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Crystalline molecular flasks

Nature Chemistry volume 3, pages 349–358 (2011)Cite this article

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Abstract

A variety of host compounds have been used as molecular-scale reaction vessels, protecting guests from their environment or restricting the space available around them, thus favouring particular reactions. Such molecular 'flasks' can endow guest molecules with reactivities that differ from those in bulk solvents. Here, we extend this concept to crystalline molecular flasks, solid-state crystalline networks with pores within which pseudo-solution-state reactions can take place. As the guest molecules can spontaneously align along the walls and channels of the hosts, structural changes in the substrates can be directly observed by in situ X-ray crystallography during reaction. Recently, this has enabled observation of the molecular structures of transient intermediates and other labile species, in the form of sequential structural snapshots of the chemical transformation. Here, we describe the principles, development and applications of crystalline molecular flasks.

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Figure 1: Schematic representations of two types of crystalline-state reactions.
Figure 2: Self-assembled cage as a crystalline molecular flask.
Figure 3: SCSC reactions within calix[4]arene crystals.
Figure 4: Guest inclusion in porous network complexes.
Figure 5: Post-synthetic modifications of porous network complexes analysed by X-ray single crystallography.
Figure 6: Modular synthesis of a porous network complex.
Figure 7: A variety of SCSC transformations within a biporous network.
Figure 8: Single crystallographic determination of a hemiaminal intermediate.

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References

  1. Yoshizawa, M., Klosterman, J. K. & Fujita, M. Functional molecular flasks: New properties and reactions within discrete, self-assembled hosts. Angew. Chem. Int. Ed. 48, 3418–3438 (2009).

    Article  CAS  Google Scholar 

  2. Cram, D. J., Tanner, M. E. & Thomas, R. The taming of cyclobutadiene. Angew. Chem. Int. Ed. Engl. 30, 1024–1027 (1991).

    Article  Google Scholar 

  3. Ramamurthy, V. & Venkatesan, K. Photochemical reactions of organic crystals. Chem. Rev. 87, 433–481 (1987).

    Article  CAS  Google Scholar 

  4. Lauher, J. W., Fowler, F. W. & Goroff, N. S. Single-crystal-to-single-crystal topochemical polymerizations by design. Acc. Chem. Res. 41, 1215–1229 (2008).

    Article  CAS  Google Scholar 

  5. Ohashi, Y. in Models, Mysteries and Magic of Molecules (eds Boeyens, J. C. A. & Ogilvie, J. F.) 109–113 (Springer, 2008).

    Book  Google Scholar 

  6. Coppens, P., Vorontsov, I. I., Graber, T., Gembicky, M. & Kovalevsky, A. Y. The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffraction. Acta Cryst. A61, 162–172 (2005).

    Article  CAS  Google Scholar 

  7. Moffat, K. Time-resolved biochemical crystallography: A mechanistic perspective. Chem. Rev. 101, 1569–1581 (2001).

    Article  CAS  Google Scholar 

  8. Kohlschutter, V. & Tuscher, J. L. Zur Kenntnis topochemischer Reaktionen. Über Bildung und Verhalten von Kupferhydroxyd. Z. Anorg. Allg. Chem. 111, 193–236 (1920).

    Article  CAS  Google Scholar 

  9. Caulder, D. L. & Raymond, K. N. Supermolecules by design. Acc. Chem. Res. 32, 975–982 (1999).

    Article  CAS  Google Scholar 

  10. Fujita, M. Metal-directed self-assembly of two- and three-dimensional synthetic receptors. Chem. Soc. Rev. 27, 417–425 (1998).

    Article  CAS  Google Scholar 

  11. Conn, M. M. & Rebek, J. Jr Self-assembling capsules. Chem. Rev. 97, 1647–1668 (1997).

    Article  CAS  Google Scholar 

  12. Hof, F., Craig, S. L., Nuckolls, C. & Rebek, J. Jr Molecular encapsulation. Angew. Chem. Int. Ed. 41, 1488–1508 (2002).

    Article  CAS  Google Scholar 

  13. Fujita, M., Tominaga, M., Hori, A. & Therrien, B. Coordination assemblies from a Pd(II)-cornered square complex. Acc. Chem. Res. 38, 369–378 (2005).

    Article  CAS  Google Scholar 

  14. Kang, J. M. & Rebek, J. Jr Acceleration of a Diels–Alder reaction by a self-assembled molecular capsule. Nature 385, 50–52 (1997).

    Article  CAS  Google Scholar 

  15. Pluth, M. D., Bergman, R. G. & Raymond, K. N. Acid catalysis in basic solution: A supramolecular host promotes orthoformate hydrolysis. Science 316, 85–88 (2007).

    Article  CAS  Google Scholar 

  16. Yoshizawa, M., Tamura, M. & Fujita, M. Diels–Alder in aqueous molecular hosts: Unusual regioselectivity and efficient catalysis. Science 312, 251–254 (2006).

    Article  CAS  Google Scholar 

  17. Batten, S. R. & Robson, R. Interpenetrating nets: Ordered, periodic entanglement. Angew. Chem. Int. Ed. 37, 1460–1494 (1998).

    Article  Google Scholar 

  18. Eddaoudi, M. et al. Modular chemistry: Secondary building units as a basis for the design of highly porous and robust metal–organic carboxylate frameworks. Acc. Chem. Res 34, 319–330 (2001).

    Article  CAS  Google Scholar 

  19. Kitagawa, S., Kitaura, R. & Noro, S. Functional porous coordination polymers. Angew. Chem. Int. Ed. 43, 2334–2375 (2004).

    Article  CAS  Google Scholar 

  20. Moulton, B. & Zaworotko, M. J. From molecules to crystal engineering: Supramolecular isomerism and polymorphism in network solids. Chem. Rev. 101, 1629–1658 (2001).

    Article  CAS  Google Scholar 

  21. Yaghi, O. M. et al. Reticular synthesis and the design of new materials. Nature 423, 705–714 (2003).

    Article  CAS  Google Scholar 

  22. Férey, G. Hybrid porous solids: Past, present, future. Chem. Soc. Rev. 37, 191–214 (2008).

    Article  Google Scholar 

  23. Fujita, M. et al. Self-assembly of 10 molecules into nanometre-sized organic host frameworks. Nature 378, 469–471 (1995).

    Article  CAS  Google Scholar 

  24. Cohen, M. D. & Schmidt, G. M. J. Topochemistry. 1. Survey. J. Chem. Soc. 1996–2000 (1964).

  25. Yoshizawa, M., Takeyama, Y., Kusukawa, T. & Fujita, M. Cavity-directed, highly stereoselective [2+2] photodimerization of olefins within self-assembled coordination cages. Angew. Chem. Int. Ed. 41, 1347–1349 (2002).

    Article  CAS  Google Scholar 

  26. Takaoka, K., Kawano, M., Ozeki, T. & Fujita, M. Crystallographic observation of an olefin photodimerization reaction that takes place via thermal molecular tumbling within a self-assembled host. Chem. Commun. 1625–1627 (2006).

  27. 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 

  28. Zheng, S. L., Messerschmidt, M. & Coppens, P. Single-crystal-to-single-crystal E→Z and Z→E isomerizations of 3-chloroacrylic acid within the nanocavities of a supramolecular framework. Chem. Commun. 2735–2737 (2007).

  29. Zheng, S. L. et al. Supramolecular solids as a medium for single-crystal-to-single-crystal E/Z photoisomerization: Kinetic study of the photoreactions of two Zn-coordinated tiglic acid molecules. Chem. Eur. J. 14, 706–713 (2008).

    Article  CAS  Google Scholar 

  30. Legrand, Y. M., van der Lee, A. & Barboiu, M. Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene by confinement in a crystalline matrix. Science 329, 299–302 (2010).

    Article  CAS  Google Scholar 

  31. Maier, G. Cyclobutadiene problem. Angew. Chem. Int. Ed. Engl. 13, 425–438 (1974).

    Article  Google Scholar 

  32. Alabugin, I. V., Gold, B., Shatruk, M. & Kovnir, K. Comment on 'Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene by confinement in a crystalline matrix'. Science 330, 1047 (2010).

    Article  CAS  Google Scholar 

  33. Scheschkewitz, D. Comment on 'Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene by confinement in a crystalline matrix'. Science 330, 1047 (2010).

    Article  CAS  Google Scholar 

  34. Legrand, Y. M., van der Lee, A. & Barboiu, M. Response to comment on 'Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene by confinement in a crystalline matrix'. Science 330, 1047 (2010).

    Article  CAS  Google Scholar 

  35. Matsuda, R. et al. Highly controlled acetylene accommodation in a metal–organic microporous material. Nature 436, 238–241 (2005).

    Article  CAS  Google Scholar 

  36. Seo, J. S. et al. A homochiral metal–organic porous material for enantioselective separation and catalysis. Nature 404, 982–986 (2000).

    Article  CAS  Google Scholar 

  37. Kawano, M. & Fujita, M. Direct observation of crystalline-state guest exchange in coordination networks. Coord. Chem. Rev. 251, 2592–2605 (2007).

    Article  CAS  Google Scholar 

  38. Lee, J. et al. Metal–organic framework materials as catalysts. Chem. Soc. Rev. 38, 1450–1459 (2009).

    Article  CAS  Google Scholar 

  39. Wang, Z. Q. & Cohen, S. M. Postsynthetic modification of metal–organic frameworks. Chem. Soc. Rev. 38, 1315–1329 (2009).

    Article  CAS  Google Scholar 

  40. Chae, H. K. et al. A route to high surface area, porosity and inclusion of large molecules in crystals. Nature 427, 523–527 (2004).

    Article  CAS  Google Scholar 

  41. Biradha, K. & Fujita, M. A springlike 3D-coordination network that shrinks or swells in a crystal-to-crystal manner upon guest removal or readsorption. Angew. Chem. Int. Ed. 41, 3392–3395 (2002).

    Article  CAS  Google Scholar 

  42. Ohmori, O., Kawano, M. & Fujita, M. Crystal-to-crystal guest exchange of large organic molecules within a 3D coordination network. J. Am. Chem. Soc. 126, 16292–16293 (2004).

    Article  CAS  Google Scholar 

  43. Cohen, M. D. & Schmidt, G. M. J. Photochromy and thermochromy of anils. J. Phys. Chem. 66, 2442–2445 (1962).

    Article  CAS  Google Scholar 

  44. Haneda, T., Kawano, M., Kojima, T. & Fujita, M. Thermo-to-photo-switching of the chromic behavior of salicylideneanilines by inclusion in a porous coordination network. Angew. Chem. Int. Ed. 46, 6643–6645 (2007).

    Article  CAS  Google Scholar 

  45. Karakas, A., Elmali, A., Unver, H. & Svoboda, I. Nonlinear optical properties of some derivatives of salicylaldimine-based ligands. J. Mol. Struct. 702, 103–110 (2004).

    Article  CAS  Google Scholar 

  46. Ohara, K., Kawano, M., Inokuma, Y. & Fujita, M. A porous coordination network catalyzes an olefin isomerization reaction in the pore. J. Am. Chem. Soc. 132, 30–31 (2010).

    Article  CAS  Google Scholar 

  47. Ohara, K., Inokuma, Y. & Fujita, M. The catalytic Z to E isomerization of stilbenes in a photosensitizing porous coordination network. Angew. Chem. Int. Ed. 49, 5507–5509 (2010).

    Article  CAS  Google Scholar 

  48. Costa, J. S. et al. Chemical modification of a bridging ligand inside a metal–organic framework while maintaining the 3D structure. Eur. J. Inorg. Chem. 1551–1554 (2008).

  49. Burrows, A. D., Frost, C. G., Mahon, M. F. & Richardson, C. Post-synthetic modification of tagged metal-organic frameworks. Angew. Chem. Int. Ed. 47, 8482–8486 (2008).

    Article  CAS  Google Scholar 

  50. Sato, H., Matsuda, R., Sugimoto, K., Takata, M. & Kitagawa, S. Photoactivation of a nanoporous crystal for on-demand guest trapping and conversion. Nature Mater. 9, 661–666 (2010).

    Article  CAS  Google Scholar 

  51. Ohmori, O., Kawano, M. & Fujita, M. A two-in-one crystal: Uptake of two different guests into two distinct channels of a biporous coordination network. Angew. Chem. Int. Ed. 44, 1962–1964 (2005).

    Article  CAS  Google Scholar 

  52. Kawano, M., Kawamichi T., Haneda, T., Kojima, T. & Fujita, M. The modular synthesis of functional porous coordination networks. J. Am. Chem. Soc. 129, 15418–15419 (2007).

    Article  CAS  Google Scholar 

  53. Haneda, T., Kawano, M., Kawamichi, T. & Fujita, M. Direct observation of the labile imine formation through single-crystal-to-single-crystal reactions in the pores of a porous coordination network. J. Am. Chem. Soc. 130, 1578–1579 (2008).

    Article  CAS  Google Scholar 

  54. Kawamichi, T., Kodama, T., Kawano, M. & Fujita, M. Single-crystalline molecular flasks: Chemical transformation with bulky reagents in the pores of porous coordination networks. Angew. Chem. Int. Ed. 47, 8030–8032 (2008).

    Article  CAS  Google Scholar 

  55. Ikemoto, K., Inokuma, Y. & Fujita, M. The reaction of organozinc compounds with an aldehyde within a crystalline molecular flask. Angew. Chem. Int. Ed. 49, 5750–5752 (2010).

    Article  CAS  Google Scholar 

  56. Kawamichi, T., Haneda, T., Kawano, M. & Fujita, M. X-ray observation of a transient hemiaminal trapped in a porous network. Nature 461, 633–635 (2009).

    Article  CAS  Google Scholar 

  57. Jones, S. C. & Bauer, C. A. Diastereoselective heterogeneous bromination of stilbene in a porous metal–organic framework. J. Am. Chem. Soc. 131, 12516–12517 (2009).

    Article  CAS  Google Scholar 

  58. Kawamichi, T., Inokuma, Y., Kawano, M. & Fujita, M. Regioselective Huisgen cycloaddition within porous coordination networks. Angew. Chem. Int. Ed. 49, 2375–2377 (2010).

    Article  CAS  Google Scholar 

  59. Ma, L., Abney, C. & Lin, W. Enantioselective catalysis with homochiral metal–organic frameworks. Chem. Soc. Rev. 1248–1256 (2009).

  60. Li, Q. W. et al. Docking in metal–organic frameworks. Science 325, 855–859 (2009).

    Article  CAS  Google Scholar 

  61. Inokuma, Y., Arai, T. & Fujita, M. Networked molecular cages as crystalline sponges for fullerenes and other guests. Nature Chem. 2, 780–783 (2010).

    Article  CAS  Google Scholar 

  62. Smaldone, R. A. et al. Metal–organic frameworks from edible natural products. Angew. Chem. Int. Ed. 49, 8630–8634 (2010).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan

    Yasuhide Inokuma & Makoto Fujita

  2. Division of Advanced Materials Science (WCU project) Pohang University of Science and Technology (POSTECH), San 31 Hyojadong, 790-784, Pohang, South Korea

    Masaki Kawano

  3. Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan

    Makoto Fujita

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  1. Yasuhide Inokuma
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Correspondence to Makoto Fujita.

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Inokuma, Y., Kawano, M. & Fujita, M. Crystalline molecular flasks. Nature Chem 3, 349–358 (2011). https://doi.org/10.1038/nchem.1031

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