Pentafluorophenol

[771-61-9]  · C6HF5O  · Pentafluorophenol  · (MW 184.07)

(preparation of pentafluorophenyl active esters for peptide synthesis;1 formylating agent; preparation of aromatic fluoro derivatives)

Physical Data: white solid, mp 34-36 °C; bp 143 °C; fp >72 °C; nD 1.4263.

Solubility: sol most organic solvents, particularly aprotic ones.

Form Supplied in: available commercially.

Handling, Storage, and Precautions: toxic and irritant. Harmful if swallowed, inhaled, or absorbed through the skin. Incompatible with strong oxidizing agents, bases, acid chlorides, and anhydrides. Keep away from heat and naked flames: combustible solid/liquid. Store in a cool, dry place.

Use in Peptide Synthesis.

Solution Techniques.

Simple alkyl esters of amino acids (which may be protected) undergo aminolysis at a rate too slow for peptide bond synthesis. Phenyl esters are more reactive and, if electronegative substituents are present on the ring, may undergo aminolysis at rates similar to those of anhydrides. The overriding requirements in peptide bond formation are efficiency and freedom from side reactions. Esters of pentafluorophenol have found wide application in the synthesis of peptides (cf. Pentachlorophenol).1a-c Pentafluorophenol (1) serves as a coupling reagent, i.e. a compound added to a mixture of carboxyl and amino components to promote condensation. However it is very difficult to find efficient coupling reagents which do not give undesirable side reactions. Kinetic studies have shown the superiority of pentafluorophenyl esters compared to other coupling reagents with respect to speed of coupling (and thus lowering or eliminating undesirable reactions, e.g. a-hydrogen abstraction leading to racemization).2a,b Relative rates are OPFP >> OPCP > ONp, corresponding to 111:3.4:1, where PFP = pentafluorophenyl; PCP = pentachlorophenyl; Np = nitrophenyl.

Pentafluorophenyl esters have been used in both solution and solid phase peptide syntheses, the difference being that solid phase synthesis involves linking the peptide to a solid support (see below), whilst solution techniques involve just one phase. There are many examples of pentafluorophenyl esters being used in peptide synthesis,1a,3a-e e.g. the peptide sequence t-Boc-Phe-Pro-Pro-Phe-Phe-Val-Pro-Pro-Ala-Phe-OMe3a and the alkaloid peptide (2)3b have been synthesized by these methods.

More recently, the base labile 9-fluorenylmethoxycarbonyl (Fmoc) group has become well established in peptide synthesis for the protection of amino functionalities.4,5 The problem associated with this group is cleavage of the Fmoc group by the free amino component to be acylated, which results in double acylations. The principal method of avoiding this now is to use the Fmoc group in association with highly reactive pentafluorophenyl esters to greatly increase the rate of coupling compared with the undesirable reactions. Formation of these esters is shown in eq 1.4

For example, this methodology was first used in the synthesis of Fmoc-glycyl-L-tryptophyl-L-leucyl-L-aspartyl-L-phenylalaninamide (Fmoc-Gly-Trp-Leu-Asp-Phe-NH2) with the isolation of all pentafluorophenyl ester intermediates in excellent yields (75-99%); the coupled amino acids were subsequently prepared stepwise, again in very good yields, with the minimum of undesirable side reactions.4

This method has since been modified and improved further by utilizing 9-fluorenylmethyl pentafluorophenyl carbonate (eq 2).5a

There is a newer alternative method of synthesizing Fmoc-protected pentafluorophenyl ester amino acids employing pentafluorophenyl trifluoroacetate (3).5b

Table 1 gives some typical examples of the N-9-Fluorenylmethoxycarbonyl (Fmoc) amino acids and their pentafluorophenyl (PFP) esters which have been prepared by these methods.4,6,7 The physical data are in agreement with either preparative method, and with early preparations of these compounds.4,5a,b

Solid Phase Peptide Synthesis (SPPS).

Pentafluorophenyl esters have been used in both solution and solid phase peptide synthesis. So far, only solution methods have been considered. The principal of SPPS is incorporation of single amino acid residues into peptide chains built on insoluble polymeric supports. The famous Merrifield paper8 started the tradition of SPPS using t-butoxycarbonyl (Boc) amino acids activated with 1,3-Dicyclohexylcarbodiimide, although this has now been superseded with the introduction of the Fmoc group in polystyrene- and polyamide-based SPPS. The theory of SPPS will not be discussed here. Needless to say, the use of pentafluorophenyl esters in SPPS was inevitable and was first reported by Atherton in 1985.9 Fmoc-amino acid pentafluorophenyl active esters were used in the polyamide solid phase series in polar DMF solutions in the presence of 1-Hydroxybenzotriazole as a catalyst.

The preparation of the decapeptide H-Val-Gln-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-OH (4) will be used as an example of pentafluorophenyl esters in SPPS.9,10 This is a good example to use since it contains normal, sterically hindered, and functionalized amino acids. All Fmoc-pentafluorophenyl esters were prepared by the method of Kisfaludy and Schön already described.4,5 Beaded polymethylacrylamide gel resin was used as the solid phase with fivefold excesses of the pentafluorophenyl esters dissolved in a minimum of DMF. The resin was first functionalized with a reference norleucine residue and then with an acid-labile linkage agent (5).

Esterification of the first residue, glycine, to the free OH used the symmetrical anhydride/4-Dimethylaminopyridine procedure.11 The subsequent peptides were all coupled using standard techniques like those already described above and are fully documented. Slightly varying conditions and catalysts were required for some of the amino acids.10 After addition of the last amino acid, the final Fmoc group was cleaved and the complete decapeptide detached from the support resin using 95% aqueous Trifluoroacetic Acid. Side chain protecting groups were also cleaved simultaneously. Crude peptide analysis was achieved by HPLC and showed the samples obtained by this method to be extremely pure.

More recently, SPPS has also been employed in glycopeptide synthesis.12 There is an excellent review of active esters in SPPS, including pentafluorophenyl esters.13

A New and Efficient Derivative of Pentafluorophenol.14

Pentafluorophenol has found many applications in both solution and solid phase peptide syntheses. Diphenylphosphinic mixed anhydrides are also well known in peptide chemistry. A new and efficient reagent has been prepared from these precursors: pentafluorophenyl diphenylphosphinate (FDPP; 6) which can be used directly as a coupling reagent without side reactions. FDPP is prepared from mixing equimolar amounts of Diphenylphosphinic Chloride, pentafluorophenol (1), and Imidazole in CH2Cl2 at room temperature (eq 3).14

FDPP may be kept refrigerated for several months and is used as an efficient coupling reagent, by simply mixing the carbonyl and amine components with a tertiary amine and FDPP in an organic solvent, of which DMF was found to be the most efficient (eq 4).

FDPP has been used in both solid and solution peptide syntheses and analysis has shown it to have the lowest rate of racemization of any of the common coupling reagents.14

Comparison of Pentafluorophenyl Active Esters with Pentachlorophenyl Esters.15

It is interesting to compare these two compounds with respect to active ester formation since they are very closely related and both have been employed in both liquid and solid phase peptide syntheses (see Pentachlorophenol). Pentachlorophenyl esters generally have higher melting points, which can be of advantage if crystallization is difficult or a compound is of low melting point, e.g. for serine and threonine the oily pentafluorophenyl esters are usually replaced by the pentachlorophenyl esters.

As already mentioned, pentafluorophenyl derivatives are much more reactive than pentachlorophenyl ones. The reason for this is still not clear. Many calculations have been performed on the net atomic energies of these esters and show that there is no significant difference between the environment of the electrophilic center in OPFP esters compared to OPCP ones. Analysis of the carbonyl stretching frequencies of these compounds is quite revealing (Table 2), i.e. there is no significant difference in the carbonyl stretching frequencies of these functionalized esters. This, plus additional evidence from MM calculations and NMR studies, suggests that electronic factors do not play a significant role in determining the reactivity of these esters.

There is however, an important steric effect, as would be expected given the differing sizes of the halogens involved (van der Waals atomic radii = 1.75 Å for Cl and 1.47 Å for F). X-ray crystal analysis is interesting in that it shows there is no intramolecular interaction in OPFP esters and the structure is an extended conformation. The main interaction is the strong dipole-dipole of a negative fluorine to a positive carbon of another PFP ring in a neighboring molecule. CO...NH interactions appear to be only minor in comparison and the carbonyl group and PFP ring are almost perpendicular. Studies have shown that the same conformation applies whether in solid or solution.

One of the explanations offered for the high reactivity of the OPFP ester is neighboring group participation of an ortho fluorine atom in accelerating the collapse of a tetrahedral intermediate transition state, i.e. anchimeric acceleration. This would explain the low solvent effect on aminolysis rates, the high second-order rate constant, and unaffected third-order rate constant. Pentahalogen esters fall midway between quinol-8-yl esters, where there is definite participation, and nitrophenol esters where there is none (from studies on the model system of phenyl acetates and piperidine).15 The PFP ester shows greater interaction than the PCP ester. There are other possible explanations: this could still be explained in steric terms, or by the high solvation of the leaving group (pentafluorophenol is much more soluble and reactive in aprotic solvents than pentachlorophenol).

Formylation Reactions.16

The problem with Acetic Formic Anhydride, the most commonly used formylating agent, is undesirable side reactions, particularly if there are acid sensitive functionalities in the compound. One of the best alternatives is to use pentafluorophenyl formate (7), an easily prepared and stable compound which reacts with N-nucleophiles in minutes at room temperature to yield the N-formyl derivative (eq 5) (Table 3). Significantly, no reaction occurs with alcohols, thiols, or sterically hindered amines.

Preparation of Aromatic Fluoro Derivatives.

Reaction of (1) with VF2, VF4, Vanadyl Trifluoride, or Xenon(II) Fluoride in HF, CFCl3, or MeCN at -30 to 20 °C yields mixtures of perfluoro-2,5-cyclohexadien-1-one together with its 2- and 4-pentafluorophenoxy derivatives and/or perfluoro-6-phenoxy-2,4-cyclohexadien-1-one, along with traces of perfluoro-2-cyclohexen-1-one or perfluoro-p-benzoquinone. Using Antimony(V) Fluoride or NbF4, however, only gives stable complexes or pentafluorophenolates.17

Pentafluorophenol (1) reacts with Phosphorus(V) Chloride in the presence of a base, triethylamine or g-collidine, to yield perfluoropentaphenoxyphosphorane (8) plus perfluorotriphenyl phosphate (9) and perfluorodiphenyl ether (10) (eq 6).18

This reaction has also been used to prepare pentafluorothiophenol phosphorus derivatives. These compounds have been utilized in 31P, 19F, and 1H variable temperature NMR studies on intramolecular ligand rearrangement processes in phosphorus compounds.18

The preparation and reactions of Polyfluoroaromatics, including pentafluorophenol derivatives, have been studied by various Russian workers, who have also evaluated the pentafluorophenoxy group as a leaving group (eq 7).19a

The main product of the reaction was the 4-substituted tetrafluoropyridine, although varying yields of the 2-, 2,6- and 2,4,6-pentafluorophenoxypyridines were obtained depending on the ratios of (11):(1) and also on the levels of Potassium Fluoride, 18-Crown-6, the reaction temperature, and solvent. This reaction has been studied in comparison with 4-NO2C6H4 (which is of similar basicity) and in competition with F- anions.

More recently it has been shown that the substitution reaction of pentafluoropyridine with (1) in the presence of Cesium Fluoride/graphite gave much better yields of (12), but still with traces of the other products. The catalyst activity was found to increase in the order: NaF < KF < RbF < CsF and was similar for the free fluorides and their graphite-supported analogs.19b


1. For examples of early work on pentafluorophenyl esters in peptide synthesis, see: (a) Kisfaludy, L.; Roberts, J. E.; Johnson, R. H.; Mayers, G. L.; Kovacs, J. JOC 1970, 35, 3563 and references therein. (b) Kisfaludy, L.; Schón, I.; Szirtes, T.; Nyéki, O.; Lów, M. TL 1974, 1785 and references therein. (c) Kovacs, J.; Kisfaludy, L.; Ceprini, M. Q. JACS 1967, 89, 183.
2. (a) For a kinetic study of coupling rates and competing reactions, see: Gross, E.; Meienhofer, J. In The Peptides-Analysis, Synthesis and Biology, 2nd ed.; Academic: New York, 1980; p 519; (b) see also Ref. 1(c).
3. There are many examples of solution peptide synthesis utilizing pentafluorophenyl esters. A few notable examples are cited here: (a) Kisfaludy, L.; Schön, I.; Szirtes, T.; Nyéki, O.; Low, M. TL 1974, 1785. (b) Schmidt, U.; Schanbacher, U. LA 1984, 6, 1205. See also Ref. 1(a). (c) Schmidt, U.; Lieberknecht, A.; Griesser, H.; Haeusler, J. LA 1982, 12, 2153. (d) Karel'skii, V. N.; Krysin, E. P.; Antonov, A. A.; Rostovskaya, G. E. Khim. Prir. Soedin. 1982, 1, 96 (CA 1982, 97, 92 730s). (e) Polevaya, L. K.; Vegners, R.; Ars, G.; Grinsteine, I.; Cipens, G. Latv. PSR Zinat. Akad. Vestis, Khim. Ser. 1981, 4, 469 (CA 1982, 96, 7059s).
4. Kisfaludy, L.; Schön, I. S 1983, 325.
5. (a) Kisfaludy, L.; Schön, I. S 1986, 303. (b) Green, M.; Berman, J. TL 1990, 31, 5851.
6. Meienhofer, J.; Waki, M.; Heimer, E. P.; Lambros, T. J.; Makofske, R. C.; Chang, C-D. Int. J. Pept. Protein Res. 1979, 13, 35.
7. Chang C-D.; Waki, M.; Ahmad, M.; Meienhofer, J.; Lundell, E. O.; Haug, J. D. Int. J. Pept. Protein Res. 1980, 15, 59.
8. Merrifield, R. B. JACS 1963, 85, 2149.
9. Atherton, E.; Sheppard, R. C. CC 1985, 165.
10. Atherton, E.; Cameron, L. R.; Sheppard, R. C. T 1988, 44, 843.
11. Atherton, E.; Logan, C. J.; Sheppard, R. C. JCS(P1) 1981, 538.
12. For the use of pentafluorophenyl esters in SPPS of glycopeptides, see: Meldal, M.; Jensen, K. J. CC 1990, 483 and references therein.
13. For a review of active esters in SPPS, see: Bodanszky, M.; Bednarek, M. A. J. Protein Chem. 1989, 8, 461.
14. Chen, S.; Jiecheng, X. TL 1991, 32, 6711.
15. Kisfaludy, L.; Low, M.; Argay, G.; Czugler, M.; Komives, T.; Sohar, P.; Darvas, F. In Peptides (Proceedings 14th European Peptide Symposium); Loffet, A., Ed.; Editions de lŽUniversité de Bruxelles: Bruxelles, 1976; p 55 and references therein.
16. Kisfaludy, L.; &OOuml;tvos, Jr., L. S 1987, 510.
17. Avramenko, A. A.; Bardin, V. V.; Karelin, A. L.; Krasil'nikov, V. A.; Tushin, P. P.; Furin, G. G.; Yakobson, G. G. ZOR 1985, 21, 822 (CA 1985, 103, 141 551n).
18. Denny, D. B.; Denney, D. Z.; Liu L-T. PS 1982, 13, 1.
19. (a) Aksenov, V. V.; Vlasov, V. M.; Yakobson, G. G. JFC 1982, 20, 439. (b) Aksenov, V. V.; Vlasov, V. M.; Danilkin, V. I.; Naumova, O. Y.; Rodionov, P. P.; Chertok, V. S.; Shnitko, G. N.; Yakobson, G. G. IZV 1984, 9, 2158 (CA 1985, 102, 131 881k).

Keith Jones

King's College London, UK



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