Volume 86 Issue 25 | pp. 37-38
Issue Date: June 23, 2008

Molecular Cage May Contain ... Nothing

Self-assembled prisms may enclose empty spaces rather than solvent
Department: Science & Technology
A molecular dynamics simulation shows the escape of nitromethane molecules placed inside a prism (purple), leaving behind an empty space. The prism and trifluoromethanesulfonate (triflate) counterions are shown as space-filling models, and nitromethane molecules outside the prism are shown as stick structures (orange).
Credit: Courtesy of Josef Michl

MOLECULAR SELF-ASSEMBLY involves the production of supramolecular structures from component parts without external direction. Get enough surfactant molecules in close proximity, for example, and they can spontaneously form into monolayers, micelles, or other nanostructures. Researchers have also devised building blocks that self-assemble in solution to form a variety of cages, in shapes ranging from cubes and dodecahedra to trigonal and tetragonal prisms.

Intuitively, one might expect that such molecular cages self-assembled in solution would encase solvent molecules.

Think again. The interiors of such structures may be voids, says a group of researchers led by Jaroslav Vacek of the Institute of Organic Chemistry & Biochemistry at the Academy of Sciences of the Czech Republic; Douglas C. Caskey and Josef Michl of the University of Colorado, Boulder; and Peter J. Stang of the University of Utah in a pair of papers recently published in the Journal of the American Chemical Society (DOI: 10.1021/ja710715e and 10.1021/ja801341m). Furthermore, the existence of such empty spaces inside molecular cages may be a more general phenomenon contributing not only to cage assembly but perhaps even to biological processes.

"The study provides a wonderful combination of novel structures, experiment, and computation," says William L. Jorgensen, a chemistry professor at Yale University.

Molecular cages, including prism-shaped ones, have applications in molecular recognition and enantioselective catalysis. To that end, Caskey and colleagues were working with several types of trigonal prisms formed from tetrapyridyl star-shaped connectors and platinum linkers. In particular, they were trying to incorporate chirality into the faces of the prisms rather than simply at the vertices.

Empty Cage
A trigonal prism self-assembled in solution from tetrapyridyl connectors and platinum linkers (green) may enclose a void rather than solvent.
Credit: Brian Northrop/U of Utah
Empty Cage
A trigonal prism self-assembled in solution from tetrapyridyl connectors and platinum linkers (green) may enclose a void rather than solvent.
Credit: Brian Northrop/U of Utah

The tetrapyridyl arms of the "stars" tend to twist in a propeller-like fashion, producing a conformational helical chirality in the cage faces once they're locked into an assembled structure. When the researchers evaluated the ability of the pyridine rings to rotate—the mechanism by which the cages stereochemically invert—they noticed that the rings in one of the prisms seemed to rotate in different ways depending on the temperature.

More specifically, the transition enthalpies and entropies for pyridine ring rotation were significantly different under low and high temperature conditions. The values at low temperatures were comparable with those for similar prisms. The researchers attributed the rotational barrier at these temperatures to conformational preferences stemming from the electronic structure of the linking Pt atom.

For pyridine rotation at higher temperatures, a high transition enthalpy led the scientists to postulate that one or two adjacent Pt–N bonds must break, thereby allowing the pyridine ring to rotate freely until the bonds re-form.

TO FURTHER EXPLAIN an "extraordinarily high" transition entropy at high temperatures, Vacek and coworkers went on to examine solvent effects through molecular dynamics calculations. They started the simulations with fully assembled cages, which they assumed would enclose solvent.

To their surprise, they found that solvent nitromethane molecules initially placed inside the prism escape the cage within a few dozen picoseconds, leaving the inside of the prism empty. The scientists now believe the interior of the prism is solvophobic and tends to expel nitromethane molecules from the structure. When Pt–N bonds break and prism vertices open, the solvophobicity is disrupted and solvent molecules refill the void, resulting in the high transition entropy values.

The authors point out that there is precedent for void formation in another molecular context—hydrophobic pockets of proteins. There, water-free bubbles collapse and contribute to high entropy values when proteins unfold. Nevertheless, Vacek and colleagues note that more experiments are needed to determine whether the void-in-prism phenomenon is real—and if so, whether it is unique to the prism in this study or is found in other self-assembled cages as well.

The authors add that the prisms may also serve as models for a recent proposal that the closing and opening of biological ion channels in membranes may be controlled by the formation and collapse of water vapor bubbles in such channels (Biophys. J., DOI: 10.1529/biophysj.107.120493).

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