An important side reaction using the thiol, 3,6-dioxa-1,8-octanedithiol (DODT), in 9-fluorenylmethoxycarbonyl-based solid phase peptide synthesis

A considerable quantity of an alkylation by‐product is observed when using 3,6‐dioxa‐1,8‐octanedithiol as a scavenger during acidic release of peptides containing the thioether amino acid methionine from the solid support. Adjustment of the cleavage conditions by replacement of 3,6‐dioxa‐1,8‐octanedithiol with ethane dithiol or by using methionine sulfoxide as an alternative to methionine resulted in no such impurity. The by‐product was detectable by liquid chromatography and mass spectrometry and characterised by NMR spectroscopy of an isolated model peptide. It could be effectively removed in a separate post cleavage step by treatment with dilute aqueous acid at 37 °C. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd. We outline a novel alkylation when using the dithiol 3,6‐dioxa‐1,8‐octanedithiol (DODT) as a scavenger in TFA‐mediated peptide cleavage from the resin. Peptides containing unprotected methionine were extensively modified by a DODT‐derived alkylating agent affording a previously unreported by‐product. Conditions for the prevention or subsequent removal of the by‐product are outlined.