Fluorenylmethyloxycarbonyl protecting group
Base-labile protecting group
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Through Base (chemistry), Amine and Acid
Protection & Formation
Fmoc-carbamate is frequently used as a protecting group for primary and secondary amines, where the Fmoc group can be introduced by reacting the amine with fluorenylmethyloxycarbonyl chloride (Fmoc-Cl), e.g.:
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.
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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.
Role in Peptide Synthesis
The use of Fmoc as a temporary protecting group for amine at the N-terminus in solid phase synthesis is very widespread for Fmoc/tBu approach, because its removal with piperidine 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−CH2−OC(O)NHR + (CH2)5NH → (CH2)5NH+2 + [C13H8−CH2−OC(O)NHR]−
- [C13H8−CH2−OC(O)NHR]− → C13H8=CH2 + −OC(O)NHR
- −OC(O)NHR + (CH2)5NH+2 → HOC(O)NHR + (CH2)5NH
- HOC(O)NHR → CO2 + RNH2
- C13H8=CH2 + (CH2)5NH → C13H9−CH2N(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.