I'd be careful about making quick assumptions that it is a consituent of the chocolate. The toxicity could be related to the added sugar from chocolate processors. Animals tend to be much more susceptible to diabetic-type complications than humans (i.e. omnivore-man and carnivore-dog). You could probably measure theobromine content by some type of chromatography technique (GC or more likely HPLC) and not have to worry about isolation by extraction.
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