I synthesized short peptide contains His(Boc) and I couldn't isolate it protected. For the first, Boc group is removed even in 10% AcOH in DCM (during the cleavage). And the mixture obtained (protected and unprotected peptide) I can't separate using HPLC. Neither Straight phase or RP.
Is it stability issue? Or just separation problem?
What conditions did you use for the normal and reverse phase chromatography? Which solvents and modifiers?
Also, how are you detecting the product? Please keep in mind that, if detection is done by mass spectroscopy, the BOC group may fragment from the molecule after initial ionization. This fragmentation gives the appearance that you are seeing only the unprotected compound.
His(Boc) is not completely stable to piperidine so it is probably coming off before cleavage. Try to keep Fmoc deprotection times as short as possible (e.g. 2x1min).
His(MBom) is a more reliable alternative.
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