Imaging of Single Organic Molecules in Motion

Abstract

High-resolution transmission electron microscopy revealed nearly atomically precise images of stepping conformational change and translational motion of single hydrocarbon molecules confined in carbon nanotubes. One or two C12 or C22 alkyl chains were tethered to a carborane end group and then embedded in the nanotubes. Images of the hydrocarbon chains interacting with each other and with a graphitic surface provide information on three-dimensional structures and dynamic molecular interactions that cannot be obtained by other analytical methods.

Imaging of Aromatic Amide Molecules in Motion

“…In the light of the present results together with the reported stability of saturated hydrocarbons, 1 we suggest that a single isolate organic molecule in a CNT retains its original atomic connectivity of its skeletal atoms for a period long enough for observation of its conformational changes. The results, therefore, raise the hope that forthcoming development of higher-resolution, faster imaging and temperature controlled TEM instruments will provide methods to study molecular structures and reactions at the single molecule level.…”

“…The contrast is as weak as the one we observed previously for single alkyl chains. 1 The molecular rotation event can be more readily seen in Movie S1 (Supporting Information) rather than in the still pictures in Figure 2. The detailed interpretation of the molecular conformations is described in the Supporting Information.…”

“…2,3 The [60]fullerene group in 1 acts as an anchor to fix the sample molecule in one position 4 and makes possible the observation of the conformational change of the amide molecules and the top and side view of the aromatic ring at the single molecule level. In our previous report, 1 we described several fundamental observations about the TEM imaging of small, labile organic molecules: (1) individual organic molecules may be vaporized in vacuum and fixed either tightly or loosely in a CNT of a suitable size, (2) the tight fixing may occur largely when the tail of a saturated hydrocarbon chain sticks by chance to a defective area of the CNT, and hence the probability of finding the molecules suitable for structural study is rather low and unpredictable, (3) single individual molecules in vacuum are much more stable than previously expected on the basis of solid-state TEM imaging of organic molecules, 5 and (4) more specifically, saturated hydrocarbon molecules maintain their structural integrity for the observation time of about one minute under the 120-kV TEM conditions. We reexamined these issues on the molecule 1 and found that we can introduce the molecules into CNTs by a solution-phase process 6 instead of the vacuum process; that is, by soaking the CNTs in a toluene solution of the sample molecules.…”

“…1 Our initial data obtained for the alkylcarborane molecules suggested that the TEM imaging is of considerable potential for the structural study of small organic molecules. As the first step toward probing this hypothesis, we herein report the TEM images of 1-aminopyrene derivative 1 encapsulated in CNTs.…”

“…Moreover, we found that the fullerene moiety in 1 serves to suppress or to significantly slow down the translational motion of the molecule in a CNT 4 for a period long enough for imaging of the conformational and rotational motions than usually expected 7 and that the amide molecule 1 are at least as stable as the hydrocarbon molecules. 1 The molecule 1 8 was encapsulated into oxidatively perforated CNTs prepared by laser ablation, 9 and the CNT sample was suspended in methanol by ultrasonication. The suspension was dropped onto a TEM-microgrid for TEM observation (JEM-2100F, operated at 120-kV and 1 Â 10 À5 Pa, with 2.3-Å resolution).…”