Fluorenylmethyloxycarbonyl chloride

Fluorenylmethoxycarbonyl (Fmoc) protecting group is used for protecting amines. One application is the synthesis of peptides. This protecting group, it is possible to protect the next amino acid in the chain growth in the direction of the N -terminal end of the peptide. The combination of N-Fmoc and tert -butyl esters or its chemically related analogs is a polymer-bound ideal orthogonal protecting group combination and is widely used in solid phase peptide synthesis.

Importance

The fluorenylmethoxycarbonyl group forms a key element in the strategy of solid phase peptide synthesis. Ideally, you should be able to in an automatable synthesis, such as those mentioned, separated all the necessary protection and leave them undisturbed apart. This concept is called orthogonality of the protecting groups.

In the peptide synthesis has to do it's usually with three sets of protecting groups: First, the protecting group in the direction of future N -terminal end, such as Fmoc. Furthermore, a protecting group for the C-terminal end; This is formed in the solid-phase peptide synthesis by a resin, to which the first amino acid is bound. A premature release of the growing peptide would significantly reduce yields. The third type are the protecting groups for the possibly existing interfering functional groups in the amino acids to be incorporated into the peptide.

Here, Fmoc by its exceptional property in an acidic stable, but on the other hand to be labile under basic conditions, an exception under the protection selcetion The majority of the other protecting groups is cleaved under acidic conditions.

In the solid phase peptide synthesis, peptides are automatically to Merrifield resin and further developments of this technique produced with the aid of synthesis robots. The case used standard protocols enable peptide coupling yields in excess of 99.99 %, which is needed to synthesize peptides in the 10 kDa range and can be purified later.

Deprotection

The protecting group can be removed under mildly basic conditions again, but is stable under acidic conditions. Therefore, it may well in connection with the so-called Boc protecting group (tert -butyloxycarbonyl ) and common in this regard protecting group for carboxylic acids, the tert-butyl ester, can be used and is complementary thereto, since the Boc- and the tert- butyl ester group is acidic (typically with concentrated trifluoroacetic acid) removed. Fmoc deprotection at the acidic hydrogen atom is removed (usually a secondary amine) with the aid of a base. In a mechanism, the said protecting group E1cb system collapses to a quasi - aromatic system and the free amine as shown ( for example, esters of a peptide ), such as in the reaction mechanism:

The proton at the 9- position of the fluorenyl ring ( pKa = 22.6 in dimethyl sulfoxide ) can be removed under mild conditions behaves as standard. Thereby, it is possible that the deprotection with 20% piperidine, a relatively weak base, in dimethylformamide ( DMF) within a few minutes ( 30 minutes ) can be carried. Because of characteristic UV absorptions at 295 nm ( ε = 7800 ), one can pursue the correct course of deprotection and thereby recognize problematic peptide couplings on the basis of slow or poor elimination of the protecting group occurs peptide synthesis using a synthesizer.

Protection of the amino function

Usually the protection of the amino function, in the absence of other interfering groups are part of the amino acid, by reaction with fluorenylmethoxycarbonyl chloride (Fmoc -Cl) or N -(9- Fluorenylmethoxycarbonyloxy ) succinimide (Fmoc -OSu ) in the presence of an aqueous sodium bicarbonate solution with the corresponding amino acid. The Fmoc derivatives of all common amino acids are commercially available.

Alternatively, the amino function of an amino acid can be protected with the Fmoc group, if instead fluorenylmethoxycarbonyl N -hydroxysuccinimide derivative of Fmoc- ONSu is used.