The 55% solution: A formula for molecular recognition in the liquid state

Chemistry - A European Journal

Volumn 4, Issue 6, 1998, Pages 1016-1022

  Mecozzi, Sandro ^a   Rebek Jr , Julius ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Host guest chemistry; Molecular dynamics; Molecular recognition; Self assembly; Supramolecular chemistry

Indexed keywords

EID: 0031832791     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3765(19980615)4:6<1016::AID-CHEM1016>3.0.CO;2-B     Document Type: Article

References (50)

1. C. J. Pedersen, J. Am. Chem. Soc. 1967, 89, 7017-7036.
2. This phrase first appears as the title of a lecture by D. J. Cram at the C. David Gutsche Symposium, Washington University, St. Louis, Missouri, May 5, 1990: for examples, see D. J. Cram, Nature 1992, 356, 29-36.
3. J. Rebek, Jr., Chem Soc. Rev. 1997, 255-264 and references therein.
4. a) L. Garel, J. Dutasta, A. Collet, Angew. Chem. 1993, 105, 1249-1251; Angew. Chem. Int. Ed. Engl. 1993, 32, 1169-1171;
5. a) L. Garel, J. Dutasta, A. Collet, Angew. Chem. 1993, 105, 1249-1251; Angew. Chem. Int. Ed. Engl. 1993, 32, 1169-1171;
6. b) A. Collet,in Comprehensive Supramolecular Chemistry Vol. 2 (Eds: J. L. Atwood, J. E. Davies, D. D. MacNicol, F. Vögtle), Elsevier, 1996, pp325-365;
7. R. Meissner, X. Garcias, S. Mecozzi, J. Rebek, Jr., J. Am. Chem. Soc. 1997, 119, 77-85.
8. a) A. Bondi, Physical Properties of Molecular Crystals, Liquids, and Glasses, Wiley, 1968; b) J. Israelachvili, Intermolecular & Surface Forces, 2nd ed., Academic Press, 1992; A. T. Kitaigorodsky, Molecular Crystals and Molecules, Academic Press, 1973, pp. 18- 19.
9. a) A. Bondi, Physical Properties of Molecular Crystals, Liquids, and Glasses, Wiley, 1968; b) J. Israelachvili, Intermolecular & Surface Forces, 2nd ed., Academic Press, 1992; A. T. Kitaigorodsky, Molecular Crystals and Molecules, Academic Press, 1973, pp. 18- 19.
10. a) A. Bondi, Physical Properties of Molecular Crystals, Liquids, and Glasses, Wiley, 1968; b) J. Israelachvili, Intermolecular & Surface Forces, 2nd ed., Academic Press, 1992; A. T. Kitaigorodsky, Molecular Crystals and Molecules, Academic Press, 1973, pp. 18- 19.
11. a) M. H. Klapper, Biochim. Biophys. Acta 1971, 229, 557-566; b) Prog. Bioorg. Chem. 1973, 2, 55-133; P. L. Privalov, S. L. Gill, Adv. Protein Chem. 1988, 39, 191-234; F. M. Richards, Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176; e) F. M. Richards, J. Mol. Biol. 1974, 82, 1-14.
12. a) M. H. Klapper, Biochim. Biophys. Acta 1971, 229, 557-566; b) Prog. Bioorg. Chem. 1973, 2, 55-133; P. L. Privalov, S. L. Gill, Adv. Protein Chem. 1988, 39, 191-234; F. M. Richards, Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176; e) F. M. Richards, J. Mol. Biol. 1974, 82, 1-14.
13. a) M. H. Klapper, Biochim. Biophys. Acta 1971, 229, 557-566; b) Prog. Bioorg. Chem. 1973, 2, 55-133; P. L. Privalov, S. L. Gill, Adv. Protein Chem. 1988, 39, 191-234; F. M. Richards, Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176; e) F. M. Richards, J. Mol. Biol. 1974, 82, 1-14.
14. a) M. H. Klapper, Biochim. Biophys. Acta 1971, 229, 557-566; b) Prog. Bioorg. Chem. 1973, 2, 55-133; P. L. Privalov, S. L. Gill, Adv. Protein Chem. 1988, 39, 191-234; F. M. Richards, Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176; e) F. M. Richards, J. Mol. Biol. 1974, 82, 1-14.
15. a) M. H. Klapper, Biochim. Biophys. Acta 1971, 229, 557-566; b) Prog. Bioorg. Chem. 1973, 2, 55-133; P. L. Privalov, S. L. Gill, Adv. Protein Chem. 1988, 39, 191-234; F. M. Richards, Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176; e) F. M. Richards, J. Mol. Biol. 1974, 82, 1-14.
16. These packing coefficients were calculated according to Equation (1), with the van der Waals radii described in the Volume calculations section.
17. C. N. Eid, Jr., D. J. Cram, J. Chem. Ed. 1993, 70, 349-351.
18. B. C. Hamann, K. D. Shimizu, J. Rebek, Jr., Angew. Chem. 1996, 108, 1425-1427; Angew. Chem. Int. Ed. Engl., 1996, 55, 1326-1329.
19. B. C. Hamann, K. D. Shimizu, J. Rebek, Jr., Angew. Chem. 1996, 108, 1425-1427; Angew. Chem. Int. Ed. Engl., 1996, 55, 1326-1329.
20. Although appropriate force field parameters for all the functional groups in molecules 1-6 do not exist, the use of the force field Amber* of MacroModel 5.5 allows a reasonable approximation for the computation and the comparison of volumes.
21. F. Mohamadi, N. G. J. Richards, W. C. Guidia, R. Liskamp, C. Caulfield, G. Chang, T. Hendrickson, W. C. Still, J. Comput. Chem. 1990, 11, 440-467.
22. A. Nicholls, K. A. Sharp, B. Honig, Proteins 1991, 11, 281-296.
23. J. C. McGowan, A. Mellors, Molecular Volumes in Chemistry and Biology: Applications Including Partitioning and Toxicity, Wiley, 1986.
24. J. C. Sherman, D. J. Cram, J. Am. Chem. Soc. 1991, 113, 2194-2204.
25. A. Collet, Tetrahedron 1987, 43, 5725-5759.
26. a) R. Grotzfeld, N. Branda, J. Rebek, Jr., Science 1996, 271, 487-489; b) K. D. Shimizu, J. Rebek, Jr., Proc. Nat. Acad. Sci. 1995, 92, 12403-12407.
27. a) R. Grotzfeld, N. Branda, J. Rebek, Jr., Science 1996, 271, 487-489; b) K. D. Shimizu, J. Rebek, Jr., Proc. Nat. Acad. Sci. 1995, 92, 12403-12407.
28. J. Kang, J. Rebek, Jr., Nature 1997, 385, 50-52.
29. R. Meissner, J. de Mendoza, J. Rebek, Jr., Science 1995, 270, 1485-1488.
30. J. Kang, J. Rebek, Jr., Nature 1996, 382, 239-241.
31. For a discussion of thermodynamics of inclusion processes see a) D. J. Cram, H-J. Choi, J. A. Bryant, C. B. Knobler, J. Am. Chem. Soc. 1992, 114, 7748-7765; b) J. D. Dunitz, Chem. Biol. 1995, 2, 709-712; B. R. Peterson, P. Wallimann, D. R. Carcanague, F. Diederich, Tetrahedron 1995, 51, 401-421; M. S. Searle, M. S. Westwell, D. H. Williams, J. Chem. Soc. Perkin Trans. 2 1995, 141-151.
32. For a discussion of thermodynamics of inclusion processes see a) D. J. Cram, H-J. Choi, J. A. Bryant, C. B. Knobler, J. Am. Chem. Soc. 1992, 114, 7748-7765; b) J. D. Dunitz, Chem. Biol. 1995, 2, 709-712; B. R. Peterson, P. Wallimann, D. R. Carcanague, F. Diederich, Tetrahedron 1995, 51, 401-421; M. S. Searle, M. S. Westwell, D. H. Williams, J. Chem. Soc. Perkin Trans. 2 1995, 141-151.
33. For a discussion of thermodynamics of inclusion processes see a) D. J. Cram, H-J. Choi, J. A. Bryant, C. B. Knobler, J. Am. Chem. Soc. 1992, 114, 7748-7765; b) J. D. Dunitz, Chem. Biol. 1995, 2, 709-712; B. R. Peterson, P. Wallimann, D. R. Carcanague, F. Diederich, Tetrahedron 1995, 51, 401-421; M. S. Searle, M. S. Westwell, D. H. Williams, J. Chem. Soc. Perkin Trans. 2 1995, 141-151.
34. For a discussion of thermodynamics of inclusion processes see a) D. J. Cram, H-J. Choi, J. A. Bryant, C. B. Knobler, J. Am. Chem. Soc. 1992, 114, 7748-7765; b) J. D. Dunitz, Chem. Biol. 1995, 2, 709-712; B. R. Peterson, P. Wallimann, D. R. Carcanague, F. Diederich, Tetrahedron 1995, 51, 401-421; M. S. Searle, M. S. Westwell, D. H. Williams, J. Chem. Soc. Perkin Trans. 2 1995, 141-151.
35. J. M. Rivera, T. Martin, J. Rebek, Jr., J. Am. Chem. Soc. 1998, 120, 66-99.
36. J. M. Rivera, T. Martin, J. Rebek, Jr., Science 1998, 279, 1021-1023.
37. O. Mogck, E. F. Paulus, V. Böhmer, I. Thondorf, W. Vogt, Chem. Commun. 1996, 2533-2534.
38. R. G. Chapman, J. C. Sherman, J. Am. Chem. Soc. 1995, 117, 9081-9082.
39. a) R. Wyler, J. de Mendoza, J. Rebek, Jr., Angew. Chem. 1993, 105, 1820-1821; Angew. Chem. Int. Ed. Engl. 1993, 32, 1699-1701;
40. a) R. Wyler, J. de Mendoza, J. Rebek, Jr., Angew. Chem. 1993, 105, 1820-1821; Angew. Chem. Int. Ed. Engl. 1993, 32, 1699-1701;
41. b) C. Valdès, U. P. Spitz, L. Toledo, S. Kubik, J. Rebek, Jr., J. Am. Chem. Soc. 1995, 117, 12733-12745;
42. N.Branda, R. Wyler, J. Rebek, Jr., Science 1994, 263, 1267-1268;
43. X. Garcias, J. Rebek, Jr., Angew. Chem. 1996, 108, 1328-1330;
44. Angew. Chem. Int. Ed. Engl. 1996, 35, 1225-1227.
45. C. Valdés, L. Toledo, U P. Spitz, J. Rebek, Jr., Chem. Eur. J. 1996, 2, 989-991.
46. a) P. Timmermann, W. Verboom, F. C. J. M. van Veggel, J. P. M. Duynhoven, D. N. Reinhoudt, Angew. Chem. 1994, 106, 2437-2440; Angew. Chem. Int. Ed. Engl. 1994, 33, 2345-2348;
47. a) P. Timmermann, W. Verboom, F. C. J. M. van Veggel, J. P. M. Duynhoven, D. N. Reinhoudt, Angew. Chem. 1994, 106, 2437-2440; Angew. Chem. Int. Ed. Engl. 1994, 33, 2345-2348;
48. b) A. M. A. van Wageningen, P. Timmerman, J. P. M. van Duynhoven, W. Verboom, F. C. J. M. van Veggel, D. N. Reinhoudt, Chem. Eur. J. 1997, 3, 639-654.
49. Calculation of the internal cavity volume for cryptophanes 8 and 9 is made difficult by the presence of large holes in the molecular surfaces of the molecules. A closed cavity could only be built by use of a probe of 1.55 Å in diameter, a probe that inevitably underestimates the cavity volumes of 8 and 9. For the same reason, not all the structures sampled during the molecular dynamics simulation could be used for volume calculations. In some cases the holes were just too large to be closed with a probe of the appropriate size.
50. R. G. Chapman, N. Chopra, E. D. Cochien, J. C. Sherman, J. Am. Chem. Soc. 1994, 116, 369-370.