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Dynamical simulation illustrates the behavior of a stiff molecule

The panels above (the first is an animated GIF) show a 10 ps MM2-based molecular mechanics simulation of the molecular physics of a stiff rod and sliding ring in vacuum (atoms: 606, length: 7.4 nm). The rod is built almost exclusively of hydrogen-terminated carbon in a diamond-like structure; the ring is built of oxygen and hydrogen-terminated silicon. In addition, both parts have several charged ammonium groups, totaling +3e on the lower surface of the rod and +6e on the upper surface of the ring. Electrostatic repulsion presses the ring upward (for contrast, see what happens when the ring starts at the bottom!).

The kinds of atoms and bonds forming the rod are the same as those in floppy structures (such as a rotaxane), but arranged differently. Comparing the simulations of the rod and the rotaxane makes clear the enormous qualitative difference between stiff and conformationally flexible structures of similar size. The molecular sciences to date have focused chiefly on structures of the latter sort, owing to the limitations of biological and solution-phase organic synthesis. Molecular manufacturing will enable the fabrication of structures that violate many of the intuitions that scientists have developed in working with floppy molecules.

Note that this is, by molecular mechanical engineering standards, a rather flexible structure because the rod is long and thin. Reliable positioning of tools with sub-bond-length accuracy at room temperature requires more rigid structures of the sort described in Nanosystems, pp. 398–409.

What is the molecular structure of the rod?

Link  Large molecules made by mechanosynthesis can be stiff

How does a similar but floppy molecule behave?

Previous  Dynamical simulation illustrates the behavior of a floppy molecule

Why does chemistry deal chiefly with floppy molecules?

Link  Most large molecules made by conventional synthesis are floppy