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I am attempting to extract certain alkaloids from green plant matter, which is very high in waxes and fats.

I understand that in this scenario it is common to first acidify and then use a non-polar solvent to de-fat the solution.

I am curious though: say I were to basicify and extract alkaloids without any de-fatting. If I were then to add HCl solution to the non-polar solvent which now contains the alkaloids, wouldn't this in theory be equivalent to the de-fatting stage? Wouldn't the alkaloids would now be in the aqueous layer, and the lipids would be stuck in the non-polar layer?

As the acid/base method is so common, I am wondering if there are any downsides to the method described above that I am unaware of. I only have enough material for one shot so I would just like to hear some input before I attempt this expedited method.

May main fear would be emulsions that wouldn't break up. Is this a valid concern that is remedied by a preliminary de-fatting stage? Are there other concerns I should be wary of?

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    $\begingroup$ You need to allow your aqueous solvent to gain access to the regions that contain alkaloids. If these are occluded by fatty matter then you have to remove them otherwise your extraction would be inefficient. The emulsions do break up, you can centrifuge to separate the phases efficiently. $\endgroup$ – WYSIWYG Sep 15 '15 at 5:21
  • $\begingroup$ I am no chemist, but a biologist. I routinely extract alkaloids from some insects. We don't follow this defatting protocol you describe to rid the mix of waxes, in fact I had never heard of it. We just use silica column separation by affinity -- our alkaloids get captured in the silica by a strongly apolar solvent which will carry the fats off, and then the silica can be washed with a more polar solvent to release alkaloids. Acidification helps a lot in removing them from the silica. Does that sound helpful? $\endgroup$ – Scientist Feb 18 '18 at 14:45
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One big risk with the method you propose is foaming and gellation turning your extractions into a huge mess. Under basic conditions, the fats (e.g. triacylglycerols or TAGs) are likely to hydrolyze, forming carboxylate salts of fatty acids. "Carboxylate salts of fatty acids" is a long way of saying soap. These soap-like compounds could lead to excessive foaming or gellation of the sample, which will hinder phase separation and gunk up your apparatus.

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