[ShedenSmith]

I have a compound that I want to purify that contains both a tertiary amine and a carboxylic acid functional group. I know for columns for amine purification, people frequently add triethylamine or ammonia to keep the amine in the neutral state so it doesn't stick to the silica. Similarly for purification of carboxylic acids by column chromatography, I've heard of people adding some acid into the eluant to keep the carboxylic acid in the neutral state. But what do I do when by compound contains both of these functional groups? It seems like no matter what I do, one of the functional groups is going to be ionized and it will stick strongly to the silica.

[Babcock_Hall]

I don't see silica working in this application, but I may be wrong.  If you can purify by ion-exchange, that might be easier.  A common trick in purifying amino acids is to use Dowex-50 in the H⁺-form and then elute with 2-3 M ammonia.  Dowex-1 in the acetate form is another possibility.  I have used both, but if your compound has a large, hydrophobic portion, polystyrene-based exchangers can be problematic.  There are some more exotic variations.