Imaging the passage of a singlehydrocarbon chain through a nanopore

MASANORI KOSHINO1, NICLAS SOLIN2†, TAKATSUGU TANAKA2, HIROYUKI ISOBE2*† ANDEIICHI NAKAMURA1,2*1Exploratory Research for Advanced Technology (ERATO), Nakamura Functional Carbon Cluster Project, Japan Science and Technology Agency (JST),

Hongo, Bunkyo-ku, Tokyo 113-0033, Japan2Department of Chemistry, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan†Present address: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, 10691 Stockholm, Sweden (N.S.); Department of

Chemistry, Tohoku University, Aoba-ku, Sendai 980-8578, Japan (H.I.)

*e-mail: isobe@mail.tains.tohoku.ac.jp; nakamura@chem.s.u-tokyo.ac.jp

Published online: 14 September 2008; doi:10.1038/nnano.2008.263

Molecular transport through nanoscale pores in films,membranes and wall structures is of fundamental importancein a number of physical, chemical and biological processes1–6.However, there is a lack of experimental methods that canobtain information on the structure and orientation of themolecules as they pass through the pore, and their interactionswith the pore during passage. Imaging with a transmissionelectron microscope is a powerful method for studyingstructural changes in single molecules as they move7,8 and forimaging molecules confined inside carbon nanotubes9. Here,we report that such imaging can be used to observe thestructure and orientation of a hydrocarbon chain as it passesthrough nanoscale defects in the walls of a single-walledcarbon nanotube to the vacuum outside, and also to study theinteractions between the chain and the nanopore. Based onexperiments at 293 K and 4 K we conclude that the majorenergy source for the molecular motions observed at 4 K is theelectron beam used for the imaging.

We synthesized10 fullerene molecules with long alkenyl chains(Fig. 1a) and long alkyl chains (Fig. 1b). The nanotubes weretreated with hot O2 gas to remove the end caps and also toproduce the nanopores or defects in the tube wall. The moleculesand nanotubes were heated together in toluene and the samplewas subjected to transmission electron microscope (TEM)analysis. Figure 2 shows three fullerene molecules with longalkenyl chains orientated head-to-tail with each other (left-to-right), and the results of computer simulations and models. Wefound in this and other images that the hydrocarbon chains inboth types of molecules were often twisted in one of twodirections to maintain contact with the surface of the nanotube toreduce the surface energy due to CH–p interactions. Figure 2a,dshows two images captured over the periods 2.1–6.3 s and8.4–12.6 s, respectively, following the start of the observation (seeSupplementary Information, Movie 1). The images were obtainedfrom samples that were held on a specimen holder kept at atemperature of 293 K under an acceleration voltage of 120 kVwith a current density of 8.0 � 104 e.nm22 s21. A 0.5-s imagingtime was followed by a 1.6-s readout time from a charge-coupled device (CCD); the clear image of the carbon chainsindicates that their motion was much slower than the 0.5-s

exposure time. The chain of the left-hand molecule has a sickle-like conformation and was observed to rotate slowly in a volumeof �1.5 nm3 (see Supplementary Information, Movie 1). Theanalysis of the movie suggests that the observed 180 8 rotation ofthe chain occurred in �15 s. During this rotation, the middle partof the chain was in contact with the tube wall and the chainterminal was in contact with the neighbouring fullerene molecule.The side chains of the other two molecules were bent morecompactly and were observed to rotate qualitatively over thesame timescale.

In observations of a number of alkenyl fullerene molecules innanotubes, we sometimes observed that the rotating chain partiallyegressed from the tube by means of a nearby defect. Figure 3a showsan example of this, with four representative frames taken from amovie over a period of 25.2 s (see Supplementary Information,Movie 2). At 2.1 s, the chain is in a bent conformation. It can alsobe seen that there is a hole defect in the top of the tube (markedwith a red arrow)11–13. The diameter of the hole is �0.5 nm, wideenough to allow a linear hydrocarbon to pass through. The sidechain rotated in the tube, retaining the bent conformation and, at6.3 s, the chain terminus entered into the pore defect. The nanoporeretarded the chain for a period (up to a time of 8.4 s), and, based onsimulations (see Supplementary Information, Fig. S1), we concludedthat this pore/chain interaction occurred around the secondmethylene groups. Although the significance of these particularpositions is unclear at this time, our observation demonstrates thepotential utility of the TEM method for the study of specificmolecular interactions on a single-molecule basis. The remainder ofthe chain underwent a small conformational change between thetimes 8.4 and 18.9 s, and the entire chain was drawn back into thenanotube after a total period of 18.9 s.

(CH2)4CH=CH(CH2)3CH3

H(trans isomer)

(CH2)11CH3

H

Figure 1 The sample molecules. Alkenyl fullerene (left) and alkyl fullerene (right).

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Figure 2 Alkenyl fullerene in a carbon nanotube. a,d, Images obtained by superimposing three sequential TEM images captured over a period of 2.1–6.3 s (a) and

8.4–12.6 s (d) (�70 88888 rotation). b,e Simulated images obtained using molecular models. c,f, Molecular models used in b and e, respectively. Scale bar, 1 nm. The

TEM images were obtained with a JEOL JEM-2100F (V ¼ 120 kV, resolution ¼ 2.3 A) operating at 293 K.

6.3 s 8.4 s 18.9 s

58.0–62.0 s

48.3 s48.3 s35.7 s35.7 s

23.0–27.0 s

2.1 s

Figure 3 Alkenyl fullerene and alkyl fullerene in a carbon nanotube. a, Sequential TEM images of alkenyl fullerene captured over a period of 25.4 s on a sample

stage at 293 K, with the corresponding molecular models shown directly below (see Supplementary Information, Fig. S1). The red arrow shows the position of the

hole on the sidewall of the nanotube. b, Images of alkyl fullerene molecule captured over the periods 23.0–27.0 s (left panel) and 58.0–62.0 s (middle panel) on a

stage at 4 K. The experimental images were obtained by superimposing five sequential TEM images. A model for 58.0–62.0 s is shown in the right panel. c,d Images

of alkyl fullerene molecule captured at 35.7 and 48.3 s on a sample stage at 293 K. Simulations and models are also shown. e, Image of alkyl fullerene attached to

the top surface of a nanotube at 293 K. The fullerene moiety can be seen in the top right-hand corner, with the alkyl chain extending to the left-hand side. Scale

bars, 1 nm. The nanotubes have a diameter of 1.4 nm. The TEM images in a,c–e were obtained with a JEOL JEM-2100F TEM (V ¼ 120 kV, resolution ¼ 2.3 A). The

images in b were taken with a JEOL JEM-2100FC TEM (V ¼ 120 kV, resolution ¼ 2.6 A).

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We can consider a priori two energy sources that could cause themolecular motions—ambient thermal conditions and/or theelectron beam. We performed experiments using a TEM thatallowed us to image the molecules on a specimen stage kept at 4 Kto remove the effects of the ambient thermal conditions. A nanotubesample containing molecules with alkyl chains was prepared in thesame way as described for molecules with alkenyl chains and thiswas analysed on a sample stage cooled to 4 K. Figure 3b showsseveral frames from a movie taken over a total observation time of80 s (see Supplementary Information, Movie 3). After a period of�60 s from the beginning of the observations, the alkyl chainmoved out of the tube in its stretched conformation, vibrated slowlyfor a period of 8 s in its linear conformation, and was then drawnback into the nanotube interior after a period of 65 s. Based on acomparison of various motion images at both 4 and 293 K, weconcluded that the observed conformational changes of themolecule occurred at approximately the same timescale of secondsat both temperatures.

Images of molecules with a long alkyl chain kept in the vacuumspace outside a nanotube (Fig. 3c–e) are now considered. The imageswere taken at 293 K. The first case is the conformational changeshown in Fig. 3c,d (see Supplementary Information, Movie 4),which illustrates two representative structures observed at 35.7 and48.3 s during the total observation time of 60.9 s. The movementtook place slowly on a timescale similar to that described for amolecule with alkenyl chains confined in a nanotube. We cantherefore conclude that the nanotube confinement is not the mainreason for the very slow movement of the alkyl chains under ourTEM conditions. The chain terminal kept touching the tubesurface throughout the 60.9 s observation time, which can beascribed to the CH–p interaction14. Another molecule with alkylchains attached to the outside of a nanotube is shown in Fig. 3e(see Supplementary Information, Movie 5)15. The conformationalchange of the alkyl chain was also very slow.

The data from the experiments discussed above led us to severalconclusions. First, and most importantly, we found that the samplestage temperature had only a small effect on the observed molecularmotions (4 K versus 293 K). Therefore, we can surmise that theelectron beam heated the nanotube locally, thereby causing theconformational change of the molecules in the tube. Note that wehave drawn this conclusion, and the remaining conclusions, basedon observations of hundreds of molecules with alkenyl and alkylchains, and related molecules, rather than just the images reportedabove. Second, we observed that the hydrocarbon chains underwenta very slow change in conformation, and kept the CH–pinteraction with the nanotube surface, whether they were locatedinside or outside of the tube. Given the success in the imaging ofan amide8,16 and of carborane derivatives7, we consider that ourTEM methodology is applicable to the study of the structure andinternal rotations of a wide range of organic and organometallicmolecules. Third, the hydrocarbon chains outside the carbonnanotube maintained their structural integrity for a period that waseffectively equal to that of the molecules inside the tube, andtherefore we conclude that confinement in a carbon nanotube doesnot provide protection of the hydrocarbons against damage by theelectrons to any significant degree. We have discussed thebackground of the radiation damage to organic molecules17

confined in a carbon nanotube in the supporting online materialsof ref. 7. The effect of charging under electron irradiation is anotherissue and will be the subject of future studies. Finally, we suggestthat TEM can provide molecular-level information on the transportof molecules through nanopores, which has so far not beenavailable using any other experimental method18. The imagesdirectly indicate that the molecular transport was a reversible

process. Of particular interest is that the hydrocarbon chain rotatingin the tube interior occasionally came out of a hole opening in thenanotube wall, and when the chain came out, the vector of thetranslational motion was nearly perpendicular to the tube wall.Although we have so far observed that the hydrocarbon chains passthrough holes in a linear conformation, they may also take the bentconformation if the hole size is much larger. The time resolution of0.5 s in this study is admittedly quite long and does not permit usto study ultrafast molecular events such as skeletal vibrations.

The observations that we have made have generated a numberof new questions. What force pushes the rotating chain out of ahole and then retracts it again into the tube interior? What is themolecular-level information that correlates to the kinetics of thetransportation process as studied using bulk materials? DoesTEM provide us with experimental tools to study the interactionsbetween a molecule and a pore of the sidewall or a tube, andcan we use this information to design functional membranesor functional porous materials such as zeolites? Obviously,this last problem needs us to seriously consider a transitionfrom the quantum mechanics of single molecules to the classicalmechanical rules that govern the motion of macroscopicsubstances. These questions are fundamental in nature and weexpect that some of these will be addressed experimentally andtheoretically in the near future.

Received 9 June 2008; accepted 6 August 2008; published 14 September 2008.

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Supplementary Information accompanies this paper at www.nature.com/naturenanotechnology.

AcknowledgementsElectron microscopy experiments were performed in collaboration with the Nanotube Research Centre,the National Institute of Advanced Industrial Science and Technology (AIST). We thank K. Yamanouchifor helpful discussions. This study was partly supported by MEXT (KAKENHI no. 18655012 to E.N.) andthe Sumitomo Foundation (to H.I.). N.S. wishes to thank the Knut och Alice Wallenbergs stiftelse(Stockholm, Sweden) for a postdoctoral fellowship and T.T. thanks the Japan Society for Promotion ofScience for a predoctoral fellowship.

Author contributionsM.K., H.I. and E.N. conceived and designed the experiments. N.S. contributed materials/analysis tools.M.K., H.I. and E.N. co-wrote the paper. All authors discussed the results and commented on themanuscript. N.S., T.T., H.I. and E.N. were responsible for synthesis of organic molecules and theiranalysis. M.K. was responsible for peapod sample preparations, TEM measurements and their analysis.

Author informationReprints and permission information is available online at http://npg.nature.com/reprintsandpermissions/.Correspondence and requests for materials should be addressed to H.I. and E.N.

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