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Fmoc protected compounds contain the fluorenylmethoxycarbonyl group attached to the nitrogen atom of organic compounds. Fmoc chloride is a chloroformate ester, used to introduce Fmoc to amino compounds as Fmoc carbamate. A superior alternative for Fmoc protection is 9-fluorenylmethyl succinimidyl carbonate (Fmoc-OSu), also referred to as Fmoc succinimde, which prevents the formation of side products. The chemistry of Fmoc is used for the protection of the alpha amino group of amino acids. Fmoc chemistry has been shown to be more reliable for producing high quality peptides.
Fmoc protection has found significant use in solid phase peptide synthesis because its removal with piperidine solution does not disturb the acid labile linker between the peptide and the resin. Piperidine also scavenges the reactive dibenzofulvene byproduct of Fmoc cleavage and prevents it from reacting with the peptide chain. Since the fluorenyl group is highly fluorescent, certain otherwise UV inactive compounds containing Fmoc are suitable for analysis by reversed phase HPLC. The Fmoc amino acids and Fmoc cleavage byproducts tend to give strong UV absorbance, allowing solid phase peptide synthesis reactions to be easily monitored by photometry. The Fmoc group has an advantage in that it is cleaved under very mild basic conditions (e.g. piperidine), but is stable under acidic conditions.