First, thank you very much for your suggestions concerning the Teledyne CombiFlash; we can also ask for some help at our institution. Second, we are working on two glycosides which are made using very different synthetic strategies. One has a phosphonate diester as an intermediate, but this portion of the molecule will be discarded in a Horner Wadsworth Emmons reaction. We still have a few more steps to go, but I could see reverse phase used after the final deprotection step.
The present synthesis used four TBDMS groups on the four carbohydrate oxygen atoms (at carbons 2, 3, 4, and 6). The final step was the use of 8 equivalents of TBAF to remove these protecting groups. We have performed this step several times with only one failure. Then we followed the procedure of Kaburagi and Kishi (J. Org. Chem. 2007) to remove the remaining fluoride ions and the tetrabutylammonium ions, some of which may be pairing with carbonate or bicarbonate anions. In brief calcium ions form CaF, and the Dowex-50 provides protons to oxygen and binds to the TBA ions. This step was partially successful, removing roughly 90% of the TBA ions by H-1 NMR (it has previously been more successful in our hands). Our job now is to remove the majority of the remaining TBA ions. Our product is electrically neutral, but I would describe it as amphipathic, having an aromatic portion and a glycosidic portion.
If I had a charged product, I might be tempted to try low pressure ion exchange using TEAB, which is volatile.