Protecting group
A protecting group or protective group is introduced into a molecule by chemical modification of a
In many preparations of delicate
Protecting groups are more common in small-scale laboratory work and initial development than in industrial production because they add additional steps and material costs. However, compounds with repetitive functional groups – generally, biomolecules like peptides, oligosaccharides or nucleotides – may require protecting groups to order their assembly. Also, cheap chiral protecting groups may often shorten an enantioselective synthesis (e.g. shikimic acid for oseltamivir).
As a rule, the introduction of a protecting group is straightforward. The difficulties honestly lie in their stability and in selective removal. Apparent problems in synthesis strategies with protecting groups are rarely documented in the academic literature.[2]
Orthogonal protection
Orthogonal protection is a strategy allowing the specific deprotection of one protective group in a multiply-protected structure. For example, the amino acid tyrosine could be protected as a benzyl ester on the carboxyl group, a fluorenylmethylenoxy carbamate on the amine group, and a tert-butyl ether on the phenol group. The benzyl ester can be removed by hydrogenolysis, the fluorenylmethylenoxy group (Fmoc) by bases (such as piperidine), and the phenolic tert-butyl ether cleaved with acids (e.g. with trifluoroacetic acid).
A common example for this application, the Fmoc peptide synthesis, in which peptides are grown in solution and on solid phase, is very important.[3] The protecting groups in solid-phase synthesis regarding the reaction conditions such as reaction time, temperature and reagents can be standardized so that they are carried out by a machine, while yields of well over 99% can be achieved. Otherwise, the separation of the resulting mixture of reaction products is virtually impossible (see also § Industrial applications).[4]
-
Schematic diagram of a solid-state peptide synthesis with orthogonal protecting groups X and Y
-
Fmoc solid state peptide synthesis with orthogonal protecting groups
A further important example of orthogonal protecting groups occurs in
Cleavage categorization
Many reaction conditions have been established that will cleave protecting groups. One can roughly distinguish between the following environments:[5]
- Acid-labile protecting groups
- Base-labile protecting groups
- Fluoride-labile protecting groups
- Enzyme-labile protecting groups
- Reduction-labile protecting groups
- Oxidation-labile protecting groups
- Protecting groups cleaved by heavy metal salts or their complexes.
- Photolabile protecting groups
- Double-layered protecting groups
Various groups are cleaved in acid or base conditions, but the others are more unusual.
Fluoride ions form very strong bonds to
Catalytic hydrogenation removes a wide variety of benzyl groups: ethers, esters, urethanes, carbonates, etc.
Only a few protecting groups can be detached oxidatively: the methoxybenzyl ethers, which oxidize to a
Allyl compounds will isomerize to a vinyl group in the presence of noble metals. The residual enol ether (from a protected alcohol) or enamine (resp. amine) hydrolyzes in light acid.
Photolabile protecting groups bear a chromophore, which is activated through radiation with an appropriate wavelength and so can be removed.[6] For examples the o-nitrobenzylgroup ought be listed here.
The rare double-layer protecting group is a protected protecting group, which exemplify high stability.
Common protecting groups
Alcohol protecting groups
The classical protecting groups for alcohols are esters, deprotected by nucleophiles; triorganosilyl ethers, deprotected by acids and fluoride ions; and (hemi)acetals, deprotected by weak acids. In rarer cases, a carbon ether might be used.
The most important esters with common protecting-group use are the
- Chloroacetyl > acetyl > benzoyl > pivaloyl
Triorganosilyl sources have quite variable prices, and the most economical is
Aliphatic methyl ethers cleave with difficulty and only under drastic conditions, so that these are in general only used with quinonic phenols. However, hemiacetals and acetals are much easier to cleave.
List
Esters:
- Acetyl (Ac) – Removed by acid or base (see Acetoxy group).
- Benzoyl(Bz) – Removed by acid or base, more stable than Ac group.
- Pivaloyl(Piv) – Removed by acid, base or reductant agents. It is substantially more stable than other acyl protecting groups.
Silyl ethers:
- Triethylsilyl — 10–100× stabler than a TMS group.[8] Cleaved with trifluoroacetic acid in water/tetrahydrofuran,[9] acetic acid in water/tetrahydrofuran,[10] or hydrogen fluoride in water or pyridine[11]
- tert-Butyldimethylsilyl (TBDMS or TBS) — Cleaved with acetic acid in tetrahydrofuran/water,tetrabutylammonium fluoride in THF.[17] Commonly protects 2'-hydroxy function in oligonucleotide synthesis.
- Triisopropylsilyl (TIPS) ethers) — Similar conditions to TBS but longer reaction times.[18]
- tert‑Butyldiphenylsilyl (TBDPS) — Similar conditions to TBS but even longer reaction times (100–250× slower than TBS and 5–10× slower than TIPS)
Benzyl ethers:
- Benzyl (Bn) — Removed by hydrogenolysis.[19]Bn group is widely used in sugar and nucleoside chemistry.
- and hydrogenolysis
- p,m‑Dimethoxybenzyl ether — Removed via oxidation with DDQ or ceric ammonium chloride[24]
Acetals:
- Dimethoxytrityl, [bis-(4-methoxyphenyl)phenylmethyl] (DMT) — Removed by weak acid. DMT group is widely used for protection of 5'-hydroxy group in nucleosides, particularly in oligonucleotide synthesis.
- Methoxytrityl [(4-methoxyphenyl)diphenylmethyl] (MMT) – Removed by acid and hydrogenolysis.
- Benzyloxymethyl — Comparable stability to MOM, MEM und SEM,[25] but also admits reductive removal: sodium in liquid ammonia,[26][27] catalytic hydrogenation (palladium hydroxide on activated carbon), or Raney nickel in ethanol[28][29]
- Ethoxyethyl ethers (EE) – Cleavage more trivial than simple ethers e.g. 1N hydrochloric acid[30]
- Methoxyethoxymethyl ether (MEM) — Removed by hydrobromic acid in tetrahydrofuran[31] or zinc bromide in dichloromethane[32]
- Methoxymethyl ether (MOM) — Removed by 6 M hydrochloric acid in tetrahydrofuran/water[33]
- Methylthiomethyl ether — Removed by acid[citation needed] or soft metal oxidants: base-buffered mercuric chloride in wet acetonitrile[36] or silver nitrate in wet tetrahydrofuran[37]
- Tris(isopropyl)silyloxymethyl (TOM) — Commonly protects 2'-hydroxy function in oligonucleotide synthesis.
- tetrabutylammonium fluoride in HMPT (Hexamethyl phosphoric acid triamide) or in tetrahydrofuran[40][41]
Other ethers:
- p-Methoxyphenyl ether (PMP) – Removed by oxidation.[citation needed]
- Tert-butyl ethers (tBu) – Removed with anhydrous trifluoroacetic acid, hydrogen bromide in acetic acid, or 4 N hydrochloric acid[42]
- Allyl — Removed with potassium tert‑butoxide[43] DABCO in methanol, palladium on activated carbon, or diverse platinum complexes – conjoined with acid workup.[44]
- Methyl ethers – Cleavage is by TMSI in dichloromethane or acetonitrile or chloroform. An alternative method to cleave methyl ethers is BBr3 in DCM
- Tetrahydrofuran (THF)[clarification needed] – Removed by acid.
1,2-Diols
The 1,2‑diols (
An exceptional case appears with the benzylideneprotecting group,which also admits reductive cleavage. This proceeds either through catalytic hydrogenation or with the hydride donor diisobutyl aluminum hydride (DIBAL). The cleavage with DIBAL deprotects one alcohol group, for the benzyl moiety stays as a benzyl ether on the second, sterically hindered hydroxy group.[45][46]
Amine protecting groups
Other, more exotic amine protectors are the
Selection
Carbamates:
- Carbamate group – Removed by acid and mild heating.
- Carbobenzyloxy (Cbz) group — Removed by hydrogenolysis: hydrogen and palladium on activated carbon,[50] or lithium or sodium in liquid ammonia.[51]
- p-Methoxybenzyloxycarbonyl (Moz or MeOZ) group – Removed by hydrogenolysis, more labile than Cbz
- solid phase peptide synthesis.
- 9-Fluorenylmethyloxycarbonyl (solid phase peptide synthesis
- Allyloxycarbamate group — Removed with complexes of metals like palladium(0) or nickel(0).[58]
Other amides:
- Benzoyl (Bz) groups — common in oligonucleotide synthesis for protection of N4 in cytosine and N6 in adenine. Removed by base, often aqueous or gaseous ammonia or methylamine. Too stable to readily remove from aliphatic amides.
- Troc (trichloroethyl chloroformate ) group – Removed by Zn insertion in the presence of acetic acid
- sodium naphthalenide)
- Other sulfonamide (Nosyl & Nps) groups — Removed by samarium iodide, thiophenol or other soft thiol nucleophiles, or tributyltin hydride[59]
Benzylamines:
- Benzyl (Bn) group – Removed by hydrogenolysis
- p-Methoxybenzyl (PMB) – Removed by hydrogenolysis, more labile than benzyl
- 3,4-Dimethoxybenzyl (DMPM) – Removed by hydrogenolysis, more labile than p-methoxybenzyl
- ammonium cerium(IV) nitrate(CAN)
Carbonyl protecting groups
The most common protecting groups for carbonyls are acetals and typically cyclic acetals with diols. The runners-up used are also cyclic acetals with 1,2‑hydroxythiols or dithioglycols – the so-called O,S– or S,S-acetals.
Overall, trans-acetalation plays a lesser role in forming protective acetals; they are formed as a rule from glycols through dehydration. Normally a simple glycol like ethylene glycol or 1,3-propadiol is used for acetalation.Modern variants also use glycols, but with the hydroxyl hydrogens replaced with a trimethylsilyl group.[60][61]
Acetals can be removed in acidic aqueous conditions. For those ends, the mineral acids are appropriate acids. Acetone is a common cosolvent, used to promote dissolution. For a non-acidic cleavage technique, a palladium(II) chloride acetonitrile complex in acetone[62] or iron(III) chloride on silica gel can be performed with workup in chloroform.[63]
Cyclic acetals are very much more stable against acid hydrolysis than acyclic acetals. Consequently acyclic acetals are used practically only when a very mild cleavage is required or when two different protected carbonyl groups must be differentiated in their liberation.[64]
Besides the O,O-acetals, the S,O- and S,S-acetals also have an application, albeit scant, as carbonyl protecting groups too. Thiols, which one begins with to form these acetals, have a very unpleasant stench and are poisonous, which severely limit their applications. Thioacetals and the mixed S,O-acetals are, unlike the pure O,O-acetals, very much stabler against acid hydrolysis. This enables the selective cleavage of the latter in the presence of sulfur-protected carbonyl groups.
The formation of S,S-acetals normally follows analogously to the O,O-acetals with acid catalysis from a dithiol and the carbonyl compound. Because of the greater stability of thioacetals, the equilibirum lies on the side of the acetal. In contradistinction to the O,O‑acetal case, it is not needed to remove water from the reaction mixture in order to shift the equilibrium.[65]
S,O-Acetals are hydrolyzed a factor of 10,000 times faster than the corresponding S,S-acetals. Their formation follows analogously from the thioalcohol. Also their cleavage proceeds under similar conditions and predominantly through mercury(II) compounds in wet acetonitrile.[66]
For aldehydes, a temporary protection of the carbonyl group the presence of ketones as hemiaminal ions is shown below. Here it is applied, that aldehydes are very much more activated carbonyls than ketones and that many addition reactions are reversible.[67][68]
Types of protectants
- Ketals– Removed by acid. Normally, the cleavage of acyclic acetals is easier than of cyclic acetals.
- Lewis acids.
- Dithianes – Removed by metal salts or oxidizing agents.
Carboxylic acid protecting groups
The most important protecting groups for carboxylic acids are the esters of various alcohols. Occasionally, esters are protected as ortho-esters or oxazolines.[69]
Many groups can suffice for the alcoholic component, and the specific cleaving conditions are contrariwise generally quite similar: each ester can be hydrolyzed in a basic water-alcohol solution. Instead, most ester protecting groups vary in how mildly they can be formed from the original acid.
Protecting groups
- Benzyl esters — Also removed by hydrogenolysis.[77]
- Benzhydryl esters — Same as benzyl, but easier to cleave[78]
- 2,6‑Dialkylphenols (e.g. DBU-catalyzed high-pressure methanolysis at room temperature.[84]
- Allyl esters — As with allyl ethers, also removed by diverse platinum complexes – connected with acid workup[85]
- organometallicreagents.
- Orthoesters– Converted to standard ester by mild aqueous acid
- Oxazoline – Removed by strong hot acid (pH < 1, T > 100 °C) or alkali (pH > 12, T > 100 °C), but not e.g. LiAlH4, organolithium reagents or Grignard (organomagnesium) reagents
Alkene
Alkenes rarely need protection or are protected. They are as a rule only involved in undesired side reactions with electrophilic attack, isomerization or catalytic hydration. For alkenes two protecting groups are basically known:
- Temporary halogenation with bromine to a trans‑1,2‑dibromoalkane: the regeneration of the alkene then follows with preservation of conformation via elemental zinc[86][87][88][89][90] or with titanocene dichloride.[91]
- Protection through a Diels-Alder reaction: the transformation of an alkene with a diene leads to a cyclic alkene, which is nevertheless similarly endangered by electrophilic attack as the original alkene. The cleavage of a protecting diene proceeds thermically, for the Diels-Alder reaction is a reversible (equilibrium) reaction.[92][93][94]
Phosphate protecting groups
- 2-cyanoethyl – removed by mild base. The group is widely used in oligonucleotide synthesis.
- Methyl(Me) – removed by strong nucleophiles e.c. thiophenole/TEA.
Terminal alkyne protecting groups
For alkynes there are in any case two types of protecting groups. For terminal alkynes it is sometimes important to mask the acidic hydrogen atom. This normally proceeds from deprotonation (via a strong base like
In order to protect the triple bond itself, sometimes a transition metal-alkyne complex with dicobalt octacarbonyl is used. The release of the cobalt then follows from oxidation.[97][98][99][100][101]
Other
-
Photolabile protecting groupsAs aphotochemical transesterification by trimethylsilyldiazomethane utilizing the kinetic isotope effect:[102] Due to this effect the quantum yieldfor deprotection of the right-side ester group is reduced and it stays intact. Significantly by placing the deuterium atoms next to the left-side ester group or by changing the wavelength to 254 nm the other monoarene is obtained.
Criticism
The use of protective groups is pervasive but not without criticism.
Industrial applications
Although the use of protecting groups is not preferred in industrial syntheses, they are still used in industrial contexts, e.g.
An important example of industrial applications of protecting group theory is the synthesis of
In order to prevent oxidation of the secondary alcohols with potassium permanganate, they are protected via acetalation with acetone and then deprotected after the oxidation of the primary alcohols to carboxylic acids.[107]
A very spectacular example application of protecting groups from
The introduction or modification of a protecting group occasionally influences the reactivity of the whole molecule. For example, diagrammed below is an excerpt of the synthesis of an analogue of
The exchange of a protecting group from a methyl ether to a MOM-ether inhibits here the opening of an epoxide to an aldehyde.
Protecting group chemistry finds itself an important application in the automated synthesis of peptides and nucleosides. The technique was introduced in the field of peptide synthesis by Robert Bruce Merrifield in 1977.[111] For peptide synthesis via automated machine, the orthogonality of the Fmoc group (basic cleavage), the tert‑butyl group (acidic cleavage) and diverse protecting groups for functional groups on the amino acid side-chains are used.[112] Up to four different protecting groups per nucleobase are used for the automated synthesis of DNA and RNA sequences in the oligonucleotide synthesis. The procedure begins actually with redox chemistry at the protected phosphorus atom. A tricoordinate phosphorus, used on account of the high reactivity, is tagged with a cyanoethyl protecting group on a free oxygen. After the coupling step follows an oxidation to phosphate, whereby the protecting group stays attached. Free OH-groups, which did not react in the coupling step, are acetylated in an intermediate step. These additionally-introduced protecting groups then inhibit, that these OH-groups might couple in the next cycle.[113]
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- ^ Peter G.M. Wuts, Theodora W. Greene: Green's Protective Groups in Organic Synthesis, 4th Ed., John Wiley & Sons Inc., Hoboken, New Jersey, pp. 10–13; ISBN 0-471-69754-0.
- J. Am. Chem. Soc., 1993, 115, pp. 6094–6100; doi:10.1021/ja00067a026.
- .
- ^ Weng C. Chan, Peter D. White: Fmoc Solid Phase Peptide Synthesis. Reprint 2004, Oxford University Press, ISBN 0-19-963724-5.
- ^ Serge L. Beaucage, Radhakrishman P. Iyer: "Advances in the Synthesis of Oligonucleotides by the Phosphoramidite Approach", in: Tetrahedron, 1992, 48, pp. 2223–2311; doi:10.1016/S0040-4020(01)88752-4.
Further reading
- Philip J. Kocieński: Protecting Groups, 1st ed., Georg Thieme Verlag, Stuttgart 1994, ISBN 3-13-135601-4.
- Peter G.M. Wuts, Theodora W. Greene: Green's Protective Groups in Organic Synthesis, 4th Ed., John Wiley & Sons Inc., Hoboken, New Jersey, ISBN 0-471-69754-0.
- Michael Schelhaas, Herbert Waldmann: "Schutzgruppenstrategien in der organischen Synthese", in: Angewandte Chemie, 1996, 103, pp. 2192–2219; doi:10.1002/ange.19961081805 (in German).
- Krzysztof Jarowicki, Philip Kocieński: "Protecting groups", in: J. Chem. Soc., Perkin Trans. 1, 1998, pp. 4005–4037; doi:10.1039/A803688H.
External links
- Introduction of protecting group and mechanism of deprotection
- Senior undergraduate study notes on this subject, from Prof. Rizzo.
- A further set of study notes in tutorial form, with guidance and comments, from Profs. Grossman and Cammers.
- A review by Prof. Kocienski.
- A user site excerpting the classic Greene and Wuts text regarding stability of a few key groups, from this reference's extensive tables.
- Organic-Reaction.com: Protecting Group
- Universität Marburg: Schutzgruppen in der organischen Synthesechemie(in German)