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Molecular snap-shots

Conformational changes of organic molecules tethered to the surface of carbon nanostructures are imaged using high resolution electron microscopy.

Obtaining structural information about the conformational changes of complex organic molecules, on the single molecule scale and with near atomic precision, has eluded chemists to date. Methods involving the encapsulation of molecules inside carbon nanotubes offer a means to achieving these goals, however, the confined environment limits the size of molecules that can be studied and, most likely, the number of possible conformations the molecules can readily adopt.

Now, Nakamura and co-workers from the Japan Science and Technology Agency and University of Tokyo1 have imaged such molecular behaviour by covalently tethering organic molecules to the surface of carbon nanohorns. Transmission electron microscopy (TEM) showed organic molecules with almost atomic precision. The molecules had long chain triamides—attached to the carbon nanohorns by an amide link—and a biotin group at the opposite end.

The triamide molecules preferentially attached to the cap regions of the nanohorns rather than the side walls of the structure and, according to Nakamura, this is the first experimental evidence to show that the curved regions are the most reactive sections of carbon nanohorns. Notably, only between one and three triamide molecules were attached to each nanohorn.

Fig. 1: TEM images showing the bent conformation of a triamide molecule attached to the cap regions a carbon nanohorn. The time corresponds to the time (seconds) since the observation begun.

TEM-based video images of the conformational changes of the molecules (Fig. 1), showed the changes to be smooth and the molecules to remain in relatively close contact with nanohorn surfaces as a result of non-covalent interactions between the biotin and π-surface of nanohorns. In addition, the contrast of the electron diffraction spots was related to the alignment of the atoms in the electron beam—the greater the number of carbon, nitrogen or oxygen atoms that lie parallel to the beam at a given point, the darker the image. The researchers coupled this experimental information with TEM simulations to create three-dimensional models of the conformers that may exist out of over one hundred million possibilities.

“We are now in a position to image how a single molecule interacts with another large molecule or materials,” says Nakamura. “In the future, we should be able to adapt this technique to visualize the dynamic structural change of peptide groups located on the surface of a small protein.”


  1. 1

    Nakamura, E. et. al. Imaging of Conformational Changes of Biotinylated Triamide Molecules Covalently Bonded to a Carbon Nanotube Surface. J. Am. Chem. Soc. 130, 7808–7809 (2008).

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Molecular snap-shots. NPG Asia Mater (2008).

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