We have a problem in synthesizing our anti-malarials that could use some feedback from some organic chemists:

Ever since we isolated our Ugi products, we've been trying to cyclize them to the diketopiperazines. As described by Hulme, we are trying to effect an intramolecular transamidation catalyzed by trifluoroacetic acid (TFA). Instead of dichloroethane we are generally using CDCl3 so that we can monitor the reaction by NMR.

The first step of removing the boc group seems to proceed very smoothly, with the appearance of t-butyl trifluoroacetate at 1.61 ppm within a few minutes or hours, depending on the concentration of TFA. Here is a H NMR from Khalid's EXP070, 13 min after addition of 50% TFA in CDCl3 showing complete deprotection: