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

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.

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

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Acknowledgements

This research was supported by the Core Research for Evolutional Science and Technology (CREST) project of the Japan Science and Technology Agency (JST) and a Grant-in-Aid for specially promoted research (24000009), of which M.F. is the principal investigator. We thank H. Sato (Rigaku) for the determination of the face indices.

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Authors and Affiliations

Authors

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.

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Correspondence to Yasuhide Inokuma or Makoto Fujita.

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The authors declare no competing financial interests.

Integrated supplementary information

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).

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

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).

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

Supplementary Figure 3 Face indices of a single crystal of crystalline sponge 1·(cyclohexane) in category B suitable for guest inclusion.

Supplementary Figure 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.

Supplementary Figure 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.

Supplementary information

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) (PDF 1946 kb)

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). (PDF 1890 kb)

Supplementary Figure 3

Face indices of a single crystal of crystalline sponge 1· (cyclohexane) in category B suitable for guest inclusion. (PDF 829 kb)

Supplementary Figure 4

Crystal structure of 1· (cyclohexane) in the different directions. (PDF 345 kb)

Supplementary Figure 5

Comparison of the crystallinity of single crystals 1· (cyclohexane) in category A and B before and after guest inclusion. (PDF 474 kb)

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Inokuma, Y., Yoshioka, S., Ariyoshi, J. et al. Preparation and guest-uptake protocol for a porous complex useful for 'crystal-free' crystallography. Nat Protoc 9, 246–252 (2014). https://doi.org/10.1038/nprot.2014.007

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