Research Article

Solid-state structures of peapod bearings composed of finite single-wall carbon nanotube and fullerene molecules

Sota Sato, Takashi Yamasaki, and Hiroyuki Isobe
PNAS June 10, 2014 111 (23) 8374-8379; first published May 27, 2014 https://doi.org/10.1073/pnas.1406518111

  1. Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved May 8, 2014 (received for review April 11, 2014)

Significance

Carbonaceous entities possessing tubular and spherical shapes spontaneously form a host–guest complex. This supramolecular complex, so-called a peapod, is unique among host–guest pairs in that it is assembled solely by van der Waals interactions at the concave–convex interface of sp2-carbon networks. Recently, a molecular version of this supramolecular system revealed the presence of the extremely tight association concomitantly with the dynamic motions of the guest in apolar media. In this paper, an atomic-level structure of the molecular peapod is revealed by a crystallographic method to show the presence of an inflection-free surface inside the tubular molecule. Enjoying rotational freedom at this smooth surface, the guest fullerene molecule rolls dynamically even in the solid state.

Abstract

A supramolecular combination of carbon nanotube and fullerene, so-called a peapod, has attracted much interest, not solely because of its physical properties but also for its unique assembled structures of carbonaceous entities. However, the detailed structural information available was not sufficient for in-depth understanding of its structural chemistry or for exploratory research inspired by novel physical phenomena, mainly because of the severely inhomogeneous nature of currently available carbon nanotubes. We herein report solid-state structures of a molecular peapod. This structure, solved with a belt-persistent finite carbon nanotube molecule at the atomic level by synchrotron X-ray diffraction, revealed the presence of a smooth, inflection-free Hirshfeld surface inside the tube, and the smoothness permitted dynamic motion of the C60 guest molecule even in the solid state. This precise structural information may inspire the molecular design of carbonaceous machines assembled purely through van der Waals contacts between two neutral molecules.

A carbonaceous supramolecular system called a peapod, i.e., a host–guest composite of a single-wall carbon nanotube (SWNT) and fullerene, is attracting considerable interest in various fields due to its unique electronic and molecular structures (1). Although interesting physical phenomena of peapods are being discovered, especially in solid-state physics (2⇓⇓–5), little fundamental and in-depth understanding of peapods has been accumulated at the molecular or atomic levels until quite recently. The first reports of structural chemistry related to peapods appeared through the studies of [10]cycloparaphenylene ([10]CPP) (6): Yamago and coworkers (7) first reported a moderate level of association (association constant Ka ∼ 103 M in o-dichlorobenzene) with C60 in the solution phase, and solid-state crystal structures were reported with C60 and C70 by Jasti and coworkers (8) and Yamago and coworkers (9). Although this moderate level of association in [10]CPP raised a question regarding the stability of peapods in general (5, 10), we recently showed that the association of belt-persistent tubular molecules, [4]cyclo-2,8-chrysenylenes ([4]CC2,8) (11⇓–13), with C60 was much higher and recorded a 106- and 109-fold higher association constant in the same medium (Ka ∼ 109 M) and in benzene (Ka ∼ 1012 M), respectively (Fig. 1A) (14, 15). The level of association in this molecular peapod was comparable to the one expected from theoretical studies with infinite SWNT peapods (10) and, to the best of our knowledge, was highest among host–guest complexes in organic media to date. The uniqueness of molecular recognition in the curved π-systems was further accentuated by the fact that this tight association does not hamper dynamic rolling motions of the guest, providing an intriguing possibility as a molecular bearing (16). To deepen the understanding of tightest host–guest complex composed of two apolar and neutral components and also to accelerate the development of carbonaceous molecular machines (17), the structural information of this molecular peapod, especially at the atomic level, is indispensable. We herein report the solid-state structures of the peapod bearing. We show that, even in the solid state, the belt-persistent tubular molecule allows the dynamic motion of the encapsulated C60 molecule. An inflection-free, smooth surface inside the tube was revealed by a combination of diffraction analysis using a high-flux X-ray beam (18) and graphical inspection using the Hirshfeld surface of the encapsulated C60 probe (19). The atomic-level structural information at the tube–sphere interface should be valuable and useful for the in-depth understanding of curved π-systems, for the discussion of peapods in the solid state, and for the design of peapod molecular machines in the future.

Fig. 1.
Fig. 1.

Solid-state NMR analysis of peapod bearing. (A) Chemical structure of (M)-(12,8)-[4]CC2,8⊃C60. (B) Spectra of C60, (M)-(12,8)-[4]CC2,8⊃C60 and a mixture of C60 and (M)-(12,8)-[4]CC2,8⊃C60 at 25 °C under MAS conditions. See SI Appendix, Fig. S1, for the whole region. (C) VT NMR spectra of (M)-(12,8)-[4]CC2,8⊃C60 under static conditions without MAS. See SI Appendix, Fig. S3, for all of the data.

Results

Solid-State NMR Analysis.

We first investigated the solid-state structure of the peapod bearing (M)-(12,8)-[4]CC2,8⊃C60 through solid-state NMR analysis. The encapsulation in [4]CC resulted in an up-field shift of the 13C resonance of C60 (Fig. 1B and SI Appendix, Fig. S1): under magic-angle spinning (MAS) conditions of 20 kHz, the resonance of naked C60 appeared at 143 ppm, whereas the resonance of (M)-(12,8)-[4]CC2,8⊃C60 appeared at 140 ppm. The 3-ppm difference was unequivocally ascribed to the encapsulation by recording two separate resonances with a mixture of C60 and (M)-(12,8)-[4]CC2,8⊃C60. Although the resonances from [4]CC under the MAS conditions were not intense, they were enhanced under the cross-polarization MAS conditions to show the corresponding resonances (SI Appendix, Fig. S2).

As demonstrated previously with naked C60, the solid-state NMR spectra provide the evidence for dynamic motion in the solid state. Due to the random orientations of the molecules fixed in the solid state against the external magnetic field, ordinary molecules affords a broad powder pattern of resonances under static NMR conditions without MAS (20), whereas C60 affords a narrow single resonance even under the static NMR conditions by cancelling out the chemical shift anisotropy through the dynamic rolling motion in the solid state (21⇓–23). When we conducted the solid-state NMR analysis of (M)-(12,8)-[4]CC2,8⊃C60 under static conditions (Fig. 1C and SI Appendix, Fig. S2), we observed a narrow single resonance of C60 at 140 ppm along with the broad powder-pattern resonances of the encapsulating [4]CC host. This observation showed that, even in the solid state, C60 in [4]CC rolled rapidly on the NMR timescale. When we conducted variable-temperature (VT) NMR analysis, the resonance maintained its symmetric peak shape, and the half-width of the C60 resonance in [4]CC was maintained at 798 ± 53 Hz (4.5 ± 0.3 ppm, 176 MHz) throughout the accessible temperature range of our conventional instrument (from 70 °C to –30 °C; SI Appendix, Fig. S3). This result indicated that the dynamic motion of C60 at the lowest reachable temperature (–30 °C) was rapid enough to average away the chemical shift anisotropy. The detailed kinetics of the motion should be further investigated, for instance, by a wide-bore NMR instrument specialized for the ultralow temperature analysis of a 13C-enriched specimen (24). It is also important to note that the half-width of the C60 resonance is much smaller than in the previous data with infinite SWNT peapods (3,500 Hz, 35 ppm; 100 MHz) (24). The broadening effect of the previous investigation should be attributable to the presence of various SWNT structures, which, in turn, confirmed the importance of discrete molecular structures for the precise structural analysis.

Molecular and Packing Structures of Vacant and Filled Tubes.

We then conducted structural analysis using crystallographic methods. The crystal structure of vacant (12,8)-[4]CC2,8 is described first. A single crystal of (12,8)-[4]CC2,8 was obtained from a racemic mixture and revealed the tubular molecular structure through diffraction analysis with monochromated X-rays (BL-1A beamline; Photon Factory) (25). The average dihedral angle at the single-bond linkages was 18.48 ± 0.16°, which described the sp2-carbon atoms on a curved plane along the cylindrical axis (Fig. 2A) (13). The average diameter of the tube was measured at the carbon atoms closest to the equator (2- and 8-positions) and was 14.03 ± 0.04 (14.101 × 2 and 13.951 × 2) Å (13, 26). The molecules were packed in a thread-in-bead entanglement between enantiomers, a packing motif similar to the packing of the (16,0)-isomer (12), but the molecules of (12,8)-isomer were further knitted to form a 2D network of the molecules by accommodating hexyl chains of two different enantiomeric molecules in the tube. Each of the enantiomers was separately stacked through an interdigitated entanglement of hexyl chains to form homochiral columns of (P)- and (M)-structures, respectively (26).

Fig. 2.
Fig. 2.

Molecular structures from synchrotron X-ray diffraction analysis of a single crystal. For molecular structures viewed from the top, the hexyl chains and C60 are shown as wireframe diagrams, and the chrysenylenes are shown in ORTEP diagrams with thermal ellipsoids at the 30% level. The numberings of carbon atoms at the 2- and 8-positions are also shown. For the packing structures viewed from the side, the (P)- and (M)-structures are colored in red and blue, respectively. Solvent molecules with disorders are omitted for clarity. (A) Molecular and packing structures of (12,8)-[4]CC2,8. For the molecular structure, the (M)-structure is shown. Disordered hexyl chains are found, and one representative structure is shown. See CCDC 993075 for the crystal data. (B) Molecular and packing structures of (M)-(12,8)-[4]CC2,8⊃C60. One of the representative structures for four disordered C60 molecules (25% occupancy) and hexyl chains are shown. See Fig. 3 for the details of the C60 disorders and CCDC 993074 for the crystal data.

The crystal structure of (M)-(12,8)-[4]CC2,8⊃C60 from X-ray diffraction analysis is described next (Fig. 2B). Although severe disorders inherent to the dynamic bearing system hampered the analysis with ordinary X-ray beams, a synchrotron macromolecular crystallography beamline (BL41XU; SPring-8) (18) allowed us to solve the complex structure of the peapod at the atomic level. In the presence of chlorine atoms of CH2Cl2 molecules in a single crystal of the chiral trigonal P32 space group at –173 °C, we unequivocally assigned the absolute configuration of (12,8)-[4]CC2,8 as (M)-helicity with a reliable Flack parameter of 0.13 (13). Note that this assignment finally confirmed the previous conclusion from the spectral and theoretical investigations (11). Upon the encapsulation of C60, the average dihedral angle at the single-bond linkages was reduced to 11.64 ± 2.18°, and the smoothness of the curved π-system was further emphasized. The average diameter was 13.95 ± 0.01 (13.976, 13.969, 13.943, and 13.925) Å and did not deviate much from the diameter found at the same position of the vacant system (see above). The small deviation indicated that the tubular structure of the vacant host was ideally preorganized for the C60 guest (14, 27). As shown in Fig. 2B, the (M)-(12,8)-[4]CC2,8⊃C60 molecules were aligned in a columnar assembly again by the interdigitated hexyl substituents (26). The encapsulation of C60 thus disturbed only the thread-in-bead entanglement without affecting the interdigitated entanglement and resulted in a similar periodic spacing of [4]CC molecules, whether vacant or filled, in the homochiral column [13.5 Å for (12,8)-[4]CC2,8 and 13.3 Å for (M)-(12,8)-[4]CC2,8⊃C60].

Disorders and Hirshfeld Surfaces of Encapsulated C60 Molecules.

One of the most remarkable features of the crystal structure was the presence of disordered C60 molecules. As shown in Fig. 3, we identified as many as four disordered structures of C60 with an identical position of the center of gravity to minimize the R factors [R1 (observed data) = 0.1111, wR2 (all data) = 0.2999]. The severe disorders among four C60 molecules may indicate a small energy difference among these structures, which should be beneficial for the dynamic motion in the solid state. Unexpectedly, close examination of the disorders revealed the presence of anomalous carbon atoms: Two carbon atoms at the opposing corners of C60 were commonly located at almost identical positions in the crystal, and, as a result, the sum of their occupancy at this position accumulated to 100%. As a result of columnar assembly of the molecules, the carbon anomalies were further aligned in the crystal. Although we do not fully understand the origin of this anomaly at this stage, this observation may indicate that a subtle difference in the shape of the tube results in biased orientations of the C60 molecules (28, 29): The two anomalous carbon atoms define the circumscribing circle of C60 by locating at the opposite sites, and the anomalous locations let the longest diameter of the guest escape from the direct contact with the tube wall.

Fig. 3.
Fig. 3.

Disorder breakdown with different colors on disordered C60 molecules in (M)-(12,8)-[4]CC2,8⊃C60. (A) Molecular structure showing the disordered C60 molecules with highlights of carbon anomalies shown in ball models. (B) Molecular structures with C60 carbon atoms in ORTEP diagrams with thermal ellipsoid at the 20% level. Although one might postulate that two anomalous atoms could function as an axis for shaft motions, the directions of the thermal ellipsoids in the disordered structures do not support such dynamic single-axis motions. The disordered structures provided static snapshots at –173 °C, and the biased orientations with anomalous positions may correspond to the presence of a local energy minimum around this location. (C) Columnar packing structures showing the positions of anomalous carbon atoms with sphere models. For the structure viewed from the side, a transparent van der Waals surface of (M)-(12,8)-[4]CC2,8⊃C60 is also shown.

Analysis of the crystal structure with the Hirshfeld surface revealed the details of the peapod assembly (19, 30). By partitioning the space of the crystal into nonoverlapping volumes of molecules, the Hirshfeld surface of a molecule graphically provides various information, for instance, about the shape of the space dominated by an electron distribution of the molecule or about the environment surrounding the molecule (19). The Hirshfeld surface of the encapsulated C60 in the molecular peapod therefore serves as an inspection probe for the inner space: It should provide information about the encapsulating space of the host as well as the interacting contacts at the surface (31).

Reflecting the void space surrounded by hexyl chains over the peapod as well as the close contacting areas surrounded by [4]CC around the belt region, the Hirshfeld surface of C60 appeared as a football-shaped surface (Fig. 4; see also SI Appendix, Fig. S5, and Movies S1–S3 for the additional details). By coloring the surface based on the curvedness, shape index, and de mappings, we abstracted information on the surrounding environments, i.e., the tubular inner space. The three color mappings of curvedness, shape index, and de, in short, show the geometric inflection of the surface, the convex and concave areas of the surface, and the distance from the surface to the external atoms, respectively. The curvedness mapping on the Hirshfeld surface showed no dividing nodes in the region wrapped by [4]CC and indicated the smoothness of the inner tubular surface without geometric inflection. The shape index mapping with blue and green areas showed the presence of concave and flat surfaces of the tube, respectively, and should represent a generally typical shape character of the inner surface of SWNT. The green lines of flat areas that appeared helically around the belt region are so significant that shows the presence of a chiral surface inside the helical tube (32). The green dots on the de mapping appeared under most of the sp2-carbon atoms of [4]CC and showed the presence of efficient Chost–Cguest contacts distributed evenly over the tube. This observation confirmed that the tightest association of the host–guest complex to date has been achieved purely by nondirectional van der Waals interactions between two neutral molecules.

Fig. 4.
Fig. 4.

Hirshfeld surface of (M)-(12,8)-[4]CC2,8⊃C60 with disordered structures. Solvent molecules with disorders are omitted for clarity. Curvedness, shape index, and de are mapped in colors over the Hirshfeld surfaces. See SI Appendix, Fig. S4, for the complementary surfaces of [4]CC and Movies S1–S3 for more detailed inspection.

A comparison with the relevant molecular peapod (7, 8), [10]CPP⊃C60, further revealed structural features that should be important for tight association and dynamic structures. Although the Hirshfeld surface revealed the presence of an inflection-free complementary surface at the interface of (M)-(12,8)-[4]CC2,8⊃C60, slipped π–π stack motifs between planar hexagons of the host and guest were observed for the crystal structure of [10]CPP⊃C60 (8). As shown in SI Appendix, Fig. S5, the Hirshfeld surface analysis of [10]CPP⊃C60 indeed showed apparent signatures of π–π stacking as the result of severe deformation with dividing nodes of inflections. The absence of disordered C60 molecules in [10]CPP⊃C60 also corresponds well to the planar facial recognition between two polygons (8). The difference in molecular recognition, i.e., tube–sphere vs. planar π–π recognitions, may thus have led to the great difference in the association (7, 14). The structural comparison disclosed a distinct difference, albeit subtle at first glance of chemical structures, in the smoothness of inner surface and demonstrated a unique nature of van der Waals interface that is highly sensitive to molecular shapes.

Discussion

Solid-state dynamic motions of C60 in a finite SWNT molecule were revealed by NMR analysis. The rapid bearing motion in the solid state suggests interesting physical phenomena to be explored in solid-state materials science, and the detailed kinetics of the motion is of immediate interest. A smooth, inflection-free inner surface of the tubular molecule was disclosed by the crystal structure of the molecular peapod, which should be a distinctive structural feature of peapods in general. This structural information on a smoothly curved π-tube shed the first light on the “mysterious world that exists inside the carbon nanotube” (4) at the atomic level by clarifying the structural origins of unique molecular recognition at the interfaces of curved π-systems. A recent polar host–guest complex of cucurbit[7]uril and ferrocenes demonstrated a unique synthetic complex assembled with a delicate match between hydrophobicity, charge, and size in aqueous media to rival the tightest complex in Nature (33, 34), and this peapod complex now added another novel entry of synthetic design for neutral host–guest complex in apolar organic media to be assembled, tightly and solely, by van der Waals interactions at the convex–concave sp2-carbon surfaces. The combination of the complementary tube–sphere shapes and nondirectional van der Waals interactions further plays a key role in the dynamic motion of the guest and should be explored for friction-free molecular machines (14⇓–16). The concomitant presence of the tight binding and the dynamic supramolecular complex should be of great interest for the theoretical studies, and the helical environment found on the Hirshfeld surface is of special interest for its effect on the dynamic motion. Furthermore, because the peapod bearing of discrete molecules provides access to a homochiral columnar assembly in the crystalline solid state, an interesting possibility of synchronized orientations of single-axis motion of the peapod bearing may be exploited (35, 36). The manipulation of the periodicity of C60 sites in the tubular column through designing the interdigitated chains as a spacer is also of great interest (37).

Materials and Methods

Synthesis.

The synthesis of [4]CC and (M)-(12,8)-[4]CC2,8⊃C60 was conducted by the methods reported in the literatures (11, 14). The racemic mixture and (M)-isomer of (12,8)-[4]CC2,8 was obtained by preparative HPLC using ODS columns (20ϕ × 250 + 250 + 250 mm; Kanto Chemical; eluent, 50% (vol/vol) methanol/CH2Cl2) and cholester columns (20ϕ × 250 + 250 mm; Nacalai Tesque; eluent, 40% (vol/vol) methanol/CH2Cl2), respectively.

Solid-State NMR Analysis.

A specimen in powder form was loaded in a 2.5ϕ × 3.5-mm rotor tube and analyzed on Bruker AVANCE III 700 spectrometer (176 MHz for 13C). The chemical shift was externally referenced to the resonance of glycine at 176.03 ppm.

Crystallographic Analysis of (12,8)-[4]CC.

A single crystal of racemic (12,8)-[4]CC was obtained from a solution in methanol/CH2Cl2 [∼1:1 (vol/vol)] at 25 °C in a loosely sealed vial. The single crystal was mounted on a thin polymer tip with cryoprotectant oil and frozen at –178 °C with flash-cooling. The diffraction analysis of a single crystal with a synchrotron X-ray source was conducted at –178 °C at the BL-1A beamline at KEK PF (25) with a diffractometer equipped with a Dectris PILATUS 2M-F PAD detector. The collected diffraction data were processed with the HKL2000 software program (38). The structure was solved by a charge flipping method (39) and refined by full-matrix least-squares on F2 using the SHELX program suite (40) running on the Yadokari-XG 2009 software program (41). Geometrical restraints on the alkyl chains and the solvent, i.e., DFIX, SADI, and SIMU, were used in the refinements. The nonhydrogen atoms in the aromatic part and the solvent were analyzed anisotropically, whereas the nonhydrogen atoms in the disordered alkyl chains were partially analyzed isotropically. Hydrogen atoms were input at calculated positions and refined with a riding model. The details of the crystal data are summarized in SI Appendix, Table S1. Two level-A alerts are suggested by the PLATON/CIF check program: Despite the use of a synchrotron source and trials for several crystals, the data quality was not high enough to avoid the alerts, and data were only collected to a resolution of ∼1.2 Å. The lack of high-angle diffraction data can be attributed to the solvent disorder.

Crystallographic Analysis of (M)-(12,8)-[4]CC2,8⊃C60.

A single crystal of (M)-(12,8)-[4]CC⊃C60 was obtained from a solution in methanol/CH2Cl2 [∼1:1 (vol/vol)] at 25 °C in a loosely sealed vial. The single crystal was mounted on a thin polymer tip with cryoprotectant oil and frozen at –258 °C with flash-cooling, and the temperature was gradually raised to –173 °C. The diffraction analysis of a single crystal with a synchrotron X-ray source was conducted at –173 °C at the BL41XU beamline at SPring-8 (18) with a diffractometer equipped with a Rayonix MX225HE CCD detector. The collected diffraction data were processed with the HKL2000 software program (38). The structure was solved by a direct method (42) and refined by full-matrix least-squares on F2 using the SHELX program suite (40) running on the Yadokari-XG 2009 software program (41). Geometrical restraints, i.e., DFIX, DANG, and SIMU on the alkyl chains and the solvent and SIMU on the four C60 molecules with 25% occupancy for each C60 modeled as rigid bodies, were used in the refinements. All of the nonhydrogen atoms were analyzed anisotropically. Hydrogen atoms were input at calculated positions and refined with a riding model. Due to the severe disorder and fractional occupancy, the electron density attributed to some solvent molecules was not properly modeled, and the structures were refined without these solvents by the PLATON Squeeze technique (43, 44). The details of the crystal data are summarized in SI Appendix, Table S2. Two level-A alerts are suggested by the PLATON/CIF check program: Despite the use of a synchrotron source and trials for several crystals, the data quality was not high enough to avoid the alerts, and data were only collected to a resolution of ∼0.95 Å. The lack of high-angle diffraction data can be attributed to the presence of the solvent disorder.

Acknowledgments

We thank Dr. Y. Nishiyama (JEOL) for helpful discussion, Dr. H. Sato (Rigaku) for his support in the diffraction analysis, KEK PF (Research 2013G640) and SPring-8 (Research 2013B0042) for the use of the X-ray diffraction instruments, Central Glass Company for the gift of hexafluoroisopropanol for the synthesis, Ms. A. Yoshii (Tohoku University) for the preparation of starting materials, and the Analytical Center for Giant Molecules (Tohoku University) for the use of the solid-state NMR instruments. This study was partly supported by Grant-in-Aid for Scientific Research, KAKENHI (24241036, 25107708, and 25102007).

Footnotes

  • ↵1To whom correspondence should be addressed. E-mail: isobe{at}m.tohoku.ac.jp.

  • Author contributions: S.S. and H.I. designed research; S.S., T.Y., and H.I. performed research; T.Y. contributed new reagents/analytic tools; S.S., T.Y., and H.I. analyzed data; and H.I. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: The atomic coordinates and structure factors have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, United Kingdom (CSD reference nos. CCDC 993074 and CCDC 993075).

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1406518111/-/DCSupplemental.

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Solid-state structures of peapod bearings
Sota Sato, Takashi Yamasaki, Hiroyuki Isobe
Proceedings of the National Academy of Sciences Jun 2014, 111 (23) 8374-8379; DOI: 10.1073/pnas.1406518111
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