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Description of Problem
The stereo bond only defines one stereocentre, although some chemists may assume that it defines the stereocentres at both ends of the bond. However, in structure databases, it is the norm for a stereo-bond to define a stereocentre at one end only - the pointed end. The "blunt" end of the bond therefore does not of itself specify any stereochemistry.
Effects & Implications
Serious effects
The stereochemistry of the "blunt" end of the bond is unspecified as far as structure databases are concerned. This may not be what the registering chemist intended.
Such compounds will not be found by structure queries that specify the diastereomer correctly.
Database users may be misled into thinking that both stereocentres are specified.
Other undesirable effects
There may be confusion over the degree to which stereochemistry has been specified.
Fixing the Problem
The stereocentres have to be specified individually to make the stereochemistry absolutely clear.
Change the ambiguous bond into a normal single bond.
Change one or more of the other bonds at each centre to appropriate stereo-bonds. However, wherever possible, avoid changing ring bonds into stereo-bonds. Instead...
Add stereo-bonded hydrogen atoms for clarity, where necessary.
How to Avoid the Problem
If there stereocentres at both ends of a bond, ensure that there are separate stereo-bonds pointing to each centre. If necessary, draw in stereo-bonded hydrogens to make the stereochemistry totally clear.
Further Information
Other ABACUS Problem Compounds
Contacts:
Peter Millington (Ext.4000) or
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Site Owner:
Peter Millington
(Ext.4000), Discovery IS - Last Updated: 16/05/2004
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