© Ravi Divakaran, 2008.

Protecting groups in organic synthesis

Protecting groups for amino, hydroxyl, thiol, carboxyl and carbonyl groups

The use of protecting groups is of great importance in synthetic organic chemistry, when we want reactions to take
place at only a particular functional group when other reactive groups are also present. This concept can be easily
illustrated by considering the synthesis of a desired dipeptide molecule from the starting aminoacid molecules (the
concept can be extended to polypeptide synthesis). Let the dipeptide to be synthesized be

H2N-A-CO-NH-B-COOH (or abbreviated as AB)

starting from

H2N-A-COOH (abbreviated as A) and NH2-B-COOH (abbreviated as B)

If one mixes together A and B and allow them to react, one can easily see that many other products such as BA,
AA, BB, AAA, BBB, ABA, BAB, AAB … will all be produced and the reaction will be a total loss. On the other
hand, if we block the amino group of A and the acid group of B,

P1-HN-A-COOH and NH2-B-COO-P2

Then only the acid group of A and the amino group of B are free to react, giving only the desired product AB. The
protecting groups are removed after reaction.

Desirable properties of a protecting group:

(1) Must react easily with the functional group to be protected under mild conditions.
(2) Must be stable to the reaction conditions after protection.
(3) Must be easily removable when required without affecting other parts of the molecule.

In peptide synthesis, after introducing the protecting groups, the amide (or peptide) linkages are produced by
reacting in presence of a coupling agent such as N,N-dicyclohexyl carbodiimide (or DCC). The water molecule
produced by the condensation of the amino and carboxylic acid group is absorbed by DCC, which is converted to a
urea derivative that can be easily removed, for example by chromatography.

N C N + H2O N C NH
H

DCC DCC.H2O

P1-HN-A-COOH + NH2-B-COO-P2 + DCC → P1-HN-A-CO-NH-B-COO-P2 + DCC.H2O

↓ deprotect

H2N-A-CO-NH-B-COOH

All these reactions are usually carried out in solution (known as solution-phase polypeptide synthesis) and
isolation / purification steps are necessary after each condensation step. This process is thus very laborious.
Professor Merrifield (Nobel Prize 1984) introduced a new easier method for peptide synthesis, in which the first
aminoacid molecule is attached to a solid resin at the COOH group (NH2 group is free). The resin is then treated
successively with the required sequence of amino-protected aminoacid solutions in presence of DCC. After each
treatment, the resin is simply washed free of the excess reagents and the protecting group at the end is removed.
The peptide chain thus “grows” as a branch from the solid polymer substrate. The protecting group usually
employed is FMOC.

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This method is commonly known as the Merrifield synthesis or solid-phase peptide synthesis (SPPS), and
automated machines that can be programmed to produce the required peptide when supplied with the aminoacid
solutions are now available (see picture on next page).

There are many reagents for protecting the amino group as the carbamate (carbamic acid is H2N-COOH), such as
the benzyloxycarbonyl group (abbreviated as Cbz or simply Z), the t-butoxycarbonyl group (abbreviated as
Boc) and the 9-fluorenylmethoxycarbonyl group (abbreviated as Fmoc). All these are stable in acid medium, but
can be easily removed by hydrogenolysis or weakly basic medium.

The Advanced ChemTech (ACT) model 396MPS automatic peptide synthesizer.

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1. Benzyloxycarbonyl group (abbreviated as Cbz [old name carbobenzyloxy] or simply Z):

The reagent used is benzyloxycarbonyl chloride.

Protection:

(1) aq. NaOH

-CH2OCOCl + H2N-R -CH2OCO-HN-R or Z-NH-R
(2) aq. H+

benzyloxycarbonyl
chloride

Deprotection:
H2
-CH2OCO-HN-R -CH3 + CO2 + H2N-R
Pd

or
HBr
-CH2OCO-HN-R -CH2Br + CO2 + H2N-R

2. t-butoxycarbonyl group (BOC): The reagent used is tertiary butoxy carbonyl azide.

Protection:

- HN3
(CH3)3C-O-CO-N3 + H2N-R (CH3)3C-O-CO- HN-R or (BOC)-NH-R

t-butoxycarbonyl
azide

Deprotection:
H2
(CH3)3 C-O-CO- HN-R (CH3)3CH + CO2 + H2N-R
Pd

or
HBr
(CH3)3C-O-CO- HN-R (CH3)2C =CH2 + CO2 + H2N-R

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3. 9-fluorenylmethoxycarbonyl group (FMOC):

Protection:

(1) aq. NaOH

-CH2 -O-CO-Cl + H2N-R -CH2-O-CO- HN-R or (FMOC)-NH-R
(2) aq. H+

9-fluorenyl methoxycarbonyl
chloride

Deprotection:

H2
-CH2-O-CO- HN-R -CH3 + CO2 + H2N-R
Pd

FMOC protecting group can also be easily removed by treating with several amines such as piperidine through a β-
elimination.

4. Triphenylmethyl group (trityl group):

The triphenylmethyl group is a good protecting group for alcohols and amines, and can be easily removed by
hydrogenolysis or mild acid hydrolysis. It is selective for primary alcohols in presence of secondary and tertiary
alcoholic groups, and has been utilized in the synthesis of adenosine triphosphate.

AlCl3
3 Ph-H + CCl4 Ph3C-Cl
- 3 HCl

H2 / Pd
Ph3C-Cl + HOCH2-R Ph3C- OCH2-R Ph3CH + HOCH2-R
trityl chloride

H2 / Pd
Ph3C-Cl + H2N-R Ph3C- HN-R Ph3CH + H2N-R

Triphenylmethyl chloride can be prepared from benzene and carbon tetrachloride through Friedel-Craft’s reaction.

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5. Phthalic anhydride:

Phthalimide has been used extensively in the Gabriel synthesis of amino acids for generating amino groups.

CO CO KOH
CO
O + NH3 NH NK
CO CO CO

R-Br

COOH CO
OH-
+ RNH2 N-R
COOH CO

The phthaloyl group can also act as a protecting group for the amino group if it can be introduced and removed
under milder conditions in which the peptide linkage is not affected. The phthaloyl group can be introduced by
heating the aminoacid with phthalic anhydride, and can be removed under mild conditions by treating with
hydrazine as shown in the following sequence of reactions:

CO heat CO
O + H2N-A-COOH N-A-COOH
CO CO

NH2-NH2
CO
NH
NH
+ H2N-A-COOH
CO

6. The benzyl group:

The benzyl group can be used to protect –COOH, -OH and –SH groups. The reagent used is usually benzyl
chloride.
H+ H+
R-COOH + HO-CH2-Ph R-CO-O-CH2-Ph R-COOH + HO-CH2-Ph
benzyl benzyl ester
alcohol
H2 / Pd
R-COOH + CH3-Ph
toluene
Na / NH3
R-SH + Cl-CH2-Ph R-S-CH2-Ph R-SH + CH3-Ph
benzyl thioether

Na / NH3
R-OH + Cl-CH2-Ph R-O -CH2-Ph R-OH + CH3-Ph
benzyl ether

Deprotection of the acid ester is achieved by acid hydrolysis or catalytic hydrogenation. The thioether and ether are
converted back to thiol and alcohol by reduction with metallic sodium in liquid ammonia.

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7. The tetrahydropyranyl group:

This is a protecting group for alcohols. The reagent used is dihydropyran, which forms an acetal with alcohols in
anhydrous acid medium. The group can be removed using aqueous mineral acid.

H+ H+
+ HO-R + HO-R
O O OR O

H+

O-R O OR
O O
+ H

8. The trialkyl silyl group:

The trimethylsilyl group is a good protecting group for amino, hydroxyl and carboxylic acid groups. The derivatives
are easily made by the reaction of the carboxylic acid, alcohol or amine with chlorotrimethylsilane (same as
trimethylsilyl chloride) in the presence of a tertiary amine base like pyridine.
CH3
| pyridine NaOH
R-CO-OH + Cl-Si-CH3 R-CO-O-Si(CH3)3 R-COONa + HO-Si(CH3)3
| - HCl
CH3
pyridine HF
R-OH + Cl-Si(CH3)3 RO-Si(CH3)3 R-OH + F-Si(CH3)3
- HCl
pyridine CH3OH
R-NH2 + Cl-Si(CH3)3 R-NH-Si(CH3)3 R-NH2 + CH3O-Si(CH3)3
- HCl

In general the trimethylsilyl ethers of alcohols are very susceptible to solvolysis in protic media and cannot endure
the reaction conditions of a multi-step synthesis. t-butyldimethylsilyl ethers give better results, and can be prepared
by the reaction of alcohols with t-butylchlorodimethylsilane in presence of imidazole.

ROH

Si(CH3)2C4H9-t
N N
+ t-C4H9(CH3)2SiCl +
ROSi(CH3)2C4H9-t
N N
H H

These derivatives are not affected by conditions of synthetic transformations and more resistant to hydrolysis than
trimethylsilyl ethers. They can be reconverted in to the alcohol by treatment with HF (cleavage of a Si-O bond by
nucleophylic attack by fluoride ion and formation of an even stronger Si-F bond).

Another advantage of t-butyldimethylsilyl ethers is that the bulky protecting group can sometimes be used to control
the stereochemistry of a reaction at a nearby functional group. For example,

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CH3 CH3
(CH3)2CuLi
O OSi(CH3)2C4H9-t O OSi(CH3)2C4H9-t

CH3

The attack of lithium dimethylcuprate on the cyclopentanone is directed entirely to the top face of the molecule.

9. The t-butyl group:

The carboxylic acid group is normally protected by converting into the t-butyl ester using isobutylene (same as 2-
methyl propene) in presence of sulphuric acid.

H+
R-CO-OH + H2C=C(CH3)2 R-CO-O-C(CH3)3

The protecting group may be removed by mild acid hydrolysis through the readily-formed carbonium ion.

H+
R-CO-O-C(CH3)3 R-CO-+O--C(CH3)3 R-CO-OH + +C(CH
3)2
|
H

- H+
+ C(CH )
3 2 + H2O HO-C(CH3)2

10. Acetals and thioacetals:

Aldhydes react with primary alcohols in anhydrous acid medium to give acetals which can be isolated. Since all
steps in the reaction are reversible, aqueous acid hydrolyses the acetal, reverting it back to the aldehyde and
alcohol. Therefore the formation of acetals can be used as protecting groups for both the carbonyl group as well as
alcohols.

R CH O R CH O H A R CH OH + A-

O O+
CH3 H CH3 H

- H+

R CH R CH +OH
2
R CH OH
- H 2O H+
+O CH3 O CH3 O CH3
hemiacetal

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H
O+ CH3 O CH3
CH3OH - H+
+CH CH R CH
R R
O CH3
O CH3 O CH3 acetal

Ketones do not give acetals with monohydric alcohols, but react with glycols (or 1,2-diols) to give cyclic ketals. Thus
ketones can form protecting groups for 1,2-diols.

O
HO H+
(CH3)2C=O + (CH3)2C + H2O
HO O

Both aldehydes and ketones give the thio-acetals and thio-ketals when treated with mercaptans in presence of
acid. Therefore both can act a protecting groups for –SH groups.

SR'
H+
(CH3)2C=O + 2 R'-SH (CH3)2C + H2O
SR'