Fluorenylmethyloxycarbonyl protecting group

The fluorenylmethoxycarbonyl protecting group (Fmoc) is a base-labile protecting group used in organic synthesis.



Protection & Formation
Fmoc carbamate is frequently used as a protecting group for amines, where the Fmoc group can be introduced by reacting the amine with fluorenylmethyloxycarbonyl chloride (Fmoc-Cl), e.g.:


 * Fmoc-L-SER-formation-2D-skeletal.png

The other common method for introducing the Fmoc group is through 9-fluorenylmethylsuccinimidyl carbonate (Fmoc-OSu), which may itself be obtained by the reaction of Fmoc-Cl with the dicyclohexylammonium salt of N-hydroxysuccinimide.

Reacting with 9-fluorenylmethyloxycarbonyl azide (itself made by reacting Fmoc-Cl with sodium azide) in sodium bicarbonate and aqueous dioxane is also a method to install Fmoc group.

Because the fluorenyl group is highly fluorescent, certain UV-inactive compounds may be reacted to give the Fmoc derivatives, suitable for analysis by reversed phase HPLC. Analytical uses of Fmoc-Cl that do not use chromatography may be limited by the requirement that excess Fmoc-Cl be removed before an analysis of fluorescence.

Cleavage & Deprotection
The Fmoc group is rapidly removed by base. Piperidine is usually preferred for Fmoc group removal as it forms a stable adduct with the dibenzofulvene byproduct, preventing it from reacting with the substrate.

Roles in SPPS
The use of Fmoc as a temporary protecting group for amine at the N-terminus in SPPS is very widespread for Fmoc/tBu approach, because its removal with piperidine solution does not disturb the acid-labile linker between the peptide and the resin. A typical SPPS Fmoc deprotection is performed with a solution of 20% piperidine in N,N-dimethylformamide (DMF).


 * C13H9\sCH2\sOC(O)NHR + (CH2)5NH  -> (CH2)5NH2+  +   [C13H8\sCH2\sOC(O)NHR]-
 * [C13H8\sCH2\sOC(O)NHR]- -> C13H8\dCH2 +  -OC(O)NHR
 * -OC(O)NHR + (CH2)5NH2+ ->  HOC(O)NHR  + (CH2)5NH
 * HOC(O)NHR -> CO2  + RNH2
 * C13H8\dCH2 +  (CH2)5NH  ->  C13H9\sCH2N(CH2)5

Common deprotection cocktails for Fmoc during SPPS:
 * 20% piperidine in DMF (Fmoc group has an approximate half life of 6 seconds in this solution)
 * 5% piperazine, 1% DBU and 1% formic acid in DMF. This method avoids the use of strictly controlled piperidine. No side product was observed for a peptide with 9 residues synthesized with this method.