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Compressed alkanes in reversible encapsulation complexes

Abstract

Simple alkanes feature fully extended conformations as their lowest-energy shapes but can assume coiled, compressed conformations in small spaces. A series of normal alkanes, C16 to C19, were encapsulated in self-assembled, hydrogen-bonded complexes. Coiling of the longer alkanes was observed by NMR spectroscopy. The coiling exerts pressure on the interior; the hydrogen bonding seams are loosened, and rotation of the capsule's components occurs on the NMR timescale. The rotation results in interconversion of mirror-image capsule assemblies (racemization). The racemization rates were determined and shown to increase with the length of the alkane, the longer alkanes exerting more pressure. Free energies of activation for racemization were determined at the coalescence temperatures, and were ΔG = 15.7, 16.7 and 17.2 kcal mol−1 for C19, C18 and C17, respectively. The shorter C16 was encapsulated in its fully extended conformation, and does not seem to exert pressure inside the capsule.

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Figure 1: Encapsulation of coiled alkanes in a cylindrical capsule.
Figure 2: Insertion of spacer elements in a dimeric capsule creates an extended, chiral capsule.
Figure 3: Coiled alkanes in an extended capsule create internal pressure.
Figure 4: Racemization of the extended capsule.

References

  1. Trembleau, L. & Rebek, J. Jr Helical conformation of alkanes in hydrophobic environments. Science 301, 1219–1220 (2003).

    Article  CAS  Google Scholar 

  2. Wilson, C. F., Eastman, M. P. & Hartzell, C. J. Hydrogen bonding in a host–guest system: C-undecylcalix[4]resorcinarene and water in benzene. J. Phys. Chem. B 101, 9309–9313 (1997).

    Article  CAS  Google Scholar 

  3. Shivanyuk, A. & Rebek, J. Jr Recognition of guests in solution by self-assembling resorcinarene subunits. Proc. Natl Acad. Sci. USA 98, 7662–7665 (2001).

    Article  CAS  Google Scholar 

  4. Shivanyuk, A. & Rebek, J. Jr Assembly of resorcinarene capsules in wet solvents. J. Am. Chem. Soc. 125, 3432–3433 (2003).

    Article  CAS  Google Scholar 

  5. Yamanaka, M., Shivanyuk, A. & Rebek, J. Jr Kinetics and thermodynamics of a hexameric capsule formation. J. Am. Chem. Soc. 126, 2939–2943 (2004).

    Article  CAS  Google Scholar 

  6. Palmer, L. C., Shivanyuk, A., Yamanka, M. & Rebek, J. Jr Resorcinarene assemblies as synthetic receptors. Chem. Commun. 857–858 (2005).

  7. Gerkensmeier, T. et al. Self-assembly of 2,8,14,20-tetraisobutyl- 5,11,17,23-tetrahydroxyresorc[4]arene. Eur. J. Org. Chem. 2257–2262 (1999).

  8. Atwood, J. L., Barbour, L. J. & Jerga, A. Hydrogen-bonded molecular capsules are stable in polar media. Chem. Commun. 2376–2377 (2001).

  9. Atwood, J. L., Barbour, L. J. & Jerga, A. Supramolecular chemistry and self-assembly special feature: organization of the interior of molecular capsules by hydrogen bonding. Proc. Natl Acad. Sci. USA 99, 4837–4841 (2002).

    Article  CAS  Google Scholar 

  10. Cave, G. W. V., Antesberger, J., Barbour, L. J., McKinlay, R. M. & Atwood, J. L. Inner core structure responds to communication between nanocapsule walls. Angew. Chem. Int. Ed. 43, 5263–5266 (2004).

    Article  CAS  Google Scholar 

  11. Hayashida, O., Sebo, L. & Rebek, J. Jr Molecular discrimination of N-protected amino acid esters by a self-assembled cylindrical capsule: spectroscopic and computational studies. J. Org. Chem. 67, 8291–8298 (2002).

    Article  CAS  Google Scholar 

  12. Scarso, A., Trembleau, L. & Rebek, J. Jr Encapsulation induces helical folding of alkanes. Angew. Chem. Int. Ed. 42, 5499–5502 (2003).

    Article  CAS  Google Scholar 

  13. Scarso, A., Trembleau, L. & Rebek, J. Jr Helical folding of alkanes in a self-assembled, cylindrical capsule. J. Am. Chem. Soc. 126, 13512–13518 (2004).

    Article  CAS  Google Scholar 

  14. Heinz, T., Rudkevich, D. M. & Rebek, J. Jr Pairwise selection of guests in a cylindrical molecular capsule of nanometre dimensions. Nature 394, 764–766 (1998).

    Article  CAS  Google Scholar 

  15. Heinz, T., Rudkevich, D. M. & Rebek, J. Jr Molecular recognition within a self-assembled cylindrical host. Angew. Chem. Int. Ed. 38, 1136–1139 (1999).

    Article  CAS  Google Scholar 

  16. Ajami, D. & Rebek, J. Jr Coiled molecules in spring loaded devices. J. Am. Chem. Soc. 128, 15038–15039 (2006).

    Article  CAS  Google Scholar 

  17. Ajami, D. & Rebek, J. Jr Expanded capsules with reversibly added spacers. J. Am. Chem. Soc. 128, 5314–5315 (2006).

    Article  CAS  Google Scholar 

  18. Ajami, D. & Rebek, J. Jr Adaptations of guest and host in expanded self-assembled capsules. Proc. Natl Acad. Sci. USA 104, 16000–16003 (2007).

    Article  CAS  Google Scholar 

  19. Mecozzi, S. & Rebek, J. Jr The 55% solution: a formula for molecular recognition in the liquid state. Chem. Eur. J. 4, 1016–1022 (1998).

    Article  CAS  Google Scholar 

  20. Ajami, D. & Rebek, J. Jr Longer guests drive the reversible assembly of hyperextended capsules. Angew. Chem. Int. Ed. 47, 6059–6061 (2008).

    Article  CAS  Google Scholar 

  21. Hollingsworth, M. D. & Harris, K. D. M. Comprehensive Supramolecular Chemistry Vol. 6, 177–237 (Elsevier, 1996).

    Google Scholar 

  22. Brown, M. E. & Hollingsworth, M. D. Stress-induced domain reorientation in urea inclusion compounds. Nature 376, 323–327 (1995).

    Article  CAS  Google Scholar 

  23. Schramm, M. P. & Rebek, J. Jr Moving targets: recognition of alkyl groups. Chem. Eur. J. 12, 5924–5933 (2006).

    Article  CAS  Google Scholar 

  24. Séneque, O., Rager, M.-N., Giorgi, M. & Reinaud, O. Calix[6]arenes and zinc: biomimetic receptors for neutral molecules. J. Am. Chem. Soc. 122, 6183–6189 (2000).

    Article  Google Scholar 

  25. Tashiro, S., Kobayashi, M. & Fujita, M. Folding of an Ala-Ala-Ala tripeptide into a β-turn via hydrophobic encapsulation. J. Am. Chem. Soc. 128, 9280–9281 (2006).

    Article  CAS  Google Scholar 

  26. Fiedler, D., Bergman, R. G. & Raymond, K. N. Supramolecular catalysis of a unimolecular transformation: aza-Cope rearrangement within a self-assembled host. Angew. Chem. Int. Ed. 43, 6748–6751 (2004).

    Article  CAS  Google Scholar 

  27. Udachin, K. A., Enright, G. D., Brouwer, E. B. & Ripmeester, J. A. t-Butylcalix[4]arene compounds with long chain guests: structures and host–guest interactions. J. Supramol. Chem. 1, 97–100 (2001).

    Article  CAS  Google Scholar 

  28. Zanotti, G., Scapin, G., Spadon, P., Veerkamp, J. H. & Sacchettini, J. C. Three-dimensional structure of recombinant human muscle fatty acid-binding protein. J. Biol. Chem. 267, 18541–18550 (1992).

    CAS  PubMed  Google Scholar 

  29. Han, G. W. et al. Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography. J. Mol. Biol. 308, 263–278 (2001).

    Article  CAS  Google Scholar 

  30. Tzlil, S., Kindt, J. T., Gelbart, W. M. & Ben-Shaul, A. Forces and pressures in DNA packaging and release from viral capsids. Biophys. J. 84, 1616–1627 (2003).

    Article  CAS  Google Scholar 

  31. Verduin, B. J. M. & Bancroft, J. B. The infectivity of tobacco mosaic virus RNA in coat proteins from spherical viruses. Virology 37, 501–506 (1965)

    Article  Google Scholar 

  32. Dong, V. M., Fiedler, D., Carl, B., Bergman, R. G. & Raymond, K. N. Molecular recognition and stabilization of iminium ions in water. J. Am. Chem. Soc. 128, 14464–14465 (2006).

    Article  CAS  Google Scholar 

  33. Ziegler, M., Brumaghim, J. L. & Raymond, K. N. Stabilization of a reactive cationic species by supramolecular encapsulation. Angew. Chem. Int. Ed. 39, 4119–4121 (2000).

    Article  CAS  Google Scholar 

  34. Yoshizawa, M., Kusukawa, T., Fujita, M. & Yamaguchi, K. Ship-in-a-bottle synthesis of otherwise labile cyclic trimers of siloxanes in a self-assembled coordination cage. J. Am. Chem. Soc. 121, 6311–6312 (2000).

    Article  Google Scholar 

  35. Iwasawa, T., Mann, E. & Rebek J. Jr A reversible reaction inside a self-assembled capsule. J. Am. Chem. Soc. 128, 9308–9309 (2006).

    Article  CAS  Google Scholar 

  36. Kawano, M., Kobayashi, Y., Ozeki, T. & Fujita, M. Direct crystallographic observation of a coordinatively unsaturated transition-metal complex in situ generated within a self-assembled cage. J. Am. Chem. Soc. 128, 6558–6559 (2006).

    Article  CAS  Google Scholar 

  37. Fiedler, D., Bergman, R. G. & Raymond, K. N. Supramolecular catalysis of a unimolecular transformation: aza-Cope rearrangement within a self-assembled host. Angew. Chem. Int. Ed. 43, 6748–6751 (2004).

    Article  CAS  Google Scholar 

  38. Murase, T., Sato, S. & Fujita, M. Nanometer-sized shell molecules that confine endohedral polymerizing units. Angew. Chem. Int. Ed. 46, 1083–1085 (2007).

    Article  CAS  Google Scholar 

  39. Chen, J. & Rebek, J. Jr Selectivity in an encapsulated cycloaddition reaction. Org. Lett. 4, 327–329 (2002).

    Article  CAS  Google Scholar 

  40. Valdés, C., Spitz, U. P., Toledo, L., Kubik, S. & Rebek, J. Jr Synthesis and self-assembly of pseudo-spherical homo- and heterodimeric capsules. J. Am. Chem. Soc. 117, 12733–12745 (1995).

    Article  Google Scholar 

  41. Brody, M. S., Schalley, C. A., Rudkevich, D. M. & Rebek, J. Jr Synthesis and characterization of an intramolecularly self-assembled capsule. Angew. Chem. Int. Ed. 38, 1640–1644 (1999).

    Article  CAS  Google Scholar 

  42. Shivanyuk, A. & Rebek, J. Jr Hydrogen-bonded capsules in polar, protic solvents. Chem. Commun. 2374–2375 (2001).

  43. Shivanyuk, A. & Rebek, J. Jr Reversible encapsulation of multiple, neutral guests in hexameric resorcinarene hosts. Chem. Commun. 2424–2425 (2001).

  44. Tucci, F. C., Rudkevich, D. M. & Rebek, J. Jr Deeper cavitands. J. Org. Chem. 64, 4555–4559 (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful to the Skaggs Institute for support.

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Correspondence to Julius Rebek Jr.

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Ajami, D., Rebek, J. Compressed alkanes in reversible encapsulation complexes. Nature Chem 1, 87–90 (2009). https://doi.org/10.1038/nchem.111

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