Question

In a variation of the Merrifield solid-phase peptide synthesis, the amino group is protected by a fluorenylmethoxycarbonyl (FMOC) group. This protecting group is removed by treatment with a weak base such as the secondary amine, piperidine. Write a balanced equation and propose a mechanism for this deprotection.

Short answer

Answer: The mechanism of deprotection involves three steps: (1) Proton transfer, where piperidine acts as a weak base and deprotonates the amine group; (2) Nucleophilic attack, where the nitrogen anion attacks the carbonyl group of FMOC, forming a tetrahedral intermediate; and (3) Elimination of FMOC-piperidine, where the intermediate collapses, releasing the deprotected amino group and the FMOC-piperidine compound.

Step-by-step solution

Draw the structures of FMOC, amino group, and piperidine

The structure of fluorenylmethoxycarbonyl (FMOC) is as follows: (latex) \text{FMOC}: \text{C}_{15}\text{H}_{11} (-\text{O}\textrm{-}\text{C(=O)}\textrm{-} \text{R})$ The amino group protected by FMOC will have the structure: (latex) \text{FMOC}\textrm{-}\text{N}\textrm{-}\text{H}\textrm{-}\text{R} And the structure of piperidine is a saturated six-membered heterocyclic ring containing a nitrogen atom: (latex) \text{Piperidine:} \text{C}_{5}\text{H}_{10}\text{N}

Write the balanced equation for the reaction

The balanced equation for the deprotection of FMOC protecting group by piperidine can be represented as: (latex) \text{FMOC}\textrm{-}\text{N}\textrm{-}\text{H}\textrm{-}\text{R} + \text{Piperidine} \rightarrow \text{N}\textrm{-}\text{H}\textrm{-}\text{R} + \text{FMOC}\textrm{-}\text{piperidine}

Propose a mechanism for the deprotection of the FMOC group by piperidine

The mechanism of deprotection consists of the following steps: 1. Proton transfer: Piperidine acts as a weak base and deprotonates the amine group, forming a nitrogen anion (amide ion) and protonated piperidine. (latex)\text{N}\textrm{-}\text{H}\textrm{-}\text{FMOC} + \text{Piperidine} \rightarrow \text{N}^{-}\textrm{-}\text{FMOC} + \text{Piperidine}^{\oplus}\text{H} 2. Nucleophilic attack: The nitrogen anion (amide ion) generated in the previous step attacks the carbonyl group of FMOC, forming a tetrahedral intermediate. (latex)\text{N}^{-}\textrm{-}\text{FMOC} \rightarrow \text{Intermediate} 3. Elimination of FMOC-piperidine: The intermediate collapses with the formation of a double bond between the nitrogen and carbonyl carbon, releasing the FMOC-piperidine compound. (latex)\text{Intermediate} \rightarrow \text{N}\textrm{-}\text{H}\textrm{-}\text{R} + \text{FMOC}\textrm{-}\text{piperidine} This proposed mechanism results in the deprotection of the amino group by removing the FMOC protecting group with the help of piperidine.

Key concepts

Solid-Phase Peptide Synthesis

Solid-phase peptide synthesis (SPPS) is a method widely used in chemistry for synthesizing peptides. This technique allows one to build peptides step-by-step on a solid support material. The process begins with anchoring the first amino acid onto this solid support, such as resin, which provides a stable platform. Once anchored, additional amino acids are sequentially added one at a time to extend the peptide chain.

This technique offers several advantages:

• Improves purity: Excess reagents and by-products are easily removed by washing.
• Efficiency: Reaction conditions can be precisely controlled, improving the efficiency of each step.
• Automation: Automated synthesizers can control the addition of each amino acid, speeding up the process.

During the synthesis, protecting groups are crucial to prevent unwanted reactions at the amino and carboxyl groups. This ensures that only the intended peptide bonds are formed. The FMOC group, for instance, is often used to protect the amino groups of the growing peptide chain during SPPS.

Protecting Groups

Protecting groups are essential components in many chemical syntheses, including peptide synthesis. They are used to temporarily block certain reactive sites within a molecule to prevent side reactions. When introducing reactants to build complex molecules, protecting groups shield sensitive areas, allowing chemists to target specific regions.

One commonly used protecting group in peptide synthesis is the FMOC (fluorenylmethoxycarbonyl) group. This group safeguards the amino group of amino acids, ensuring they do not react before the appropriate step.

• FMOC is particularly favored because it is stable under acidic conditions but removable under mild basic conditions.
• This allows for selective protection and deprotection, crucial in multi-step peptide synthesis.

The removal of a protecting group, such as FMOC deprotection, is a strategic step. It is typically carried out once it is necessary for the amino group to engage in subsequent reactions. The goal is to remove the group efficiently without affecting the fragile peptide chain still under construction.

Nucleophilic Attack

Nucleophilic attack is a fundamental concept in organic chemistry, where a nucleophile, or electron-rich species, donates a pair of electrons to an electrophile, or electron-deficient site, to form a chemical bond. During FMOC deprotection, nucleophilic attack plays a vital role.

In the context of the FMOC mechanism, once a weak base like piperidine deprotonates the nitrogen atom, forming an anion, this sets the stage for a nucleophilic attack.

• The negatively charged nitrogen (amide ion) acts as a nucleophile.
• It attacks the carbonyl carbon in the FMOC group, forming an intermediate state.
• This attack leads to the collapse of the intermediate, releasing the FMOC group as FMOC-piperidine.

This entire sequence highlights the importance of understanding nucleophilic attack. It demonstrates how carefully timed reactions lead to efficient deprotection, freeing the amino group for its next task in peptide synthesis.