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First Ever Rearrangement Of Atomic Bonds In A Single Molecule

By adjusting the voltage pulses on an atomic force microscope, chemists have succeeded in rearranging the bonds between atoms in a single molecule.


Stephen Luntz

Stephen has a science degree with a major in physics, an arts degree with majors in English Literature and History and Philosophy of Science and a Graduate Diploma in Science Communication.

Freelance Writer

These three shapes, bent alkyne, diradical and cyclobutadiene, can be selected by applying differing voltages to bonds in between.
They may look like ghosts but (L to R) bent alkyne, diradical, and cyclobutadiene are three molecules of the same composition with different bonds. Image Credit: Leo Gros/IBM

For chemists, the capacity to change the bonds within individual molecules, changing the molecule's shape in the process, would be close to the ultimate power. The capacity to do just that using a (homebuilt) scanning tunneling microscope and an adjustable voltage has been demonstrated for the first time, albeit for one rather distinctive molecule.

Building complex molecules is currently a very inefficient process. In a Perspective in Science, it's described by Professor Igor Alabugin and Chaowei Hu of Florida State University as like dumping Lego blocks in a washing machine and hoping they come out in the right combination, “either by complete chance or under the guidance of other molecular-sized objects – i.e., catalysts.”


Help may be at hand, however. The same edition of Science contains the paper Alubugin and Hu are commenting on, which describes a much more exact process, shaping an atom bond by bond by adjusting the charge on a tiny copper-tipped probe. Dr Florian Albrecht of IBM Research Europe and co-authors succeeded in creating three different products starting from the same basic form, just by choosing different voltage combinations and applying them to bonds within the molecule. Indeed, they even found the products could be switched back and forth at will.

The paper describes a process beginning with a substance called 5,6,11,12-tetrachlorotetracene (C18H8Cl4), from which four chlorine atoms were removed, leaving behind carbon atoms with at least one unpaired electron known as radical centers. The radical centers then pair up creating carbon-carbon bonds but two unpaired electrons.

The system is designed so the unpaired electrons cannot reconnect to make a further carbon-carbon bond, as would normally occur. Depending on the voltage applied, the system can maintain its initial form, known as diradical, or become either cyclobutadiene or bent alkyne. Each of these have the same composition, but a different arrangement of atoms and bonding combinations.

“The potential to interact with a different set of partners makes this shape-shifting molecular system a Swiss Army knife with three distinct and useful chemical tools,” Alabugin and Hu write. Each is capable of performing a different chemical function, such as serving as a binding site for transition metals or participating in redox reactions. The three could even be used as logic gates in molecular electronics.


Having conducted the experiment at −268° C (−450° F), a temperature where molecules can be relied on to barely move, replication at something approaching room temperature may prove more difficult. Other molecules may also prove harder nuts to crack. Nevertheless, the demonstration opens the path to precise control of molecular shape in at least some cases.

Moreover, the work will help us understand redox reactions, which retain plenty of mystery, despite their important role in organic, and inorganic chemistry.


spaceSpace and Physicsspacechemistry
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