“This is no cartoon. It’s a real molecule, with all the interactions
taking place correctly,” said Anatoly Kolomeisky as he showed an animation
of atoms twisting and turning about a central hub like a carnival ride gone
Kolomeisky, a Rice
Univ. associate professor
of chemistry, was offering a peek into a molecular midway where atoms dip, dive,
and soar according to a set of rules he is determined to decode.
Kolomeisky and Rice graduate student Alexey Akimov have taken a large step
toward defining the behavior of these molecular whirligigs with a new paper in
the American Chemical Society’s Journal
of Physical Chemistry C. Through molecular dynamics simulations, they
defined the ground rules for the rotor motion of molecules attached to a gold
It’s an extension of their work on Rice’s famed nanocars, developed
primarily in the lab of James Tour, Rice’s T.T. and W.F. Chao Chair in
Chemistry as well as a professor of mechanical engineering and materials
science and of computer science, but for which Kolomeisky has also constructed
Striking out in a different direction, the team has decoded several key
characteristics of these tiny rotors, which could harbor clues to the ways in
which molecular motors in human bodies work.
The motion they described is found everywhere in nature, Kolomeisky said.
The most visible example is in the flagella of bacteria, which use a simple
rotor motion to move. “When the flagella turn clockwise, the bacteria move
forward. When they turn counterclockwise, they tumble.” On an even smaller
level, ATP-synthase, which is an enzyme important to the transfer of energy in
the cells of all living things, exhibits similar rotor behavior—a Nobel
Understanding how to build and control molecular rotors, especially in
multiples, could lead to some interesting new materials in the continuing
development of machines able to work at the nanoscale, he said. Kolomeisky
foresees, for instance, radio filters that would let only a very finely tuned
signal pass, depending on the nanorotors’ frequency.
“It would be an extremely important, though expensive, material to
make,” he said. “But if I can create hundreds of rotors that move
simultaneously under my control, I will be very happy.”
The professor and his student cut the number of parameters in their computer
simulation to a subset of those that most interested them, Kolomeisky said. The
basic-model molecule had a sulfur atom in the middle, tightly bound to a pair
of alkyl chains, like wings, that were able to spin freely when heated. The
sulfur anchored the molecule to the gold surface.
While working on a previous paper with researchers at Tufts Univ.,
Kolomeisky and Akimov saw photographic evidence of rotor motion by scanning
tunneling microscope images of sulfur/alkyl molecules heated on a gold surface.
As the heat rose, the image went from linear to rectangular to hexagonal,
indicating motion. What the pictures didn’t indicate was why.
That’s where computer modeling was invaluable, both on the Kolomeisky lab’s
own systems and through Rice’s SUG@R platform, a shared supercomputer cluster.
By testing various theoretical configurations—some with two symmetrical chains,
some asymmetrical, some with only one chain—they were able to determine a set
of interlocking characteristics that control the behavior of single-molecule
First, he said, the symmetry and structure of the gold surface material (of
which several types were tested) has a lot of influence on a rotor’s ability to
overcome the energy barrier that keeps it from spinning all the time. When both
arms are close to surface molecules (which repel), the barrier is large. But if
one arm is over a space—or hollow—between gold atoms, the barrier is
Second, symmetric rotors spin faster than asymmetric ones. The longer chain
in an asymmetric pair takes more energy to get moving, and this causes an
imbalance. In symmetric rotors, the chains, like rigid wings, compensate for
each other as one wing dips into a hollow while the other rises over a surface
Third, Kolomeisky said, the nature of the chemical bond between the anchor
and the chains determines the rotor’s freedom to spin.
Finally, the chemical nature of rotating groups is also an important factor.
Kolomeisky said the research opens a path for simulating more complex rotor
molecules. The chains in ATP-synthase are far too large for a simulation to
wrangle, “but as computers get more powerful and our methods improve, we
may someday be able to analyze such long molecules,” he said.
The Welch Foundation, the National Science Foundation and the National
Institutes of Health funded the research.