Natural Science Forum / Chemistry / Organic Synthesis / July 2005

Maybe your contamination is structurally related and then sublimation
might not work, whatever the temperature. So you might have to resort
to using the (reversed or normal phase) HPLC, and with your compound
that shouldn't be a problem.

Have you considered converting your amidine derivative to the HCl salt
then trying the recrystallization?  Amidines in general are very polar
(pKa ~11-12) and as the freebase can absorb CO2 from the atmosphere.
The HCl salt will be more crystalline and less susceptible to
atmospheric CO2 (but more likely to be hygroscopic).  You may have
better luck recystallizing the material from a mixture of ethanol and
diethyl ether, which may serve to remove the impurities.

Purification by reverse-phase HPLC is a viable option but in my
experience, low molecular weight amidines tend to elute at the solvent
front when a C18 column is used.  You will need to do some method
development to identify a suitable stationary phase for the HPLC
separation.

Lastly, your sublimation apparatus may not be suitable for a true
sublimation.  This looks more like an Abderhalden drying pistol (used
to remove solvents from samples) rather that a true sublimation
apparatus.  If you are still committed to trying sublimation of the
freebase of the amidine, please consider an apparatus from a glassware
vendor such as ChemGlass or Ace Glass (e.g.
http://www.aceglass.com/page.php?page=8022).  The sample is placed on
the lower portion of the vessel and the sublimed material will collect
on the cold finger (cooled with water or dry ice as in the example in
the above link) once heat and vacuum are applied.