A novel graphite-like stacking structure in a discrete molecule and its molecular recognition behavior

Article abstract of DOI:10.1039/c8nj01315b

A graphite-like stacking structure was nicely reproduced in a discrete molecule that was prepared by 2+2 macrocyclic Schiff base formation. In the crystal structure, two hexabenzocoronene planes are closely stacked with displacement, yielding the intramolecular stacking structure similar to an AB- or ABC-stacking pattern in natural graphite. This molecule showed a recognition ability toward electron-deficient aromatic molecules in solution.

Full text of DOI:10.1039/c8nj01315b

View Article Online
View Journal
NJC
Accepted Manuscript
This article can be cited before page numbers have been issued, to do this please use: S. Akine, T.
Onuma and T. Nabeshima, New J. Chem., 2018, DOI: 10.1039/C8NJ01315B.
This is an Accepted Manuscript, which has been through the
Royal Society of Chemistry peer review process and has been
accepted for publication.
Volume 40 Number
1 January 2016 Pages 1–846
NJC
Accepted Manuscripts are published online shortly after
New Journal of Chemistry
www.rsc.org/njc
A journal for new directions in chemistry
acceptance, before technical editing, formatting and proof reading.
Using this free service, authors can make their results available
to the community, in citable form, before we publish the edited
article. We will replace this Accepted Manuscript with the edited
and formatted Advance Article as soon as it is available.
You can find more information about Accepted Manuscripts in the
author guidelines.
Please note that technical editing may introduce minor changes
to the text and/or graphics, which may alter content. The journal’s
standard Terms & Conditions and the ethical guidelines, outlined
in our author and reviewer resource centre, still apply. In no
event shall the Royal Society of Chemistry be held responsible
for any errors or omissions in this Accepted Manuscript or any
consequences arising from the use of any information it contains.
ISSN 1144-0546
PAPER
Jason B. Benedict et al.
The role of atropisomers on the photo-reactivity and fatigue of
diarylethene-based metal–organic frameworks
rsc.li/njc

Please do not adjust margins
New Journal of Chemistry
Page 1 of 5
View Article Online
DOI: 10.1039/C8NJ01315B
Journal Name
COMMUNICATION
Novel graphite-like stacking structure in a discrete molecule and
its molecular recognition behavior
Shigehisa Akine,*a Takahiro Onuma b and Tatsuya Nabeshima*b
Received 00th January 20xx,
Accepted 00th January 20xx
DOI: 10.1039/x0xx00000x
www.rsc.org/
Graphite-like stacking structure was nicely reproduced in
a
discrete molecule that was prepared by 2+2 macrocyclic Schiff
base formation. In the crystal structure, two hexabenzocoronene
planes are closely stacked with displacement, yielding the
intramolecular stacking structure similar to AB- or ABC-stacking
pattern in natural graphite. This molecule showed recognition
ability toward electron-deficient aromatic molecules in solution.
Graphite is one of the allotropes of carbon that has a layered
structure of sp2 carbon atoms. Each of the layers has a
hexagonal honeycomb structure called a graphene sheet,
which has recently attracted the increasing interests of
researchers.1 Along with the infinite graphene sheet, there is a
class of nano-sized discrete analogues, e.g., polycyclic aromatic
hydrocarbons (PAHs) with a finite π-surface, which can be
synthesized as pure organic compounds.2 Hexa-peri-
hexabenzocoronene (HBC, hereafter) is one of the
representative examples that has been well studied as a nano-
sized graphene. While the chemistry of nanographenes has
been well established,2 it has been difficult to reproduce the
stacking columns are found in the crystal structure of a simple
unsubstituted nanographene derivative,8 while discrete
dimeric and trimeric stacks are observed in the crystal of
nanographene derivatives with peripheral bulky substituents.9
However, it has been difficult to control the number of stacked
molecules via self-assembly due to the formation of an infinite
polymeric stack or dissociation equilibrium10 with the
monomer in solution, while some double-decker graphenes
are reported to show unique physical and electrical
properties.11 In this context, it would be advantageous to
covalently link a limited number of nanographene subunits12,13
so that the number of stacks is controlled both in solution and
in the crystalline state. In fact, a discrete dimeric sack was
efficiently formed by using a macrocyclic bis(HBC) compound,
although its stacking pattern was ambiguous.12 We designed a
graphite-like stacking in
a discrete nano-sized molecule.
Nevertheless, it should be interesting to know how nano-sized
graphene molecules are stacked and how the stacked sheets
interact with each other, while it has been well understood
that graphite has a layered structure with a 3.35 Å separation
in a staggered (AB or ABC-stacking) pattern3 rather than an
eclipsed (AA-stacking) one.4
To obtain a layered nanographite structure, the bottom-up
assembling of nanographene subunits would be effective. In
general, nanographene molecules tend to form stacking
structures due to π-stacking interactions,5–7 but the number of
stacks depends on the molecular structures. Parallel infinite
macrocyclic HBC dimer
1 as a unimolecular nanographite, in
which two nanographene moieties are connected with two
diimine linkages (Figure 1). The two HBC planes, which are
slightly curved and each facing its convex side, are stacked in a
staggered fashion, which nicely reproduces the AB- or ABC-
stacking structures found in natural graphite. The
This journal is © The Royal Society of Chemistry 20xx
J. Name., 2013, 00, 1-3 | 1
Please do not adjust margins

Please do not adjust margins
New Journal of Chemistry
Page 2 of 5
View Article Online
DOI: 10.1039/C8NJ01315B
COMMUNICATION
Journal Name
intermolecular interaction between
1 and some electron-
deficient planar molecules was also investigated.
For efficient synthesis of the macrocyclic molecular
graphite, we used the Schiff base formation, because the
reversible feature of the Schiff base formation is known to be
effective for high-yield macrocyclization (Scheme 1).14 Suzuki-
16
coupling of diiodide 215 and 4-bromophenylboronic acid (
3)
using a palladium catalyst afforded dibromide
The HBC derivative 517 was synthesized by the oxidation of
with iron(III) chloride in 97% yield. The precursor having two
3-formylphenyl groups was synthesized by Suzuki coupling of
4 in 81% yield.
4
7
the dibromo-HBC
yield.
5 with 3-formylphenylboronic acid (6) in 52%
The reaction of the diformyl precursor
7 with an equimolar
18
amount of the diamines with different chain lengths (8a
–8c)
planes are closely stacked on top of each other. In the UV-vis
absorption spectra, 1b and 1c showed absorption maxima at
363 and 377 nm (Figure S8, S9), respectively, while mono-HBC
was investigated in CDCl3 by 1H NMR spectroscopy. After
mixing, the peak for the formyl group (10.3 ppm) completely
disappeared and a new peak for the aldimine functionality was
observed for each reaction mixture. This indicated that a single
macrocyclic product was formed in each of the reaction
mixtures. Mass spectrometric measurements (MALDI-TOF MS)
clearly indicated the molecular ions at m/z 1957.0 (for 1a),
2044.8 (for 1b), and 2132.8 (for 1c) corresponding to the 2+2
macrocyclic products consisting of two HBC units.
derivative 7 showed the corresponding band at 366 nm (Figure
S10). This suggests that the HBC planes in 1c are more
efficiently interacting with each other.
The X-ray crystallographic analysis of 1b‡ confirmed the
close stacking of the two HBC planes (Figure 2a,b) that are
linked with two CH2CH2OCH2CH2 chains to afford the 2+2
macrocyclic structure. The molecule of 1b has
a
Each of the 1H NMR spectra of the macrocyclic HBC dimers
crystallographically-imposed center of symmetry at the
midpoint of the two HBC planes. Interestingly, the two HBC
planes did not perfectly overlap, but are displaced from each
other by 2.79 Å, which nearly corresponds to twice the
average C–C bond lengths. For example, the centroid of the
six-membered ring C1–C6, which is at the center of one of the
HBC planes, is almost exactly above C19* of the counterpart
HBC plane (Figure 2c). Due to this displacement, the two HBC
1a–1c showed three peaks assignable to the HBC skeletal
protons at 8.7–8.9 ppm (Figure S3), which were significantly
upfield shifted compared to the corresponding protons of the
mono-HBC derivative
7 at around 9.3 ppm (Figure S2).
Obviously, the upfield shifts are ascribed to the shielding effect
of the counterpart HBC plane. This suggests that the dimers
1a–1c are likely to adopt a structure in which the two HBC
2 | J. Name., 2012, 00, 1-3
This journal is © The Royal Society of Chemistry 20xx
Please do not adjust margins

Please do not adjust margins
New Journal of Chemistry
Page 3 of 5
View Article Online
DOI: 10.1039/C8NJ01315B
Journal Name
COMMUNICATION
of the yellow solution of 1c with
a red solution of
isoviolanthrone (B). In the UV-vis absorption spectra,
a
structured CT band centered at 510, 546, 591, and 650 nm was
observed (Figure 3b, S12). The association constant was
determined to be log Ka = 2.64 ± 0.10.
It is known that π-aromatic molecules often form D–A–D–A
alternate stacking structures due to donor (D) acceptor (A)
interactions. However, repeating patterns other than D–A–D–
A structures have been generally difficult to be obtained when
we use simple monomeric π-aromatic molecules. As
demonstrated in this study, the dimeric HBC molecule 1c
showed a high affinity toward some electron-deficient π-
aromatic molecules. Although the structure of the charge-
transfer complexes 1c•A and 1c•B were not elucidated,
planes were stacked in a staggered fashion, which nicely
reproduces the AB- or ABC-stacking pattern observed for
natural graphite. This is the first crystallographic analysis of a
macrocyclic HBC dimer that allows stacking of the two HBC
planes. The arrangement of the two HBC planes is very similar
to that observed in the crystal of hexa-tert-butyl derivative,9a
while unsubstituted HBC forms an infinite column with a non-
natural stacking pattern.8
dimeric HBC derivatives, such as 1c, would be useful to
construct stacking structures having various kinds of stacking
patterns such as D–D–A–D–D–A, some of which are known to
show unique semiconducting properties.19
In conclusion, we have synthesized a new series of HBC
dimers 1a–1c using the macrocyclic Schiff base formation. In
the crystalline state, the molecule of 1b showed a unique
intramolecular stacking structure with the shortest interplane
distance of about 3.30 Å. The two HBC planes are stacked in a
staggered fashion as observed in natural graphite with the AB-
or ABC-stacking pattern. In addition, 1c was found to form
donor-acceptor complexes with some electron-deficient planar
molecules. The intermolecular interaction of the dimeric unit
of 1c with aromatic molecules would enable the formation of
various stacking patterns. Further investigation of the
structures of donor-acceptor complexes and their electronic
properties is now in progress.
The two HBC planes are slightly bent and each facing their
convex side so that the atoms on lines 4 and 4* (see Figure
2b,c) are close to each other. The interplane distances
between lines 4 and 4* were in the range of 3.30–3.38 Å,
which were comparable to the interlayer distance of natural
graphite (3.35 Å).3 Since the two HBC planes are bent, the
interplane distances at the periphery were longer (lines 3–5*,
3.40–3.44 Å; lines 2–6*, 3.49–3.61 Å; lines 1–7* 3.73–3.80 Å),
but still indicative of the π–π interaction. The steric demand of
the tert-butyl groups at C16, C22, C34, and C40 should
elongate the interplane distances at the periphery. As a result,
the four outer six-membered rings (C13–C18, C19–C24, C31–
C36, and C37–C42) attached to the tert-butyl groups were
outwardly bent with the dihedral angles of 5.7–10.7 deg.
It is noteworthy that the molecules of 1b did not form an
intermolecular π-stacking structure in the crystal packing,
leaving discrete dimeric structures isolated from other
molecules (Figure S13). In general, extended π-aromatic
molecules have a strong tendency to form intermolecular
stacking structures such as an infinite assembly,8 but in the
case of 1b, such an intermolecular stacking was not favored
probably due to the tert-butyl groups at the periphery.
However, π-aromatic molecules smaller than the HBC π-
surface would efficiently interact with the dimeric compounds
This work was supported in part by JSPS KAKENHI (Grant
Number JP15K13638, JP16H06510 and JP26288022),
Kanazawa University CHOZEN Project, and World Premier
International Research Centre Initiative (WPI), MEXT, Japan.
Conflicts of interest
There are no conflicts to declare.
Notes and references
‡ Single crystal of 1b (0.25 × 0.15 × 0.10 mm3, C156H140Cl12N4O4 =
C152H132N4O2•2H2O•4CHCl3 (2560.11) was obtained by slow
evaporation of the solution in chloroform/hexane. The intensity
data were collected on a Bruker Smart APEX II Ultra at 120 K
using Mo Kα radiation (λ = 0.71073 Å). The data were corrected
for Lorentz and polarization factors, and for absorption based on
symmetry equivalent and repeated reflections. The structure
was solved by direct methods (SHELXD20) and refined by full-
matrix least-squares on F2 using SHELXL 2014.21
1a
some electron-deficient planar compounds such as
As expected, when we mixed a yellow solution of 1c with
an orange solution of perylenebisimide derivative , the color
–
1c. Thus, we investigated the interaction between 1c and
A
and
B.
A
of the solution changed to red. In the UV-vis absorption
spectra, a broad band was observed at 600–750 nm (Figure 3a,
S11). The absorption band can be ascribed to the charge-
Crystallographic data: crystal system, monoclinic, space group,
P21/n, a = 16.0494(3), b = 19.0406(3), c = 21.7646(4) Å, α = 90.00,
β = 105.1990(10), γ = 90.00 deg, V = 6418.4(2) Å3, Z = 2, Dcalcd
1.325 g/cm3, Collected reflections, 68324, unique, 14013, Rint
=
=
transfer interaction between 1c and
A. The association
constant was determined to be log Ka = 4.59 ± 0.10 (Ka in M–1)
by nonlinear least-squares analysis of the titration curve.
Similarly, a dark green solution was obtained upon the mixing
0.0384, 2θmax = 54.00 deg, F000 = 2680, μ(Mo Kα) = 0.319,
Limiting indices, –20 ≤ h ≤ 20, –24 ≤ k ≤ 24, –27 ≤ l ≤ 27,
Parameters/restraints, 1091/365, Goodness of fit (F2) = 1.119, R1
This journal is © The Royal Society of Chemistry 20xx
J. Name., 2013, 00, 1-3 | 3
Please do not adjust margins

Please do not adjust margins
New Journal of Chemistry
Page 4 of 5
View Article Online
DOI: 10.1039/C8NJ01315B
COMMUNICATION
Journal Name
(I > 2σ(I)) = 0.0903, wR2 (I > 2σ(I)) = 0.2059, R1 (all data) = 16 G. W. Kabalka, U. Sastry, K. A. R. Sastry, F. F. Knapp, Jr. and P.
0.1332, wR2 (all data) 0.2388. CCDC-1818716 contains the C. Srivastava, J. Organomet. Chem., 1983, 259, 269–274.
supplementary crystallographic data for this paper. These data 17 C. M. Thompson, G. T. McCandless, S. N. Wijenayake, O.
can be obtained free of charge from The Cambridge
Crystallographic Data Centre via
www.ccdc.cam.ac.uk/data_request/cif.
Alfarawati, M. Jahangiri, A. Kokash, Z. Tran and R. A.
Smaldone, Macromolecules, 2014, 47, 8645–8652.
18 Y. Li, C. Zhang and S. Zheng, Eur. Polym. J., 2011, 47, 1550–
1562.
1
2
3
For reviews, see: a) K. S. Novoselov, V. I. Fal'ko, L. Colombo,
P. R. Gellert, M. G. Schwab and K. Kim, Nature, 2012, 490
192–200; b) M. J. Allen, V. C. Tung and R. B. Kaner, Chem.
Rev., 2010, 110, 132–145.
For reviews, see: a) J. Wu, W. Pisula and K. Müllen, Chem.
Rev., 2007, 107, 718–747; b) H. Seyler, B. Purushothaman, D.
J. Jones, A. B. Holmes and W. W. H. Wong, Pure Appl. Chem.,
2012, 84, 1047–1067.
a) J. D. Bernal, Proc. Roy. Soc., 1924, A106, 749–773; b) O.
Hassel and H. Mark, Z. Phys., 1924, 25, 317–337; c) J. B.
Nelson and D. P. Riley, Proc. Phys. Soc., 1945, 57, 477–485.
I. Lobato and B. Partoens, Phys. Rev. B, 2011, 83, 165429.
a) W. Pisula, A. Menon, M. Stepputat, I. Lieberwirth, U. Kolb,
A. Tracz, H. Sirringhaus, T. Pakula and K. Müllen, Adv. Mater.,
2005, 17, 684–689; b) V. Lemaur, D. A. da Silva Filho, V.
Coropceanu, M. Lehmann, Y. Geerts, J. Piris, M. G. Debije, A.
M. van de Craats, K. Senthilkumar, L. D. A. Siebbeles, J. M.
Warman, J.-L. Brédas and J. Cornil, J. Am. Chem. Soc., 2004,
126, 3271–3279; c) A. M. van de Craats, N. Stutzmann, O.
Bunk, M. M. Nielsen, M. Watson, K. Müllen, H. D. Chanzy, H.
Sirringhaus and R. H. Friend, Adv. Mater., 2003, 15, 495–499;
d) L. Schmidt-Mende, A. Fechtenkötter, K. Müllen, E. Moons,
R. H. Friend and J. D. MacKenzie, Science, 2001, 293, 1119–
1122.
19 a) J. Zhang, W. Xu, P. Sheng, G. Zhao and D. Zhu, Acc. Chem.
Res., 2017, 50, 1654−1662; b) H. Endres, A. Bongart, D.
Nöthe, I. Hennig, D. Schweitzer, H. W. Helherg and H. Schäfer,
Mol. Cryst. Liq. Cryst. 1985, 120, 365−368; c) Q. Qin, J. T.
Mague, K. Z. Moses, E. M. Carnicom and R. J. Cava
CrystEngComm, 2017, 19, 6355−6364.
,
20 G. M. Sheldrick, Acta Cryst., 2010, D66, 479–485.
21 G. M. Sheldrick, Acta Cryst., 2015, C71, 3–8.
4
5
6
7
a) J. P. Hill, W. Jin, A. Kosaka, T. Fukushima, H. Ichihara, T.
Shimomura, K. Ito, T. Hashizume, N. Ishii and T. Aida, Science
2004, 304, 1481–1483; b) Y. Yamamoto, T. Fukushima, Y.
Suna, N. Ishii, A. Saeki, S. Seki, S. Tagawa, M. Taniguchi, T.
Kawai and T. Aida, Science, 2006, 314, 1761–1764.
a) M. Kastler, W. Pisula, D. Wasserfallen, T. Pakula and K.
Müllen, J. Am. Chem. Soc., 2005, 127, 4286–4296; b) S. Ito,
M. Wehmeier, J. D. Brand, C. Kübel, R. Epsch, J. P. Rabe and
K. Müllen, Chem. Eur. J., 2000, 6, 4327–4342; c) S. Xiao, M.
Myers, Q. Miao, S. Sanaur, K. Pang, M. L. Steigerwald and C.
Nuckolls, Angew. Chem. Int. Ed., 2005, 44, 7390–7394.
R. Goddard, M. W. Haenel, W. C. Herndon, C. Krüger and M.
Zander, J. Am. Chem. Soc., 1995, 117, 30–41.
a) P. T. Herwig, V. Enkelmann, O. Schmelz and K. Müllen,
Chem. Eur. J., 2000, 6, 1834–1839; b) A. Matsumoto, M.
8
9
Suzuki, D. Kuzuhara, H. Hayashi, N. Aratani and H. Yamada,
Angew. Chem. Int. Ed., 2015, 54, 8175–8178.
10 J. Wu, A. Fechtenkötter, J. Gauss, M. D. Watson, M. Kastler,
C. Fechtenkötter, M. Wagner and K. Müllen, J. Am. Chem.
Soc., 2004, 126, 11311–11321.
11 a) Y. Gao, T. Cao, F. Cellini, C. Berger, W. A. de Heer, E.
Tosatti, E. Riedo and A. Bongiorno, Nature Nanotech., 2018,
13, 133–138; b) Y.-M. Lin and P. Avouris, Nano Lett., 2008, 8,
2119–2125.
12 M. D. Watson, F. Jäckel, N. Severin, J. P. Rabe and K. Müllen,
J. Am. Chem. Soc., 2004, 126, 1402–1407.
13 For a review on cyclophanes containing polycyclic aromatic
hydrocarbons, see: P. G. Ghasemabadi, T. Yao and G. J.
Bodwell, Chem. Soc. Rev.,2015, 44, 6494–6518.
14 a) N. E. Borisova, M. D. Reshetova and Y. A. Ustynyuk, Chem.
Rev., 2007, 107, 46–79; b) M. J. MacLachlan, Pure Appl.
Chem., 2006, 78, 873–888; c) S. Akine, J. Inclusion Phenom.
Macrocycl. Chem., 2012, 72, 25–54; d) S. Akine and T.
Nabeshima, Dalton Trans., 2009, 10395–10408.
15 S. Shah, T. Concolino, A. L. Rheingold and J. D. Protasiewicz,
Inorg. Chem., 2000, 39, 3860–3867.
4 | J. Name., 2012, 00, 1-3
This journal is © The Royal Society of Chemistry 20xx
Please do not adjust margins

Page 5 of 5
New Journal of Chemistry
View Article Online
DOI: 10.1039/C8NJ01315B
TOC text (within 20 words)
Macrocyclic imines containing two hexabenzocoronene planes adopted a unique intramolecular stacking
structure, similar to the stacking pattern in natural graphite.
TOC graphic