U-shaped aromatic ureadicarboxylic acids as versatile building blocks: Construction of ladder and zigzag networks and channels

Article abstract of DOI:10.1021/cg200988w

In order to examine versatility of ureadicarboxylic acids as U-shaped building blocks for crystal engineering, their crystal structures and cocrystals with pyridine derivatives were investigated. H-bonding networks created by a sequential linking of H-bon

Full text of DOI:10.1021/cg200988w

ARTICLE
pubs.acs.org/crystal
U-Shaped Aromatic Ureadicarboxylic Acids as Versatile Building
Blocks: Construction of Ladder and Zigzag Networks and Channels
Shugo Hisamatsu,† Hyuma Masu,‡ Isao Azumaya,§ Masahiro Takahashi,† Keiki Kishikawa,† and
Shigeo Kohmoto*,†
†Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho,
Inage-ku, Chiba 263-8522, Japan
‡Chemical Analysis Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
§Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
S Supporting Information
b
ABSTRACT: In order to examine versatility of ureadicarboxylic
acids as U-shaped building blocks for crystal engineering, their
crystal structures and cocrystals with pyridine derivatives were
investigated. H-bonding networks created by a sequential linking
of H-bonded carboxylic acid dimers resulted in the formation of
ladder-type networks in the crystals of N,N0-diethyl-N,N0-diphe-
nylureadicarboxylic acid (2) and N,N0-diallyl-N,N0-diphenylur-
eadicarboxylic acid (3). A zigzag type H-bonding network with
wedging of water molecules into carboxyꢀcarboxy H-bonding
was observed for N,N0-dibenzyl-N,N0-diphenylureadicarboxylic
acid (4). Cocrystals of N,N0-dimethyl-N,N0-diphenylureadicarboxylic acid (1) with 2,5-di(pyridine-4-yl)thiazolo[5,4-d]thiazole
(5) and 2 with 4,40-dipyridyl (6) afforded zigzag-type assembled structures. Two types of channel structures were created in the
cocrystals of 1 and dipyridylurea (7) by inclusion of water molecules together with either methanol or ethanol. The former afforded a
straight-type one-dimensional channel, while the latter afforded a fishnet-type two-dimensional channel.
’ INTRODUCTION
adopt two distinctive conformations, either a linear trans,trans- or
a folding cis,cis-conformation. Substitution of the hydrogen atom
to other groups at the urea nitrogen atom causes a drastic change
in the conformation of aromatic urea compounds from the linear
to the folding one (Chart 1a).11 As the intermolecular interaction
for supramolecular assembling, we chose carboxyꢀcarboxy
H-bonding.12 It can roughly be classified into two types, dimeric
and catemeric.13 It is interesting that the same building block can
take dual types of H-bonding patterns, which results in the
creation of differing H-bonding networks and polymorphs. Our
preliminary results showed that ureadicarboxylic acid 1 afforded
double catemeric H-bonding networks in its crystal structure10
(Chart 1b). Two sets of H-bonding networks were created
independently among the carboxys of the upper and among
those of the bottom of the U-shaped 1. There will be two patterns
of networks in dimeric H-bonding depending on the orientation
of ureadicarboxylic acids. The first type is the dimeric H-bonding
created among the upper carboxys and the bottom carboxys
of the neighboring ureadicarboxylic acids depicted as dimeric
type A in Chart 1c. The second type, dimeric type B, involves
H-bonding amonguppercarboxys or bottom carboxys (Chart 1d).
In the dimeric type A, utilization of one of the carboxys for
Development of simple and unique building blocks and an
appropriate choice of intermolecular interactions are essential for
the progress of crystal engineering.1 They can be utilized as key
elements to design crystal lattice structure. Metal coordination has
a strong power to regulate crystal lattices because of their rigidity
and the controllable direction of coordination. Therefore, inten-
sive studies on metalꢀorganic frameworks (MOFs) have been
carried out to design tailor-made functional materials, such as
nanoporous materials.2 Organic crystals without metal coordina-
tion lack these advantages. However, diversity of weak intermo-
lecular interactions operating in there is attractive, which generates
a variety of crystal structures including polymorphs.3 We are
interested in building blocks to create aromatic architectures with
folding,4 especially a column of zigzag-type aromatic networks5 in
a supramolecular way. Piling of aromatics can create potential
electrically conductive molecular wires.6 Among the known aro-
matic folded building blocks, ureas,7 guanidines,8 and imides,9 we
employed ureas. For this purpose we developed N,N0-dimethyl-N,
N0-diphenylureadicarboxylicacid1 and applied it to the fabrication
oftriple helicesby inclusion of dipyridylaromatic compounds.10 In
this paper, we report on further studies on the versatility of
aromatic ureadicarboxylic acids as U-shaped building blocks for
the creation of diversified aromatic architectures.
Received: July 30, 2011
It is known that conformation of arylureas has a characteristic
feature. Depending on the substituents at the nitrogen atom, they
Revised:
Published: October 24, 2011
October 22, 2011
r
2011 American Chemical Society
5387
dx.doi.org/10.1021/cg200988w Cryst. Growth Des. 2011, 11, 5387–5395
|

Crystal Growth & Design
ARTICLE
Chart 1. Conformations of Aromatic Ureadicarboxylic-Acids (a) and Their H-Bonding Networks, Catemeric (b) and Two Types
of Dimeric, Type A (c) and Type B (d)
1
H-bonding with the carbonyl of the ureylene moiety affords a
ladder-type H-bonding network. Inclusion of linear spacer mol-
ecules by pinching with two carboxys results in the formation of an
extended zigzag H-bonding network. We have chosen bipyridyl
derivatives as spacer molecules since carboxy-pyridine H-bonding
is a well-known and reliable intermolecular interaction in crystal
engineering.14 Inclusion of a fluorescent spacer is especially
interesting from the viewpoint of the construction of a fluorescent
column with tuning of fluorescent color.15 In the dimeric-type B,
inclusion of such spacer molecules by pinching gives a helical
H-bonding network which leads the formation of triple helices as
we have reported preliminarily.
purification. H and 13C NMR spectra were recorded for samples in
CDCl3 with Me4Si as an internal standard.
Synthesis. Ureadicarboxylic acid 110 and dipyridylurea 716 were pre-
pared according to the literature.
4,40-(Carbonylbis(ethylazanediyl))dibenzoic Acid (2). The
compound was prepared by saponification of 4,40-(carbonylbis-
(ethylazanediyl))dibenzoate (1H NMR (300 MHz, CDCl3) δ 7.71 (d, J =
8.7 Hz, 4H), 6.84 (d, J = 8.6 Hz, 4H), 4.32 (q, J = 7.1 Hz, 4H), 3.72 (q, J =
7.1 Hz, 4H), 1.36 (t, J = 7.1 Hz, 6H), 1.17 (t, J = 6.8 Hz, 6H)) which was
synthesized by ethylation of 4,40-(carbonylbis-(azanediyl))dibenzoate in
80% yield. To a solution of diethyl 4,40-(carbonylbis(ethylazanediyl))-
dibenzoate (133 mg, 0.32 mmol) in EtOH (10 mL) was added a solution
of KOH (108 mg, 1.9 mmol) in water (1 mL). The resulting mixture was
refluxed for 8 h. After the reaction, the solvent was evaporated and to the
residue was added water and aqueous 1 M HCl solution. The precipitate
formed was filtered off and dried to give 2 (65 mg, 57%). Mp 276ꢀ
280 °C; IR (KBr) 2971 (w), 2935 (w), 1715 (s), 1692 (s), 1589 (s), 1244
(s) cmꢀ1; 1H NMR (300 MHz, (CD3)2CO) δ 7.75 (d, J = 8.7 Hz, 4H),
’ EXPERIMENTAL SECTION
Materials and Methods. All the reagents and solvents employed
were commercially available and used as received without further
5388
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
7.04 (d, J = 8.6 Hz, 4H), 3.78 (q, J = 7.1 Hz, 4H),1.17 (t, J = 7.1 Hz, 6H);
13C NMR (125 MHz, DMSO-d6) δ 167.3, 158.8, 147.7, 130.4,
126.7, 125.3, 45.7, 13.8; HRMS (ESI), calcd for C19H19N2O5 [M ꢀ H]ꢀ
355.1299, found 355.1303.
Chart 2. N,N0-Disubstituted Aromatic Ureadicarboxylic
Acids for Crystallographic Study and Dipyridyl Derivatives
Examined for the Preparation of Cocrystals with Them
4,40-(Carbonylbis(allylazanediyl))dibenzoic Acid (3). In a
similar manner as for the synthesis of 2, saponification of the corre-
sponding diethyl ester gave 3 in a yield of 84%. Mp 272ꢀ274 °C; IR
(KBr) 3078 (w), 2983 (w), 1711 (s), 1684 (s), 1591 (s) cmꢀ1; 1H NMR
(300 MHz, (CD3)2CO) δ 7.75 (d, J = 8.4 Hz, 4H), 7.08 (d, J = 8.7 Hz,
4H), 5.99 (ddt, J = 17.3 Hz, J = 9.9 Hz, J = 6.3 Hz, 2H), 5.14 (dd, J =
1.5 Hz, J = 17.1 Hz, 2H), 5.09 (dd, J = 1.5 Hz, J = 10.2 Hz), 4.35 (d, J =
6.0 Hz, 4H); 13C NMR (125 MHz, DMSO-d6) δ 167.6, 159.1, 149.3,
147.6, 134.5, 130.3, 126.8, 125.3, 118.5, 53.2; HRMS (ESI), calcd for
C21H19N2O5 [M ꢀ H]ꢀ 379.1299, found 379.1300.
4,40-(Carbonylbis(benzylazanediyl))dibenzoic Acid (4). In
a similar manner as for the synthesis of 2, saponification of the correspond-
ing ditethyl estergave4 in a yield of 90%. Mp 225ꢀ229 °C; IR(KBr) 3248
(br. w), 3032(w), 2944 (m), 2905(m), 1689 (s), 1603 (s), 1425(m), 1280
(m) cmꢀ1; 1H NMR (300 MHz, (CD3)2CO) δ 7.63 (d, J = 8.7 Hz, 4H),
7.39ꢀ7.35 (m, 4H), 7.28ꢀ7.19 (m, 4H), 7.00 (d, J = 8.7 Hz, 4H), 4.99
(s, 4H); 13C NMR (75 MHz, DMSO-d6) δ 167.5, 160.4, 147.5, 138.5,
130.5, 129.1, 128.0, 127.0, 125.6, 53.9; HRMS(ESI), calcd for C29H25-
N2O5 [M + H]+ 481.1769, found 481.1748.
respectively) were obtained by recrystallization of 1 or 2 with the
corresponding bipyridyl derivatives (Chart 2). Their crystal data
including angles (θ) and torsion angles (j) between the planes
of two phenyl rings of aromatic ureadicarboxylic acids are
summarized in Table 1. All of them have U-shaped molecular
2,5-Di(pyridine-4-yl)thiazolo[5,4-d]thiazole (5)17. A solution
of rubeanic acid (100 mg, 0.83 mmol) and 4-pyridinecarboxaldehyde
(0.20 mL, 2.2 mmol) in anhydrous DMF (5 mL) was refluxed for 2.5 h at
153 °C. Upon cooling, the product was recrystallized out from the
resulting solution. Filtration and washing with water afforded 5 as yellow
needles (174 mg, 71%). Mp over 300 °C; IR (KBr) 3426 (s), 3038 (w),
structures with cis,cis-conformation. Cocystals 1 7 MeOH and
3 3
1 7 EtOH contained trans,cis-conformation together with cis,
3 3
cis-conformation. Conformations of their U-shaped molecular
structures are very different. The degree of distortion is ranged
with θ and j of 18ꢀ37° and 12ꢀ50°, respectively. This could be
originated in the flexible molecular structures of aromatic
ureadicarboxylic acids. The values of j are smaller than that
observed in the previously reported 1 (j = 58°), which showed a
zipper-type double catemeric network as depicted in Chart 1b.10
In contrast, ureas 2, 3, and 4 gave crystal structures based on
H-bonding of the dimeric type A as shown in Chart 1c. The
2923 (w), 2853 (w), 1591 (s), 1442 (s), 1234 (s), 815 (s), 696 (s) cmꢀ1
;
1H NMR (300 MHz, CDCl3) δ 8.79 (d, J = 6.0 Hz, 2H), 7.88 (d, J =
6.4 Hz, 4H); HRMS (ESI), calcd for C14H9N4S2 [M + H]+ 297.0263,
found 297.0261.
Recrystallization. Recrystallization was carried out at room tem-
perature by a vapor diffusion method. A vessel containing 3ꢀ10 mg of
sample dissolved in 3ꢀ6 mL of solvent was placed in a jar in which
solvent to be vaporized was added. After the sample stood for several
OꢀH OdC H-bonding between the carboxy and ureylene
3 3 3
moieties, together with this dimeric type A carboxyꢀcarboxy
H-bonding, creates ladder-type H-bonding networks in the
crystal structures of 2 and 3 (Figure 1). They have almost
identical network structures.
days, single crystals of compounds 2, 3, and 4, and cocrystals 2 6 and
3
1 7 MeOH (containing 1, 7, methanol, and water in a ratio, 2:3:4:9.5,
3
3
respectively) were obtained from methanol with diffusion of water
vapor. Single crystals of 1 5 were obtained from chloroform/ethanol
3
One of the carboxy moieties participates in the dimeric type
H-bonding with the neighboring carboxy moiety with the oxy-
genꢀoxygen atomic distance of 2.64 Å. The other carboxy moiety
interacts with the neighboring carbonyl oxygen atom of the
ureylene moiety via H-bonding with the oxygenꢀoxygen atomic
distance of 2.62 Å. Sequential interactions of these furnish a ladder-
type structure. Figure 1b,e shows the packing structures for 2 and
3, respectively, viewed from the direction of the c-axis. A gear-like
structure is created by gathering of the ladders as shown in the
space-filling models (Figure 1c,f). The cavities of the ladders
are filled with the ethyl or allyl groups of the ureylene moieties
of the neighboring ladders. It is interesting that a slight difference
in the size of the substituents at the urea nitrogen atom, either
methyl or ethyl, could change their crystal structures from the
double catemeric to the ladder structure. The oxygenꢀoxygen
atomic distances for H-bonding of the carboxylic acid dimers for 2
with diffusion of hexane vapor. Cocrystals 1 7 EtOH (containing 1, 7,
3
3
ethanol, and water in a ratio, 2:3:3:5.5, respectively) were recrystallized
from ethanol with diffusion of water vapor.
X-ray Crystallography. X-ray diffraction data for the crystals were
measured on CCD diffractometers. Data collections were carried out at
low temperature by using liquid nitrogen. All structures were solved by
direct methods SHELXS-97,18 and the non-hydrogen atoms were
refined anisotropically against F2, with full-matrix least-squares methods
SHELXL-97.18 All hydrogen atoms except that in water molecules were
positioned geometrically and refined as riding. The positions of hydro-
gen atoms in water molecules were determined based on the electron
density distribution. Other details of refinements of the crystal structures
are described in Supporting Information.
’ RESULTS AND DISCUSSION
Ureadicarboxylic acids 2, 3, and 4 (Chart 2) were prepared by
ethylation, allylation, and benzylation of 4,40-(carbonylbis-
(azanediyl))dibenzoic acid ethyl ester, respectively, followed by
hydrolysis. All of them gave single crystals suitable for crystallographic
analysis. Cocrystals 1 5, 2 6, 1 7 MeOH (containing 1, 7,
and 3 are 2.64 and 2.63 Å, respectively, and those for CdO
interaction between the carboxy moiety and the carbonyl oxygen
atom are 2.62 Å for both ureadicarboxylic acids.
H
3 3 3
A zigzag-type assembling is created in the crystal structure of
4 H2O by applying a modified H-bonding (dimeric type A).
3
3
3 3
3
methanol, and water in a ratio, 2:3:4:9.5, respectively), and
Two molecules of water are wedged into one of the dimeric type
1 7 EtOH (containing 1, 7, ethanol, and water in a ratio, 2:3:3:5.5,
H-bonding of carboxys (Figure 2a). The OꢀO atomic distances
3 3
5389
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
Table 1. Crystallographic Data for Aromatic Ureadicarboxylic Acids and Their Complexes with Pyridine Derivatives
compound
2
3
4 H2O
1 5
2 6
1 7 MeOH
1 7 EtOH
3
3
3
3
3
3 3
formula
C
19H20N2O5
C21H20N2O5
monoclinic
P21/n
C29 H27 N2 O5
monoclinic
P21/n
C31 H24 N6 O5S2
monoclinic
P21/c
C29H28N4O5
monoclinic
C2/c
C71H97N16O26.5
monoclinic
C2/c
C73H91N16O21.5
crystal system
space group
a (Å)
monoclinic
P21/n
9.5177(7)
17.235(3)
10.909(2)
90
orthorhombic
Pbca
9.4088(2)
18.474(2)
10.940(1)
90
9.9661(1)
18.3254(2)
14.3623(2)
90
8.3904(1)
15.0050(2)
22.5231(3)
90
11.842(3)
16.252(3)
14.325(4)
90
22.746(3)
31.072(4)
25.140(4)
90
25.6980(4)
19.7165(4)
30.1786(6)
90
b (Å)
c (Å)
α (°)
β (°)
γ (°)
V (Å3)
93.011(3)
90
95.535(1)
90
101.586(1)
90
96.430(1)
90
109.151(2)
90
115.475(1)
90
90
90
1787.05(5)
1.325
1892.7(4)
1.335
2569.58(5)
1.250
2817.77(6)
1.473
2604.2(11)
1.307
16041(4)
1.301
15290.7(5)
1.335
8
Dc (Mg mꢀ3
)
Z
4
4
4
4
4
8
T (K)
150
120
173
173
150
150
173
R1 [I > 2σ(I)]
wR2 [I > 2σ(I)]
angle θ (°)a
0.0377
0.0907
32
0.0375
0.0867
35
0.0415
0.1120
26
0.0492
0.1213
33
0.0465
0.1045
18
0.0668
0.1867
37
0.0630
0.1801
23
torsion angle j (°)b
46
42
50
30
41
34
12
a Angles (θ) between the planes of two phenyl rings of ureadicarboxylic acids. b Torsion angles (j) between the planes of two phenyl rings of
ureadicarboxylic acids.
for the dimeric type H-bonding of carboxys are 2.59 Å and those
between the carboxys and the wedged water molecules are 2.57
and 2.71 Å. The H-shaped packing of the three zigzag networks is
observed from the direction of [101] (Figure 2b). A similar type
of hydrate of carboxylic acid was reported in the crystal structure
of 2-chloro-4-nitrobenzoic acid.19 Tetrameric motif involving
two molecules each of 2-chloro-4-nitrobenzoic acid and water
created 2D sheet structure.
We have found that the size of the substituents at the urea
nitrogen atom is sensitive to the type of H-bonding network to be
created, the double catemeric or dimeric structure. The latter
affords the ladder or the zigzag-type folding. The results
prompted us to examine the effect of the substituent and the
spacer molecule to be pinched on the supramolecular assembly.
In order to explore further this zigzag-type assembling, we have
prepared cocrystals of 1 and 5, and also 2 and 6. Single crystal
X-ray structural analysis of these showed that the composite
ratios of ureadicarboxylic acids and dipyridyl derivatives are 1:1
for both cocrystals. Zigzag-type H-bonding networks were
formed in both cases. The H-bonding between the carboxy
and the nitrogen atom of the pyridyl works well to sandwich
dipyridyl derivatives with ureadicarboxylic acids via the dimeric
type A pattern. They did not give triple helices observed in the
cocrystals of 1 and dipyridyl derivatives (the dimeric type B
pattern).
carboxy and the pyridyl moieties is 2.66 Å. The torsion angle j in
the cocrystal 1 5 is 41°. Zigzag strands are stacked in the
3
direction of the a-axis with sliding (Figure 3b). The layer
distances between the adjacent thiazole derivative 5 is 3.67 Å
and the distance between the centroids of 1 and 5 is 3.74 Å. The
zigzag pitch, 23.1 Å, is slightly longer than that (ca. 20 Å)
observed in the cocrystals of 1 and 4,40-bipyridyl derivatives
(1:1).10 It is interesting that even the inclusion of the longer
dipyridyl derivative affects a little on the zigzag pitch. As we
referred to previously in the formation of triple helices, the zigzag
pitch should remain almost the same independent of the length
of dipyridyl derivatives employed as spacers. Since the widths of
the linear aromatic spacers are nearly the same, the zigzag with
nearly the same pitch will be generated but with different widths
of the zigzag depending on the length of the spacer molecules.
The present case is a similar situation as in the formation of triple
helices.
The crystal structure of cocrystal 2 6 afforded a zigzag-type
3
H-bonding network (Figure 4a). However, the pattern of zigzag
folding is different from that of 1 5 even though the way of
3
pinching is the same (the dimeric type A pattern). The distance
between the carboxy oxygen atom and the pyridyl nitrogen atom
is 2.67 Å. As shown in Figure 4b, a cross-patterned H-bonding
network is created, which results in the formation of a eight-
shaped-type zigzag-sequence with the zigzag pitch of 14.3 Å. The
Figure 3a shows the zigzag-type H-bonding network observed
pitch is fairly smaller than that of 1 5. We observed the formation
3
in 1 5. The OꢀN atomic distance for H-bonding between the
of a triple helix in the cocrystal 1 6.10 It is interesting that a small
3
3
5390
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
Figure 2. Crystal structures of 4 H2O. Packing diagram showing
3
(a) the zigzag-type H-bonding network and (b) the front view along
the [101] direction. Oxygen atoms of the wedged water molecules are
indicated by spheres of arbitrary size. H-bonds are indicated with blue
lines together with the OꢀO atomic distances.
H-bonding to furnish channels. The interval between the
U-shaped building blocks could be available as a vacancy for
the channel. For a candidate of the straight scaffold, we employed
bipyridylurea 7. Bipyridylureas were utilized as diverse structural
scaffolds in crystal engineering.20 It was reported that 7 could
assemble linearly in the presence of dicarboxylic acids.21 Proton-
ation of one of the pyridyl moieties of 7 by carboxylic acids
generates pyridinium which creates a H-bond with the remaining
pyridyl moiety. The sequential H-bonding affords the linear array
of 7. Carboxylates generated after protonation interacts with the
urea moiety by H-bonding resulting in the formation of channels.
Two carboxylates of the U-shaped building block connect the
two straight scaffolds.
Figure 1. Crystal structures of 2 and 3. Ladder-type H-bonding
networks of 2 (a) and 3 (d) in which H-bonds are indicated with blue
lines together with the OꢀO atomic distances. Packing diagrams of 2
(b) and 3 (e) viewing along the c-axis and side views of 2 (c) and 3 (f)
indicated by a space-filling model in which each ladder is colored
differently.
Recrystallization of 1 in the presence of 7 from methanol with
diffusion of water vapor gave solvated cocrystals 1 7 MeOH
3 3
with a large unit cell volume. Molar ratio of 1, 7, and methanol
was 2:3:4, which was also observed by 1H NMR analysis. Crystal
structure of the complex showed a channel structure in which
methanol and water molecules were included. Figure 5a shows
nanometer-size channels viewed along the c-axis in which
included methanol and water molecules are omitted for clarity.
Two conformations of 1, cis,cis- and trans,cis-confromations, exist
in the cocrystals. In Figure 5, they are colored light green (cis,cis)
and pink (trans,cis), respectively. DFT calculations (B3LYP/
6-31(G)d) of three possible conformations of 1, cis,cis-, trans,cis-,
and trans,trans-conformations, were carried out. Urea cis,cis-1 is
slightly more stable than trans,cis-1 and trans,trans-1 is least stable
one. Their relative energies are 0.90 and 1.55 kcal/mol for trans,
difference in the size of the substituent at the urea nitrogen atom,
either methyl or ethyl, causes a significant difference in the
creation of zigzag architecture. The zigzag strands are stacked
together to cover their zigzag gaps (Figure 4c,d).
In order to demonstrate the versatility of the ureadicarboxylic
acid as a potential U-shaped building block, we applied it to the
construction of channel structures. The folding shape of the
building block could be favorable to prepare space for channels.
Our design of a channel structure is as follows. The first step is the
creation of a straight scaffold arranged with hydrogen bonding
sites at a constant interval. The second step is the insertion of the
U-shaped units between the straight scaffolds by two-point
5391
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
Figure 3. Crystal structure of 1 5. (a) Zigzag-type H-bonding network. (b) Packing diagram viewed from the direction of the a-axis. (c) The layer
3
distance between the adjacent 5 and the distance between the centroids of 1 and 5.
Figure 4. Crystal structure of 2 6. (a) Supramolecularly assembled zigzag H-bonding network. (b) A cross-patterned network viewed along the c-axis.
3
Packing diagrams, (c) a side view and (d) a front view in which strands are colored bright pink and green for clarity.
cis-1 and trans,trans-1, respectively, in comparison with cis,cis-1 as
0 kcal/mol.
Pyridinium derived from the protonation of 7 by 1 creates a
linear array of 7 via H-bonding between the pyridinium and
pyridine moieties of protonated 7. Figure 5b shows the 2D
sheet generated on the ac plane by assembling of the linear
array of protonated 7. Between these arrays the carboxylates
derived from 1 possessing cis,cis-conformation are located as
binders to connect the arrays. Figure 5c,d shows the way of
H-bonding between the arrays of protonated 7 and the
carboxylate of 1 viewed from the direction of [101] and
the c-axis, respectively. The first and the third rows and also
5392
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
Figure 5. Single crystal X-ray structure of 1 7 MeOH. cis,cis- and trans,cis-conformations of 1 are indicated with light green and pink colors,
3
3
respectively. (a) The channel structure viewed along the c-axis in which methanol and water molecules included in the channels are omitted for clarity.
(b) A view along the b-axis to show the 2D sheet of 7. H-bonding networks viewed from (c) the direction of [101], (d) the c-axis, and (e) the b-axis.
H-bonds are indicated with blue lines.
the second and the fourth rows of the array of protonated 7 are
connected by the two-point-H-bonding with the carboxylates
of cis,cis-1. The layer distance between the alternate arrays is
6.6ꢀ6.7 Å, which is twice the thickness of the pyridine ring
(Figure 5e). The results indicate that efficient stacking is taking
place between the arrays. The angle θ and torsion angle
j between the planes of two phenyl rings in cis,cis-1 are 36.6
and 33.4°, respectively. The remaining fifth and sixth rows
are H-bonded with the carboxylates possessing trans,cis-
conformation.
When the solvent of recrystallization of 1 and 7 was changed
from methanol to ethanol with diffusion of water vapor, we
obtained a different type of channel structure. In a sense, a
pseudopolymorphic channel was created. In contrast to a straight
1D channel obtained from methanol with diffusion of water
vapor, an unusual fishnet-type 2D channel was furnished.
Fishnet-type 2D channels are created on the ab plane
(Figure 6c). The crossing angle of channels is about 75°. Each
sheet of 2D channels was separated by the wall of assembled
arrays of protonated 7. Figure 6d shows a schematic representa-
tion of fishnet-type 2D channels. The difference between the 1D
and the 2D channels originates in the way of H-bonding of the
carboxylate to the ureylene moiety of protonated 7. The
carboxylates pinch the neighboring two arrays of protonated
7 by H-bonding in the 2D channels while they pinch the two
alternate arrays of protonated 7 in the 1D channels (Figure 6e).
The layer distance between the two neighboring arrays of
protonated 7 in the 2D channels is 3.2ꢀ3.3 Å, which is
equivalent to the thickness of the pyridine ring. The angle
θ and torsion angle j in the cis,cis-conformation of carboxylate
1 are 23.2 and 12.1°, respectively. These values are fairly small
compared to those of other aromatic ureadicarboxylic acids.
Owing to its flexible molecular structure, 1 can adapt its
conformation to the desirable one for channels, which results
in unusual pseudopolymorphic channels.
Figure 6a,b shows packing structures of 1 7 EtOH viewed from
3 3
the direction of (a) [110] and (b) [110] in which ethanol and
water molecules included in the channels are omitted for clarity.
5393
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
’ REFERENCES
(1) (a) Wuest, J. D. Chem. Commun. 2005, 5830–5837.
(b) Reichenb€acher, K.; S€uss, H. I.; Hulliger, J. Chem. Soc. Rev. 2005,
34, 22–30.
(c) Desiraju, G. R. Angew. Chem., Int. Ed. 2007, 46, 8342–8356.
(d) Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Terraneo, G.
Angew. Chem., Int. Ed. 2008, 47, 6114–6127. (e) Custelcean, R. Chem.
Commun. 2008, 295–307. (f) Gilli, P.; Pretto, L.; Bertolasi, V.; Gilli, G.
Acc. Chem. Res. 2009, 42, 33–44. (g) Bishop, R. Acc. Chem. Res. 2009,
42, 67–78. (h) Price, S. L. Acc. Chem. Res. 2009, 42, 117–126.
(2) (a) Uemura, K.; Saito, K.; Kitagawa, S.; Kita, H. J. Am. Chem. Soc.
2006, 128, 16122–16130. (b) Kawano, M.; Kawamichi, T.; Haneda, T.;
Kojima, T.; Fujita, M. J. Am. Chem. Soc. 2007, 129, 15418–15419.
(c) Horike, S.; Bureekaew, S.; Kitagawa, S. Chem. Commun.
2008, 471–473. (d) Luo, J.; Xu, H.; Liu, Y.; Zhao, Y.; Daemaen, L. L.;
Brown, C.; Timofeeva, T. V.; Ma, S.; Zhou, H.-C. J. Am. Chem. Soc. 2008,
130, 9626–9627. (e) Furukawa, H.; Kim, J.; Ockwig, N. W.; O’Keef, M.;
Yaghi, O. M. J. Am. Chem. Soc. 2008, 130, 11650–11661. (f) Zhang, J.;
Bu, J. T.; Chen, S.; Wu, T.; Zheng, S.; Chen., Y.; Nieto, R. A.; Feng, P.;
Bu, X. Angew. Chem., Int. Ed. 2010, 49, 8876–8879.
(3) (a) Stahly, G. P. Cryst. Growth Des. 2007, 7, 1007–1062.
(b) Nangia, A. Acc. Chem. Res. 2008, 41, 595–604. (c) Kitamura, M.
CrystEngComm 2009, 11, 949–964. (d) Yu, L. Acc. Chem. Res. 2010,
43, 1257–1266. (e) Aaker€oy, C. B.; Champness, N. R.; Janiak, C.
CrystEngComm 2010, 12, 22–43. (f) Bernstein, J. Cryst. Growth Des.
2011, 11, 632–650.
(4) (a) Huc., I. Eur. J. Org. Chem. 2004, 17–29. (b) Li., Z.-T.; Hou,
J.L.; Li, C.; Yi, H.-P. Chem. Asian J. 2006, 1, 766–778. (c) Gillies, E. R.;
Deiss, F.; Staedel, C.; Schmitter, J.-M.; Huc, I. Angew. Chem., Int. Ed.
2007, 46, 4081–4084. (d) Smaldone, R. A; Moore, J. S. Chem.—Eur.
J. 2008, 14, 2650–2657. (e) Amemiya, R.; Yamaguchi, M. Org. Biomol.
Chem. 2008, 6, 26–35. (f) Saraogi, I.; Hamilton, A. D. Chem. Soc. Rev.
2009, 38, 1726–1743. (g) Juwarker, H.; Suk, J.; Jeong, K.-S. Chem. Soc.
Rev. 2009, 38, 3316–3325. (h) Sanchez-Garcia, D.; Kauffmann, B.;
Kawanami, T.; Ihara, H.; Takefuji, M.; Delville, M.-H.; Huc, I. J. Am.
Chem. Soc. 2009, 131, 8642–8648. (i) Fischer, L.; Guichard, G. Org.
Biomol. Chem. 2010, 8, 3101–3117. (j) Ni, B.-B.; Yan, Q.; Ma, Y.; Zhao,
D. Coord. Chem. Rev. 2010, 254, 954–971. (k) Zhao, X.; Li, Z.-T. Chem.
Commun. 2010, 46, 1601–1616.
Figure 6. Single crystal X-ray structure of 1 7 EtOH. cis,cis- and trans,
3
3
cis-conformations of 1 are indicated with light green and pink colors,
respectively. (a) The channel structure presented by space-filling model
viewed from the direction of (a) [110] and (b) [110] in which ethanol
and water molecules included in the channels are omitted for clarity. (c)
A view along the c-axis showing fishnet-type 2D channels created on the
ab plane in which ethanol and water molecules are colored blue.
Hydrogen atoms of water molecules are not included. (d) Schematic
representation of fishnet-type channels in a crystal. (e) The layer
structure viewed along the c-axis.
(5) Masu, H.; Kohmoto, S. Yuki Gosei Kagaku Kyokaishi 2007,
65, 139–150.
ꢀ
(6) (a) Bayard, E.; Hamel, S.; Rochefort, A. Org. Electron. 2006,
’ CONCLUSION
7, 144–154. (b) Enozawa, H.; Hasegawa, M.; Takamatsu, D.; Fukui, K.;
Iyoda, M. Org. Lett. 2006, 8, 1917–1929. (c) Zeidan, T. A.; Wang, Q.;
Fiebig, T.; Lewis, F. D. J. Am. Chem. Soc. 2007, 129, 9848–9849.
(d) Wakayama, Y.; Hayakawa, R.; Chikyow, T.; Machida, S.; Nakayama,
T.; Egger, S.; Oteyza, D. G.; Dosch, H.; Kobayashi, K. Nano Lett. 2008,
8, 3273–3277. (e) Smeu, M.; Wolkow, R. A.; Guo, H. J. Am. Chem. Soc.
2009, 131, 11019–11026. (f) Hansen, M. R.; Schnitzler, T.; Pisula, W.;
Graf, R.; M€ullen, K.; Spiess, H. W. Angew. Chem., Int. Ed. 2009,
48, 4621–4624.
(7) (a) Yamaguchi, K.; Matsumura, G.; Kagechika, H.; Azumaya, I.;
Ito, Y.; Itai, A.; Shudo, K. J. Am. Chem. Soc. 1991, 113, 5474–5475.
(b) Krebs, F. C.; Jorgensen, M. J. Org. Chem. 2002, 67, 7511–7518.
(c) Lewis, F. D.; Santos, G. B. D.; Liu, W. J. Org. Chem. 2005,
70, 2974–2979. (d) Zeidan, T. A.; Wang, Q.; Fiebig, T.; Lewis, F. D.
J. Am. Chem. Soc. 2007, 129, 9848–9849. (e) Clayden, J.; Pickworth, M.;
Jones, L. H. Chem. Commun. 2009, 547–549. (f) Kudo, M.; Hanashima,
T.; Muranaka, A.; Sato, H.; Uchiyama, M.; Azumaya, I.; Hirano, T.;
Kagechika, H.; Tanatani, A. J. Org. Chem. 2009, 74, 8154–8163. (g)
Fischer, L.; Claudon, P.; Pendem, N.; Miclet, E.; Didierjean, C.; Ennifar,
E.; Guichard, G. Angew. Chem., Int. Ed. 2010, 49, 1067–1070.
(8) Tanatani, A.; Yamaguchi, K.; Azumaya, I.; Fukutomi, R.; Shudo,
K.; Kagechika, H. J. Am. Chem. Soc. 1988, 120, 6433–6442.
Wehave demonstratedthe usefulness andversatility ofaromatic
ureadicarboxylic acids as U-shaped building blocks for crystal
engineering. Self-assembled ladder-type and zigzag-type structures
can be generated depending on the choice of the substituents on
the urea nitrogen atom. Supramolecularly assembled zigzag archi-
tectures are created in cocrystalsof them with dipyridyl derivatives.
Especially interesting is the creation of pseudopolymorphic chan-
nels by assembling with dipyridilyurea. Two types of channels,
straight-type 1D and fishnet-type 2D channels, were obtained by
inclusion of methanol and ethanol, respectively.
’ ASSOCIATED CONTENT
S
Supporting Information. The crystallographic information
b
files (CIF) and crystal data of compounds 2, 3, and 4 H2O and
cocrystals, 1 5, 2 6, 1 7 MeOH, and 1 7 EtOH. This information
is available free of charge via the Internet at http://pubs.acs.org/.
3
3
3
3 3
3 3
’ AUTHOR INFORMATION
Corresponding Author
*Phone: +81-43-290-3420. Fax: +81-290-3422. E-mail: kohmoto@
faculty.chiba-u.jp.
(9) (a) Kohmoto, S.; Ono, Y.; Masu, H.; Yamaguchi, K.; Kishikawa,
K.; Yamamoto, M. Org. Lett. 2001, 3, 4153–4155. (b) Masu, H.; Sakai,
M.; Kishikawa, K.; Yamamoto, M.; Yamaguchi, K.; Kohmoto, S. J. Org.
5394
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395

Crystal Growth & Design
ARTICLE
Chem. 2005, 70, 1423–1431. (c) Masu, H.; Mizutani, I.; Kato, T.;
Azumaya, I.; Yamaguchi, K.; Kishikawa, K.; Kohmoto, S. J. Org. Chem.
2006, 71, 8037–8044. (d) Masu, H.; Mizutami, I.; Ono, Y.; Kishikawa,
K.; Azumaya, I.; Yamaguchi, K.; Kohmoto, S. Cryst. Growth Des. 2006,
6, 2086–2091. (e) Kohmoto, S.; Takeichi, H.; Kishikawa, K.; Masu, H.;
Azumaya, I. Tetrahedron Lett. 2008, 49, 1223–1227. (f) Kohmoto, S.;
Hisamatsu, S.; Mitsuhashi, H.; Takahashi, M.; Masu, H.; Azumaya, I.;
Yamaguchi, K.; Kishikawa, K. Org. Biomol. Chem. 2010, 8, 2174–2179.
(10) Hisamatsu, S.; Masu, H.; Azumaya, I.; Takahashi, M.; Kishikawa,
K.; Kohmoto, S. Cryst. Growth Des. 2011, 11, 1453–1457.
(11) Clayden, J.; Hennecke, U.; Vincent, M. A.; Hillier, I. H.;
Helliwell, M. Phys. Chem. Chem. Phys. 2010, 12, 15065–15064.
(12) (a) Desiraju, G. R. Nature 2001, 412, 397–340. (b) Ivasenko,
O.; Perepichka, D. F. Chem. Soc. Rev. 2011, 40, 191–206.
(13) (a) Beyer, T.; Price, S. L. J. Phys. Chem. B 2000, 104, 2647–2655.
(b) Das, D.; Jett, R. K. R.; Boese, R.; Desiraju, G. R. Cryst. Growth Des.
2003, 3, 675–681. (c) Centore, R.; Tuzi, A. Cryst. Eng. 2003, 6, 87–97.
(d) Das, D.; Desiraju, R. Chem. Asian J. 2006, 1, 231–244. (e) Chen, J.;
Trout, B. L. J. Phys. Chem. B 2008, 112, 7794–7802.
(14) (a) Geib, S. J.; Vicent, C.; Fan, E.; Hamilton, A. D. Angew.
Chem., Int. Ed. Engl. 1993, 32, 119–121. (b) Du, M.; Zhang, Z.-H.; Zhao,
X.-J. Cryst. Growth Des. 2005, 5, 1199–1208. (c) MacGillivray, L. R.
J. Org. Chem. 2008, 73, 3311–3317. (d) Men, Y.-B.; Sun, J.; Huang, Z.-T.;
Zheng, Q.-Y. Angew. Chem., Int. Ed. 2009, 48, 2873–2876.
(15) (a) Mizobe, Y.; Miyata, M.; Hisaki, I.; Hasegawa, Y.; Tohnai, N.
Org. Lett. 2006, 8, 4295–4298. (b) Hong, Y.; Lam, J. W. Y.; Tang, B. Z.
Chem. Commun. 2009, 4332–4353.
(16) Weilandt, T.; Troff, R. W.; Sazell, H.; Rissanen, K.; Schalley,
C. A. Inorg. Chem. 2008, 47, 7588–7598.
(17) Knighton, R. C.; Hallett, A. J.; Kariuki, B. M.; Pope, S. J. A.
Tetrahedron Lett. 2010, 51, 5419–5422.
(18) Sheldrick, G. M. Acta Crystallogr. 2008, A64, 112–122.
(19) Aitipamula, S.; Chow, P. S.; Tan, R. B. H. CrystEngComm 2011,
13, 1037–1045.
(20) Chandran, S. K.; Nath, N. K.; Cherukuvada, S.; Nangia, A.
J. Mol. Stuct. 2010, 968, 99–107.
(21) Adarsh, N. N.; Kumar, D. K.; Dastidar, P. Tetrahedron 2007,
63, 7386–7396.
5395
dx.doi.org/10.1021/cg200988w |Cryst. Growth Des. 2011, 11, 5387–5395