Carbodiimide

A carbodiimide is a functional group consisting of the formula N=C=N. Carbodiimides hydrolyze to form ureas, which makes them rarely found in nature.

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Carbodiimide formation

Carbodiimides are formed by dehydration of ureas or from thioureas.

Uses of carbodiimides

In synthetic organic chemistry, compounds containing the carbodiimide functionality are dehydration agents and are often used to activate carboxylic acids towards amide or ester formation. Additives, such as N-hydroxybenzotriazole or N-hydroxysuccinimide, are often added to increase yields and decrease side reactions.

Carbodiimides can also react with amines to form guanidines.

Amide formation mechanism

The formation of an amide using a carbodiimide is straightforward, but with several side reactions complicating the subject. The acid 1 will react with the carbodiimide to produce the key intermediate: the O-acylisourea 2, which can be viewed as a carboxylic ester with an activated leaving group. The O-acylisourea will react with amines to give the desired amide 3 and urea 4.

The side reaction of the O-acylisourea 2 produce both desired and undesired products. The O-acylisourea 2 can react with an addition carboxylic acid 1 to give a acid anhydride 5, which can react further to give the desired amide 3. The main undesired reaction pathway involves the rearrangement of the O-acylisourea 2 to the stable N-acylurea 6. The use of solvents with low-dielectric constants such as dichloromethane or chloroform can minimize this side reaction.

DCC

Main article: Dicyclohexylcarbodiimide

DCC (acronym for N,N'-dicyclohexylcarbodiimide) was one of the first carbodiimides developed. It is widely used for amide and ester formation, especially for solid-phase peptide synthesis. DCC has achieved popularity mainly because of its high yielding amide coupling reactions and the fact that it is quite inexpensive.

However, DCC does have some serious drawbacks, and its use is often avoided unless necessary, for several reasons:

1. The byproduct N,N'-dicyclohexylurea is mostly removed by filtration, but trace amounts remain and are often difficult to remove.
2. DCC is incompatible with traditional solid-phase peptide synthesis. The formed N,N'-dicyclohexylurea is mostly insoluble and is difficult to separate from the peptide resin.
3. Most importantly, DCC is a potent allergen, thus contact with skin can lead to a potentially dangerous allergic reaction.

DIC

Main article: N,N'-Diisopropylcarbodiimide

DIC (acronym for N,N'-diisopropylcarbodiimide) was developed as an alternative to DCC. DIC is identical to DCC in nearly every way except:

1. As a liquid, DIC is easier to handle than DCC (which is a waxy solid).
2. The product, N,N'-diisopropylurea, is soluble in organic solvents and is easily removed by extraction. Hence, DIC is more often used in solid-phase synthesis.
3. Most importantly, DIC will not induce an allergic reaction.

EDC

EDC or EDAC (acronym for 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) is a water soluble carbodiimide which is typically employed in the 4.0-6.0 pH range. It is generally used as a carboxyl activating agent for the coupling of primary amines to yield amide bonds. Additionally, EDC can also be used to activate phosphate groups. Common uses for this carbodiimide include peptide synthesis, protein crosslinking to nucleic acids and preparation of immunoconjugates. EDC is often used in combination with N-hydroxysuccinimide (NHS) or sulfo-NHS to increase coupling efficiency or create a stable amine-reactive product.

EDC also used in organic chemistry to couple a carboxylic acid to alcohol using DMAP as a catalyst.

References

• Nakajima, N; Ikada, Y; Bioconjug Chem. 1995, 6(1), 123-130. Abstract

• Skotnicki, S; Tetrahedron Lett. 1994, 35(2), 197-200. [1]