Identifying and suppressing peptide side reactions is the key to mastering peptide purity. This collection details the mechanisms of common synthetic artifacts—from backbone cyclizations to protecting group modifications—providing the diagnostic mass shifts and chemical preventions needed to troubleshoot failed syntheses.
Cyclization & Backbone Rearrangement
Aspartimide Formation
A base-catalyzed cyclization occurring primarily at Asp–Gly/Ser motifs. Details the mechanism of ring closure and strategies to suppress it using HMB backbone protection or optimized bases.
Diketopiperazine (DKP)
A side reaction common at the dipeptide stage (especially with Pro/Gly), where the N-terminal amine attacks the C-terminal ester. Covers mechanism, mass loss, and prevention during loading.
Pyroglutamate (pGlu)
The spontaneous or acid-triggered cyclization of N-terminal Glutamine (or Glutamic Acid) into pyroglutamate. Explains the -17 Da mass shift and impact on biological activity.
Reactive Intermediates & Adducts
DBF Alkylation (+178 Da)
A common Fmoc deprotection artifact where residual dibenzofulvene (DBF) reacts with free amines. Focuses on identifying the characteristic +178 Da mass shift and improving washing protocols.
Arg-Sulfonyl Adducts
Details how Pbf/Pmc protecting groups generate reactive electrophiles during cleavage. Explains the modification of Trp, Cys, and Tyr residues and the necessary scavenger cocktails to prevent it.
Racemization & Epimerization
Cysteine Racemization
Base-catalyzed epimerization in Fmoc-SPPS, focusing on cysteine α-proton abstraction, mechanistic pathways, LC–MS detection, and practical strategies to suppress D-Cys formation during synthesis.
Histidine Racemization
Activation-stage epimerization in Fmoc-SPPS driven by α-proton abstraction and oxazolone intermediates. Covers mechanisms, LC–MS detection, and practical strategies to suppress D-His formation during peptide synthesis.