Carboxylic Acid Protecting Groups¶
Alkyl Esters¶
Alkyl esters are the most prominent type of carboxylate protecting group. Most of the carbamates used to protect amines have an analogous ester used for protecting the carboxylate. Esters are more easily cleaved with aqueous base than are carbamates. They are easily installed and allow a wide variety of deprotection conditions. Usually, formation entails DCC/DMAP ester coupling or alkylation of carboxylate using alkyl halide. The Mitsunobu reaction is another option.
Me (Methyl)¶
Installation and removal of the methyl protecting group is usually straightforward. Deprotection requires aqueous base. Base-mediated epimerization at the alpha-carbon of amino acids is a concern but the methyl remains one of the most popular C-terminus protecting groups in solution because LiOH generally does not cause epimerization. The methyl ester can usually be cleaved in the presence of other esters. However, if the conformation of an amide is constrained such that there is loss of resonance, even amides may be unexpectedly cleaved by LiOH. Chemists have gone to extreme lengths to cleave methyl esters while keeping delicate molecules intact and labile chiral centers unepimerized.
tBu (tert-Butyl)¶
The tBu group is a staple in SPPS (the Fmoc/tBu method). tBu esters are installed under a variety of conditions: isobutylene/H2SO4, tBuOH/DCC/DMAP, etc. Many classical esterification techniques may fail. Unlike most esters, tBu is not readily cleaved with base or nucleophile and is therefore fully orthogonal to Fmoc. tBu is removed by acids. Usually moderately strong acids are required, but formic acid at room temperature has been used.
Tip
Including scavengers is generally a good idea to quench reactive tBu cation and isobutylene. Any environment of sufficient acidity to remove a Boc group will also cleave a tBu ester. Often, amino acids with a tBu carboxylate protecting group are commercially available.
Allyl¶
The allyl ester is frequently used by our lab as an Fmoc and acid orthogonal carboxylate protecting group. It is removed by palladium(0)-catalyzed allyl transfer to a nucleophilic scavenger.
Propargyl¶
Propargyl deserves mention because its removal with benzyltriethylammonium tetrathiomolybdate in acetonitrile is very orthogonal to almost any other protecting group. Protection (propargyl bromide, K2CO3) and deprotection are compatible with Boc, Fmoc, Z, and allyl ester. Only a slight excess of the tetrathiomolybdate is required. This protecting group appears to be compatible with classical solution-phase peptide synthesis (DCC/HOBt/NMM/MeCN), although compatibility with Fmoc deprotection may not be as good.
Bn (Benzyl)¶
Benzyl esters are prepared by methods typical of esters. Benzyl esters are useful because they may be cleaved by hydrogenolysis, including transfer hydrogenolysis. The combination of silane and Pd(OAc)2 converted Boc-L-allylglycine benzyl ester to Boc-L-allylglycine silyl ester (easily hydrolyzed) in 100% yield.
PMB (para-Methoxybenzyl)¶
PMB esters are removed by oxidative conditions (DDQ) or by strong acids.
DMB (2,4-Dimethoxybenzyl)¶
DMB esters are similar to PMB but more acid-labile due to the additional methoxy group.
pNB (para-Nitrobenzyl)¶
pNB esters are removed by reductive conditions (zinc, SnCl2) or by hydrogenolysis.
Trt (Trityl)¶
Trityl esters are extremely labile to acids and should not be regarded as a general use protecting group. However, the conditions of Fmoc SPPS are consistently basic, and trityl protecting groups are useful, particularly trityl-type resins. Trityl esters are cleaved with weak or dilute acids. The trityl-type protecting groups afford excellent protection against nucleophilic attack, unlike most esters.
2CT (2-Chlorotrityl)¶
Mainly recognized as the basis for 2-chlorotrityl polystyrene resin used heavily in most peptide synthesis labs, 2CT is a highly acid-sensitive protecting group (although not as sensitive as trityl). 2CT esters are easily formed from 2-chlorotrityl chloride and carboxylate salts. 2CT resin is usually cleaved using 1 or 2% TFA in DCM or 20-30% HFIP in DCM.
Fm (Fluorenyl)¶
The Fm protecting group is removed under conditions similar to those used to remove Fmoc (piperidine or diethylamine in DMF or DCM). It is essentially the carboxylic acid protecting counterpart to the Fmoc group. It is installed and removed from the C-terminus without epimerization.
TCE (2,2,2-Trichloroethyl)¶
The TCE ester is formed under the usual conditions and cleaved rapidly using various metals (usually zinc dust) in various solvents. The zinc is then removed by filtration.
TMSE (2-Trimethylsilylethyl)¶
TMSE is removed with fluoride sources or acids. The TMSE ester has been retained during Boc removal -- Boc was removed in the presence of TMSE protection using 4 M HCl (probably in dioxane) in 99% yield. However, if simultaneous Boc and TMSE removal is desired, 10% TFA/DCM may be used. It has been used in the synthesis of complex cyclic peptides. TMSE is compatible with catalytic hydrogenation conditions.
Dmnb (Dimethoxynitrobenzyl)¶
Dmnb is a photolabile protecting group for carboxylic acids, removed by UV irradiation.