Reactions with Amines

Amide bond formation is one of the most common reactions in organic synthesis. Carboxylic acid derivatives + amines give amides, with the specific conditions depending on which derivative you start with.

Acyl Halide + Amine (Fastest)

R-COCl + R’-NH₂ + pyridine → R-CO-NHR’ + pyridinium chloride.

Pyridine acts as a base to absorb the HCl that forms; without it, the amine would get protonated to its ammonium form and lose nucleophilicity.

This reaction is fast (minutes at room temperature), irreversible, and high-yielding. It is the standard lab method for amide bonds when the starting acid is easily converted to its chloride.

Anhydride + Amine

R-CO-O-CO-R + R’-NH₂ → R-CO-NHR’ + R-COOH.

Half of the anhydride becomes the amide; the other half becomes the carboxylic acid byproduct. Slower than acyl halide + amine but still fast at room temperature.

Ester + Amine (Slower)

R-COOR’ + R”-NH₂ → R-CO-NHR” + R’-OH.

This “aminolysis” of esters requires heat and time. Rate depends on the ester’s structure: methyl esters react faster than bulky esters. For peptide synthesis, ester intermediates are sometimes used as “active esters” - N-hydroxysuccinimide (NHS) esters or pentafluorophenyl esters are common examples. They are more reactive than methyl/ethyl esters because their LG (NHS anion or pentafluorophenolate) is a weak base.

Carboxylic Acid + Amine Directly (Slow)

R-COOH + R’-NH₂ ⇌ R-CO-NHR’ + H₂O.

This equilibrium is unfavorable at room temperature because:

1. The carboxylic acid protonates the amine, turning both into unreactive zwitterion forms.
2. Even if they do come together, the -OH is a poor LG.

To force this reaction, you need extreme heat (150°C+) with water removal. A cleaner alternative is DCC coupling (see below).

DCC Coupling (Standard for Peptide Synthesis)

DCC (dicyclohexylcarbodiimide, C₆H₁₁-N=C=N-C₆H₁₁) activates the carboxylic acid at room temperature:

Step 1: R-COOH + DCC → O-acylisourea (activated intermediate).
Step 2: O-acylisourea + R’-NH₂ → amide + DCU (dicyclohexylurea, insoluble byproduct).

Mechanism in detail:

1. DCC’s central carbon is highly electrophilic.
2. The COOH’s oxygen attacks it, forming a C-O bond and breaking one of the C=N bonds.
3. The resulting O-acylisourea has a greatly activated acyl carbonyl.
4. The amine attacks this activated acyl carbon.
5. The N=C-N portion of the DCC rearranges to give urea (DCU), which precipitates out.

DCC is the “gold standard” for peptide synthesis because it is done at room temperature, does not racemize chiral alpha-centers (a big concern in peptide chemistry), and DCU can be filtered off.

Related coupling reagents:

• EDC (ethyl-(dimethylaminopropyl)carbodiimide): water-soluble, easier workup.
• HATU, HBTU, PyBOP: more reactive, used for difficult couplings.
• BOP, TBTU: similar applications.

All follow the same acid-activation-then-amine-attack logic.

Peptide Bond Formation in Biology

Cells make peptide bonds via the ribosome. The mechanism is essentially:

1. Amino acid is esterified onto tRNA via ATP activation (forming aminoacyl-tRNA).
2. The activated amino acid’s carbonyl is more electrophilic than a free acid.
3. The next amino acid’s -NH₂ attacks the activated acyl carbonyl.
4. The tRNA is kicked out as the LG.
5. Result: new peptide bond + empty tRNA.

The ribosome’s peptidyl transferase center (PTC) is actually a ribozyme - the catalysis is done by RNA, not protein. The chemistry is the same NAS mechanism you just learned, just with tRNA as the leaving group (instead of chloride or alkoxide) and ribosome positioning for specificity.