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Double-Helix Supramolecular Nanofibers Assembled from NegativelyCurved NanographenesKenta Kato, Kiyofumi Takaba, Saori Maki-Yonekura, Nobuhiko Mitoma, Yusuke Nakanishi, Taishi Nishihara,Taito Hatakeyama, Takuma Kawada, Yuh Hijikata, Jenny Pirillo, Lawrence T. Scott, Koji Yonekura,Yasutomo Segawa, Kenichiro Itami
Submitted date: 22/11/2020 • Posted date: 23/11/2020Licence: CC BY 4.0Citation information: Kato, Kenta; Takaba, Kiyofumi; Maki-Yonekura, Saori; Mitoma, Nobuhiko; Nakanishi,Yusuke; Nishihara, Taishi; et al. (2020): Double-Helix Supramolecular Nanofibers Assembled from NegativelyCurved Nanographenes. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.13270607.v1
The layered structures of graphite and related nanographene molecules play key roles in their physical andelectronic functions. However, the stacking modes of negatively curved nanographenes remains unclear,owing to the lack of suitable nanographene molecules. Herein we report the synthesis and one-dimensionalsupramolecular self-assembly of negatively curved nanographenes without any assembly-assistingsubstituents. This curved nanographene self-assembles in various organic solvents and acts as an efficientgelator. The formation of nanofibers was confirmed by microscopic measurements, and an unprecedenteddouble-helix assembly by continuous π-π stacking was uncovered by three-dimensional electroncrystallography. This work not only reports the discovery of an all-sp2-carbon supramolecular π-organogelatorwith negative curvature, but also demonstrates the power of three-dimensional electron crystallography for thestructural determination of submicrometer-sized molecular alignment.
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Double-helix supramolecular nanofibers assembled from negatively curved nanographenes
Kenta Kato,1,† Kiyofumi Takaba,2,† Saori Maki-Yonekura,2,† Nobuhiko Mitoma,1,3,4 Yusuke Nakanishi,5 Taishi Nishihara,1,3,6 Taito Hatakeyama,7 Takuma Kawada,7 Yuh Hijikata,1,8,9 Jenny Pirillo,8,9 Lawrence T. Scott,10 Koji Yonekura,2,11,* Yasutomo Segawa,1,3,12,13,* and Kenichiro 5 Itami1,3,8,*
Affiliations: 1 Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan 2 Biostructural Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan 10 3 JST, ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Nagoya 464-8602, Japan 4 RIKEN Center for Emergent Matter Science, Wako 351-0198, Japan 5 Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Japan 6 Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan 15 7 Central Research Laboratory Technology and Development Division, Kanto Chemical Co., Inc., Saitama 340-0003, Japan 8 Institute of Transformative Bio-Molecules (WPI-ITbM) Nagoya University, Nagoya 464-8602, Japan 9 Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, 20 Sapporo, Hokkaido 001-0021, Japan 10 Department of Chemistry, University of Nevada, Reno, NV 89557-0216, USA 11 Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan 12 Institute for Molecular Science, Myodaiji, Okazaki, 444-8787, Japan 25 13 Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, 444-8787, Japan * Correspondence to: [email protected] (K.Y.), [email protected] (Y.S.), [email protected] (K.I.) † These authors contributed equally. 30 Abstract: The layered structures of graphite and related nanographene molecules play key roles in their physical and electronic functions. However, the stacking modes of negatively curved nanographenes remains unclear, owing to the lack of suitable nanographene molecules. Herein we 35 report the synthesis and one-dimensional supramolecular self-assembly of negatively curved nanographenes without any assembly-assisting substituents. This curved nanographene self-assembles in various organic solvents and acts as an efficient gelator. The formation of nanofibers was confirmed by microscopic measurements, and an unprecedented double-helix assembly by continuous π-π stacking was uncovered by three-dimensional electron crystallography. This work 40 not only reports the discovery of an all-sp2-carbon supramolecular π-organogelator with negative curvature, but also demonstrates the power of three-dimensional electron crystallography for the structural determination of submicrometer-sized molecular alignment.
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Main Text: The layered structures of graphite and related nanographene molecules play a key role in their
physical and electronic properties (1–6). The well-ordered molecular alignment of nanographenes and its structural determination are of interest in order to gain insight into a variety of carbon materials. It is well known that the one-dimensional (1D) assembly of planar nanographenes (e.g. 5 hexa-peri-hexabenzocoronene) can be achieved by introducing suitable peripheral substituents that tune solubility (Figure 1A) (7). The 1D assembly of bowl-shaped nanographenes was also achieved by convex-concave π-π stacking along with non-covalent interactions (8–10). However, the stacking modes of negatively curved nanographenes remains unclear, owing to the lack of suitable nanographene molecules. In 2013, our group reported warped nanographene (WNG), a 10 large nonplanar nanographene containing five seven-membered rings (Figure 1C) (11). In spite of its large structure with 80 carbon atoms (C80H30), WNG is soluble in various organic solvents because its negative curvature hinders π-π stacking. During related works on WNGs (12–15), we found that a synthetic intermediate of WNG (1-biph) efficiently forms stacked π-π dimers in the crystalline state (12). Considering the high solubility of the WNG family and the existence of a π-15 π stacking mode, we hypothesized that substituent-free 1D assemblies could be realized by using negatively curved nanographenes (Figure 1B).
Figure 1. 1D assemblies of nanographenes. (A) Assembly of planar nanographenes with peripheral substituents. (B) Assembly of negatively curved nanographenes (hypothesis). (C) 20 Structures of warped nanographene (WNG) and its analogues (1-H, 1-biph).
Herein, we report the synthesis and 1D self-assembly of a newly designed nanographene 1-H (C68H28), a negatively curved PAH with 12 carbon atoms fewer than WNG (Figure 1C). Serendipitously, we discovered that 1-H self-assembles in various organic solvents and works as 25 a highly efficient gelator that forms organic gels at concentrations of <1 wt%. Transmission
R
A B
C
No π-π stacking
1D-assemblingnegatively curved PAH
this work
1D assembly ofplanar nanographenes
1D assembly of negativelycurved nanographenes
(hypothesis)
π-π stacked dimerin the crystalline state
WNG
1-H 1-biph(R = 2-biphenylyl)
3
electron microscopy (TEM) and atomic force microscopy (AFM) measurements confirm that 1-H forms fibers with diameters of ~2.8 nm. The presence of efficient π-π interactions in the fiber structures is supported by a bathochromic shift in the fluorescence spectrum of the gel state relative to that of dilute solutions of 1-H. Finally, using three-dimensional (3D) electron crystallography, the double-helix π-π stacking mode of 1-H in the supramolecular nanofiber was revealed. 5
The synthesis of 1-H was accomplished by a synthetic route analogous to that used to prepare WNG as shown in Figure 2 (11). We selected tetrakis(biphenyl-2-yl)corannulene (2) as the precursor of 1-H. Fourfold Suzuki–Miyaura coupling of a regioisomeric mixture of tetraborylcorannulene 3 (16) with 2-bromobiphenyl afforded 2. A Scholl reaction (17,18) of 2 was brought about by the action of 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and CF3SO3H to 10 generate 1-H as a yellow solid in 56% yield based on 3. The 1H NMR and 13C NMR spectroscopic analysis of 1-H suggest a C2-symmetric structure in solution, and high-resolution mass spectra confirm a molecular formula of C68H28 for 1-H.
Figure 2. Synthesis of 1-H. Reaction conditions: (i) Pd2(dba)3·CHCl3, SPhos, K3PO4, 15 toluene/water, 100 °C, 24 h; (ii) DDQ, CF3SO3H, 0 °C, 3 h. Abbreviations: DDQ = 2,3-dichloro-5,6-dicyanobenzoquinone; Bpin = 4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl; dba = dibenzylideneacetone; SPhos = 2-dicyclohexylphosphino-2',6'-dimethoxybiphenyl.
During recrystallization experiments, it was discovered that 1-H works as an efficient 20 organogelator. When a CH2Cl2 solution of 1-H was slowly evaporated over the course of 1 day, an organogel was formed (Figure 3A,B). To the best of our knowledge, there is no report of any unfunctionalized aromatic hydrocarbon that works as an organogelator (19–26). Intrigued by this unique behavior, we conducted a detailed investigation of the gelating ability of 1-H in various organic solvents (Figure 3C). Some chloroalkanes and aromatic solvents yield transparent gels at 25 low critical gelation concentrations (CGC; 0.2–0.8 wt%), indicating the high gelation efficiency of 1-H. Slow diffusion of pentane vapor into solutions of 1-H in tetrahydrofuran (THF) and 1,1,2,2-tetrachloroethane (TCE) affords translucent gels with slightly higher CGCs (2.3 and 1.8 wt%, respectively) reflecting the high solubility of 1-H in THF and TCE. In hydrocarbons and polar solvents (triethylamine, acetonitrile, alcohols, dimethyl sulfoxide, and water), no gels are 30 formed. In no case could single crystals of 1-H be obtained. This behavior stands in sharp contrast to the structurally similar derivative 1-Cl, which readily forms single crystals (for details, see Supplementary Materials (SM)).
1-H(i)
Bpin(ii)
23
56%based on 3
Br
pinB
pinB
Bpin
4
Figure 3. Gel formation of 1-H. (A) Gelation of 1-H. (B) Photo of the yellow organogel obtained by partial evaporation of a solution of 1-H in CH2Cl2. (C) Gelation properties of 1-H in organic solvents. a CGC: critical gelation concentration. b J = jelly precipitate. (D) A UV–Vis absorption spectrum (abs; solid line) and fluorescence spectra (FL; dotted lines) of 1-H in CH2Cl2 and in the 5 gel state. The inserted photographs show the solution (left) and gel (right) under irradiation with UV light (l = 365 nm). Fluorescence spectra were recorded upon excitation at 350 nm (solution) or 390 nm (gel). (E) A TEM image of a dried gel obtained from a CH2Cl2 solution of 1-H. (F) An AFM image of a dried gel obtained from a CH2Cl2 solution of 1-H and the cross-sectional height profile taken along the dotted line in the AFM image. 10
The photophysical properties of 1-H support the existence of intermolecular π-π interactions in the gel state. In solution (CH2Cl2), 1-H shows absorption maxima at 264, 320, 369, 390, and 460 nm and exhibits blue fluorescence, with peaks at 475 and 502 nm and a low fluorescence quantum yield (ΦF = 0.20) upon excitation at 350 nm (Figure 3D). These results in solution are 15 similar to those obtained for WNG (11). By contrast, in the gel state, 1-H exhibits yellow fluorescence, with the longest wavelength fluorescence peaks shifted bathochromically to 489 nm and 521 nm (Figure 3D). These aggregation-dependent changes in the fluorescence spectrum signify strong π-π interactions among the molecules of 1-H in the gel state (27-29).
In imaging experiments, the fibrous structure of 1-H in the organogel was observed using both 20 TEM and AFM (Figure 3E,F). The TEM image shown in Figure 3E establishes that 1-H forms nanofiber structures in the gel state. The diameter of the thinnest fiber determined by the cross-sectional height profile in the AFM image (Figure 3F) measures ca. 2.8 nm.
Finally, the nanofiber structure was fully analyzed by 3D electron crystallography. Needle-shaped microcrystals of 1-H were collected from the supernatant of the gel obtained from a TCE 25 solution at room temperature. As shown in Figure 4A, the needle-shaped microcrystals were found
5
by TEM measurement to have widths of around 0.5 µm. Electron diffraction patterns were recorded at a specimen temperature of ~98 K (Figure 4B and SM for detail) by the electron energy-filtered diffraction (eEFD) method (30). A total of 46 datasets were merged, and the high-resolution limit was determined to be 0.85 Å. The initial structure was successfully solved with a space group P42 by molecular replacement, starting from the structure of 1-Cl, and direct phasing 5 also gave the same solution. As shown in Figure 4C, the molecular structure of 1-H was confirmed as expected.
In the crystal, four crystallographically nonequivalent molecules (1-H-a–d in Figure 4D) were found. Two of the four (1-H-a and 1-H-b) have the same helical chirality around the seven-membered-ring moieties (PMP), whereas the other two (1-H-c and 1-H-d) have the opposite 10 chirality (MPM). Continuous π-π stacking of alternating 1-H-a and 1-H-b units (Figure 4E) results in the formation of homochiral nanofibers that mesh in the needle-shaped microcrystals with adjacent nanofibers composed entirely of molecules having the opposite chirality (1-H-c and 1-H-d, Figure 4F). Figures 4G and 4H provide a closer look at the molecular alignment structures within a single nanofiber. Each nanofiber comprises a double helix structure wherein 1-H 15 molecules of the same chirality are stacked with 45° twist angles. Judging from the result that the diameters of a single nanofiber (2.8 nm, Figure 4G) matches the height of the thin nanofiber found in the AFM measurement (2.8 nm, Figure 3F), this supramolecular double helix alignment beautifully accounts for the structure of the nanofibers found in the gel state. The pitch length of the helix is 3.1 nm, and 8 molecules constitute a helical repeat unit (Figure 4H). These findings 20 clearly demonstrate the power of 3D electron crystallography for the structural determination of nanometer-sized molecular alignments, even for cases in which single crystals suitable for x-ray crystallography cannot be obtained.
6
Figure 4. Structure of the nanofibers of 1-H revealed by 3D electron crystallography. (A) A cryo-EM image of fibrous microcrystals distributed on a holey carbon film. (B) Representative frames of electron diffraction patterns in a rotation angle of –4° ~ –3°. Concentric circles indicate 3.0, 1.5, 1.0, and 0.8 Å resolution rings. (C) ORTEP drawing of 1-H with 50% probability 5 determined by eEFD. (D) Four crystallographically inequivalent molecules of 1-H; helical chiralities (P or M) around the seven-membered-ring moieties are indicated. (E) A π-π stacking mode of 1-H-a and 1-H-b. (F) Packing structure of 1-H along c axis; a unit cell is shown in gray. (G) A double-helix nanofiber with its diameter and twist angle. (H) A double-helix nanofiber with its helix pitch; a unit cell is shown in gray. 10
To prepare supramolecular stacks of nanographenes, chemists have historically relied heavily on the use of assembly-assisting substituents. We have now discovered the first-in-class polycyclic π-system, consisting solely of sp2-hybridized carbon atoms, that spontaneously stacks without any assembly-assisting substituents. Our new, well-designed nanographene with negative curvature 15 self-assembles efficiently with offset π-π stacking (45° twist angles in the present case), ultimately creating beautiful, double-helix, supramolecular nanofibers. Based on this discovery and its revelation of a new guiding principle in supramolecular self-assembly, we expect that a number of negatively curved nanographenes can be developed for new applications in materials science and
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biology. Moreover, this work not only reports the discovery of an all-sp2-carbon supramolecular π-organogelator with negative curvature, but it also showcases the power of 3D electron crystallography for the structural determination of submicrometer-sized hydrocarbon molecular assemblies. This ability to elucidate the layered structures adopted by negatively curved nanographenes at the molecular level will accelerate the future development of carbon-based 5 materials science and technology.
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13 H.-A. Lin, Y. Sato, Y. Segawa, T. Nishihara, N. Sugimoto, L. T. Scott, T. Higashiyama, K. Itami, A water-soluble warped nanographene: Synthesis and applications for photoinduced cell death. Angew. Chem., Int. Ed. 57, 2874-2878 (2018). 35
14 K. Kato, H.-A. Lin, M. Kuwayama, M. Nagase, Y. Segawa, L. T. Scott, K. Itami, Two-step synthesis of a red-emissive warped nanographene derivative via a ten-fold C–H borylation. Chem. Sci. 10, 9038-9041 (2019).
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15 H.-A. Lin, K. Kato, Y. Segawa, L. T. Scott, K. Itami, Synthesis and structural features of thiophene-fused analogues of warped nanographene and quintuple helicene. Chem. Sci. 10, 2326-2330 (2019).
16 M. N. Eliseeva, L. T. Scott, Pushing the Ir-catalyzed C–H polyborylation of aromatic compounds to maximum capacity by exploiting reversibility. J. Am. Chem. Soc. 134, 15169-5 15172 (2012).
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19 E. R. Draper, D. J. Adams, Low-molecular-weight gels: the state of the art. Chem 3, 390-410 (2017).
20 N. M. Sangeethaz, U. Maitra, Supramolecular gels: Functions and uses. Chem. Soc. Rev. 34, 821-836 (2005). 15
21 T. Kato, Y. Hirai, S. Nakaso, M. Moriyama, Liquid-crystalline physical gels. Chem. Soc. Rev. 36, 1857-1867 (2007).
22 S. S. Babu, V. K. Praveen, A. Ajayaghosh, Functional π-gelators and their applications. Chem. Rev. 114, 1973-2129 (2014).
23 P. Terech, R. G. Weiss, Low molecular mass gelators of organic liquids and the properties of 20 their gels. Chem. Rev. 97, 3133-3159 (1997).
24 D. J. Abdallah, R. G. Weiss, Organogels and low molecular mass organic gelators. Adv. Mater. 12, 1237-1247 (2000).
25 P. Dastidar, Supramolecular gelling agents: Can they be designed? Chem. Soc. Rev. 37, 2699-2715 (2008). 25
26 A. Dawn, T. Shiraki, S. Haraguchi, S.-I. Tamaru, S. Shinkai, What kind of “soft materials” can we design from molecular gels? Chem. Asian J. 6, 266-282 (2011).
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29 Z. Zhao, J. W. Y. Lam, B. Z. Tang, Self-assembly of organic luminophores with gelation-enhanced emission characteristics. Soft Matter 9, 4564-4579 (2013).
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Acknowledgments:
This work was supported by the ERATO program from JST (JPMJER1302 to K.I.), the Funding Program for KAKENHI from MEXT (JP1905463 to K.I.; JP16K05771, JP19H02701, and JP19K22183 to Y.S.), a grant-in-aid for Scientific Research on Innovative Areas “π-Figuration”
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from the JSPS (JP17H05149 to Y.S.), the Cyclic Innovation for Clinical Empowerment (CiCLE) from the Japan Agency for Medical Research and Development, AMED (to K.Y.), Toyoaki Scholarship Foundation (to Y.S.), Daiko Foundation (to Y.S.), and the US National Science Foundation (CHE-1149096 to L.T.S.). K.K. thanks the IGER Program in Green Natural Sciences (Nagoya University) and the JSPS for a fellowship for young scientists. The authors thank S. Seki, 5 Y. Tsutsui T. Uchihashi, S. Ogi, H. Sakamoto, J. Shim, E. Ito, J. Shirasaki, K. Yamanoue, M. Toya, N. Yasuda, and RIGAKU Co. for fruitful discussions and support with the measurements. ITbM is supported by the World Premier International Research Center Initiative (WPI), Japan.
Supplementary Materials: Materials and Methods 10 Figures S1-S7 Tables S1-S2 References (31-47)
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Supplementary Materials for
Double-helix Supramolecular Nanofibers Assembled from Negatively Curved
Nanographenes
Kenta Kato,1,† Kiyofumi Takaba,2,† Saori Maki-Yonekura,2,† Nobuhiko Mitoma,1,3,4 Yusuke Nakanishi,5 Taishi Nishihara,1,3,6 Taito Hatakeyama,7 Takuma Kawada,7
Yuh Hijikata,1,8,9 Jenny Pirillo,8,9 Lawrence T. Scott,10 Koji Yonekura,2,11,* Yasutomo Segawa,1,3,12,13,* and Kenichiro Itami1,3,8,*
Correspondence to: [email protected] (K.Y.), [email protected] (Y.S.), [email protected] (K.I.) † These authors contributed equally.
This PDF file includes:
Materials and Methods Figs. S1 to S7 Tables S1 to S2 References 28 to 44
2
Materials and Methods Synthesis, purification, and identification
Unless otherwise noted, all materials including dry solvent were obtained from commercial suppliers and used without further purification. All reactions were performed using standard vacuum-line and Schlenk techniques. Work-up and purification procedures were carried out with reagent-grade solvents under air. 1,3,5,7,9-Pentakis(pinacolatoboryl)corannulene (S2) and tetrakis(pinacolatoboryl)corannulene 3 (regioisomeric mixture) were synthesized according to the reported procedure (16).
Analytical thin-layer chromatography (TLC) was performed using E. Merck silica gel 60 F254 precoated plates (0.25 mm). The developed chromatograms were analyzed by UV lamp (254 or 365 nm). Flash column chromatography was performed with E. Merck silica gel 60 (230–400 mesh). Preparative recycling gel permeation chromatography (GPC) was performed with a JAI LC-9204 instrument equipped with JAIGEL-2HR columns using chloroform as an eluent. The high-resolution mass spectra (HRMS) were conducted on a Bruker Daltonics Ultraflex III TOF/TOF (MALDI-TOF MS). Melting points were measured on an MPA100 Optimelt automated melting point system. Nuclear magnetic resonance (NMR) spectra were recorded on a JEOL ECA 600II spectrometer with UltraCool probe (1H 600 MHz, 13C 150 MHz) spectrometer. Chemical shifts for 1H NMR are expressed in parts per million (ppm) relative to C2HDCl4 (d 5.98 ppm). Chemical shifts for 13C NMR are expressed in ppm relative to C2D2Cl4 (d 73.79 ppm). Data are reported as follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, m = multiplet, br = broad), coupling constant (Hz), and integration. Atomic force microscopy (AFM) measurement of the fibrous structures of 1-H
AFM measurements were performed using a Dimension FastScan (Bruker) at room temperature and under atmospheric conditions with a silicon tip on silicon nitride cantilevers (FastScan-C, Bruker) in tapping mode. Organogels of 1-H were formed on a SiO2 substrate by slowly evaporating the CH2Cl2 solution of 1-H.
Transmission electron microscopy (TEM) measurement of the fibrous structures of 1-H
High-resolution TEM observation was performed on a JEOL JEM-2100F at an acceleration voltage of 80 kV under a pressure of 10–5 Pa. The gel of 1-H in CH2Cl2 was broken by shaking, and 5 drops of the supernatant were deposited onto carbon-coated copper grids. Prior to the observation, the sample was dried under vacuum for 30 min at ambient temperature. TEM images were recorded on a Gatan MSC 794 1k × 1k CCD camera with a typical exposure time of 0.3 s.
Photophysical Measurements
UV-vis absorption spectrum of the CH2Cl2 solution of 1-H was recorded on a Shimadzu UV-3600 spectrometer with a resolution of 0.5 nm. Emission spectra of the CH2Cl2 solution of 1-H was recorded on an F-4500 Hitachi spectrometer with a resolution of 0.4 nm and automatically corrected by instrumental function. Dilute solutions in degassed spectral grade CH2Cl2 in a 1 cm square quartz cell were used for measurements. Absolute fluorescence quantum yield was determined with a Hamamatsu C9920-02 calibrated integrating sphere system equipped with multichannel spectrometer (PMA-11). Emission spectra of the gel and solid state of 1-H were recorded using a monochromator attached to a thermoelectrically cooled charge-coupled device camera (Princeton Instruments, ProEM). The excitation light source was a wavelength-tunable
3
optical parametric amplifier system based on a Yb:KGW (potassium gadolinium tungstate) regenerative amplified laser with a pulse duration of 200 fs and repetition rate of 200 kHz.
X-ray crystallography of 1-Cl
Details of the crystal data and a summary of the intensity data collection parameters for 1-Cl are listed below. A suitable crystal of 1-Cl obtained from the 1,2-dichloroethane solution was mounted with mineral oil on a MiTeGen MicroMounts and transferred to the goniometer of the kappa goniometer of a RIGAKU XtaLAB Synergy-S system with 1.2 kW MicroMax-007HF microfocus rotating anode (Graphite-monochromated Mo Ka radiation (l = 0.71073 Å)) and PILATUS200K hybrid photon-counting detector. Cell parameters were determined and refined, and raw frame data were integrated using CrysAlisPro (Agilent Technologies, 2010). The structures were solved by direct methods with (SHELXT) (28) and refined by full-matrix least-squares techniques against F2 (SHELXL-2018/3) (29) by using Olex2 software package (30). The intensities were corrected for Lorentz and polarization effects. The non-hydrogen atoms were refined anisotropically. Hydrogen atoms were placed using AFIX instructions. The CIF data can be obtained free of charge from Crystallographic data and structure refinement details of 1-Cl are summarized in Table S1. The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif (CCDC 2039243).
Electron diffraction crystallography of 1-H 1. Sample screening and data collection of rotational electron diffraction patterns
Sample solution (1,1,2,2-tetrachloroethane) containing the crystalline nanofiber bundles of 1-H was dispersed with ethanol and applied onto a holey carbon-coated copper grid (Quantifoil R1.2/1.3, Quantifoil Micro Tools GmbH) with 200 mesh. Excess solution on the grid was blotted off with filter paper from the back side and dried at room temperature. Crystals on the grids were then screened at a cryogenic temperature of ~100 K with a JEM-2100 electron microscope (JEOL Ltd., Japan). Needle-shaped crystals obtained from one sample solution showed good diffraction patterns, and this was selected for 3D data collection.
The sample containing well-diffracting nanofiber bundles was prepared as above and examined with a CRYO ARM 300 microscope (JEOL Ltd., Japan) operated at an accelerating voltage of 300 kV and equipped with an in-column type energy filter. Diffraction patterns were recorded on a scintillator-based CMOS camera (XF416, TVIPS GmbH, Germany) at a specimen temperature of ~ 98 K. One crystal was parallel illuminated with a ~5 µm beam and no selected area aperture inserted at an electron dose rate of ~0.02 e–/Å2·s. Sequential diffraction frames were collected from one crystal by continuously rotating the sample stage from –68º to 68º at a goniometer rotation speed of 1°/s. Total 55 rotational series were collected in a semi-automated manner by combined use of SerialEM (31) and ParallEM (27,32). A report on details of this data collection protocol was described in (33). All datasets were taken with an energy slit adjusted to select only electrons with energy loss less than 10 eV. The camera length was calibrated to be 1245 mm from gold sputtered on carbon film as a standard. 2. Data processing and structure determination
Diffraction stacks, each of which comprises 140 raw frames with 4k × 4k pixels, were first × 2 binned (2048 × 2048 pixels) for speeding up the following steps. Diffraction datasets were then subjected to automatic processing with KAMO (34), which carried out indexing, integration, scaling and merging by using XDS (35), Pointless (36), XSCALE (37), and BLEND (38). Total 46 datasets were merged and the high-resolution limit was determined to be 0.85 Å, where a CC1/2
4
(the correlation coefficient between random half data sets) value was greater than 50% (39). The lattice group was determined to be tetragonal with lattice parameters of a = b = 34.61 Å, c = 16.51 Å. Data collection statistics and crystal parameters are summarized in Table S2.
An initial structure was solved with a space group P42 by molecular replacement starting from the structure of a 1-Cl using Phaser (40). An asymmetric unit contained four 1-H molecules (Z’ = 4). The same solution was obtained with this space group setting by the direct method using SHELXD (41). The structure was then refined with Phenix (42) and SHELXL (29) using anisotropic displacement parameters for all carbon atoms. Dependence on the experimental wavelength (λ) of an empirical extinction correction factor (EXTI (43)) was not clear for electron diffraction. Here we excluded diffraction data in a lower resolution range (d > 7 Å) and used a λ value of 1.0 Å in the formula below,
Fc’ = Fc k [1 + 0.001 x Fc2 (1.0)3 / sin(2θ)]–1/4 , where k is the overall scale factor and x is extinction factor to be refined. This provisional
correction significantly reduced an error factor (R) between the model and the experimental data, and less affected the atomic positions. The positions of all hydrogen atoms were generated as a riding model with AFIX instructions. C–C bond distances were restrained based on the structure of 1-H. Restraints in atomic displacement parameters (ADPs) were adjusted with RIGU, SIMU and ISOR instructions so that ADPs were within reasonable values. Probably due to disordering, solvent molecules (1,1,2,2-tetrachloroethane) could not be placed suitably to solvent accessible voids. The final R1 value is 0.1647. The CIF data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif (CCDC 2039244).
5
Synthesis of 1-H
To a solution of Pd2(dba)3·CHCl3 (77.6 mg, 75.0 µmol, 5.0 mol%) and SPhos (61.6 mg, 150
µmol, 10 mol%) in toluene (20 mL) were added (Bpin)4corannulene 3 (2.26 g, 3.00 mmol, 1.0 equiv), 2-bromobiphenyl (3.50 g, 15.0 mmol, 5.0 equiv) and solution of K3PO4 (6.37 mg, 30.0 mmol, 10 equiv, in 5.0 mL water), and the resultant mixture was stirred at 100 °C for 24 h under nitrogen. After cooling the mixture to room temperature, the reaction mixture was extracted with CH2Cl2. The combined organic layer was dried over MgSO4, and the solvent was removed under reduce pressure. The crude material was purified by silica-gel column chromatography (eluent: hexane/CH2Cl2 = 10:0 to 6:4) to afford a mixture of 1,3,5,8- and 1,3,6,8-tetrakis(biph)corannulene (2), which was used in the next reaction without further purification.
A solution of mixture of 2 (773 mg) and 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ; 1.45 g, 6.39 mmol, 7.1 equiv) in dry CH2Cl2 (81 mL) was added dropwise to the mixture of dry CH2Cl2 (4.5 mL) and trifluoromethanesulfonic acid (TfOH; 4.5 mL) at 0 °C for 30 min. After stirring for an additional 2.5 hours, the reaction mixture was quenched by Et3N (4.5 mL) and the solvent was removed under reduced pressure, then separated by silica-gel column chromatography (eluent: CHCl3). The compound 1-H was obtained as a yellow powder by purification of the crude material by GPC (494 mg, 56% yield based on 3).
1H NMR (600 MHz, C2D2Cl4, 25 °C) δ 9.30 (d, J = 7.8 Hz, 1H), 8.71 (s, 1H), 8.67 (d, J = 7.2 Hz, 1H), 8.60 (d, J = 7.2 Hz, 1H), 8.57 (d, J = 8.4 Hz, 2H), 7.81 (t, J = 6.0 Hz, 1H), 7.79 (t, J = 6.6 Hz, 1H), 7.72 (t, J = 7.2 Hz, 1H), 7.71 (t, J = 7.2 Hz, 1H), 7.67 (t, J = 7.8 Hz, 1H), 7.46 (d, J = 7.8 Hz, 1H), 7.42 (d, J = 7.8 Hz, 1H), 7.21 (d, J = 6.6 Hz, 1H); 13C NMR (150 MHz, C2D2Cl4, 25 ºC) δ 139.44 (4°), 139.41 (4°), 138.82 (4°), 134.08 (4°), 134.05 (4°), 133.08 (4°), 133.26 (4°), 132.61 (4°), 132.55 (4°), 132.08 (CH), 131.75 (4°), 131.02 (4°), 130.91 (4°), 130.83 (4°), 130.80 (4°), 130.75 (CH), 130.61 (CH), 130.43 (4°), 130.01 (4°), 129.43 (4°), 129.08 (4°), 129.00 (CH), 128.60 (CH), 128.01 (CH, 2C), 127.61 (CH), 127.50 (CH), 127.43 (4°), 127.27 (4°), 126.87 (4°), 126.70 (CH), 123.29 (CH), 121.44 (CH), 121.39 (CH, 2C), one carbon (4°) could not be determined; HRMS (MALDI-TOF MS) m/z calcd for C68H28 [M·]+: 844.2191, found: 844.2191; mp: >300 ºC.
2-bromobiphenyl (5.0 equiv)Pd2(dba)3·CHCl3 (2.5 mol%)
SPhos (5.0 mol%)K3PO4 (10 equiv)
toluene/water = 4:1100 °C, 24 h
3 (regioisomeric mixture)
2
DDQ (7.1 equiv)
CH2Cl2/TfOH = 19:10 °C, 3 h
1-H56% based on 3
Bpin
pinB
pinB
Bpin
pinB
pinB
Bpin
Bpin
6
Synthesis of 1-Cl
A solution of S2 (1.10 g, 1.25 mmol, 1.0 equiv) and N-chlorosaccharin (43) (712 mg, 3.27
mmol, 2.6 equiv) in CH2Cl2 (12.5 mL) was stirred at rt for 1 h. Hexane (60 mL) was added to the reaction mixture to precipitate saccharin derivatives. The suspension was filtered by Celite and the solution was evaporated under reduced pressure. Additional hexane (75 mL) was added and filtered by Celite® pad. The filtrate was concentrated under reduced pressure. The compound S3 was obtained as a yellow foam (1.01 g), which was used for the next reaction without further purification.
To a solution of Pd2(dba)3 (7.3 mg, 8.0 µmol, 10 mol%) and tris(4-methoxyphenyl)phosphine (5.6 mg, 16 µmol, 20 mol%) in toluene (1.33 mL) were added S3 (63.0 mg, 80.0 µmol, 1.0 equiv), 2-iodobiphenyl (112 mg, 400 µmol, 5.0 equiv) and a solution of K3PO4 (170 mg, 800 µmol, 10 equiv) in water (0.67 mL). The reaction mixture was stirred at 70 °C for 24 h under argon. After quenching the reaction by adding water (5.0 mL), the reaction mixture was extracted with CH2Cl2. The combined organic layer was dried over Na2SO4, and the filtrate was concentrated under reduce pressure. The residue was washed by MeOH and hexane to afford S4 (44.9 mg), which was used for the next reaction without further purification.
A solution of mixture of S4 (44.9 mg) and 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ; 81.0 mg, 360 µmol) in dry CH2Cl2 (8.5 mL) was added dropwise to mixture of dry CH2Cl2 (1.0 mL) and CF3SO3H (0.5 mL) at 0 °C for 30 min. After stirring for additional 20 hours, the reaction mixture was quenched by Et3N (1.0 mL) and the volatile was removed under reduced pressure. Methanol (20 mL) was added and the resultant suspension was filtered. The residue was purified by silica-gel column chromatography (eluent: CHCl3) to afford 1-Cl as a yellow powder (22.0 mg, 22% yield based on S2).
1H NMR (600 MHz, C2D2Cl4, 25 ºC) δ 9.07 (d, J = 7.8 Hz, 1H), 8.76 (d, J = 7.2 Hz, 1H), 8.63-8.61 (m, 4H), 8.55 (d, J = 7.8 Hz, 1H), 8.49 (d, J = 8.4 Hz, 1H), 8.46 (br s, 1H), 8.40-8.38 (m, 2H), 8.29 (s, 1H), 7.92 (t, J = 7.2 Hz, 2H), 7.88-7.82 (m, 3H), 7.72-7.67 (m, 2H), 7.52 (t, J = 7.8 Hz, 2H), 7.42 (d, J = 8.4 Hz, 1H), 7.38 (d, J = 7.2 Hz, 1H), 7.27 (br s, 1H), 7.18 (d, J = 7.8 Hz, 1H), 7.04 (br s, 1H), 6.98 (d, J = 6.6 Hz, 1H); 13C NMR (150 MHz, C2D2Cl4, 25 °C) δ 140.02 (4°), 139.53 (4°), 139.32 (4°), 138.99 (4°), 138.76 (4°), 137.99 (4°), 137.87 (4°), 136.19 (4°), 135.86 (4°), 134.149 (4°), 133.86 (4°), 133.10 (CH), 132.59 (4°), 132.55 (4°), 132.22 (4°), 132.12 (4°), 132.07 (4°), 131.75 (CH), 131.71 (CH), 131.68 (4°), 131.54 (CH), 131.39 (4°), 131.33 (4°), 131.23 (CH), 131.00 (4°), 130.86 (4°), 130.77 (4°), 130.65 (4°), 130.49 (4°), 130.40 (4°),130.19 (4°), 130.13 (CH), 129.96. (4°), 129.53 (CH), 129.51 (4°), 129.29 (4°), 129.13 (4°), 128.86. (CH), 128.67. (4°), 128.63 (4°), 128.60 (4°), 128.56 (4°), 128.40 (CH), 128.35 (CH), 128.16 (4°), 127.86 (CH), 127.73. (CH), 127.56 (4°), 127.17 (CH), 126.97 (4°), 126.80 (4°), 126.76 (CH), 126.43 (4°), 125.32 (CH), 123.59 (CH), 122.70 (CH), 122.37 (CH), 121.74 (CH), 121.53 (CH), 121.41 (CH), 120.54 (CH), 120.19 (4°), four carbon atoms (4°×2, CH×2) could not be observed; HRMS (MALDI-TOF MS) m/z calcd for C68H27Cl [M·]+: 878.1801, found: 878.1776; mp: >300 ºC.
2-iodobiphenyl (5.0 equiv)Pd2(dba)3 (10 mol%)
PMP3P (20 mol%)K3PO4 (10 equiv)
toluene/water = 2:170 °C, 24 h
Bpin
Bpin
Cl
pinB
pinB
ClS3 S4
DDQ (7.1 equiv)
CH2Cl2/CF3SO3H = 19:1
0 °C, 20 h
1-Cl22% based on S2
Cl
Bpin
Bpin
Bpin
pinB
pinB
(2.6 equiv)
CH2Cl2rt, 3 h
S2
SN
O
Cl
O O
7
Table S1. Crystallographic Data and Structure Refinement Details of 1-Cl.
1-Cl·2.5C2H4Cl2 formula C141H64Cl17
fw 2006.07 T (K) 123(2) l (Å) 0.71073
cryst syst Triclinic space group P-1
a (Å) 14.0110(7) b (Å) 14.8283(6) c (Å) 25.9612(9) a (deg) 79.517(3) b (deg) 82.011(4) g (deg) 61.809(5) V (Å3) 4665.8(3)
Z 2 Dcalc (g·cm–3) 1.428 µ (mm–1) 0.275 F(000) 2058
cryst size (mm) 0.03 × 0.03 × 0.02 2q range (deg) 4.736–49.998 reflns collected 54449 indep reflns/Rint 16225/0.1500
params 1379 GOF on F2 1.053
R1, wR2 [I>2s(I)] 0.1185, 0.2889 R1, wR2 (all data) 0.2539, 0.3644
8
Fig. S1. (A) ORTEP drawing of 1-Cl with 50% probability determined by X-ray crystallography. One of two crystallographically inequivalent parts, hydrogen atoms, and solvent molecules (1,1,2,2-tetrachloroethane) are omitted for clarity. (B) Packing structure of 1-Cl. (C) The C–C short contacts (Å) seen in the π-π dimer of 1-Cl.
A
B C
3.35 Å3.31 Å
3.30 Å
9
Fig. S2. A typical image of fibrous microcrystals distributed on the holey carbon film. Take at 400×. Diffraction patterns were collected from single fibrous microcrystal with a diameter of ≤ 1 µm.
Fig. S3. Representative frames of energy-filtered electron diffraction (eEFD) patterns in a rotation angle of –4° ~ –3° (left) and +7° ~ +8° (right). Concentric circles indicate 3, 1.5, 1.0 and 0.8 Å resolution rings.
10
Table S2. Data and refinement statistics of the electron diffraction of 1-H.
Experimental details λ (Å) 0.0197 (300 kV) T (K) 98 Oscillation angle (°) 1.00 Tilt range (°) -68.00 to 68.00 (137) Exposure time per frame (s) 1.00 Spot size 7 Illumination angle size (α) 5 Beam size (µm) ~ 5 Camera length (mm) 1245 No. of rotation datasets 46 Crystallographic data Crystal system Tetragonal Resolution (Å) 17.31 – 0.85
(0.87 – 0.85) θ range (°) 0.081 – 0.66 h, k, lmax 40, 40, 19 No. of total reflections 3,226,335 No. of unique reflections 17,516 Completeness (%) 100.0 (100.0) <I/σ(I)> 15.56 (8.48) CC1/2 (%) 99.3 (58.0) Rsym (%) 56.1 (81.9) Refinement Chemical formula (refined) C272H112 Formula weight 3379.61 Space group P42 a = b, c (Å) 34.61 (4), 16.510 (17) V (Å3) 19777 (45) Z 4 Dcalc (g/cm3) 1.135 F (000) 6976.0 Resolution (Å) 7.0 – 0.85 No. of reflections for refinement 17466 Refined parameters 2450 R1, wR2 for Fo > 4σ (Fo) (all data) 0.1647, 0.3722 Goodness of fit 1.929
11
Fig. S4. 1H NMR spectrum of 1-H (600 MHz, C2D2Cl4)
abundance02.04.06.08.010.012.014.016.018.020.022.024.026.0 X
: pa
rts p
er M
illio
n : P
roto
n
10.0
9.0
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
0-1
.0
9.308 9.295
8.707 8.607 8.595 8.575 8.561 7.818 7.816 7.736 7.725 7.689 7.481 7.469 7.446 7.433 7.236 7.225
5.980
5.309
2.145
1.635
0.064
2.00
2.00 2.00 1.00
1.00
1.001.00
1.00
1.00 1.00 1.00
abundance01.02.0 X
: pa
rts p
er M
illio
n : P
roto
n
9.0
8.0
7.0
9.308 9.295
8.707 8.671 8.659 8.607 8.595 8.575 8.561
7.840 7.830 7.818 7.816 7.804 7.748 7.736 7.725 7.713 7.701 7.689 7.676 7.481 7.469 7.446 7.433
7.278 7.236 7.225
2.00
2.002.00
1.00
1.00
1.00
1.00
1.00
1.001.001.00
1-H
12
Fig. S5. 13C NMR spectrum of 1-H (150 MHz, C2D2Cl4)
abundance01.02.03.04.05.06.07.08.0 X
: pa
rts p
er M
illio
n : C
arbo
n13
220.
021
0.0
200.
019
0.0
180.
017
0.0
160.
015
0.0
140.
013
0.0
120.
011
0.0
100.
090
.080
.070
.060
.050
.040
.030
.020
.010
.00
-10.
0-2
0.0
139.435 139.406 138.822 134.082 134.054 131.746 130.913 130.827 130.798 130.750 130.434 129.429 128.998 128.012 127.428 127.265 126.872 121.386
73.790
abundance-0.0100.010.020.030.040.050.060.070.080.090.10.110.120.130.140.150.160.170.180.190.2 X
: pa
rts p
er M
illio
n : C
arbo
n13
140.
013
9.0
138.
013
7.0
136.
013
5.0
134.
013
3.0
132.
013
1.0
130.
012
9.0
128.
012
7.0
126.
012
5.0
124.
012
3.0
122.
012
1.0
139.435 139.406
138.822
134.082 134.054
133.259
132.608 132.550
132.081 131.746
131.018 130.913 130.827 130.798 130.750 130.607 130.434 130.013 129.429 129.084 128.998 128.596
128.012 127.610 127.504 127.428 127.265 126.872 126.700
123.292
121.444 121.386
1-H
13
Fig. S6. 1H NMR spectrum of 1-Cl (600 MHz, C2D2Cl4)
abundance01.02.03.0
X :
parts
per
Mill
ion
: Pro
ton
12.0
11.0
10.0
9.0
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
0-1
.0-2
.0
9.0668.6318.6258.6188.6118.5518.5388.4998.4858.3988.3848.2877.9247.9127.8437.8367.7097.6967.6827.5177.428
5.980
3.97
3.032.052.03
2.07
2.01
1.060.99 0.98
0.97
0.93
1.000.930.94 0.94
1.04 1.030.92
abundance-0.0100.010.020.030.040.050.060.070.080.090.10.110.120.130.140.150.160.17 X
: pa
rts p
er M
illio
n : P
roto
n
9.0
8.0
7.0
9.0799.066
8.7618.749
8.6258.6188.6118.5518.5388.4998.4858.3988.3848.375
8.287
7.9377.9247.9127.8847.8717.8577.8437.8367.8247.7227.7097.6967.6827.669
7.5297.5177.5057.4287.4167.3827.370
7.267
7.1827.169
7.0426.9846.973
3.97
3.03
2.05
2.03
2.07
2.01
1.06
0.990.98
0.97
0.93
1.00
0.93
0.940.94
1.04
1.03
0.92
1-Cl
Cl
14
Fig. S7. 13C NMR spectrum of 1-Cl (150 MHz, C2D2Cl4)
abundance0.10.20.30.4
X :
parts
per
Mill
ion
: Car
bon1
3
220.
021
0.0
200.
019
0.0
180.
017
0.0
160.
015
0.0
140.
013
0.0
120.
011
0.0
100.
090
.080
.070
.060
.050
.040
.030
.020
.010
.00
-10.
0-2
0.0
140.019133.010132.550131.746131.708130.999130.645130.396129.132128.864128.634128.596128.558128.395128.347127.859127.169121.530121.405120.189
73.790
(thousandths)01.02.03.04.05.0 X
: pa
rts p
er M
illio
n : C
arbo
n13
140.
013
9.0
138.
013
7.0
136.
013
5.0
134.
013
3.0
132.
013
1.0
130.
012
9.0
128.
012
7.0
126.
012
5.0
124.
012
3.0
122.
012
1.0
120.
0
140.019
139.530139.320138.994138.755
137.989137.874
136.189135.988
134.149133.862
133.010132.589132.550132.215132.119131.746131.708131.679131.334131.229130.999130.856130.769130.645130.396129.965
129.506129.132128.864128.673128.634128.596128.558128.395128.347128.156127.859127.562127.169126.968126.796126.758126.432
125.321
123.588
122.698122.372
121.740121.530121.405
120.544
120.189
1-Cl
Cl
15
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