Purifying ionic compounds by flash column chromatography

One of the more challenging purifications is that of water-soluble, ionizable compounds. Typically, normal-phase with silica is not used because of the probable non-reversible interactions, especially between the ionized amines interacting and the ionizable silanols.  With normal-phase out of the purification solution that leaves ion exchange and reversed-phase as chromatographic options.

In this post I will discuss the use of reversed-phase and the influence pH and buffers have on the chromatography of some ionic, water soluble compounds.

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Published by

Bob Bickler

Technical Specialist, Biotage

2 thoughts on “Purifying ionic compounds by flash column chromatography”

  1. I need to add 0.1% TFA to my eluent (10% MeCN in H2O up to 100% MeCN) to get my compounds purified, as they have four trimethylammonium groups. This works pretty good and I can get rid of my byproducts. But after removing the solvent, I always find a white powder (looks like silica) in my flasks additionally. Is it to much TFA? Does some of the solvent material dilute in my mixture? For good purifications I need at least 100 CVs. Is this the problem? I hope someone can help me.

    1. Hi Stefanie,

      The addition of 0.1% TFA to reversed-phase mobile phases is fairly common but it is quite acidic. It is not likely the white residue is silica but may be hydrolyzed bonded phase. Have you tried reducing your TFA concentration, perhaps to 0.01%?

      Best regards,


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