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Stereochemistry

  • To: Chemical information in core CIF <corecifchem@iucr.org>
  • Subject: Stereochemistry
  • From: Peter Murray-Rust <pm286@cam.ac.uk>
  • Date: Thu, 23 Dec 2004 12:46:25 +0000
At 14:49 22/12/2004 -0500, David Brown wrote:
>Thank you Peter and Howard.  I will work through your suggestions as I 
>recover for ODing on turkey and other holiday fare, but at first glance it 
>seems that we should be able to make big strides in the next round.
>I am beginning to realize that I know nothing about stereochemistry.  It 
>would help if Howard could supply us with good definitions of all thet 
>terms so we all understand what we are talking about.

One of the problems with stereochemistry is the degree of certainty. This 
is more of a problem for chemistry than crystallography, since chemistry 
often provides only parts of the stereochemistry as knowns. If we elaborate 
the taxonomy of Rumsfeld [1] we may say:

There are compounds whose chirality we know
There are compounds which we know are chiral but we don't know the chirality
There are compounds which we know are not chiral (achiral)
There are compounds which are not known to be achiral but we do not know 
whether they are chiral

We can convolute this with partial knowledge of relative and absolute 
stereocentres. The chemist has to consider (at least)

For one stereocentres (the centre) in a molecule with other centres
- we know the absolute chirality of all centres
- we know the relative chirality of all centres but we don't know the 
absolute chirality of the molecule
- we know the absolute chirality of the centre but we don't know its 
relative chirality to the molecule
- we know we don't know the chirality of a centre relative to a molecule 
whose chirality we know
- we know we don't know the chirality of a centre relative to a molecule 
whose chirality we don't know

See how the following fit:
- we have one (rigid) molecule per asymmetric unit in P212121
- we have one (rigid) molecule per asymmetric unit in P21/c
- we have one molecule with potentially hindered rotation in P212121
- we have a molecule with a disordered group representing two epimers (e.g. 
alpha and beta sugars in the same crystal) in P212121

Some of these are known knowns, some are known unknowns. Remember that few 
crystallographers measure the optical rotation of the crystal they select 
and this is an unknown known. Most publications unfortunately involve 
unreported knowns which then become unknown knowns.

Cheers

P.

[1]

—Feb. 12, 2002, Department of Defense news briefing
As we know,
There are known knowns.
There are things we know we know.
We also know
There are known unknowns.
That is to say
We know there are some things
We do not know.
But there are also unknown unknowns,
The ones we don't know
We don't know.

>In the meantime, enjoy the holidays and I will be in touch in the new year.
>
>David
>
>
>
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Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069

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