. $\endgroup$ – Martin - マーチン Nov 14 '18 at 14:18

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