Boc Protecting Group: N-Boc Protection & Deprotection Mechanism

What is the Boc Protecting Group?

Boc stands for tert-butyloxycarbonyl and protects amines as carbamates. More rarely, it is also used to protect alcohols as their carbonates.
Boc is resistant to basic hydrolysis, many nucleophiles as well as catalytic hydrogenation. The fact that it can be removed with mild acid makes it orthogonal to other key protecting groups (see below).

Boc Protection Mechanism

The main method of Boc protection is use of Boc anhydride. Base is not strictly needed for the reaction with Boc₂O (tert-butanol formed as product). However, bases like triethylamine or NaOH (amino acids) are sometimes used, depending on the system.

The mechanism is straight-forward: attack of the nucleophilic amine to the electrophilic anhydride. The carbonate leaving group can release CO₂, providing a strong driving force for the reaction. This step is the same as for other carbamate protecting groups such as Cbz.

As we have seen for PMB, many variants of activated agents can exist. The same is true for Boc: while Boc anhydride is the most common reagent, others like the cheaper Boc-Cl (t-butyl chloroformate) or Boc-ON (oxyimino-nitrile reagent).
As a common theme for protecting groups: Remember that amines are more nucleophilicity than alcohols, so you can selectively protect them in many cases.

Boc DeProtecTION Mechanism WITH Acid

Acids like TFA, HCl… can deprotect Boc groups. Protonation into the oxocarbenium triggers fragmentation into a stabilized tertiary cation (inductive effect). It later deprotonates to form gaseous isobutene.
The fragmented carbamate can decarboxylate, releasing CO₂ (here you have a parallel of Boc anhydride introduction and its removal) and giving the free amine.

Given the high steric hindrance of the carbamate, the Boc group is not base-labile like methyl esters, for instance.

A potential issue are intermolecular side reactions of the intermediary t-butyl cation. An example from peptide chemistry is alkylation of nucleophilic amino acids methionine or tryptophan. That’s why you might see conditions which employ scavengers like thiophenol, anisole, cresol… to remove the reactive intermediate.

Boc protecting group Orthogonality

Boc protection is a key tool for heterocycle and peptide synthesis. In solid phase peptide synthesis (SPPS), it is used as a protecting group for alpha-amino groups and amino acids lysine, tryptophan and histidine.

Due to its acidic deprotection, it is orthogonal to other important amino acid protecting groups:

• Fmoc (9-fluorenylmethoxycarbonyl) – removed with base
• Cbz / Z (benzyloxycarbonyl) – removed with H₂ reduction
• Alloc (allyloxycarbonyl) – removed with transition metal catalysis (Pd)

However, Boc is not stable to Lewis acids or oxidative conditions. We have seen that the O-PMB protecting group is removable with DDQ. In one case [1], treatment of the PMB ether did not result in any desired deprotection.

Can you explain why this side reaction and overoxidation might have occurred?

Boc side reactions

In organic chemistry, surprises wait around every corner. Don’t assume that protecting groups stay on forever, and only cleave on demand!

Before, we have mentioned that alcohols are less nucleophilic than amines, allowing selective protections. In this example [2], the authors observed a N-O Boc transfer when preparing a chiral oxazolidinone auxiliary. Upon deprotection of the TBDMS group, the highly nucleophilic alkoxide grabs the Boc group from the nitrogen!

Overman et al used a more conscious Boc-participation in their synthesis towards the diazatricyclic core of sarain marine alkaloids. [3]
Base generates the alkoxide which again attacks Boc. This time however, the group is not transferred (the negative charge would not be stabilized on the nitrogen, unlike the previous example). Instead, we see an intramolecular cyclization.

Boc in Peptide Synthesis

As alluded to above – particularly in the early days – the Boc protecting group proved very useful for solid-phase peptide synthesis (SPPS). However, in the late 20th century, the Fmoc protecting group started to replace Boc methodology.

Fmoc deprotection is generally milder than the moderate/ strong acidolysis steps used for Boc. More specifically, Fmoc proved more compatible with synthesis of amino acids that are susceptible to acid-catalysed side reactions.

A good example is the synthesis of the peptide gramicidin A which contains four acid-sensitive tryptophan residues. Using Boc chemistry, yields were in the range of 5-24%. Switching to Fmoc dramatically improved the yields, in some cases to 87% [4].

Closing Remarks

The Boc group is pretty cool, and its deprotection mechanism is a must-know for every organic chemistry student. The orthogonality to base- or reduction-labile protecting groups make it a top pick for many total and peptide syntheses.

However, like all protecting groups, it has its downsides. The carbamate carbon remains somewhat nucleophilic which opens avenues for surprising reactions, particularly intramolecular. Also, the acidic conditions and reactive tert-butyl-cations used can pose challenges to some systems. As always, smart planning and workarounds might be needed.

BOC Protection experimental procedure [5]

One pot Cbz->Boc switch
“To a solution of Cbz-carbamate SM (3.5 g, 6.81 mmol) in MeOH (25 mL) were added Pd/C (10 % w/w, 200 mg, 0.19 mmol) and Boc2O (2.17 g, 9.9 mmol) at room temperature. The reaction mixture was stirred under a hydrogen atmosphere (balloon) at room temperature for 6 h. The reaction mixture was filtered through a pad of celite, and then concentrated in vacuo. Flash column chromatography (silica gel, hexanes:EtOAc 10:1 → 7:1) afforded Boc-carbamate 42 (2.94 g, 90 %) as an oil.”

BOC deprotection experimental procedure [6]

“Boc-L-allo-End(Cbz)2-OtBu (597 mg, 1 mmol) was dissolved in a mixture of TFA (10 mL) and water (1.0 mL). The mixture was stirred at room temperature for 3 h, then concentrated to give a brown oil. The resulting crude oil was azeotroped with toluene (3 x 10 mL) and concentrated in vacuo to remove any residual TFA.”

BOC Protecting Group References

• [1] S. M. Bauer, R. W. Armstrong, J. Am. Chem. Soc. 1999, 121, 6355 | Total Synthesis of Motuporin (Nodularin-V)
• [2] S.P Bew, S.D Bull, S.G Davies, Tetrahedron Lett. 2000, 41, 7577 | Polymer supported oxazolidin-2-ones derived from L-serine – A cautionary tale
• [3] R. Downham, F. W. Ng, L. E. Overman, J. Org. Chem 1998, 63, 9096 | Asymmetric Construction of the Diazatricyclic Core of the Marine Alkaloids Sarains A−C
• [4] M. Stawikowski, G. B. Fields, Curr. Protoc. Protein Sci. 2002, 18.1 | Introduction to Peptide Synthesis
• [5] Chem. Asian J. 2008, 3, 413 | Total Synthesis of Thiopeptide Antibiotics GE2270A, GE2270T, and GE2270C1
• [6] Org. Chem. Front., 2018, 5, 1431 | Total synthesis of teixobactin and its stereoisomers
• C. Agami, F. Couty, Tetrahedron 2002, 58, 2701 | The reactivity of the N-Boc protecting group: an underrated feature
• P. Kocienski, Protecting Groups (Thieme Verlag)
• P. Wuts, T. Greene, Greene’s Protective Groups in Organic Synthesis (Wiley)