Kinetic analysis of the Rebek self-replicating system: Is there a controversy?

Journal of the American Chemical Society

Volumn 118, Issue 29, 1996, Pages 6880-6889

  Reinhoudt, David N ^a   Rudkevich, Dmitry M ^a   De Jong, Feike ^a  

^a UNIVERSITY OF TWENTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; COMPLEX FORMATION; REACTION ANALYSIS; REACTION TIME;

EID: 0029955316     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja960324g     Document Type: Article

References (34)

1. (a) von Kiedrowski, G. Angew. Chem., Int. Ed. Engl. 1986, 25, 932-935.
2. (b) von Kiedrowski, G.; Wlotzka, B.; Helbing, J.; Matzen, M.; Jordan, S. Angew. Chem., Int. Ed. Engl. 1991, 30, 423-426.
3. (c) Terfort, A.; von Kiedrowski, G. Angew. Chem., Int. Ed. Engl. 1992, 31, 654-656.
4. (d) Sievers, D.; von Kiedrowski, G. Nature 1994, 369, 221-224.
5. For timely reviews on the problem, see: (a) Hoffmann, S. Angew. Chem., Int. Ed. Engl. 1992, 31, 1013-1016. (b) Orgel, L. E. Acc. Chem. Res. 1995, 28, 109-118.
6. For timely reviews on the problem, see: (a) Hoffmann, S. Angew. Chem., Int. Ed. Engl. 1992, 31, 1013-1016. (b) Orgel, L. E. Acc. Chem. Res. 1995, 28, 109-118.
7. (a) Tjivikua, T.; Ballester, P.; Rebek, J., Jr. J. Am. Chem. Soc. 1990, 112, 1249-1250.
8. -1 at 8.2 mM initial concentration. According to Rebek, three processes contribute to the formation of the product: the background bimolecular reaction, the base-paired bimolecular reaction, and the termolecular template-catalyzed reaction (via a termolecular complex). For a short overview of Rebek's work, see: Wintner, E. A.; Conn, M. M.; Rebek, J., Jr. Acc. Chem. Res. 1994, 27, 198-203.
9. -1 at 8.2 mM initial concentration. According to Rebek, three processes contribute to the formation of the product: the background bimolecular reaction, the base-paired bimolecular reaction, and the termolecular template-catalyzed reaction (via a termolecular complex). For a short overview of Rebek's work, see: Wintner, E. A.; Conn, M. M.; Rebek, J., Jr. Acc. Chem. Res. 1994, 27, 198-203.
10. Menger, F. M.; Eliseev, A. V.; Khanjin, N. A. J. Am. Chem. Soc. 1994, 116, 3613-3614. It was shown that primary amides (e.g., acetamide, 2-naphthamide) and secondary N-methylpropionamide also catalyze the reaction between 1 and 2. The authors stated that, since Rebek's template 3 is an amide itself, the reaction is not self-replicating but simply amide-catalyzed.
11. 8 Secondly, Rebek et al. used the HPLC technique and Menger et al. employed NMR spectroscopy. Thirdly, Menger et al. never tested Rebek's model compounds (e.g., 6-8).
12. In a later communication. Rebek et al. demonstrated that not all amides do accelerate the reaction of 1 and 2. Thus, model compounds 6-8 which have the structural fragments of template 3, namely, trans-secondary amide, Kemp's imide, and adenosine, respectively, show no catalysis in the reaction between 1 and 2 when the reactions are performed at 2.2 mM initial concentration. Since there is no primary amide function present in the reaction mixture, acetamide and 2-naphthamide were rejected as incorrect models. See: Conn, M. M.; Wintner, E. A.; Rebek, J., Jr. J. Am. Chem. Soc. 1994, 116, 8823-8824.
13. Wintner, E. A.; Tsao, B.; Rebek, J., Jr. J. Org. Chem. 1995, 60, 7997-8001.
14. See, for example: (a) Titskii, G. D.; Litvinenko, L. M. Zh. Gen. Chem. USSR (Russ. Ed.) 1970, 40, 2680-2688. (b) Su, C.-W.; Watson, J. J. Am. Chem. Soc. 1974, 96, 1854-1857.
15. See, for example: (a) Titskii, G. D.; Litvinenko, L. M. Zh. Gen. Chem. USSR (Russ. Ed.) 1970, 40, 2680-2688. (b) Su, C.-W.; Watson, J. J. Am. Chem. Soc. 1974, 96, 1854-1857.
16. Kolb, M.; Danzin, C.; Barth, J.; Claverie, N. J. Med. Chem. 1982, 25, 550-556. For the review on Mitsunobu reaction see: Mitsunobu, O. Synthesis 1981, 1-28.
17. Kolb, M.; Danzin, C.; Barth, J.; Claverie, N. J. Med. Chem. 1982, 25, 550-556. For the review on Mitsunobu reaction see: Mitsunobu, O. Synthesis 1981, 1-28.
18. Hampton, A. J. Am. Chem. Soc. 1961, 83, 3640-3645.
19. 1H NMR spectra at 8.25, 16.5, and 30 mM concentrations.
20. t=0. We calculated the latter on the basis of corresponding kinetic equations from the composition of the mixtures at time t = 0 and the determined reaction rate constants. Therefore, the initial rates can only be used to compare relative catalytic trends.
21. Essentially higher than observed by Rebek et al. initial rates at 8.25 mM can be reasonably explained by hydrolysis which (for some reason) took place under their conditions (yielding only ca. 65% of 3 after > 1500 min). See ref 3b.
22. -1 rate at 8.2 mM which is 5.6 times lower than the rate Rebek et al. reported at 8.2 mM for the reaction between 1 and 2. See ref 5.
23. This is in agreement with Rebek's observation that the nonbinding N-methylated analog of 1 showed a ca. 6.5-fold decrease of the background rate. In fact, Rebek used the latter reaction as the background reaction in his kinetic modeling.
24. The results show that, with the current set of parameters, the concentrations of species composed of four components are very low up to 50 mM concentration.
25. For typical examples from the Rebek group see: (a) Askew, B.; Ballester, P.; Buhr, C.; Jeong, K. S.; Jones, S.; Parris, K.; Williams, K.: Rebek, J., Jr. J. Am. Chem. Soc. 1989, 111, 1082-1090. (b) Williams, K.; Askew, B.; Ballester, P.; Buhr, C.; Jeong, K. S.; Jones, S.; Rebek, J., Jr. J. Am. Chem. Soc.1989, 111, 1090-1094.
26. For typical examples from the Rebek group see: (a) Askew, B.; Ballester, P.; Buhr, C.; Jeong, K. S.; Jones, S.; Parris, K.; Williams, K.: Rebek, J., Jr. J. Am. Chem. Soc. 1989, 111, 1082-1090. (b) Williams, K.; Askew, B.; Ballester, P.; Buhr, C.; Jeong, K. S.; Jones, S.; Rebek, J., Jr. J. Am. Chem. Soc.1989, 111, 1090-1094.
27. 19 suggest that two molecules of 3, being quite flexible, fit much better in the linear than in the cyclic dimer structure.
28. Brooks, B. R.; Bruccoleri, R. E.; Olafsen, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187. Quanta was bought from Molecular Simulations Inc., Burlington, MA.
29. 2 signal of the adenine fragment is found at 5.69 ppm; see ref 3b.
30. Theoretical curves were calculated on the basis of the model derived in the supporting information, on a normal PC using Lotus 123 software. Conversion as a function of time was calculated taking 4 min intervals.
31. 2 of 3.0 and 10.7, respectively.
32. In the so-called "self-replicating molecules of second generation" Rebek et al. forced the reaction to the template-catalyzed mechanism by restraining the preassociative bimolecular pathway. See: Wintner, E. A.; Conn, M. M.; Rebek, J., Jr. J. Am. Chem. Soc. 1994, 116, 8877-8884.
33. +-H and the template carbonyl C=O group is 1.65 Å in this case.
34. de Boer, J. A. A.; Reinhoudt, D. N.; Harkema, S.; van Hummel, G. J.; de Jong, F. J. Am. Chem. Soc. 1982, 104, 4073-4076.