[sehling0708]

EDC (N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride) is commonly used to couple carboxylic acids to amines.

I found that when I mix EDC with certain amines (before addition of the carboxylic acid to be coupled), an orange-red color develops. This should not happen as it indicates a chemical reaction between EDC and the amine. I dissolved the EDC in pyridine-HCl buffer. The color develops more slowly as the pH is lowered and it no longer develops at pH less than 3.

I tested the following amines and the color developed with all of them:

3-picolylamine
N-methylbenzylamine
Isoniazid

The color did NOT develop with o-benzylhydroxylamine. This is the only amine which successfully coupled to all carboxylic acids I tried so far.

[rolnor]

It could be good to mix amine and acid before the EDC is added. The yellow color can be small impurities. How do you monitor the reaction? TLC can be a simple way to see what is happening. Normaly, a protected peptide will move on silica-TLC with EtOAc or EtoAce1:Hexane2 or a system with polarity somewhere bewetween these systems. It depends on the PG-groups and what aminoacids are used. It seems a little bit unessecary to use a pyridine buffer, you can just use DMF. I have used HOBT as catalyst and its effective. Maybe you have a aminoacid that is hard to disslove in DMF.

[Babcock_Hall]

Perhaps the bases are deprotonating an impurity and therefore changing its behavior as a chromophore.  This hypothesis does not explain why one base would not show a color change.

Are you following a particular literature protocol?

[rolnor]

A hydroxylamine is not very basic, its around pKa 6