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X-ray analysis on the nanogram to microgram scale using porous complexes

A Corrigendum to this article was published on 21 August 2013

Abstract

X-ray single-crystal diffraction (SCD) analysis has the intrinsic limitation that the target molecules must be obtained as single crystals. Here we report a protocol for SCD analysis that does not require the crystallization of the sample. In our method, tiny crystals of porous complexes are soaked in a solution of the target, such that the complexes can absorb the target molecules. Crystallographic analysis clearly determines the absorbed guest structures along with the host frameworks. Because the SCD analysis is carried out on only one tiny crystal of the complex, the required sample mass is of the nanogram–microgram order. We demonstrate that as little as about 80 nanograms of a sample is enough for the SCD analysis. In combination with high-performance liquid chromatography, our protocol allows the direct characterization of multiple fractions, establishing a prototypical means of liquid chromatography SCD analysis. Furthermore, we unambiguously determined the structure of a scarce marine natural product using only 5 micrograms of the compound.

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Figure 1: X-ray crystallographic observation of liquid guest molecules using crystalline sponges.
Figure 2: Nanogram-scale guest inclusion with a crystal of crystalline sponge3.
Figure 3: Crystal structures of a variety of guests determined using a one-crystal-scale inclusion protocol.
Figure 4: The crystal structure of a chiral guest, santonin, trapped in a crystalline sponge.
Figure 5: LC–SCD analysis of natural flavonoids.
Figure 6: Structural determination of miyakosyne A.

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References

  1. Ooi, L. Principles of X-Ray Crystallography (Oxford Univ. Press, 2010)

    Google Scholar 

  2. Sheldrick, G. M. A short history of SHELX . Acta Crystallogr. A 64, 112–122 (2008)

    Article  ADS  CAS  Google Scholar 

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

    Book  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  7. Fujita, M., Kwon, Y. J., Washizu, S. & Ogura, K. Preparation, clathration ability and catalysis of a two-dimensional square network material composed of cadmium(II) and 4,4′-bipyridine. J. Am. Chem. Soc. 116, 1151–1152 (1994)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  9. 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 

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

    Article  ADS  CAS  Google Scholar 

  11. Inokuma, Y., Kojima, N., Arai, T. & Fujita, M. Bimolecular reaction via the successive introduction of two substrates into the crystals of networked molecular cages. J. Am. Chem. Soc. 133, 19691–19693 (2011)

    Article  CAS  Google Scholar 

  12. 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 

  13. 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 

  14. 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 

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

    Article  Google Scholar 

  16. Li, J.-R., Kuppler, R. J. & Zhou, H.-C. Selective gas adsorption and separation in metal–organic frameworks. Chem. Soc. Rev. 38, 1477–1504 (2009)

    Article  CAS  Google Scholar 

  17. Chen, B., Xiang, S. & Qian, G. Metal-organic frameworks with functional pores for recognition of small molecules. Acc. Chem. Res. 43, 1115–1124 (2010)

    Article  CAS  Google Scholar 

  18. Kondo, M. et al. Three-dimensional framework with channeling cavities for small molecules: {[M2(4,4′-bpy)3(NO3)4]•xH2O} n (M = Co, Ni, Zn). Angew. Chem. Int. Edn Engl. 36, 1725–1727 (1997)

    Article  CAS  Google Scholar 

  19. 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 

  20. Inokuma, Y., Kawano, M. & Fujita, M. Crystalline molecular flasks. Nature Chem. 3, 349–358 (2011)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  22. Kim, H., Chun, H., Kim, G.-H., Lee, H.-S. & Kim, K. Vapor phase inclusion of ferrocene and its derivative in a microporous metal-organic porous material and its structural characterization by single crystal X-ray diffraction. Chem. Commun. 2759–2761 (2006)

  23. Halder, G. J. & Kepert, C. J. In situ single-crystal X-ray diffraction studies of desorption and sorption in a flexible nanoporous molecular framework material. J. Am. Chem. Soc. 127, 7891–7900 (2005)

    Article  CAS  Google Scholar 

  24. 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 

  25. Kitaura, R. et al. Formation of a one-dimensional array of oxygen in a microporous metal-organic solid. Science 298, 2358–2361 (2002)

    Article  ADS  CAS  Google Scholar 

  26. Cahn, R. S., Ingold, C. & Prelog, V. Specification of molecular chirality. Angew. Chem. Int. Edn Engl. 5, 385–415 (1966)

    Article  CAS  Google Scholar 

  27. Seco, J. M., Quiñoá, E. & Riguera, R. The assignment of absolute configuration by NMR. Chem. Rev. 104, 17–118 (2004)

    Article  CAS  Google Scholar 

  28. Freedman, T. B., Cao, X., Dukor, R. K. & Nafie, L. A. Absolute configuration determination of chiral molecules in the solution state using vibrational circular dichroism. Chirality 15, 743–758 (2003)

    Article  CAS  Google Scholar 

  29. Bijvoet, J. M., Peerdeman, A. F. & van Bommel, A. J. Determination of the absolute configuration of optically active compounds by means of X-rays. Nature 168, 271–272 (1951)

    Article  ADS  CAS  Google Scholar 

  30. Flack, H. D. & Bernardinelli, G. Absolute structure and absolute configuration. Acta Crystallogr. A 55, 908–915 (1999)

    Article  CAS  Google Scholar 

  31. Corey, E. J. The stereochemistry of santonin, β-santonin, and artemisin. J. Am. Chem. Soc. 77, 1044–1045 (1955)

    Article  CAS  Google Scholar 

  32. Deschamps, J. R. X-ray crystallography of chemical compounds. Life Sci. 86, 585–589 (2010)

    Article  CAS  Google Scholar 

  33. Takayanagi, H., Sudou, M. & Ogura, H. Crystal structure of 1α,2β-dibromo-1,2-dihydro-α-santonin. Anal. Sci. 7, 183–184 (1991)

    Article  CAS  Google Scholar 

  34. Inayama, S. et al. Unusual bromination of tetrahydro-(–)-α-santonins and new santonin isomers: X-ray crystal and molecular structure of 2β,14-dibromo-4α,5β,6β,11βH-tetrahydrosantonin. J. Chem. Soc. Chem. Commun. 495–496. (1980)

  35. Green, C. O., Wheatley, A. O., Osagie, A. U., Morrison, E. Y. S. A. & Asemota, H. N. Determination of polymethoxylated flavones in peels of selected Jamaican and Mexican citrus (Citrus spp.) cultivars by high-performance liquid chromatography. Biomed. Chromatogr. 21, 48–54 (2007)

    Article  CAS  Google Scholar 

  36. Han, S. et al. Isolation and identification of polymethoxyflavones from the hybrid Citrus, Hallabong. J. Agric. Food Chem. 58, 9488–9491 (2010)

    Article  CAS  Google Scholar 

  37. Hitora, Y., Takada, K., Okada, S. & Matsunaga, S. Miyakosynes A–F, cytotoxic methyl branched acetylenes from a marine sponge Petrosia sp. Tetrahedron 67, 4530–4534 (2011)

    Article  CAS  Google Scholar 

  38. Sampietro, D. A., Catalan, C. A. N. & Vattuone, M. A. Isolation, Identification, and Characterization of Allelochemicals/Natural Products (Science Publ., 2009)

    Book  Google Scholar 

  39. Croue, J.-P., Korshin, G. V. & Benjamin, M. M. Characterization of Natural Organic Matter in Drinking Water 73–374 (Am. Water Works Assoc., 1999)

    Google Scholar 

  40. Ahuja, S. & Alsante, K. Handbook of Isolation and Characterization of Impurities in Pharmaceuticals (Academic, 2003)

    Google Scholar 

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Acknowledgements

This research was supported by Grants-in-Aid for Specially Promoted Research (24000009) and Young Scientists (B) (23750146), and by the CREST project of the Japan Science and Technology Agency. The experiment involving X-ray crystallography with 80 ng of guest molecules was performed using VariMax optics with a RAPID image plate detector system, courtesy of Rigaku Corporation. We thank M. Yamasaki and H. Sato for support for X-ray measurements.

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Authors and Affiliations

Authors

Contributions

Y.I. and M.F. designed the project, analysed results and wrote the manuscript. S.Y., J.A. and T.A. performed the experimental work and crystallographic analysis. Y.H., S.M. and K.T. selected and provided a natural product sample for analysis. K.R. confirmed the validity of the X-ray crystallographic analysis of all data.

Corresponding author

Correspondence to Makoto Fujita.

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Competing interests

The authors declare no competing financial interests.

Additional information

The X-ray crystallographic coordinates for structures reported in this paper have been deposited at the Cambridge Crystallographic Data Centre, under deposition numbers CCDC 910380, 910381, 910382, 910383, 910384, 910385, 910386, 910387, 910388, 910389, 910390, 910391, 910392, 910393 and 910394. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre (http://www.ccdc.cam.ac.uk/data_request/cif).

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Text and Data Supplementary Figures 1-5 and additional references. (PDF 3503 kb)

Supplementary Data

This file contains the crystallographic data. This file was added online on 8 April, 2013. (TXT 774 kb)

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Inokuma, Y., Yoshioka, S., Ariyoshi, J. et al. X-ray analysis on the nanogram to microgram scale using porous complexes. Nature 495, 461–466 (2013). https://doi.org/10.1038/nature11990

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