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Dynamical simulation illustrates the behavior of a floppy molecule

The panels above (the first is an animated GIF) show a 10 ps, MM2-based molecular mechanics simulation of the behavior of a “rotaxane” molecule in vacuum (atoms: 340, initial length: 7.0 nm). The simulation starts with the molecule held in an elongated conformation at roughly room temperature. Subsequent thermal motion tends to make the configuration more random, as initially straight chains bend, kink, and shorten. In a good solvent, the configuration would move endlessly among many trillions of these random configurations, a few of which would resemble the extended starting state. In vacuum, however, interatomic forces tend to pull the structure together into a more compact mass. These motions result chiefly from rotation around single bonds. Other structures can be more stable. These include floppy molecules that fold into specific structures (e.g., proteins) and inherently stiff molecules with networks of covalent bonds.

The example shown above is one of many rotaxanes. It has thick, branched ends linked by a slim chain which threads through a small ring (located slightly above the middle in the first panel). The ring has an electric charge of +4e. Variations in charge on the linking chain can move the ring between two different positions. Although many molecules contain parts that move in response to changes in charge, the presence of sliding rings — unusual in chemistry — has led to rotaxanes like the above being called “molecular machines”, with fanciful artwork and animations:

(Images from an article in Chemical & Engineering News; see also a news article in Science [pdf].)

Why are current rotaxanes floppy?

Link  Most large molecules made by conventional synthesis are floppy

How are stiff covalent structures organized?

Previous  Large molecules made by mechanosynthesis can be stiff

What progress has been made in designing and making stiff structures from biomolecules?

Link  Selected publications on the engineering of atomically precise structures from biomolecular materials