Scope and Limitations of the Use of Methanesulfonic Acid (MSA) as a Green Acid for Global Deprotection in Solid‐Phase Peptide Synthesis

Abstract N,N‐dimethylformamide (DMF) and trifluoroacetic acid (TFA) are the two solvents/reagents most widely used in solid‐phase peptide synthesis (SPPS). While DMF is already regulated in Europe, TFA – a member of the polyfluoroalkyl substances (PFAS) family – is expected to face similar restrictions soon. These compounds break down slowly and pose risks to human health and the environment. Herein, the use of the so‐called “green acid par excellence”, methanesulfonic acid (MSA), in substitution of TFA is discussed. As MSA is stronger than TFA, it is diluted with a solvent for use. The effectivity of MSA depends on the solvents used. When dichloromethane (DCM) is used, 1.5 % MSA removes all side‐chain protecting groups, except the trityl (Trt) group of His. In the presence of acetic acid (AcOH) and dimethylcarbonate (DMC), more concentrated solutions of MSA (8–16 %) are required. The removal of the Trt group of Asn/Gln continues to be a challenge even with these solutions, and aspartimide formation can occur in Asp‐containing peptides.