Synthesis and Bowl-in-Bowl Assembly of a Geodesic Phenylene Bowl

Article abstract of DOI:10.1002/anie.201702063

A phenylene multiring with a corannulenoidal skeleton was synthesized. Geodesic constraints over 20 phenylene panels resulted in its nanometer-sized, bowl-shaped molecular structure, which was unequivocally revealed by crystallographic analysis. The crystal structure also showed the presence of a bowl-in-bowl dimeric assembly, which was driven by entropic factors in solution.

Full text of DOI:10.1002/anie.201702063

Angewandte
Communications
Chemie
International Edition: DOI: 10.1002/anie.201702063
German Edition: DOI: 10.1002/ange.201702063
Molecular Recognition Very Important Paper
Synthesis and Bowl-in-Bowl Assembly of a Geodesic Phenylene Bowl
Koki Ikemoto, Ryo Kobayashi, Sota Sato, and Hiroyuki Isobe*
Dedicated to Professor Teruaki Mukaiyama on the occasion of his 90th birthday
Abstract: A phenylene multiring with a corannulenoidal
skeleton was synthesized. Geodesic constraints over 20 phen-
ylene panels resulted in its nanometer-sized, bowl-shaped
molecular structure, which was unequivocally revealed by
crystallographic analysis. The crystal structure also showed the
presence of a bowl-in-bowl dimeric assembly, which was
driven by entropic factors in solution.
T
he chemistry of cycloarylenes is flourishing, with various
molecular structures having been synthesized. Currently,
multiring systems constructed with phenylene panels are
being exploited to design nanometer-sized carbon-rich mol-
ecules with unique three-dimensional shapes. For example,
cage- or ball-shaped phenylene multirings have been synthe-
sized through a combination of para- and meta-linked
phenylene panels (Figure 1).[1,2] The three-dimensional
molecular shapes were constructed by connecting multiple
para-phenylene hoops with meta-phenylene hubs. Geometry
constraints for the three-dimensional shapes thus originated
from the curved hoops that were forcibly connected by the
hubs. We herein introduce a geodesic design with phenylene
multirings for the construction of unique three-dimensional
shapes. The geodesic architecture with trigonal planarity
allows for the construction of rigid, curved three-dimensional
shapes without structural stresses.[3] By using sp2-hybridized
carbon atoms as the basic trigonal planar units, chemists have
successfully synthesized a series of geodesic polyarenes such
as corannulene.[4] Herein, we used solely meta-linked phenyl-
enes as the trigonal planar basis and synthesized bowl-shaped
molecule 1 by using geodesic constraints analogous to
corannulene. The nanometer-sized, bowl shape of 1 was
unequivocally revealed by crystallographic analysis. The
crystallographic analysis further revealed bowl-in-bowl
assembly in the crystalline state. The dimerization in solution
was driven by entropic gains, which might be instructive for
understanding the assembly of bowl-shaped nanocarbons.
Figure 1. Structures of phenylene multirings possessing unique three-
dimensional molecular shapes.
We synthesized the bowl-shaped multiring 1 by expanding
[5]cyclo-meta-phenylene ([5]CMP) with multiple meta-linked
phenylene units.[5] Thus, terphenylene 5 was synthesized as
the outer-rim units from tert-butylchlorobenzene 2[6] through
ꢀ
a three-step transformation involving direct C H boryla-
tion,[7] Suzuki coupling,[8] and halogenation[9] reactions
(Scheme 1). Five rim units 5 were then coupled with borylated
[5]CMP 6[10] to afford chlorinated precursor 7 in 56% yield.
The final cyclization to complete the geodesic skeleton was
performed by using a Ni-mediated Yamamoto-type cou-
pling,[11] with fivefold intramolecular homocoupling reactions
affording the target 1 in 32% yield.
A single crystal of 1 was obtained from a toluene solution
by gradual diffusion of methanol vapor, and was subjected to
synchrotron X-ray diffraction experiments (BL17A beam line
of KEK Photon Factory). The crystallographic analysis
revealed that two molecules with slightly different conforma-
tions were stacked to form a dimer (1outꢁ1in) assembled in
a bowl-in-bowl fashion (Figure 2).[12] These two molecules
dimerized in a staggered orientation (see Figure 3c), which
[*] Dr. K. Ikemoto, Dr. S. Sato, Prof. Dr. H. Isobe
Department of Chemistry, The University of Tokyo
JST, ERATO, Isobe Degenerate p-Integration Project
Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 (Japan)
E-mail: isobe@chem.s.u-tokyo.ac.jp
R. Kobayashi, Prof. Dr. H. Isobe
Advanced Institute for Materials Research, Tohoku University
Aoba-ku, Sendai 980-8577 (Japan)
Supporting information and the ORCID identification number(s) for
the author(s) of this article can be found under:
https://doi.org/10.1002/anie.201702063.
Angew. Chem. Int. Ed. 2017, 56, 1 – 5
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
1
These are not the final page numbers!

Angewandte
Communications
Chemie
Figure 2. Crystal structures of 1. a) Two molecular structures found in
the bowl-in-bowl assembly. The numbers show the average POAV
values of the hub. b) Packing structure. See also Figure 3c for details
of the dimer structure.
72%, 1out = 76%; Figure S1). The onset of the UV/Vis
absorption of 1 was at l = 330 nm, thus red-shifted from
that of [5]CMP (l = 311 nm; Figure S3). The structural
expansion with the meta-linked phenylenes, therefore,
resulted in planar but curved conjugated systems. Bowl-
inversion processes involving conformational changes of 20
phenylene panels connected through 25 biaryl bonds are of
interest and will be investigated, for example, through careful
designs of periphery structures.[18,19]
Analyses of 1 in [D]chloroform (10 mm) by 1H NMR
spectroscopy revealed the formation of bowl-in-bowl dimers
(1outꢁ1in) in solution. The spectrum recorded at 243 K showed
seven singlet resonances (Figure 3a; with intensities of
1:2:2:2:1:2:2 from the downfield to upfield regions), which
were ascribed to the highly symmetric monomeric species
(1mono). Interestingly, additional resonances from new species
appeared when the temperature was elevated. For example, at
313 K, 13 additional singlet resonances appeared with inten-
sities of 1:4:2:2:2:2:1:2:2:2:2:1:1 together with the original
resonances of 1mono. From the bowl-in-bowl dimeric structure
observed in the crystal, 14 singlet resonances were expected: 4
resonances of intensity 1, and 10 resonances of intensity 2.
The observed resonances of the new species thus matched
well with this structure under the assumption that two
resonances of intensity 2 were overlapped. From the agree-
ment of the diffusion-ordered spectroscopy (DOSY) with
a bowl-in-bowl dimeric structure (see below), we concluded
that the new species observed at elevated temperatures was
the bowl-in-bowl dimer. The observation of two sets of
resonances for two equilibriating species showed that the
activation energy was considerably high to slow the exchange
processes on the NMR time scale.
Scheme 1. Synthesis of 1. cod=1,5-cyclooctadiene, dba=dibenzyli-
deneacetone.
was most likely due to steric hindrance between the tert-butyl
substituents. As a result, the bowl-in-bowl assembly did not
result in infinite columnar stacks of bowls,[13] and the dimers
were packed in a face-to-face orientation. Similar bowl-in-
bowl dimerization motifs have been observed with smaller
bowl-shaped polyarenes.[12,13] Structural deviations of the
phenylene panels from trigonal planar were evaluated by
using the p-orbital axis vectors at the sp2-hybridized carbon
atoms of the hub (POAV; Figure 2).[14] The POAV values
decreased from 4.78 in the central region to negligible values
below 18 toward the periphery of the molecule. The small
POAV values imply that the strain energy in these bowl-
shaped structures is not high. In contrast, the POAV values
for the smaller geodesic polyarenes corannulene and suma-
nene have been reported to be 8.28 and 9.08, respectively.[15,16]
The geometry constraints from the geodesic skeleton also
affected the biaryl torsions. The biaryl linkages of the original
[5]CMP molecule were mostly synclinal (sc; 60%),[5,17]
whereas those of 1 were mostly synperiplanar (sp; 1in =
2
www.angewandte.org
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2017, 56, 1 – 5
These are not the final page numbers!

Angewandte
Communications
Chemie
structures. Thus, the diameter (d) was 32 ꢂ for both 1mono
and 1outꢁ1in, and the thicknesses (t) were 13 and 19 ꢂ for 1mono
and 1outꢁ1in, respectively (Figure 3c and Figure S2). These
structural parameters can be converted into the expected
hydrodynamic radius through Equation (1) to afford the
expected values of 15 ꢂ for 1mono and 16 ꢂ for 1outꢁ1in. This
result also confirmed the formation of the bowl-in-bowl dimer
in solution.[25]
"
!
#
rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
ꢀ1
ꢀ ꢁ
ꢀ ꢁ
2
2
3
4
t
d
d
t
t
d
t
d
t
d
ð1Þ
Rh ¼
d
1 þ
þ
ln
þ
1 þ
ꢀ
In summary, we have synthesized a nanometer-sized,
carbon-rich multiring by assembling 20 phenylene panels with
25 biaryl bonds under geodesic constraints. The geodesic
design was applied for the first time to phenylene multirings
and resulted in the bowl-shaped molecular structure. The
large, anomalous molecular shape facilitated concave–convex
recognition for formation of the bowl-in-bowl dimer in the
crystalline state. The dimerization as well as its thermody-
namics were investigated spectroscopically to reveal an
entropy-driven assembly in solution. Geodesic arylene mul-
tirings may be of interest for exploring carbon-rich materials
with unique three-dimensional molecular shapes.
Figure 3. Bowl-in-bowl assembly of 1. a) VT 1H NMR spectra of 1 in
CDCl3 (10 mm). New resonances appearing at 313 K are marked with
asterisks. b) Thermodynamics of bowl-in-bowl assembly from the
van’t Hoff analysis. c) Molecular size of the bowl-in-bowl dimer in the
crystal.
Acknowledgements
This study was partly supported by JST ERATO
(JPMJER1301) and KAKENHI (24241036, 25102007,
16K04864). We thank Dr. M. Oinuma, Dr. S. Takahashi, and
C. Yang (ERATO) for the large-scale preparation of [5]CMP,
and KEK PF (Research 2015G097) for the use of their X-ray
diffraction instruments.
We then investigated the association thermodynamics of
the dimer formation through variable-temperature (VT)
NMR spectroscopy. The concentrations of 1mono and 1outꢁ1in
were determined from the spectra at each temperatures and
were converted into association constants through the equa-
tion Ka = [1outꢁ1in]/[1mono]2 (e.g. Ka = 55mꢀ1, 298 K; Table S2).
The temperature-dependent Ka values were further analyzed
by a 1/TꢀlnKa plot (Figure S4),[20] which revealed an associ-
ation enthalpy (DH) of + 9.6 kcalmolꢀ1 and an association
entropy (DS) of + 40.2 kcalmolꢀ1 Kꢀ1 through a vanꢀt Hoff
analysis (Figure 3b). The entropy contribution for the asso-
ciation energy (ꢀTDS) was thus ꢀ12.0 kcalmolꢀ1, which
showed the entropy-driven assembly of 1outꢁ1in. We believe
that this entropy-driven assembly originated from desolvation
of the curved carbon-rich planes, which has also been
observed with other curved p-systems.[21] Similar entropy
gains from the desolvation may be crucial for the assembly of
gigantic bowl-shaped nanocarbons such as carbon nano-
cones.[22]
Finally, we analyzed the diffusion constants (D) of 1mono
and 1outꢁ1in at 298 K by DOSY. The D values were (2.8 ꢂ
0.1) ꢁ 10ꢀ10 and (2.4 ꢂ 0.1) ꢁ 10ꢀ10 m2 sꢀ1 for 1mono and 1outꢁ1in,
respectively (Figure S5), which were consistent with the
monomer/dimer structures of different molecular weights.[23]
By applying these values in the Stokes–Einstein relation-
ship,[24] we determined apparent hydrodynamic radii (Rh) of
(14.4 ꢂ 0.6) ꢂ for 1mono and (16.5 ꢂ 0.7) ꢂ for 1outꢁ1in. The
apparent hydrodynamic radius is an equivalent radius of
spherical objects and matches well with the expected hydro-
dynamic radii calculated from the nonspherical crystal
Conflict of interest
The authors declare no conflict of interest.
Keywords: macrocycles · meta-phenylene ·
molecular recognition · nanostructures · self-assembly
[1] K. Matsui, Y. Segawa, T. Namikawa, K. Kamada, K. Itami,
Chem. Sci. 2013, 4, 84 – 88.
[2] E. Kayahara, T. Iwamoto, H. Takaya, T. Suzuki, M. Fujitsuka, T.
Majima, N. Yasuda, N. Matsuyama, S. Seki, S. Yamago, Nat.
Commun. 2013, 4, 2694.
[3] H. Kenner, Geodesic Math and How to Use It, 2nd edition,
University of California Press, Berkeley, 2003.
[4] L. T. Scott, H. E. Bronstein, D. V. Preda, R. B. M. Ansems, M. S.
Bratcher, S. Hagen, Pure Appl. Chem. 1999, 71, 209 – 219.
[5] J. Y. Xue, K. Ikemoto, N. Takahashi, T. Izumi, H. Taka, H. Kita,
S. Sato, H. Isobe, J. Org. Chem. 2014, 79, 9735 – 9739.
[6] J. A. Hartsel, D. T. Craft, Q.-H. Chen, M. Ma, P. R. Carlier, J.
Org. Chem. 2012, 77, 3127 – 3133.
[7] a) T. Ishiyama, J. Takagi, K. Ishida, N. Miyaura, N. R. Anastasi,
J. F. Hartwig, J. Am. Chem. Soc. 2002, 124, 390 – 391; b) I. A. I.
Angew. Chem. Int. Ed. 2017, 56, 1 – 5
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
3
These are not the final page numbers!

Angewandte
Communications
Chemie
Mkhalid, J. H. Barnard, T. B. Marder, J. M. Murphy, J. F.
Hartwig, Chem. Rev. 2010, 110, 890 – 931; c) J. F. Hartwig,
Chem. Soc. Rev. 2011, 40, 1992 – 2002.
[18] a) L. T. Scott, M. M. Hashemi, M. S. Bratcher, J. Am. Chem. Soc.
1992, 114, 1921 – 1923; b) A. Sygula, A. H. Abdourazak, P. W.
Rabideau, J. Am. Chem. Soc. 1996, 118, 339 – 343; c) T. J. Seiders,
K. K. Baldridge, G. H. Grube, J. S. Siegel, J. Am. Chem. Soc.
2001, 123, 517 – 525.
[19] a) P. Sarkar, S. Sato, S. Kamata, T. Matsuno, H. Isobe, Chem.
Lett. 2015, 44, 1581 – 1583; b) P. Sarkar, Z. Sun, T. Tokuhira, M.
Kotani, S. Sato, H. Isobe, ACS Cent. Sci. 2016, 2, 740 – 747.
[20] S. Hitosugi, W. Nakanishi, H. Isobe, Chem. Asian J. 2012, 7,
1550 – 1552.
[8] a) N. Miyaura, K. Yamada, A. Suzuki, Tetrahedron Lett. 1979, 20,
3437 – 3440; b) N. Miyaura, A. Suzuki, Chem. Rev. 1995, 95,
2457 – 2483.
[9] R. A. Benkeser, A. Torkelson, J. Am. Chem. Soc. 1954, 76, 1252 –
1253.
[10] K. Ikemoto, A. Yoshii, T. Izumi, H. Taka, H. Kita, J. Y. Xue, R.
Kobayashi, S. Sato, H. Isobe, J. Org. Chem. 2016, 81, 662 – 666.
[11] a) T. Yamamoto, Y. Hayashi, A. Yamamoto, Bull. Chem. Soc.
Jpn. 1978, 51, 2091 – 2097; b) T. Yamamoto, Prog. Polym. Sci.
1992, 17, 1153 – 1205; c) W. Nakanishi, T. Yoshioka, H. Taka,
J. Y. Xue, H. Kita, H. Isobe, Angew. Chem. Int. Ed. 2011, 50,
5323 – 5326; Angew. Chem. 2011, 123, 5435 – 5438.
[12] E. A. Jackson, B. D. Steinberg, M. Bancu, A. Wakamiya, L. T.
Scott, J. Am. Chem. Soc. 2007, 129, 484 – 485.
[21] H. Isobe, S. Hitosugi, T. Yamasaki, R. Iizuka, Chem. Sci. 2013, 4,
1293 – 1297.
[22] a) A. Krishnan, E. Dujardin, M. M. J. Treacy, J. Hugdahl, S.
Lynum, T. W. Ebbesen, Nature 1997, 388, 451 – 454; b) M. Endo,
Y. A. Kim, T. Hayashi, Y. Fukai, K. Oshida, M. Terrones, T.
Yanagisawa, S. Higaki, M. S. Dresselhaus, Appl. Phys. Lett. 2002,
80, 1267 – 1269.
[13] S. Lampart, L. M. Roch, A. K. Dutta, Y. Wang, R. Warshaman-
age, A. D. Finke, A. Linden, K. K. Baldridge, J. S. Siegel, Angew.
Chem. Int. Ed. 2016, 55, 14648 – 14652; Angew. Chem. 2016, 128,
14868 – 14872.
[14] R. C. Haddon, L. T. Scott, Pure Appl. Chem. 1986, 58, 137 – 142.
[15] J. C. Hanson, C. E. Nordman, Acta Crystallogr. Sect. B 1976, 32,
1147 – 1153.
[23] C. S. Johnson, Jr., Prog. Nucl. Magn. Reson. Spectrosc. 1999, 34,
203 – 256.
[24] J. T. Edward, J. Chem. Educ. 1970, 47, 261 – 270.
[25] N. A. Mazer, G. B. Benedek, M. C. Carey, Biochemistry 1980, 19,
601 – 615.
[16] H. Sakurai, T. Daiko, H. Sakane, T. Amaya, T. Hirao, J. Am.
Chem. Soc. 2005, 127, 11580 – 11581.
[17] E. L. Eliel, S. H. Willen, Stereochemistry of Organic Compounds,
Wiley, New York, 1994.
Manuscript received: February 24, 2017
Final Article published: && &&, &&&&
4
www.angewandte.org
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2017, 56, 1 – 5
These are not the final page numbers!

Angewandte
Communications
Chemie
Communications
Molecular Recognition
Shape sorting: Geodesic constraints
arising from the coupling of trigonal
planar phenylenes into a pentagon sur-
rounded by five hexagons resulted in
a nanometer-sized bowl-shaped mole-
cule. Concave–convex molecular recog-
nition resulted in the molecules assem-
bling in a bowl-in-bowl fashion. The
shape recognition was driven by an
entropy gain for the assembly of the large
120 p-systems.
K. Ikemoto, R. Kobayashi, S. Sato,
H. Isobe*
&&&& — &&&&
Synthesis and Bowl-in-Bowl Assembly of
a Geodesic Phenylene Bowl
Angew. Chem. Int. Ed. 2017, 56, 1 – 5
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
5
These are not the final page numbers!