Application of isomorphous replacement in the structure determination of a cubic liquid crystal phase and location of counterions

A second generation monodendron with dodecyl end-groups based on the AB(3) monomer 3,4,5-trihydroxy benzoate has previously been shown to form a thermotropic cubic phase with Pmthremacr;n symmetry (Balagurusamy et al., J. Am. Chem. Soc. 1997, 119, 1539). A structure consisting of spherical "micelles" was proposed originally, but an alternative choice of structure factor phases, giving a structure of interlocked squashed columns, could not be ruled out by diffraction data on the original material alone. We have therefore synthesized two selectively fluorinated equivalent compounds, the carboxylic acid and its Rb salt, to be able to apply a variant of the isomorphous replacement crystallographic technique. On the basis of the electron density maps of the new labeled compounds, reconstructed using small-angle X-ray diffraction intensities, the interlocking columns model is unequivocally rejected and the spheres model is upheld. Furthermore, the location of the metal cation in the center of the "micelles" is directly confirmed. Micellar diameter was shown to decrease on fluorination of the dodecyl chain ends, and increase significantly on introduction of Rb. This is interpreted in terms of changes in the number of wedge-shaped dendrons fitting into a spherical micelle due to their changing taper angle. It was found that the Rb-rich regions at the centers of six out of eight "micelles" in the unit cell are elongated in the direction of their closest packing. This adds support to the suggestion of a partial "column-like" character of stacked rows of such micelles, consistent with the position of the Pmthremacr;n phase next to the columnar phase in the phase sequence of most taper-shape compounds. The results illustrate the potential of isomorphous replacement, used a great deal in protein crystallography, in structure investigation of liquid crystals and supramolecular soft matter.