Crystallography without Crystals – Using Molecular “Cages” to Study Non-crystallizable Compounds

A team of Japanese researchers have developed a novel platform for capturing the structure of labile intermediate species in chemical reactions with an unprecedented level […]

A team of Japanese researchers have developed a novel platform for capturing the structure of labile intermediate species in chemical reactions with an unprecedented level of resolution. This exciting new finding, which made use of the established technique X-ray crystallography, could provide new insights into chemical reaction mechanisms.

X-ray crystallography has long been the ultimate weapon for the structural identification of important compounds in a synthetic chemist’s arsenal. When X-rays are fired at a single crystal of a compound of interest, they will be diffracted into many specific directions, and a crystallographer can use the information in the angles and intensities of these diffracted rays to determine the three-dimensional structure of the compound. Nonetheless, X-ray crystallography cannot provide informative data for compounds that fail to form sufficiently large, well-defined crystal structures. Many of the intermediate compounds formed in chemical reactions fall into this category and so efforts to elucidate their structure at high resolution have been consistently frustrated.

Makoto Fujita’s group at the University of Tokyo devised a novel method to sidestep this problem. The researchers inserted a chemical substrate species into regularly-spaced “pores” of a crystallizable molecular scaffold and held in place by strong Van der Waals forces. This created a platform for addition of a reactant to the crystalline substrate-scaffold complex; this allowed the scientists to follow the progress of a reaction – assuming it was sufficiently slow – in real-time, using crystallography.
Fujita’s group used the technique to probe the mechanism of a palladium-catalyzed aromatic bromination reaction that is of great synthetic importance. They successfully captured the structure of an acetonitrile-containing intermediate which cannot be otherwise observed due to the rapid dissociation and precipitation of its component moiety. Nonetheless, the researchers do not claim that this finding is conclusive, given that a molecular scaffold provides a highly artificial platform for investigating the progress of a reaction. In the real world, distinct reaction mechanisms may be involved.

Source: K Ikemoto et al, J. Am. Chem. Soc., 2014, DOI: 10.1021/ja502996h

Leon Kong

About Leon Kong

Organic chemist and one-time synthetic biologist. Bringing you the latest scoop in chemistry, biomedicine, and materials.