Preparation and guest-uptake protocol for a porous complex useful for 'crystal-free' crystallography

Journal name:
Nature Protocols
Volume:
9,
Pages:
246–252
Year published:
DOI:
doi:10.1038/nprot.2014.007
Published online

Abstract

We recently reported a new method for single-crystal X-ray diffraction (SCD) analysis that does not require the crystallization of the target compound. In this 'crystal-free' crystallography, a tiny crystal of a porous complex is soaked in the solution of the target guest. The guest molecules are absorbed and oriented in the crystal pores and can be analyzed by X-ray diffraction. We describe here a detailed synthetic protocol for the preparation of uniform single crystals of the porous host complex and for the subsequent guest uptake. The protocol describes our most versatile porous complex, which is prepared from commercially available ZnI2 and 2,4,6-tri(4-pyridyl)-1,3,5-triazine. The host complex has large pores with a cross-section of 8 × 5 Å2. Single crystals of the complex are grown from layered solutions of the two components. The pores of the as-synthesized complex are filled with nitrobenzene, which is replaced with the inert solvent cyclohexane. This solvent exchange is essential for the rapid and effective inclusion of target compounds. The most crucial and delicate step is the selection of high-quality single crystals from the mixture of crystals of various shapes and sizes. We suggest using the facial indices of the single crystals as a criterion for crystal selection. Single-crystal samples for X-ray analysis can be prepared by immersing the selected crystals in a cyclohexane/dichloromethane solution of target compound. After a very slow evaporation of the solvent, typically over 2 d, the final crystal can be picked and directly subjected to SCD analysis. The protocol can be completed within ∼16 d.

At a glance

Figures

  1. Synthesis of crystalline sponge 1 and the preparation of single-crystal samples loaded with target molecules 3 and 4.
    Figure 1: Synthesis of crystalline sponge 1 and the preparation of single-crystal samples loaded with target molecules 3 and 4.
  2. X-ray crystal structures of inclusion complexes.
    Figure 2: X-ray crystal structures of inclusion complexes.

    (a,b) Shown are 1·3 (a) and 1·4 (b). On the top left are single-crystal samples prepared by the described procedure, whereas on the top right are ORTEP drawings of the target compounds 3 and 4 at the 50% probability level (C, gray; H, white; N, blue). Bottom, network structures; guest molecules 3 and 4 are drawn as space-filling models.

  3. Experimental procedures for the synthesis of crystalline sponge 1 and the preparation of single-crystal samples for X-ray analysis.
    Figure 3: Experimental procedures for the synthesis of crystalline sponge 1 and the preparation of single-crystal samples for X-ray analysis.

    (a) Slow addition of ZnI2 solution onto ligand 2 solution in a test tube. (b) Crystals of complex 1 appears on the wall around the interface after 1 week. Some of the crystals fall off and accumulate at the bottom of the test tube. (c) Equipment setup for the solvent exchange. (d) Microscope photograph of crystalline sponge 1·(cyclohexane). Red arrows indicate suitable crystals for guest accommodation. (e) Picking high-quality crystals by looking through a microscope. (f) A microvial containing a crystalline sponge 1·(cyclohexane) and a solution of guest 3. (g) Micrograph of the single crystal 1·3 on the bottom of the microvial.

  4. An example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane).
    Supplementary Fig. 1: An example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane).

    The bottom pictures show the close-up views of the area surrounded by the dotted frame in the top pictures.

  5. Another example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane).
    Supplementary Fig. 2: Another example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane).

    The bottom pictures show the close-up views of the area surrounded by the dotted frame in the top pictures.

  6. Face indices of a single crystal of crystalline sponge 1·(cyclohexane) in category B suitable for guest inclusion.
    Supplementary Fig. 3: Face indices of a single crystal of crystalline sponge 1·(cyclohexane) in category B suitable for guest inclusion.
  7. Crystal structure of 1·(cyclohexane) in the different directions.
    Supplementary Fig. 4: Crystal structure of 1·(cyclohexane) in the different directions.

    Solvent molecules are omitted for the clarity. Crystallographic data for 1·(cyclohexane): C36H24N15Zn3I6·2.5(C6H12), Mr = 1792.57, Monoclinic, space group, C2/c, a = 34.071(4), b = 14.9350(18), c = 29.989(4) Å, β = 100.564(2)°-, V = 15001(3) Å3, T = 90 K, Z = 8, 8336 unique reflections out of 15426 with I> 2σ(I), 775 parameters, 1.22 < θ < 26.45°, final R factors R1 = 0.1106 and wR2 = 0.3790 for all data.

  8. Comparison of the crystallinity of single crystals 1·(cyclohexane) in category A and B before and after guest inclusion.
    Supplementary Fig. 5: Comparison of the crystallinity of single crystals 1·(cyclohexane) in category A and B before and after guest inclusion.

    Even though the crystallinity of the initial crystal is good, cracking was observed after the guest inclusion for crystals in category A.

References

  1. Sheldrick, G.M. A short history of SHELX. Acta. Cryst. A64, 112122 (2008).
  2. Ohashi, Y. Structural determination of unstable species. in Models, Mysteries and Magic of Molecules (eds. Boeyens, J.C.A. & Ogilvie, J.F.) 109113 (Springer, 2008).
  3. Inokuma, Y. et al. X-ray analysis on the nanogram to microgram scale using porous complexes. Nature 495, 461466 (2013).
  4. Stallforth, P. & Clardy, J. One size fits most. Nature 495, 456457 (2013).
  5. Kitagawa, S., Kitaura, R. & Noro, S. Functional porous coordination polymers. Angew. Chem. Int. Ed. 43, 23342375 (2004).
  6. Batten, S.R. & Robson, R. Interpenetrating nets: ordered, periodic entanglement. Angew. Chem. Int. Ed. 37, 14601494 (1998).
  7. Yaghi, O.M. et al. Reticular synthesis and the design of new materials. Nature 423, 705714 (2003).
  8. Fujita, M. et al. Self-assembly of ten molecules into nanometre-sized organic host frameworks. Nature 378, 469471 (1995).
  9. Yoshizawa, M., Klosterman, J.K. & Fujita, M. Functional molecular flasks: new properties and reactions within discrete, self-assembled hosts. Angew. Chem. Int. Ed. 48, 34183438 (2009).
  10. Inokuma, Y., Arai, T. & Fujita, M. Networked molecular cages as crystalline sponges for fullerenes and other guests. Nat. Chem. 2, 780783 (2010).
  11. 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, 1629216293 (2004).
  12. 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, 33923395 (2002).
  13. 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, 3031 (2010).
  14. Inokuma, Y. et al. Corrigendum: X-ray analysis on the nanogram to microgram scale using porous complexes. Nature 501, 262 (2013).
  15. Spek, A.L. Structure validation in chemical crystallography. Acta. Cryst. D65, 148– (2009).
  16. Sluis, P.V.D. & Spek, A.L. BYPASS: an effective method for the refinement of crystal structures containing disordered solvent regions. Acta. Cryst. A46, 194 (1990).

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Author information

Affiliations

  1. Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan.

    • Yasuhide Inokuma,
    • Shota Yoshioka,
    • Junko Ariyoshi,
    • Tatsuhiko Arai &
    • Makoto Fujita

Contributions

Y.I. and M.F. designed the project, analyzed results and wrote the manuscript. S.Y., J.A. and T.A. performed the experimental work and crystallographic analysis.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

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Supplementary information

Supplementary Figures

  1. Supplementary Figure 1: An example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane). (252 KB)

    The bottom pictures show the close-up views of the area surrounded by the dotted frame in the top pictures.

  2. Supplementary Figure 2: Another example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane). (225 KB)

    The bottom pictures show the close-up views of the area surrounded by the dotted frame in the top pictures.

  3. Supplementary Figure 3: Face indices of a single crystal of crystalline sponge 1·(cyclohexane) in category B suitable for guest inclusion. (147 KB)
  4. Supplementary Figure 4: Crystal structure of 1·(cyclohexane) in the different directions. (363 KB)

    Solvent molecules are omitted for the clarity. Crystallographic data for 1·(cyclohexane): C36H24N15Zn3I6·2.5(C6H12), Mr = 1792.57, Monoclinic, space group, C2/c, a = 34.071(4), b = 14.9350(18), c = 29.989(4) Å, β = 100.564(2)°-, V = 15001(3) Å3, T = 90 K, Z = 8, 8336 unique reflections out of 15426 with I> 2σ(I), 775 parameters, 1.22 < θ < 26.45°, final R factors R1 = 0.1106 and wR2 = 0.3790 for all data.

  5. Supplementary Figure 5: Comparison of the crystallinity of single crystals 1·(cyclohexane) in category A and B before and after guest inclusion. (103 KB)

    Even though the crystallinity of the initial crystal is good, cracking was observed after the guest inclusion for crystals in category A.

PDF files

  1. Supplementary Figure 1 (1,992 KB)

    An example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane)

  2. Supplementary Figure 2 (1,936 KB)

    Another example of high-quality crystals (category B; indicated by red arrows) found in as-synthesized crystals of crystalline sponge 1·(cyclohexane).

  3. Supplementary Figure 3 (849 KB)

    Face indices of a single crystal of crystalline sponge 1· (cyclohexane) in category B suitable for guest inclusion.

  4. Supplementary Figure 4 (353 KB)

    Crystal structure of 1· (cyclohexane) in the different directions.

  5. Supplementary Figure 5 (486 KB)

    Comparison of the crystallinity of single crystals 1· (cyclohexane) in category A and B before and after guest inclusion.

Additional data