Origins of Life and Evolution of Biospheres

, Volume 41, Issue 5, pp 399–412 | Cite as

The Relative Rates of Thiol–Thioester Exchange and Hydrolysis for Alkyl and Aryl Thioalkanoates in Water

  • Paul J. Bracher
  • Phillip W. Snyder
  • Brooks R. Bohall
  • George M. Whitesides
Prebiotic Chemistry


This article reports rate constants for thiol–thioester exchange (k ex), and for acid-mediated (k a), base-mediated (k b), and pH-independent (k w) hydrolysis of S-methyl thioacetate and S-phenyl 5-dimethylamino-5-oxo-thiopentanoate—model alkyl and aryl thioalkanoates, respectively—in water. Reactions such as thiol–thioester exchange or aminolysis could have generated molecular complexity on early Earth, but for thioesters to have played important roles in the origin of life, constructive reactions would have needed to compete effectively with hydrolysis under prebiotic conditions. Knowledge of the kinetics of competition between exchange and hydrolysis is also useful in the optimization of systems where exchange is used in applications such as self-assembly or reversible binding. For the alkyl thioester S-methyl thioacetate, which has been synthesized in simulated prebiotic hydrothermal vents, k a = 1.5 × 10−5 M−1 s−1, k b = 1.6 × 10−1 M−1 s−1, and k w = 3.6 × 10−8 s−1. At pH 7 and 23°C, the half-life for hydrolysis is 155 days. The second-order rate constant for thiol–thioester exchange between S-methyl thioacetate and 2-sulfonatoethanethiolate is k ex = 1.7 M−1 s−1. At pH 7 and 23°C, with [R″S(H)] = 1 mM, the half-life of the exchange reaction is 38 h. These results confirm that conditions (pH, temperature, pK a of the thiol) exist where prebiotically relevant thioesters can survive hydrolysis in water for long periods of time and rates of thiol–thioester exchange exceed those of hydrolysis by several orders of magnitude.


Thiol–thioester exchange Thioesters Origin of life Prebiotic chemistry Hydrolysis Dynamic covalent chemistry 



P.J.B. thanks the Harvard Origins-of-Life Initiative for the fellowship that supported his work in this area, and both P.J.B. and B.R.B. thank the National Science Foundation for graduate research fellowships. P.J.B. is currently supported by a National Science Foundation American Competitiveness in Chemistry postdoctoral fellowship (Award CHE–0936996).

Supplementary material

11084_2011_9243_MOESM1_ESM.pdf (423 kb)
ESM 1 Experimental procedure for the synthesis of thioester 3, experimental details of the kinetics experiments, representative plots for the analysis of kinetics data. (PDF 423 kb)


  1. Barnett R, Jencks WP (1969) The rates of hydrolysis of two thiol esters in water. J Org Chem 34:2777–2779. doi: 10.1021/jo01261a070 CrossRefGoogle Scholar
  2. Bruice TC, Benkovic SJ (1966) Bioorganic mechanisms: volume I. W.A. Benjamin, Inc, New YorkGoogle Scholar
  3. Carreras CW, Pieper R, Khosla C (1997) The chemistry and biology of fatty acid, polyketide, and nonribosomal peptide biosynthesis. In: Bioorganic chemistry deoxysugars, polyketides and related classes: synthesis, biosynthesis, enzymes. Springer-Verlag Berlin, Berlin 33, pp. 85–126Google Scholar
  4. Castro EA (1999) Kinetics and mechanisms of reactions of thiol, thiono, and dithio analogues of carboxylic esters with nucleophiles. Chem Rev 99:3505–3524. doi: 10.1021/cr990001d PubMedCrossRefGoogle Scholar
  5. Castro EA (2007) Kinetics and mechanisms of reactions of thiol, thiono, and dithio analogues of carboxylic esters with nucleophiles. An update. J Sulfur Chem 28:401–429. doi: 10.1080/17415990701415718 CrossRefGoogle Scholar
  6. Committee on the Limits of Organic Life in Planetary Systems, Committee on the Origins and Evolution of Life, The National Research Council (2007) The limits of organic life in planetary systems. The National Academies, WashingtonGoogle Scholar
  7. Corbett PT, Leclaire J, Vial L, West KR, Wietor JL, Sanders JKM, Otto S (2006) Dynamic combinatorial chemistry. Chem Rev 106:3652–3711. doi: 10.1021/cr020452p PubMedCrossRefGoogle Scholar
  8. Danehy JP, Noel CJ (1960) The relative nucleophilic character of several mercaptans toward ethylene oxide. J Am Chem Soc 82:2511–2515. doi: 10.1021/ja01495a028 CrossRefGoogle Scholar
  9. Dawson PE, Kent SBH (2000) Synthesis of native proteins by chemical ligation. Annu Rev Biochem 69:923–960. doi: 10.1146/annurev.biochem.69.1.923 PubMedCrossRefGoogle Scholar
  10. Dawson PE, Muir TW, Clark-Lewis I, Kent SBH (1994) Synthesis of proteins by native chemical ligation. Science 266:776–779PubMedCrossRefGoogle Scholar
  11. Dawson PE, Churchill MJ, Ghadiri MR, Kent SBH (1997) Modulation of reactivity in native chemical ligation through the use of thiol additives. J Am Chem Soc 119:4325–4329. doi: 10.1021/ja962656r CrossRefGoogle Scholar
  12. de Duve C (1991) Blueprint for a cell. Neil Patterson Publishers, BurlingtonGoogle Scholar
  13. Fedor LR, Bruice TC (1965) Nucleophilic displacement reactions at the thiol ester bond. IV. General base catalyzed hydrolysis of ethyl trifluoroacetate. Kinetic evidence for the formation of a tetrahedral intermediate. J Am Chem Soc 87:4138–4147. doi: 10.1021/ja01096a024 CrossRefGoogle Scholar
  14. Greig LM, Philp D (2001) Applying biological principles to the assembly and selection of synthetic superstructures. Chem Soc Rev 30:287–302. doi: 10.1039/b104962n CrossRefGoogle Scholar
  15. Hadley EB, Gellman SH (2006) An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface. J Am Chem Soc 128:16444–16445. doi: 10.1021/ja067178r PubMedCrossRefGoogle Scholar
  16. Huber C, Wächtershäuser G (1997) Activated acetic acid by carbon fixation on (Fe, Ni)S under primordial conditions. Science 276:245–247. doi: 10.1126/science.276.5310.245 PubMedCrossRefGoogle Scholar
  17. Huber C, Wächtershäuser G (1998) Peptides by activation of amino acids with CO on (Ni, Fe)S surfaces: implications for the origin of life. Science 281:670–672. doi: 10.1126/science.281.5377.670 PubMedCrossRefGoogle Scholar
  18. Hupe DJ, Jencks WP (1977) Nonlinear structure-reactivity correlations. Acyl transfer between sulfur and oxygen nucleophiles. J Am Chem Soc 99:451–464. doi: 10.1021/ja00444a023 CrossRefGoogle Scholar
  19. Jencks WP (1969) Catalysis in chemistry and enzymology. McGraw-Hill, Inc, New YorkGoogle Scholar
  20. Jencks WP, Cordes S, Carriuolo J (1960) Free energy of thiol ester hydrolysis. J Biol Chem 235:3608–3614PubMedGoogle Scholar
  21. Kelley DS, Karson JA, Fruh-Green GL, Yoerger DR, Shank TM, Butterfield DA, Hayes JM, Schrenk MO, Olson EJ, Proskurowski G, Jakuba M, Bradley A, Larson B, Ludwig K, Glickson D, Buckman K, Bradley AS, Brazelton WJ, Roe K, Elend MJ, Delacour A, Bernasconi SM, Lilley MD, Baross JA, Summons RT, Sylva SP (2005) A serpentinite-hosted ecosystem: the lost city hydrothermal field. Science 307:1428–1434. doi: 10.1126/science.1102556 PubMedCrossRefGoogle Scholar
  22. King JF, Rathore R, Lam JYL, Guo ZR, Klassen DF (1992) pH optimization of nucleophilic reactions in water. J Am Chem Soc 114:3028–3033. doi: 10.1021/ja00034a040 CrossRefGoogle Scholar
  23. Krupp R, Oberthür T, Hirdes W (1994) The early precambrian atmosphere and hydrosphere: thermodynamic constraints from mineral deposits. Econ Geol 89:1581–1598. doi: 10.2113/gsecongeo.89.7.1581 CrossRefGoogle Scholar
  24. Larsson R, Pei ZC, Ramström O (2004) Catalytic self-screening of cholinesterase substrates from a dynamic combinatorial thioester library. Angew Chem Int Ed 43:3716–3718. doi: 10.1002/anie.200454165 CrossRefGoogle Scholar
  25. Leclaire J, Vial L, Otto S, Sanders JKM (2005) Expanding diversity in dynamic combinatorial libraries: simultaneous exchange of disulfide and thioester linkages. Chem Commun: 1959–1961. doi: 10.1039/b500638d
  26. Macleod G, McKeown C, Hall AJ, Russell MJ (1994) Hydrothermal and oceanic pH conditions of possible relevance to the origin of life. Orig Life Evol Biosph 24:19–41PubMedCrossRefGoogle Scholar
  27. Maruyama H, Hiraoka T (1986) A stereocontrolled synthesis of thienamycin from 6-aminopenicillanic acid. J Org Chem 51:399–402. doi: 10.1021/jo00353a025 CrossRefGoogle Scholar
  28. Otto HH, Schirmeister T (1997) Cysteine proteases and their inhibitors. Chem Rev 97:133–171. doi: 10.1021/cr950025u PubMedCrossRefGoogle Scholar
  29. Rowan SJ, Cantrill SJ, Cousins GRL, Sanders JKM, Stoddart JF (2002) Dynamic covalent chemistry. Angew Chem Int Ed 41:898–952. doi: 10.1002/1521-3773(20020315)41:6<898::AID-ANIE898>3.0.CO;2-E CrossRefGoogle Scholar
  30. Ura Y, Al-Sayah M, Montenegro J, Beierle JM, Leman LJ, Ghadiri MR (2009) Dynamic polythioesters via ring-opening polymerization of 1,4-thiazine-2,5-diones. Org Biomol Chem 7:2878–2884. doi: 10.1039/b903612a PubMedCrossRefGoogle Scholar
  31. Von Damm KL, Buttermore LG, Oosting SE, Bray AM, Fornari DJ, Lilley MD, Shanks WC III (1997) Direct observation of the evolution of a seafloor ‘black smoker’ from vapor to brine. Earth Planet Sci Lett 149:101–111CrossRefGoogle Scholar
  32. Wächtershäuser G (1992) Groundworks for an evolutionary biochemistry—the iron sulfur world. Prog Biophys Mol Biol 58:85–201PubMedCrossRefGoogle Scholar
  33. Walker JCG (1983) Possible limits on the composition of the Archean ocean. Nature 302:518–520. doi: 10.1038/302518a0 CrossRefGoogle Scholar
  34. Weber AL (1984) Prebiotic formation of energy-rich thioesters from glyceraldehyde and N-acetylcysteine. Orig Life Evol Biosph 15:17–27. doi: 10.1007/BF01809390 PubMedCrossRefGoogle Scholar
  35. Weber AL (1998) Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. Orig Life Evol Biosph 28:259–270. doi: 10.1023/A:1006524818404 PubMedCrossRefGoogle Scholar
  36. Woll MG, Gellman SH (2004) Backbone thioester exchange: a new approach to evaluating higher order structural stability in polypeptides. J Am Chem Soc 126:11172–11174. doi: 10.1021/ja046891i PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Paul J. Bracher
    • 1
  • Phillip W. Snyder
    • 1
  • Brooks R. Bohall
    • 1
  • George M. Whitesides
    • 1
  1. 1.Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUSA

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