Question

An Fmoc protecting group can be removed from an amino acid by treatment with the amine base piperidine. Propose a mechanism. Fmoc-protected amino acid

Short answer

Piperidine initiates deprotonation and nucleophilic attack, resulting in Fmoc cleavage.

Step-by-step solution

Identify the components involved

First, identify the Fmoc protecting group and the piperidine base used in the reaction. The Fmoc group typically consists of a fluorenylmethoxycarbonyl moiety attached to the nitrogen of the amino acid, while piperidine is a secondary amine.

Base Deprotonation

Piperidine, acting as a base, initially attacks the hydrogen of the N-hydrogen of Fmoc. This causes the carbonyl group of the carbamate linkage to become more nucleophilic.

Nucleophilic Attack and Cleavage

The lone pair on the nitrogen of the carbamate linkage attacks the carbonyl carbon, breaking the bond between the Fmoc moiety and the nitrogen atom, leading to the departure of the fluorenyl moiety. This results in cleavage of the Fmoc-protected group from the amino acid.

Formation of Byproducts

This mechanism leads to the formation of a free amine (original amino acid) and a fluorenyl group with a piperidine attached as byproducts.

Conclusion of the Mechanism

The complete mechanism involves nucleophilic attack, deprotonation, and bond cleavage, effectively removing the Fmoc group from the amino acid leaving behind the amino group and piperidine modified fluorenylmethoxy group as byproducts.

Key concepts

Amino Acid Chemistry

Amino acids are the building blocks of proteins. Each amino acid consists of a central carbon atom, also known as the alpha carbon, to which an amino group ( H_2N ), a carboxyl group ( COOH ), a hydrogen atom, and a distinctive R group or side chain are attached. When an amino acid is protected by an Fmoc group, the nitrogen of the amino group is linked to a fluorenylmethoxycarbonyl moiety. This is a common protective strategy during peptide synthesis as it temporarily prevents unwanted reactions at the amino group. To remove the Fmoc group, a specific mechanism is followed, allowing the amino acid to regain its original form and function in further reactions.

Nucleophilic Attack

Nucleophilic attack is a key step in many chemical reactions, particularly in organic synthesis. It involves the interaction between a nucleophile, a molecule or ion with a pair of electrons to donate, and an electrophile, which has an electron-deficient center. In the removal of the Fmoc group, the nucleophile is typically the nitrogen atom in the carbamate linkage, which has lone pairs of electrons. It targets the electron-deficient carbonyl carbon atom in the Fmoc group. This results in bond formation with the carbon and eventual cleavage of the Fmoc from the nitrogen.

Deprotonation

Deprotonation refers to the removal of a proton ( H^+ ) from a molecule, making it more negatively charged or electron-rich. In the context of Fmoc protection removal, deprotonation is an initial step where piperidine, a secondary amine with basic properties, abstracts a proton from the nitrogen attached to the Fmoc group. This increases the nucleophilicity of the nitrogen atom, making it more reactive and ready to participate in the nucleophilic attack, which is necessary for the release of the Fmoc protecting group.

Carbamate Linkage

A carbamate linkage is a functional group characterized by the formula O=C(O-)NR_2 . It acts as a key intermediary structure in the Fmoc protection scheme on amino acids. In the Fmoc-protected amino acid, the carbamate linkage connects the amino group of the amino acid with the protective Fmoc group. During deprotection, the carbamate linkage plays a critical role as its carbonyl carbon becomes the site of nucleophilic attack. This facilitates the breaking of the linkage and the subsequent removal of the Fmoc group.

Piperidine Mechanism

Piperidine, as a secondary amine, is commonly used to remove Fmoc groups from amino acids. Its role involves acting both as a base and facilitator in the mechanism. Initially, piperidine accepts a proton from the nitrogen atom of the Fmoc-protected amino acid, enhancing the nucleophilic characteristics of the nitrogen. Through this mechanism, piperidine not only aids in deprotonation but also sets the stage for the nucleophile to attack the carbonyl carbon of the carbamate linkage, leading to the cleavage of the Fmoc group and yielding the free amino acid.