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Re: Absolute structure

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: Absolute structure
  • From: Howard Flack <Howard.Flack@cryst.unige.ch>
  • Date: Wed, 14 Jan 1998 10:31:51 GMT
David Brown wrote:
> preparation.  I would therefore like to add to Howard's definition,
> presumably at the end of the first paragraph, the following:
>         'For non-molecular crystals it is recommended that the absolute
> configuration determined by diffraction methods be related to some other
> physical property, such as morphology, that can be used to distinguish
> between crystals of opposite chirality.'

I wish to make comments at two levels:  
  (i) general for coredmg and 
  (ii) technical concerning absolute structure and absolute
configuration. Before I do so I wish to make it clear that I agree with
the spirit of David's new paragraph recommending physical measurements
in conjunction with absolute structure or absolute configuration
determination. Indeed the provision of the CIF data name
chemical_optical_rotation was a small step in this direction.

 (i) The general comment for coredmg has been posted as a separate text
under the thread "Modus operandi of .....". In a few words, I do not
think that coredmg should be issuing recommendations of this sort even
if they are justifiable or perhaps justified.

 (ii) Molecular crystals as well can show the property that David
ascribes to non-molecular crystals i.e. be in a space group without
improper symmetry operations and from diffraction measurements give a
clear indication of the enantiomorph. The most common case occurs where
the chirality of the molecule (in the crystal) is due to a conformation
(loosely speaking there are no 'asymmetric carbon atoms') for which the
energy barrier between the two enantiomeric conformations is low. In
this case the rate of racemisation in solution is very high leading to
an optical rotation of zero. It is probably strictly incorrect to speak
of spontaneous resolution in a case such as this since one will not
obtain an enantiomerically pure compound by selecting a set crystals of
the same enantiomorph and then dissolving them in solution. There are
also other cases where the asymmetric unit of a space group containing
only pure rotation operations consists of two achiral molecules placed
in a chiral arrangement.

  It is questionable as well whether the term 'absolute configuration'
should be applied to non-molecular crystals such as SiO2, quartz, (the
classic case). Certainly it does not seem to be encompassed by the
definition that I quoted in the text of _chemical_absolute_configuration
unless one is prepared to accept that the 'molecule' of (SiO2)n in
question is the whole crystal and that the measurement of optical
rotation applies to the solid state and not to solution. Glazer and
Stadnicka [Acta Cryst. (1989). A45, 234-238] in an article called "On
the Use of the Term 'Absolute' in Crystallography" have produced a whole
set of terms to try and describe the different cases that apply really
in crystal physics rather than in crystallography. They also have a list
of 'chiral' directions. Whilst in agreement with them on the
desirability of physical measurements in relation to absolute structure
determination, I find their choice of terms widely open to criticism.
Moreover I now think that their terms concern a rather small user base
of crystal physicists and that there is no real advantage in having so
many terms for so few people. They just need to describe exactly what
they have done in each particular experiment. On the other hand the term
'absolute configuration' is widely used by chemists and appears often in
journals such as Acta Cryst. C. The definition I quoted is from a book
by chemists and should thus correspond to what they need and what they
are supposed to be doing. 

 In my recent reading of all the papers in Acta C (1996), certainly
there are cases of the type described by David. But there are more where
an absolute configuration is claimed to have been determined but where
the compound name does not contain the preliminary sign + or -, and the
absolute configuration has not indicated in Cahn, Ingold, Prelog
notation. As with David's recommendation, one has to admit that there is
a problem but I do not think it falls within the mandate of coredmg to
make recommendations for its resolution.

D> between crystals of opposite chirality.
  should correctly be replaced by
    between enantiomorphs.
  I'll explain why if you really want to know.


Howard Flack        http://www.unige.ch/crystal/ahdf/Howard.Flack.html
Laboratoire de Cristallographie               Phone:(+41 22) 702 62 49
24 quai Ernest-Ansermet             mailto:Howard.Flack@cryst.unige.ch
CH-1211 Geneva 4, Switzerland                   Fax:(+41 22) 781 21 92

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