Peptide/amide bond formation
Carbodiimide-mediated amide (peptide) coupling
How the Carbodiimide-mediated amide (peptide) coupling works, in 3 steps. Each step shows the structures and the curved arrows that move the electrons.
In short. A 3-step mechanism. Typical reagents: R–CO₂H, R′–NH₂, DCC (dicyclohexylcarbodiimide). Conditions: CH₂Cl₂ or DMF, 0 °C → 25 °C (often + HOBt/DMAP). Bonds formed: C(O)–N amide; C=O of urea; bonds broken: O–H of acid; C=N π of DCC. Stereochemistry: Racemisation of α-stereocentres possible via oxazolone (HOBt suppresses). Rate and selectivity: O-Acylisourea is short-lived; DCU precipitates and drives the reaction.
At a glance
Step 1: Acid adds to DCC
A carboxylic acid's oxygen attacks the central, highly electrophilic carbon of DCC (dicyclohexylcarbodiimide), forming an O-acylisourea — an activated ester with a far better leaving group than plain hydroxide.
Step 2: Amine attacks the activated carbonyl
An amine's nitrogen lone pair attacks this activated carbonyl carbon, forming a tetrahedral intermediate exactly as in any nucleophilic acyl substitution.
Step 3: Collapse: amide + urea
Collapse of the tetrahedral intermediate expels a stable, neutral urea byproduct (dicyclohexylurea) and forms the new amide bond — the core reaction used to synthesize peptides and countless pharmaceuticals.
Abbreviations and terms
- R
- R group. Any carbon substituent (alkyl, aryl…) whose identity does not matter for the mechanism.
- Cy
- Cyclohexyl. –C₆H₁₁.
- DMF
- N,N-Dimethylformamide. Polar aprotic solvent – dissolves ionic nucleophiles but does not H-bond to them, speeding SN2 and SNAr.
- DCM
- Dichloromethane. Common non-polar-ish solvent for reactions that need no nucleophilic or protic solvent.
- DMAP
- 4-Dimethylaminopyridine. Hypernucleophilic acyl-transfer catalyst – forms a very reactive N-acylpyridinium.
- H2
- Hydrogen gas. Reductant for catalytic hydrogenation.
- DCC
- N,N′-Dicyclohexylcarbodiimide. Dehydrating coupling agent: activates RCO₂H as an O-acylisourea; byproduct DCU precipitates.
- DCU
- Dicyclohexylurea. Insoluble by-product of DCC couplings.
- HOBt
- 1-Hydroxybenzotriazole. Additive that suppresses racemisation in amide coupling.
How it compares with related reactions
| Carbodiimide-mediated amide (peptide) coupling | Diazotization of aniline | Acetic acid transfers a proton to water | |
|---|---|---|---|
| Reagents | R–CO₂H, R′–NH₂, DCC (dicyclohexylcarbodiimide) | NaNO₂, HCl (HONO in situ) | Acetic acid (pKa 4.76) + water |
| Conditions | CH₂Cl₂ or DMF, 0 °C → 25 °C (often + HOBt/DMAP) | H₂O, 0–5 °C (ice bath) | Aqueous solution, 25 °C |
| Stereochemistry | Racemisation of α-stereocentres possible via oxazolone (HOBt suppresses) | None | None (achiral species) |
| Rate / selectivity | O-Acylisourea is short-lived; DCU precipitates and drives the reaction | Keep cold: diazonium salts decompose above ~5 °C | Equilibrium: Ka = 1.8 × 10⁻⁵, lies mostly left |
Test yourself
Try to answer each question before opening it.
Which reagents and conditions are typical for the Carbodiimide-mediated amide (peptide) coupling?
R–CO₂H, R′–NH₂, DCC (dicyclohexylcarbodiimide). Conditions: CH₂Cl₂ or DMF, 0 °C → 25 °C (often + HOBt/DMAP).
Which bonds are formed and which are broken?
Formed: C(O)–N amide; C=O of urea. Broken: O–H of acid; C=N π of DCC.
What is the stereochemical outcome?
Racemisation of α-stereocentres possible via oxazolone (HOBt suppresses)
What controls the rate or the selectivity?
O-Acylisourea is short-lived; DCU precipitates and drives the reaction
Study guides that help with this reaction
- Carbonyl chemistry: addition, acyl substitution and enolates
- SN1, SN2, E1 or E2? How to decide which mechanism wins
- Nucleophiles, electrophiles and leaving groups: what makes a reaction go