Self-assembled dimerization of bis(crown ether)-2,2′-bibenzimidazoles

Article abstract of DOI:10.1246/bcsj.20130173

Bis(crown ether)-2,2′-bibenzimidazole 1 and its 1-substituted derivatives were synthesized as new self-assembled motifs. UV-vis and ¹HNMR titration experiments of 1 with potassium ions in a mixture of chloroform and methanol (1:1) were carried out. The stoichiometries and curve fitting analysis showed that a 2:2 complex of 1 with potassium ions was formed in a face-to-face fashion. 1-Monosubstituted bis(crown ether)-2,2′- bibenzimidazole 6a having a (dodecylaminocarbonyl)methyl group also gave a 2:2 complex with potassium ions. Structural analysis of the 2:2 complex of 6a with potassium ions was performed using various two-dimensional NMR techniques. Results suggested that, of eight or more possible conformational isomers, the one having the two substituent groups diagonally opposite each other was predominantly formed. Reversible association and dissociation of the 2:2 complex was observed after adding potassium ions and then removing them with an 18-crown-6-ether.

Full text of DOI:10.1246/bcsj.20130173

88
Bull. Chem. Soc. Jpn. Vol. 87, No. 1, 88-97 (2014)
© 2013 The Chemical Society of Japan
Self-Assembled Dimerization of Bis(crown ether)-2,2¤-bibenzimidazoles
Akiharu Satake,*1 Kazuo Tanaka,1 Hiroki Asakura,1 Masahiro Okano,1 Tsutsumu Hashimoto,1
You Matsuura,1 Yusuke Inaba,2 Tetsuhisa Oda,2 Shun Hirota,2 and Hiroyuki Koshino3
1Department of Chemistry, Faculty of Science Division II, Tokyo University of Science,
1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601
2Graduate School of Materials Science, Nara Institute of Science and Technology,
8916-5 Takayama, Ikoma, Nara 630-0101
3Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
Received June 18, 2013; E-mail: satake@rs.kagu.tus.ac.jp
Bis(crown ether)-2,2¤-bibenzimidazole 1 and its 1-substituted derivatives were synthesized as new self-assembled
1
motifs. UV-vis and H NMR titration experiments of 1 with potassium ions in a mixture of chloroform and methanol
(1:1) were carried out. The stoichiometries and curve fitting analysis showed that a 2:2 complex of 1 with potassium
ions was formed in a face-to-face fashion. 1-Monosubstituted bis(crown ether)-2,2¤-bibenzimidazole 6a having a
(dodecylaminocarbonyl)methyl group also gave a 2:2 complex with potassium ions. Structural analysis of the 2:2
complex of 6a with potassium ions was performed using various two-dimensional NMR techniques. Results suggested
that, of eight or more possible conformational isomers, the one having the two substituent groups diagonally opposite
each other was predominantly formed. Reversible association and dissociation of the 2:2 complex was observed after
adding potassium ions and then removing them with an 18-crown-6-ether.
Stable self-assembled dimers are key components to con-
bonding interaction between N-H and the neighboring co-
imidazole nitrogen.8 Therefore, if two 15-crown-5-ether moie-
ties are introduced into a bibenzimidazole, the two 15-crown-5-
ether moieties in the same plane will work cooperatively and
give stable sandwich complexes upon addition of potassium
ions (A dimer in Figure 1). Further, if such a coplanar con-
formation can be kept by only hydrogen-bonding interaction,
then introduction of a substituent group (shown as R in the B in
Figure 1) is allowable on one of the two imidazole nitrogen
atoms. Substitution on both imidazole nitrogen atoms will not
give a coplanar conformation due to lack of intramolecular
hydrogen bonding. Molecule B, which gives a two-directional
self-assembled dimer (B dimer in Figure 1), will be useful as a
versatile supramolecular motif.
struct supramolecular systems. Various self-assembled systems
have been reviewed,1 in which multiple hydrogen-bonding
interaction,2 transition-metal-ligand coordination,3 dipole-di-
pole interaction,4 and macrocyclic host-guest interaction1d,1f,5
were frequently observed. A supramolecular strategy, using
such dynamic noncovalent interactions, is advantageous for
the construction of giant and relatively complicated molec-
ular systems. The development of new self-assembled dimers,
which are sufficiently stable in solution and do not interfere
with other self-assembled motif, is important. Crown ether-
based self-assembled systems are known as noninterferable
supramolecular motifs, unaffected by hydrogen bonding and
transition-metal-ligand coordination. Therefore, simple and
stable crown ether-based modules are attractive for combina-
tion with other self-assembled systems. We investigated a new
and simple crown ether-based supramolecular motif created by
the addition of potassium ions. Sandwich-type dimers com-
posed of two bis(crown ether)-2,2¤-bibenzimidazoles and two
potassium ions are reported.
Results and Discussion
Synthesis. Bis(crown ether)-2,2¤-bibenzimidazole 1 was
prepared as shown in Scheme 1. Benzo-15-crown-5-ether (2)
was bisnitrated with nitric acid, followed by fuming nitric acid
in acetic acid. After recrystallization, pure 4,5-dinitrobenzo-15-
crown-5-ether (3) was obtained in 66% yield. Dinitro com-
pound 3 was hydrogenated in the presence of palladium/carbon
to afford the diamino compound 4, which was then immedi-
ately reacted with methyl 2,2,2-trichloroacetimidate to afford 1
in 21% yield from compound 3. The reason for the low yield
is probably the ease of oxidation of diamino compound 4 and
formation of by-products, including imine and 2,3-quinoxaline-
dione derivatives.
Molecular Design
The formation of a 2:1 sandwich-type complex of a 15-
crown-5-ether unit and potassium ions is well known,6 but the
stability constants are insufficient to permit their use in solution.
Combining two or more 15-crown-5-ether moieties in a mole-
cule allows stable complexes to be formed with potassium ions
even in solution.7 We designed bis(crown ether)-2,2¤-bibenz-
imidazole A, as shown in Figure 1. It is known that non-
substituted 2,2¤-bibenzimidazole takes a coplanar conformation
between the two benzimidazoles by intramolecular hydrogen-
1-Mono- and 1,1¤-bissubstituted compounds 6 and 7 were
prepared from 1 by addition of 2-chloro-N-alkylacetamide in
the presence of sodium hydride. Long alkyl chains, n-dodecyl
Published on the web October 31, 2013; doi:10.1246/bcsj.20130173

A. Satake et al.
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
89
Sandwich complex
Bis(crown ether)-2,2 -bibenzimidazole
H
O
O
O
O
O
N
N
N
O
H
O
O
O
O
O
O
O
O
O
N
O
K+
O
N
N
N
N
O
O
H
H
O
O
K+
O
K+
O
O
O
N
N
H
- K+
O
O
N
N
O
O
H
O
A
Coplanar
K+
K+
A dimer
Monosubstitution
R
R
O
O
O
O
N
N
N
O
O
O
O
O
O
O
O
O
N
O
O
K+
O
N
N
N
O
H
H
O
K+
O
O
K+
O
N
O
O
O
N
N
N
H
- K+
O
O
N
O
O
O
O
R
R
R
Coplanar
B dimer
B
K+
K+
R
Figure 1. Structures of bis(crown ether)-2,2¤-bibenzimidazoles A (nonsubstituted) and B (monosubstituted), and their sandwich-type
complexes with potassium ions A dimer and B dimer.
H2
(5 atm)
Pd/C
O
O
O
O
conc.HNO3
O
O
NH2
NH2
O
O
O
O
O
O
NO2
NO2
and Fuming HNO3
O
O
O
AcOH
AcOH(cat.)
EtOH
2
3
4
NH
5
O
O
O
H
1) NaH, DMF
O
O
N
N
MeO
CCl3
O
O
2) ClCH2C(O)NHR
N
N
H
O
O
conc.AcOH
then,K2CO3
O
MeOH
1
O
R
O
R
N
N
H
N
H
O
O
O
O
O
O
O
O
O
O
O
O
N
N
N
N
N
N
+
O
O
O
O
N
H
O
O
O
O
H
N
6a: R=-C12H25
6b: R= (S)-CH(CH
R
7a: R=-C12H25
O
3)C6
H5
Scheme 1.
groups, were introduced into 6a and 7a to increase their
solubility in organic media, and a chiral substituent having an
asymmetric carbon center was introduced into 6b.
Complexation of 1 and 6a. UV-vis Titration: UV-vis
titration of 1 with potassium ions was carried out in a mixture of
chloroform (CHCl3) and methanol (CH3OH) (1:1). The mixed
solvent system was required to dissolve 1 and a potassium com-
plex of 1. The resulting spectral change is shown in Figure 2a.
The peak observed initially at 359 nm was now shifted to 348
nm, and the peak at 373 nm decreased significantly. Since an
isosbestic point was observed at 352 nm, the spectral change can
be considered as equilibrium between two states.
¢
11
½1:1ꢀ complex 1 þ Kþ ꢀ 1 Kþ
ð1Þ

90
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
Bis(crown ether)-2,2¤-bibenzimidazole
Figure 3. (a) Nonsubstituted bis(crown ether)-2,2¤-bibenz-
imidazole 1, (b) monosubstituted bis(crown ether)-2,2¤-
bibenzimidazole 6a, (c) bissubstituted bis(crown ether)-
2,2¤-bibenzimidazole 7a, in the absence (solid line) and
presence (broken line) of KBF4 in chloroform/metha-
nol = 1/1.
equivalents of added KBF4. We assumed that the supramolec-
ular organization of 1 and the potassium ions was 1:1, 2:2, or
3:3. The three eqs 1-3 correspond to the equilibria of the 1:1,
2:2, and 3:3 complexes with association constant ¢nn, respec-
tively. Curve-fitting analysis of the experimental data was
carried out for various ¢nn values in the cases of the 1:1, 2:2, and
3:3 complexes. The experimental results showed a gentle S-
shape, indicating positive allosteric behavior. The curve for the
2:2 complex (solid line) is well fitted to the experimental results.
Figure 2. a) UV-vis titration of 1 (2.42 © 10¹5 M in
chloroform/methanol = 1/1, 298 K) with KBF4 (0-8
equiv), b) Job’s plot of complexation of 1 and KBF4
([1] + [KBF4] = 5.95 © 10¹5 M), c) curve-fitting analysis
of the spectral change in Figure 2a, open circle: exper-
imental results, fitting curves for 1:1 complex with ¢11
=
¹1
8.3 © 104 M
(a dash-dotted line), 2:2 complex with
This result suggests that the supramolecular 12K+ dimer is
¢
¢
22 = 1.6 © 1014
33 = 1.1 © 1024
M
M
¹3 (a plain line), and 3:3 complex with
2
formed as expected (Figure 1). From the curve-fitting analysis,
¹5
(a dotted line).
¹3
the association constant ¢22 = 1.6 © 1014
M
was obtained.
UV-vis titration of monosubstituted 6a with KBF4 was also
carried out. Similar to the case of 1, formation of a 2:2 complex
of 6a and potassium ions was suggested by curve-fitting
¢
22
½2:2ꢀ complex 2 ð1Þ þ 2 ðKþÞ ꢀ 12 Kþ
ð2Þ
ð3Þ
2
3
¢
33
½3:3ꢀ complex 3 ð1Þ þ 3 ðKþÞ ꢀ 13 Kþ
analysis, in a similar UV-vis titration. The association constant
¹3
To estimate the stoichiometry of 1 and the potassium ions,
a Job’s plot was drawn as shown in Figure 2b. Here, the total
concentration of 1 and potassium ions was 5.95 © 10¹5 M, and
the molar ratio had changed. As the peak maximum in the Job’s
plot was observed at [1]/{[1] + [KBF4]} = 0.5, the composi-
tion was determined as 1/KBF4 = 1. However, from this result,
we were unable to determine whether the supramolecular struc-
ture was 1:1, 2:2, 3:3, etc. Therefore, curve-fitting analysis was
carried out, as shown in Figure 2c. The open circles indicate
absorption change at 359 nm as a function of the number of
¢
22 = 2.0 © 1015
M
was obtained.
UV-vis spectra of three kinds of 2,2¤-bibenzimidazoles,
nonsubstituted 1, monosubstituted 6a, and bissubstituted 7a
were compared, as shown in Figure 3. UV-vis spectra of 1 and
6a gave a peak at 359 nm accompanied by two shoulders at
around 342 and 373 nm. After addition of potassium ions, the
band structures were retained, but the maximum peak was
shifted to a shorter wavelength. On the other hand, bandless
and broad spectra were obtained in the case of bissubstituted
7a. Results suggest that 7a exists as a mixture of conforma-

A. Satake et al.
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
91
Figure 4. 1H NMR (600 MHz in CDCl3:CD3OD (1:1)
at 298 K) A: 1 (4.1 mM), B: A + KBF4 (0.5 equiv),
C: A + KBF4 (0.75 equiv), D: A + KBF4 (1 equiv).
Figure 5. 1H NMR (600 MHz) spectra of 6a (14 ¯M as
a monomer) (a) in CDCl3 at 25 °C, (b) with KBF4
(ca. 17 ¯M) in CD3CN:CDCl3 (3.5:1) at ¹20 °C. Asterisks
indicate aryl protons of 2,2¤-bibenzimidazole parts.
tional isomers originating from rotation around the C-C bond
between the two benzimidazole moieties. Coplanar confor-
mation is missing due to the absence of hydrogen-bonding
interaction, and also due to steric hindrance between substitu-
ents after formation of a face-to-face complex. In a mixture of
acetonitrile/CHCl3 (3.5/1) instead of CH3OH/CHCl3 (1/1),
clearer band structures were observed in the case of 6a and a
6a/KBF4 complex, suggesting that the intramolecular hydro-
gen-bonding interaction is enhanced in an aprotic solvent
(Supporting information is provided in Figure S1.).
6a and the 6a/KBF4 complex were collected in CDCl3 and
a mixture of CD3CN:CDCl3 (3.5:1), respectively. Figure 5b
1
shows the H NMR spectrum collected at ¹20 °C. Signals in
this spectrum are slightly sharper than the signals of the
spectrum recorded at 25 °C (Figure S3). If we assume that the
spectral change due to the solvent effect between CDCl3 alone
and a mixture of CD3CN and CDCl3 in the NMR experiments
is smaller than that due to the transformation from 6a to a
6a/KBF4 complex, the structure of the 6a/KBF4 complex can
be discussed based on the spectral change. The imidazole N-H
signal at 14 ppm was significantly upfield shifted to 11.7 ppm,
and the shifted signal was sharper. Other signals of the amide
N-H (9.2 ppm) and aryl C-H (marked as asterisks) were also
upfield shifted, suggesting a ring current effect resulting from
a face-to-face dimer. Geminal methylene protons connected to
one of imidazole nitrogens were observed separately at 6.3 and
4.9 ppm. One of the geminal protons was downfield shifted,
indicating that the proton was located in a deshielded region
of an aromatic group. These sharp and well-differentiated
signals of the 6a/KBF4 complex indicated that both the 2,2¤-
bibenzimidazole moieties, and parts of the amide side chains
were fixed. Besides the above major signals, unidentified small
signals were observed at 11.2, 8.1, and 7.7-4.5 ppm. These
signals probably originated from minor conformational iso-
1H NMR Titration of Complex of 1 and KBF4. Spectra
1
of H NMR titration of 1 with KBF4 are shown in Figure 4.
A mixture of CDCl3/CD3OD (1/1) was used as solvent to
dissolve 1, and also a complex of 1 and KBF4. An imidazole
N-H proton signal disappeared by proton-deuteron exchange
in CD3OD. Upon addition of KBF4, the Ar-H signal originally
appearing at 7.1 ppm broadened and shifted upfield. The shift
ceased upon addition of 1 equiv of KBF4, indicating that the
stoichiometry of the complex is 1/KBF4 = 1 (Figure S2). This
stoichiometry is consistent with that determined by UV-vis
experiments. When 2 equiv of NaBF4 was added instead of
KBF4 under the same conditions, the Ar-H signal shifted
downfield to 7.25 ppm. Therefore, the upfield shift of the Ar-H
signal observed in the case of addition of KBF4 is not due to
the complexation of alkali metal ions with the crown ether
moieties. The shielding arising from the ring current effect
in the other 2,2¤-bibenzimidazole in a face-to-face fashion
contributes the upfield shift. This result also indicates that
the observed supramolecular structure is not a head-to-tail
polymer. Since the sharp signal (7.1 ppm) of free 2,2¤-bibenz-
imidazole 1 was broadened upon the addition of 0.5 equiv of
KBF4, ligand exchange between free 2,2¤-bibenzimidazole 1
and 1/KBF4 complex occurs at 25 °C on the NMR time scale.
Structural Analysis of Monosubstituted 2,2¤-Bibenzimi-
dazole Molecules 6a and 6b. 1H NMR spectra of mono-
substituted 6a in the absence and presence of KBF4 are shown
in Figure 5. Because there is no good solvent that dissolves
6a and the complex of 6a with KBF4, 1H NMR spectra of
1
mers. The H NMR spectrum nonetheless indicates that one of
the conformational isomers is predominantly formed. Due to
low symmetry of the monosubstituted compound 6a, various
isomers were considered in their 2:2 complexes. As illustrated
in Figure 6, anti- and syn-conformers are defined as anti and
syn relationships of the direction of the imidazole 1-H and 1¤-
substituent. When two anti-conformers form 2:2 complexes
with potassium ions, four structural isomers (AA, AB, AC, and
AD) are possible. Similarly, four other possible isomers (EE,
EF, EG, and EH) can be derived from two syn-conformers.
In addition, combination of anti- and syn-conformers gives
some different structural isomers upon 2:2 complexation with

92
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
Bis(crown ether)-2,2¤-bibenzimidazole
R
R
H
O
O
O
O
O
O
O
O
O
O
R
N
N
N
N
O
O
O
O
N
N
N
N
O
O
O
R
H
O
O
O
H
anti
H
syn
H
R
H
R
R
H
R
H
R
R
R
R
R
E
E
EE
+
A
A
A
A
+
AA
H
R
H
H
H
H
R
H
R
R
H
R
F
EF
E
E
AB
AC
AD
+
B
C
+
H
H
H
H
H
R
R
H
+
+
G
EG
+
+
H
R
H
R
H
R
R
H
R
R
H
H
H
EH
D
E
A
H
H
R
R
H
R
R
Figure 6. Possible structures of face-to-face 2:2 complexes of 6a and potassium ion. (Left hand side): combination of two anti-
components of 6a; (Right hand side): combination of two syn-components of 6a.
1
potassium ions. However, the H NMR data showed predom-
inantly one set of signals for 2,2¤-bibenzimidazole, suggesting
the formation of one symmetric isomer out of the many
possible isomers (AA-AD and EE-EH).
Referring to the assignments of free 6a, assignments and
structural analysis of the 6a/KBF4 complex were carried out by
using ROESY (Figure S11), HSQC (Figure S12), and HMBC
(Figure S13) spectra. The assignments of 1H and 13C NMR
signals and rotating Overhauser enhancement (ROE) corre-
lations are depicted in Figure 8. ROESY spectra of the 6a/
KBF4 complex differed from those of free 6a; specific ROE
correlations were observed between 6.10 and 6.83, and between
6.17 and 6.96, respectively. These two correlations are difficult
to explain intramolecularly, indicating that the corresponding
protons were closely located intermolecularly in the face-to-
face dimer. Therefore, the 6a/KBF4 complex takes one of the
structural isomers as shown in Figure 9. It corresponds to
isomer AC in Figure 6. No chemical exchange was observed
between 6.96 and 6.10, suggesting that rotation along the C-C
bond between the two benzimidazole moieties was suppressed
in the face-to-face dimer.
Monomeric compound 6a is achiral, but two of four
conformational isomers become chiral when anti-form com-
pounds of 6a produce face-to-face dimers with potassium ions.
Thus, AB and AD are chiral (C2-symmetry), while AA and AC
are achiral. When a chiral center is introduced on the substituent
group in 1-monosubstituted bis(crown ether)-2,2¤-bibenzimida-
zole, additional information is available. Compound 6b having
a chiral center on the side chain was synthesized (Scheme 1).
If AA or AC is formed from 6b as a predominant conforma-
tional isomer, only one diastereomer will be produced. On the
other hand, if AB or AD is formed from 6b as a predominant
conformational isomer, two diastereomers will be produced.
To determine the structure, assignment of all the 1H and
13C NMR signals, except the overlapping crown and dodecyl
signals, was carried out by two-dimensional NMR techniques,
such as double-quantum filtered correlation spectroscopy
(DQF-COSY), nuclear Overhauser effect correlated spectros-
copy (NOESY) (or rotating Overhauser enhancement and
exchange spectroscopy (ROESY)), heteronuclear single quan-
tum coherence (HSQC), and heteronuclear multiple-bond
connectivity (HMBC). The assignment of free 6a and nuclear
Overhauser effect (NOE) correlations are depicted in Figure 7a.
Significant NOE correlations were observed between one of the
aryl protons (7.26 ppm) and the methylene protons (5.33 ppm)
originating from the side chain, and one of the aryl protons
(7.19 ppm) and the amide N-H (9.23 ppm). Chemical exchange
between protons at 6.77 and 7.19 was observed in the NOESY
spectrum. The behavior indicates that both rotation along the C-
C bond between the two benzimidazole moieties and tautom-
erization of the benzimidazole part on the right-hand side occur.
It is noted that the anti-conformer was observed predominantly
although the chemical exchange was observed. This result
suggests that the anti-conformer is stabilized by intramolecular
hydrogen-bonding interaction (B in Figure 1).8 Based on the
assignment of aryl protons (7.26, 7.19, and 6.77 ppm), all the
aryl 1H and 13C NMR signals could be assigned by using HSQC
and HMBC data, as shown in Figure 7.

A. Satake et al.
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
93
C10H21
a)
167.29 (C)
39.68(CH2
)
O
H
5.33
N
H
H
NOE
7.19
H
9.23
H
7.26
H
H
50.07(CH2)
O
O
O
95.45
103.36
NOE
O
O
N
N
141.29
131
135
137.4
128.6
149.2
147.6
148.9
O
O
141.70
O
NOE
Chemical
148.1
N
N
O
102.93
exchange
96.05
H
14.1
O
H
7.04
H
6.77
C10H21
b)
167.29 (C)
39.68(CH
)
2
O
H
HMBC
5.33
N
H
H
7.26
H
7.19
9.23
H
H
H
50.07(CH2)
141.29
O
O
95.45
103.36
O
O
137.4
N
N
131
149.2
147.6
148.9
O
O
141.70
O
135
148.1
N
N
128.6
O
102.93
96.05
O
H
14.1
O
H
7.04
H
6.77
1
Figure 7. Assignment of H (bold numbers) and 13C (plain numbers) NMR signals of 6a in CDCl3 and correlation observed in
(a) NOESY and (b) HMBC NMR study.
C10H21
ROE
29.6
6.10
6.17
O
6.38
ROE
168.7
ROE
H
39.8
4.95
N
H
ROE
6.83
H
6.96
H
H
N
O
47.8
ROE
ROE
8.07
O
98.6
104.2
ROE
O
137.3
O
N
142.1
130.0
137.2
N
144.5
146.2
146.2
O
O
O
145.5
N
128.5
O
103.6
96.6
11.4 H
O
O
ROE
6.10
6.17
H
H
ROE
ROE
6.83
6.96
Figure 8. Assignment of 1H (bold numbers) and 13C (plain numbers) NMR signals of 6a/KBF4 complex in CDCl3:CD3CN (1:3.5)
and correlation observed in ROESY NMR study.
Therefore, if the number of diastereomers is counted for the
6b/KBF4 complex, its organized state will be distinguishable
between AA or AC, and AB or AD. 1H NMR spectra of 6b were
recorded in the absence and presence of KBF4 (Figure 10).
Similar to the 1H NMR spectral change of 6a in Figure 5,
the imidazole N-H, amide N-H, and eight aryl protons were
shifted upfield, and the methylene protons connected to one of
the imidazolyl nitrogens were split upfield and downfield. In
contrast to the 6a/KBF4 complex, two sets of signals corre-
sponding to imidazole N-H, amide N-H, diastereotopic methyl-

94
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
Bis(crown ether)-2,2¤-bibenzimidazole
ene protons (6.71 and 6.42; 5.16 and 5.02 ppm) and aryl protons
(indicated as asterisks) were observed in the 6b/KBF4 complex.
Thus, the originally identical protons in two free 6b molecules
became nonequivalent in the face-to-face dimer of 6b/KBF4.
This result indicates that only one diastereomer was formed
in the 6b/KBF4 complex, as shown in Figure 11. Although the
result indicates that the predominant dimers is either an AA or
AC form, ROE correlations observed in the two-dimensional
NMR studies for the 6a/KBF4 complex clearly showed
formation of an AC conformer. Finally, the AC isomer is the
most plausible structure for the dimeric structures of mono-
substituted bis(crown ether)-2,2¤-bibenzimidazole.
In order to consider the reason why the AC isomer was
formed predominantly among eight or more possible conforma-
tional isomers, energy minimized molecular models of AA-
EH (R = CH3) in Figure 6 were calculated using a semi-
empirical molecular orbital method under vacuum condition
(Figures S20-S22). In the case of dimers AA-AD composed
of two anti-conformers, the two 2,2¤-bibenzimidazole moieties
in each dimer were almost parallel, while they were not
parallel and twisted in dimers EE-EH composed of two syn-
conformers. The latter dimers, EE-EH, seem less stable due to
lack of coplanarity. By comparing values of heat of formation
of AA-AD, AC showed the smallest one. Two intermolecular
hydrogen-bonding interactions between the amide carbonyl
and the imidazole NH groups can be observed in this model
(Figures S20 and S22).
C10H21
O
H
N
H
H
H
H
O
O
O
O
N
N
O
O
N
N
O
O
H
O
O
H
H
ROE
H
ROE
H
O
K+
H
N
O
K+
O
O
N
O
O
N
O
N
O
O
H
O
H
H
H
N
Switching Function.
To be useful as supramolecular
H
O
components, a reversible association/dissociation function of
bis(crown ether)-2,2¤-bibenzimidazole 1 by outer stimuli is
desirable. For removing potassium ions from 1/K+ complexes,
the macrocylic ligand 18-crown-6 (18C6) was proposed as a
strong host for potassium ions to give a 1:1 complex. Because
the dimensions of the association constants of 18C6 and of 1
with the potassium ion are different (K (M¹1) = [18C6/K+]/
([18C6][K+] versus ¢22 (M¹3) = [1/K+]/([1]2[K+]2), these
values cannot be compared directly. Therefore, the equivalents
of potassium ions to give a 5:95 ratio of 18C6:18C6/K+
complexes and 1:1/K+ complexes, respectively, were calcu-
lated to carry out experiments. At the same concentration of
host molecules of 18C6 or 1 (2.0 mol L¹1), 12 equiv of potas-
sium ions are required for 1 to give a 5:95 ratio of 1:1/K+
C10H21
Figure 9.
A proposed structure of 6a/KBF4 complex
corresponding “AC” in Figure 6.
complexes on the basis of ¢22 = 1.6 © 1014
M
¹3, and 1.7 equiv
are sufficient for 18C6 to give a 5:95 ratio of 18C6:18C6/K+
¹1
on the basis of K = 1.2 © 106 M (in methanol).9 Therefore,
18C6 was expected to be a good reagent to remove potassium
ions from a [1/K+] complex.
Complexation of 1 and potassium ions was monitored
experimentally by UV-vis spectroscopy. In a cuvette (2-
mm light pathway), bis(crown ether)-2,2¤-bibenzimidazole 1
(6.94 © 10¹6 M in CH3OH/CHCl3 (1/1), 0.6 mL) was pre-
¹1
Figure 10. 1H NMR (500 MHz) spectra of 6b (ca. 17 ¯M
as a monomer) (a) in CDCl3 at 25 °C, (b) with KBF4
(ca. 20 ¯M) in CD3CN:CDCl3 (3.5:1) at 25 °C. Asterisks
indicate aryl protons of 2,2¤-bibenzimidazole parts.
pared. To the cuvette, 10 equiv of KBF4 in DMSO (0.102 M
,
10 ¯L) solution were added followed by the same amount of
18C6 in CH3OH/CHCl3 (1/1) (0.100 M¹1, 10 ¯L). At the
points of addition, the maximum wavelength of the UV-vis
(S)
Me
O
H
N
N
H
H
H
O
H
H
O
O
O
O
N
Me (S)
O
K+
O
O
O
H
N
N
O
O
N
H
H
O
O
H
H
O
O
H
H
H
H
H
H
O
non-equivalent
O
O
N
N
H
H
O
O+
K
K+
O
O
H
O
N
N
N
O
N
O
O
O
H
O
H
H
N
O
N
O
O
H
H
N
H
H
chiral
O
Me
(S)
Figure 11. Structure of 6b (left) and 6b/KBF4 complex (right), in which the two 6b moieties are nonequivalent.

A. Satake et al.
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
95
were monitored on silica gel 60 F254 TLC plates (Merck) or
aluminum oxide (Merck). The silica gel utilized for column
chromatography was purchased from Kanto Chemical Co.,
Inc.: Silica Gel 60N (Spherical, Neutral) 60-210 and 40-210
¯m (Flash). The alumina used for column chromatography was
purchased from Merck: aluminum oxide 90 (activity II).
4,5-Dinitrobenzo-15-crown-5 (3).11
To a solution of
benzo-15-crown-5 (1.0 g, 3.7 mmol) in acetic acid (4.0 mL),
nitric acid (69%, 4.0 mL) was added at 10 °C slowly. The
color turned to yellow. The mixture was stirred at rt until the
starting material disappeared. Then, the mixture was cooled to
10 °C. To the mixture, fuming nitric acid (4.0 mL) was added
dropwise. The mixture was stirred at rt. The yellow color
turned orange gradually. At this stage, mono nitro compound
was converted to dinitro compound. The mixture was poured
to ice water (40 mL), and the organic layer was extracted
with chloroform. The yellow extracts was dried over anhydrous
MgSO4, and concentrated under reduced pressure. The residue
was recrystallized from ethyl acetate to give 4,5-dinitrobenzo-
15-crown-5 (0.86 g, 66%) as yellow crystals.
4,5-Diaminobenzo-15-crown-5 (4). 4,5-Dinitrobenzo-15-
crown-5 (0.50 g, 1.4 mmol), degassed ethanol (23 mL), and
degassed acetic acid (2 mL) were placed in a 100 mL stainless
autoclave. Nitrogen gas was bubbled to the mixture for more
than 5 min to remove air. Palladium carbon (10 wt %, 71 mg,
ca. 70 ¯mol) was added to the mixture, and the mixture was
stirred under hydrogen atmosphere (1.0 MPa) at rt for 2 days.
Methanol (20 mL) was added to the autoclave. The mixture was
passed through a column packed with Celite 545μ to remove
palladium carbon by using methanol (10 mL) as an eluent. The
filtrate was diluted with methanol (95 mL). The filtrate was
directly used for the next reaction without concentration or
purification.
Bibenzimidazole-15-crown-5 (1). To the solution con-
taining 4,5-diaminobenzo-15-crown-5 prepared in the last step,
methyl 2,2,2-trichloroacetimidate (90 ¯L, 0.70 mmol) was
added. The mixture was stirred at rt shielded from light. After
9 h, K2CO3 (6.0 g) was added to the mixture. The mixture was
stirred for 11 h. The solvent was evaporated to give brown
solid. Deionized water (70 mL) was added to the solid, and the
mixture was stirred at rt for 5 h. The precipitate was filtered on
Celite 545μ, and washed with deionized water. The precipitate
was eluted with a mixture of CHCl3/MeOH (1/1). The solution
was concentrated under reduced pressure to give light brown
solid, which was passed through a short alumina column
chromatography by using a mixture of CHCl3/MeOH (10/1) as
an eluent. The fractions were concentrated, and the residue
was recrystalized from acetic acid to give 1 (104 mg, 21%) as
pale yellow crystal. HRMS (FAB) m/z ([M + Na]+) 637.2486,
calcd for C30H38N4O10Na 637.2486. 1H NMR (600 MHz,
CDCl3): ¤ 7.05 (s, 4H, Ar), 3.96 (br, 8H, crown), 3.86 (br,
8H, crown), 3.75 (br, 16H, crown); 13C NMR (150 MHz,
CDCl3): ¤ 148.19 (C), 142.92 (C), 133.03 (C), 99.26 (CH),
70.81 (CH2), 70.15 (CH2), 69.22 (CH2), 69.07 (CH2).
Figure 12. Plots of the maximum peaks in UV-vis spectra
of 1 by alternate addition of KBF4 (on) and 18-crown-6-
ether (off).
spectrum was plotted as a function of the points of addition
(Figure 12). Reversible association and dissociation was
observed in this system upon adding and removing potassium
ions. In this system, concentration of compound 1 gradually
decreased by the addition of KBF4 and 18C6 solution, and
accumulation of DMSO including in the KBF4 solution pre-
vents gradually the complexation of 1 with KBF4. Therefore,
the association process of 1 with potassium ions in Figure 12
becomes unfavorable during repetition of the association and
dissociation processes. Using other potassium ions which can
be dissolved well in methanol or acetonitrile instead of DMSO
may improve the reversible experiment.
Conclusion
A new supramolecular motif of bis(crown ether)-2,2¤-
bibenzimidazole was prepared from a combination of 2,2¤-
bibenzimidazole and 15-crown-5-ether. The alternative addi-
tion of potassium ions and 18C6 showed reversible formation
of 2:2 bis(crown ether)-2,2¤-bibenzimidazole 1/K+ complex
in a face-to-face fashion. Monosubstituted 6a also gave a 2:2
complex of 6a and potassium ions. Of eight or more possible
conformational isomers, the one having the two substituent
groups diagonally opposite each other was predominantly
formed. This feature is useful as it provides supramolecular
components that can be induced by outer stimuli.
Experimental
General Procedure. All chemicals and solvents were of
commercial reagent quality, and used without further purifi-
cation unless otherwise stated. Dry DMF (Super Dehydrated
N,N-dimethylformamide) was purchased from Wako chemical
company. Benzo-15-crown-5 (2) was prepared by according to
a literature.10
NMR spectra were recorded on JEOL ECA-600, JEOL ECP-
600, JEOL Lamda-500, JEOL AL-300, or Bruker AVANCE
400M, and chemical shifts were recorded in parts per million
(ppm) relative to tetramethylsilane. UV-vis absorption spectra
were recorded on a UV-3100PC spectrometer (Shimadzu) or a
V-650 spectrometer (JASCO). Fluorescence emission spectra
were recorded on a Hitachi F-4500 spectrometer. The fluo-
rescence intensities were normalized at the absorption of their
excitation wavelength. UV-vis λmax (log ε) values are reported
in nm. MALDI-TOF mass spectra were obtained on Bruker
autoflex II or JEOL JMS S-3000 with dithranol (Aldrich) as
the matrix. FAB mass spectra were obtained on JEOL JMS-700
MStation with m-nitrobenzyl alcohol as the matrix. Reactions
2-Chlorododecylacetamide.
Dodecylamine (0.69 g, 3.7
mmol) and ethyldiisopropylamine (0.49 g, 3.7 mmol) were dis-
solved in THF (25 mL). To the mixture, chloro acetylchloride
(0.43 g, 3.7 mmol) was added at 0 °C. The mixture was stirred
at rt for 5 h. Water (50 mL) was added to the mixture, and the

96
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
Bis(crown ether)-2,2¤-bibenzimidazole
organic layer was extracted with ethyl acetate. The organic
layer was washed with 1 M HCl solution, saturated NaHCO3
solution, and brine. The solution was dried over anhydrous
Na2SO4, and concentrated under reduced pressure to give 2-
chlorododecylacetamide (0.92 g, 37%). 1H NMR (600 MHz,
CDCl3): ¤ 6.56 (br, 1H), 4.05 (s, 2H), 3.30 (dt, 2H, J =
6.00 Hz, J = 6.30 Hz), 1.54 (m, 2H), 1.29 (m, 18H, e), 0.88
(t, 3H, J = 7.2 Hz).
Substituted Compounds 6a and 7a. To a suspension of
NaH (as 60% oil suspension, 17 mg, 0.39 mmol) in dry DMF
(2 mL), a solution of compound 1 (120 mg, 0.195 mmol) in dry
DMF (10 mL) was added. After evolution of hydrogen bubble,
a solution of 2-chlorododecylacetamide (51 mg, 0.195 mmol)
in DMF (5 mL) was added. After 20 h, a spot corresponding to
monosubstituted compound 6a became major accompanied
with spots corresponding to bissubstituted compound 7a and
starting material 1. Distilled water was added to stop the
reaction, and the mixture was concentrated to remove DMF.
Water was added to the mixture, and the organic layer was
extracted with CHCl3. The organic layer was dried over
anhydrous Na2SO4, and concentrated under reduced pressure.
The residue was purified by aluminum column chromatography
(eluent: CHCl3:MeOH = 10:1) to give 6a, (34 mg, 21%) and
7a (29 mg, 14%) as pale yellow solid.
6a: HRMS (FAB) m/z ([M + Na]+) 862.4580, calcd for
[C44H65N5O11Na]+ 862.4578. 1H NMR (600 MHz, CDCl3):
¤ 9.05 (br, 1H, NH), 7.25 (s, 1H, Ar), 7.22 (s, 1H, Ar), 7.11 (s,
1H, Ar), 6.84 (s, 1H, Ar), 5.35 (s, 2H), 4.27 (br, 2H), 4.21 (br,
2H), 4.05 (br, 4H), 3.98 (br, 4H), 3.90 (br, 4H), 3.78 (m, 16H),
3.26 (dt, 2H, J = 6.60 Hz, J = 7.50 Hz), 1.51 (m, 2H), 1.24 (m,
18H), 0.862 (m, 3H); 13C NMR (600 MHz, CDCl3): ¤ 167.19
(C, C=O), 149.25 (C), 148.95 (C), 148.11 (C), 147.55 (C),
141.63 (C), 141.17 (C), 137.36 (C), 135.14 (C), 130.90 (C),
128.50 (C), 103.35 (CH), 102.90 (CH), 95.98 (CH), 95.41
(CH), 71.37-68.95 (CH2), 50.03 (CH2), 39.60 (CH2), 31.91
(CH2), 29.71 (CH2), 29.64 (CH2), 29.62 (CH2), 29.59 (CH2),
29.34 (CH2), 29.33 (CH2), 29.17 (CH2), 27.06 (CH2), 22.69
(CH2), 14.12 (CH3).
7a: HRMS (MALDI-TOF, dithranol) m/z (M+) 1064.661,
calcd for [C58H92N6O12]+ 1064.677, ([M + Na]+) 1087.673,
calcd for [C58H92N6O12Na]+ 1087.667. 1H NMR (500 MHz,
CDCl3): ¤ 9.19 (s, 2H, NH), 7.18 (s, 2H, Ar), 7.09 (s, 2H, Ar),
5.06 (s, 4H, CH2), 4.21 (br s, 4H, crown CH2), 4.13 (br s, 4H,
crown CH2), 3.91 (br s, 8H, crown CH2), 3.72 (br s, 16H,
crown CH2), 3.18 (m, 4H, CH2), 1.46 (m, 4H, CH2), 1.20-1.15
(m, 36H), 0.80 (t, 6H, J = 7.2 Hz); 13C NMR (125 MHz,
CDCl3): ¤ 166.6 (C=O), 149.1 (C), 147.6 (C), 139.8 (C), 135.0
(C), 130.1 (C), 94.91 (Ar-CH), 70.72 (crown-CH2), 70.64
(crown-CH2), 70.12 (crown-CH2), 69.99 (crown-CH2), 69.34
(crown-CH2), 69.18 (crown-CH2), 68.94 (crown-CH2), 68.76
(crown-CH2), 49.83 (CH2), 39.25 (CH2), 31.51 (CH2), 29.32
(CH2), 29.26 (CH2), 29.22 (CH2), 29.04 (CH2), 28.95 (CH2),
28.82 (CH2), 26.68 (CH2), 22.29 (CH2), 13.71 (CH3).
stituted spot became major accompanied with bissubstituted
compound and starting material. Distilled water was added to
stop the reaction, and the mixture was concentrated to remove
DMF. Similar to the procedures of extraction and purification
of 6a, 6b (18.8 mg 24%) was obtained as pale yellow solid.
6b; [α]D ¹40° (24.5 °C, CHCl3, 9.2 © 10¹3 mol L¹1), HRMS
(MALDI-TOF, dithranol) m/z [M]+ 775.3350, calculated for
[C40H49N5O11]+ 775.3423, [M + Na]+ 798.3385, calculated
for [C40H49N5O11Na]+ 798.3320. 1H NMR (500 MHz, CDCl3):
¤ 14.04 (br, 1H), 9.97 (d, 1H, J = 6 Hz), 7.34-7.18 (5H,
m), 7.26 (s, 1H), 7.04 (s, 1H), 7.02 (s, 1H), 6.77 (s, 1H), 5.46
(d, 1H, J = 13.5 Hz), 5.17 (d, 1H, J = 13.5 Hz), 5.06 (dq, 1H,
J = 6.0 Hz, J = 7.5 Hz), 4.4-3.6 (m, 32H), 0.94-0.87 (m, 3H);
13C NMR (125 MHz, CDCl3): ¤ 166.4 (C=O), 149.1 (C), 148.8
(C), 148.0 (C), 147.9 (C), 143.2 (C), 141.5 (C), 141.3 (C), 139.5
(C), 135.2 (C), 130.9 (C), 128.6 (ph-CH), 127.2 (ph-CH), 126.2
(ph-CH), 103.1 (Ar-CH), 102.9 (Ar-CH), 96.0 (Ar-CH), 95.3
(Ar-CH), 71.0 (crown-CH2), 70.4 (crown-CH2), 70.3 (crown-
CH2), 69.5 (crown-CH2), 69.3 (crown-CH2), 69.3 (crown-CH2),
69.2 (crown-CH2), 68.2 (crown-CH2), 50.1 (CH2), 49.6 (CH),
22.4 (CH3).
6a/KBF4 Complex. Monosubstituted compound 6a (6.0
mg, 14.3 © 10¹3 mmol) was placed in a NMR tube. To the
NMR tube, CD3CN (0.35 mL) and CDCl3 (0.1 mL) was added
in a 3.5:1 ratio. To the NMR tube, a solution of KBF4 (1.0
¹1
equiv, 0.48 mol L in DMSO-d6) was added. The NMR tube
was shaken well for NMR measurements. The NMR data are
represented in Figures 7 and 8.
6b/KBF4 complex was prepared from 6b in a similar
manner to 6a/KBF4 complex. 6b/KBF4 complex: 1H NMR
(500 MHz, CD3CN: CDCl3 = 3.5/1): ¤ 11.53 (ImNH, brs, 1H),
11.45 (ImNH, brs, 1H), 8.57 (AmNH, d, J = 6.1 Hz), 8.54
(AmNH, d, J = 6.1 Hz), 7.68-7.33 (Ph, m, 10H), 7.09 (ArH, s,
1H), 7.00 (ArH, s, 1H), 6.94 (ArH, s, 1H), 6.71 (d, 1H, J =
15.9 Hz), 6.61 (ArH, s, 1H), 6.42 (d, 1H, J = 15.9 Hz), 6.33
(ArH, s, 1H), 6.24 (ArH, s, 1H), 6.10 (ArH, s, 1H), 5.79 (ArH,
s, 1H), 5.16 (d, 1H, J = 15.9 Hz), 5.02 (d, 1H, J = 15.9 Hz),
5.41-5.33 (m, 1H), 4.34-3.50 (m, 64H), 1.76-1.64 (m, 6H);
ArH HMQC correlation (1H-13C) 7.09-106.17, 6.99-98.80,
6.94-105.12, 6.61-97.75, 6.33-105.12, 6.24-96.70, 6.10-
105.12, 5.79-97.75.
UV-vis and Fluorescence Titrations. Titration experi-
ments were carried out in a quartz cell (1 cm light pass) with a
cap at 298 K. A mixture of chloroform and methanol (1:1) was
used as a solvent to dissolve both crown-ether derivatives and
their alkaline metal complex. Stock-solutions containing differ-
ent concentration of NaBF4 and KBF4 in DMSO were prepared.
Appropriated stock-solution was added to suppress increasing
the total volume in a quartz cell. Obtained data were analyzed
according to reference.13
This work was supported by KAKENHI (No. 24510140)
from the Japan Society for the Promotion of Science (JSPS).
High-performance computing resources were provided by
Tokyo University of Science.
Compound 6b. To a suspension of NaH (as 60% oil sus-
pension, 13.2 mg, 0.335 mmol) in dry DMF (5 mL), a solution
of compound 1 (60.8 mg, 0.098 mmol) in dry DMF (10 mL)
was added. After evolution of hydrogen bubbles, a solution of
(S)-N-(1-phenylethyl)chloroacetamide12 (20.8 mg, 0.106 mmol)
in DMF (5 mL) was added. After 19 h, a desired monosub-
Supporting Information
Supporting Information for this article is available. It
contains data for UV-vis spectra of 1, NMR date for 6a and

A. Satake et al.
Bull. Chem. Soc. Jpn. Vol. 87, No. 1 (2014)
97
5
a) A. Harada, M. Kamachi, Macromolecules 1990, 23,
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free of charge on the web at http://www.csj.jp/journals/bcsj/.
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