Hi all,
I've synthesised peptides using COMU as coupling reagent. Could someone explain me, why during coupling step with amino acids which contain aromatic ring (e.g.phenylalanine, Arg(Pbf)) the color of solution became red? In other amino acids I have also noticed the color change, solution was yellow. But only in case of amino acids with aromatic ring the color was more intensive (here red).
I'll be really gratefull for Your answers.
I believe COMU is designed so that it’s byproducts give off color indicating when the reaction is complete. The color and intensity of color could be due to solvent or the amount of COMU converted to its byproducts. For example I would imagine a reaction that has only progressed 50% would be different color than 100%.
While performing peptide couplings with stronger Uronium based agents(HATU, HCTU, HBTU etc) and similar ones such as COMU, the carboxyl term gets activated but only in the presence of a base (secondary amines like DIPEA usually). I believe during the course of the reaction there is the generation of charge transfer type complexes between an electron rich aromatic system and the electron deficient activating agents and that leads to the generation of an intense color (dark yellow to dark red). While using HBTU, I always see this dark coloration as soon I add the base to activate the amino acid (while coupling Phe, Arg, Ser etc.) Usually it doesn't occur while coupling hydrophobic amino acid like Val, Ala.
I think this color comes from the reaction between the activator(like HATU or HBTU) and the base(DIPEA). I once did a simple experiment to put only activator and base together without peptides or amino acid, and it also gets dark color. And with time going, the color became darker.
Hi all,
I have got the resin color converted to a color close to reddish brown after coupling of Asn (whose side chain is not protected) to the last AA which was proline. This is of course in addition to having the same color was noticed during reaction. I wonder if this is normal or something wrong may have occurred the peptide sequence that was done so far.
Of note that, the amount of DIPEA added was a little bit higher than usual.
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