We have a tertiary-butyl protected amino acid in which nitrogen is protected with FMOC.  We removed the FMOC group with diethyl amine, and we used rotary evaporation plus a toluene strip to remove the volatiles.  We attempted to purify over a short column of silica.  We were able to remove a fast-moving impurity (presumably dibenzofulvene or a derivative) using 40:60 EtOAc/hexanes, then switched to 99:1 hexanes/TEA in the hope of eluting the N-deprotected product, still bearing the carboxylate protecting group, but the product was not soluble in EtOAc or in DCM (it might have been a suspension).  We eluted with 90:10 DCM/methanol and saw two products by TLC.  They were not completely separated.  I am interested in soliciting ideas for what we should do differently next time.

In retrospect a lower percentage of methanol would have been an improvement.  I wonder whether or not the solubility of the amine would have been better in chloroform than it was in DCM.  I realize that some people do not purify at all at this stage, but instead couple the crude product with another amino acid.  We also want to couple to another amino acid. 

We tried a silica column after using diethyl amine to deprotect.  We obtained two pools, but we did not obtain our product.  We are short on mass.  It seems like time for a rethink regarding the best purification method.

Edited March 16, 20223 yr by BabcockHall

We have tried both diethyl amine and 4-methylpiperidine in the deprotection.  Most recently we removed the white precipitate with centrifugation in Corex centrifuge tubes.  This was an improvement over having a bunch of precipitate sit on the top of the silica column.

Is RP chromatography a possibility? I normally use C18 cartridges on an MPLC unit for any of my peptide work and haven’t had an issue. I would also normally use 20% piperidine in DMF for Fmoc removal, but this is for SPPS so possibly not as easy in solution phase. The other option, which might be a bit much if this is just a single amide bond you’re making or your starting material is precious, is to load it onto a resin and do the synthesis that way.