N-Acylurea formation (DIC byproduct)

DIC-mediated activation generates O-acylisourea, which can rearrange (instead of being aminolyzed) into N-acylurea — a stable, dead-end species. The peptide stays at residue n; coupling fails silently.

Why it happens (mechanism)

Carboxyl + DIC → O-acylisourea (active intermediate). If the next amine is slow to attack (poor solvation, sterics, low concentration), the O-acylisourea rearranges by 1,3-acyl migration to the inactive N-acylurea. The N-acyl now sits on a urea N; can't be aminolyzed. Coupling stops.

When it strikes (triggers)

DIC without HOBt/HOAt/Oxyma additive. Low temperature (rearrangement is slow but aminolysis is even slower). Hindered C-terminus (Aib, MeVal, etc.). Aggregated peptide on resin.

How to spot it (MS signature)

Truncation at residue n on the resin (peptide doesn't elongate further). Plus a small +N,N'-diisopropylurea adduct on the activated peptide is sometimes identified as a polar HPLC peak.

How to prevent it

• Always use HOBt or Oxyma with DIC (or HCTU/HATU which include benzotriazole equivalents). The OBt-active ester resists rearrangement.
• Pre-form the active ester briefly (5 min) before adding the amine partner.
• Higher reactant concentration (≥0.3 M).
• Double-couple hindered residues.

If it already happened (salvage)

• Re-couple the failed step with fresh activator + HOBt. If the resin has accumulated multiple incomplete steps, often need to start over.

Source

Yi Yang, Side Reactions in Peptide Synthesis (Elsevier, 2016), Chapter 5, §5.1.