1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide

1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC, EDAC or EDCI) is a water-soluble carbodiimide usually handled as the hydrochloride.[1]

1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
Skeletal formula of EDC
Ball-and-stick model of the EDC molecule
Names
Preferred IUPAC name
3-{[(Ethylimino)methylidene]amino}-N,N-dimethylpropan-1-amine
Identifiers
3D model (JSmol)
ChemSpider
ECHA InfoCard 100.015.982
UNII
  • InChI=1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3 checkY
    Key: LMDZBCPBFSXMTL-UHFFFAOYSA-N checkY
  • InChI=1/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3
    Key: LMDZBCPBFSXMTL-UHFFFAOYAH
  • CCN=C=NCCCN(C)C
Properties
C8H17N3
Molar mass 155.245 g·mol−1
Hazards
Safety data sheet (SDS) External MSDS (HCl Salt)
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
checkY verify (what is checkY☒N ?)
Infobox references

It 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. While other carbodiimides like dicyclohexylcarbodiimide (DCC) or diisopropylcarbodiimide (DIC) are also employed for this purpose, EDC has the advantage that the urea byproduct formed (often challenging to remove in the case of DCC or DIC) can be washed away from the amide product using dilute acid. Additionally, EDC can also be used to activate phosphate groups in order to form phosphomonoesters and phosphodiesters. Common uses for this carbodiimide include peptide synthesis, protein crosslinking to nucleic acids, but also in the preparation of immunoconjugates. EDC is often used in combination with N-hydroxysuccinimide (NHS) for the immobilisation of large biomolecules. Recent work has also used EDC to assess the structure state of uracil nucleobases in RNA.[2][3]

Preparation

EDC is commercially available. It may be prepared by coupling ethyl isocyanate to N,N-dimethylpropane-1,3-diamine to give a urea, followed by dehydration:[4]

Mechanism
The scheme above shows the general mechanistic steps for EDC-mediated coupling of carboxylic acids and amines under acidic conditions. The tetrahedral intermediate and the aminolysis steps are not shown explicitly.

EDC couples primary amines, and other nucleophiles,[5] to carboxylic acids by creating an activated ester leaving group. First, the carbonyl of the acid attacks the carbodiimide of EDC, and there is a subsequent proton transfer. The primary amine then attacks the carbonyl carbon of the acid which forms a tetrahedral intermediate before collapsing and discharging the urea byproduct. The desired amide is obtained.[6]

References
  1. Richard S. Pottorf, Peter Szeto (2001). "1-Ethyl-3-(3'-dimethylaminopropyl)carbodiimide Hydrochloride". E-EROS Encyclopedia of Reagents for Organic Synthesis. doi:10.1002/047084289X.re062.
  2. Mitchell, D; Renda, A; Douds, C; Babitzke, P; Assmann, S; Bevilacqua, P (2019). "In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)". RNA. 25 (1): 147–157. doi:10.1261/rna.067868.118. PMC 6298566. PMID 30341176.
  3. Wang, PY; Sexton, AN; Culligan, WJ; Simon, MD (2019). "Carbodiimide reagents for the chemical probing of RNA structure in cells". RNA. 25 (1): 135–146. doi:10.1261/rna.067561.118. PMC 6298570. PMID 30389828.
  4. Sheehan, John; Cruickshank, Philip; Boshart, Gregory (1961). "A Convenient Synthesis of Water-Soluble Carbodiimides". J. Org. Chem. 26 (7): 2525. doi:10.1021/jo01351a600.
  5. Tsakos, Michail; Schaffert, Eva S.; Clement, Lise L.; Villadsen, Nikolaj L.; Poulsen, Thomas B. (2015). "Ester coupling reactions – an enduring challenge in the chemical synthesis of bioactive natural products". Natural Product Reports. 32 (4): 605–632. doi:10.1039/C4NP00106K. PMID 25572105.
  6. "Carbodiimide Crosslinker Chemistry - US". www.thermofisher.com. Retrieved 2019-05-10.

Further reading
  • López-Alonso, JP; Diez-Garcia, F; Font, J; Ribó, M; Vilanova, M; Scholtz, JM; González, C; Vottariello, F; Gotte, G; Libonati, M; Laurents, DV (2009). "Carbodiimide EDC Induces Cross-Links That Stabilize RNase A C-dimer against Dissociation: EDC Adducts Can Affect Protein Net Charge, Conformation and Activity". Bioconjugate Chemistry. 20 (8): 1459–1473. doi:10.1021/bc9001486. PMID 19606852.
  • Nakajima, N; Ikada, Y (1995). "Mechanism of Amide Formation by Carbodiimide for Bioconjugation in Aqueous Media". Bioconjugate Chemistry. 6 (1): 123–130. doi:10.1021/bc00031a015. PMID 7711098.
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