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X-ray observation of a transient hemiaminal trapped in a porous network


X-ray crystallography is the method of choice for the direct structural analysis of crystalline compounds1. Extending its use to the in situ mapping of chemical transformations could provide valuable insights, as illustrated by time-resolved X-ray crystallography studies2,3; however, the transient nature of unstable reaction intermediates often poses a significant challenge. It has recently been demonstrated that standard chemical reactions can occur within the pores of porous coordination networks4,5,6 and that the robust crystallinity of these networks facilitates in situ X-ray analysis of the adducts and products7,8,9,10,11. Here we show that such systems even enable X-ray observations of reaction intermediates that are usually transient and non-isolable. Our proof-of-concept demonstration examines the simple and ubiquitous reaction between an amine and an aldehyde, which normally form a very short-lived hemiaminal that then yields the Schiff-base product. The mechanism of this reaction has been exhaustively examined, but the hemiaminal intermediate has only rarely been observed12,13,14,15,16. We first determine the structure of a porous network with an aromatic amine embedded in it, then diffuse an aldehyde substrate into the material to transform the amine into a hemiaminal intermediate that is kinetically trapped and thus amenable to X-ray analysis, and finally raise the temperature of the system to obtain the imine product and determine its structure. These results establish that porous network materials provide a means of obtaining sequential X-ray-based snapshots of the structural transformations that occur during chemical reactions.

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Figure 1: A reaction profile of imine formation.
Figure 2: Preparation of porous coordination network {[(ZnI2)3(2)2(3)]· x (G)}n (1; G = ethyl acetate, x = 4).
Figure 3: Direct crystallographic observation of imine formation from acetaldehyde and embedded 1-aminotriphenylene within the pores of 1.
Figure 4: Experimental device for the in situ hemiaminal formation in the crystal of 1.
Figure 5: Disorder of embedded amine 3 before the reaction.

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This research was supported by the CREST project of the Japan Science and Technology Agency, of which M.F. is the principal investigator, and also in part by KAKENHI, the Japan Society for the Promotion of Science, the Global COE Program (Chemistry Innovation through Cooperation of Science and Engineering), MEXT, Japan, and Koei Chemical Co. Ltd. This work has been approved by the Photon Factory Program Advisory Committee.

Author Contributions M.K. and M.F. designed the project, analysed the results and wrote the manuscript. T.K. and T.H. performed the experimental work.

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Correspondence to Masaki Kawano or Makoto Fujita.

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 725638 (1), CCDC 725639 (6) and CCDC 725640 (7). These data can be obtained free of charge from the Cambridge Crystallographic Data Centre (

Supplementary information

Supplementary Information

This file contains Crystallographic Data for 1, 6 and 7 and Supplementary Figures for S1-S9 with Legends. (PDF 3842 kb)

Supplementary Data

This file is the Crystallographic Information File (CIF) for the coordination networks 1, 4, and 5 and it shows that the molecular modelling software reproduces the crystal structures. (TXT 165 kb)

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

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