Crystal structures of S-shaped phenylenediurea dibenzoic acids and their cocrystals with melamine: Unusual zigzag tape of H-bonded melamine network

Article abstract of DOI:10.1021/cg401754q

Phenylenediurea dibenzoic acid derivatives 1, 2, 3, and 5 and an amide derivative 4 were synthesized, and their molecular structures were elucidated to be an S-shape by single crystal X-ray analysis. Crystals of 1 were obtained as a DMF solvate, while those of 2 and 3 were not. Sheet and ladder structures were created in the crystal packing of 1 and 3, and 2, respectively. Unlike the para-substituted diureas 1-3 which possessed meso-conformation, the meta-substituted diurea 5 exhibited helical-conformation in its crystal structure. The way of crystal packing of 4 is analogous to that of the corresponding dicarboxylic acid derivative 2. A water cluster of a chair-shaped hexagonal array of water molecules was created in the crystal structure of 4. Diureas 1 and 2 gave cocrystals with melamine recrystallized from DMF/ethyl acetate and DMF/H₂O, respectively. Unusual zigzag tapes of a H-bonding network of melamine were created in both cocrystals. The zigzag tapes were connected with S-shaped diureas by H-bonding to furnish an interpenetrated fishnet-type crystal structure.

Full text of DOI:10.1021/cg401754q

Article
pubs.acs.org/crystal
Crystal Structures of S‑Shaped Phenylenediurea Dibenzoic Acids and
Their Cocrystals with Melamine: Unusual Zigzag Tape of H‑Bonded
Melamine Network
Shigeo Kohmoto,*,† Shingo Sekizawa,† Shugo Hisamatsu,† Hyuma Masu,†,‡ Masahiro Takahashi,†
and Keiki Kishikawa†
†Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku,
Chiba 263-8522, Japan
‡Center for Analytical Instrumentation, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
S
* Supporting Information
ABSTRACT: Phenylenediurea dibenzoic acid derivatives 1, 2, 3, and 5 and an amide derivative 4 were synthesized, and their
molecular structures were elucidated to be an S-shape by single crystal X-ray analysis. Crystals of 1 were obtained as a DMF
solvate, while those of 2 and 3 were not. Sheet and ladder structures were created in the crystal packing of 1 and 3, and 2,
respectively. Unlike the para-substituted diureas 1−3 which possessed meso-conformation, the meta-substituted diurea 5
exhibited helical-conformation in its crystal structure. The way of crystal packing of 4 is analogous to that of the corresponding
dicarboxylic acid derivative 2. A water cluster of a chair-shaped hexagonal array of water molecules was created in the crystal
structure of 4. Diureas 1 and 2 gave cocrystals with melamine recrystallized from DMF/ethyl acetate and DMF/H2O,
respectively. Unusual zigzag tapes of a H-bonding network of melamine were created in both cocrystals. The zigzag tapes were
connected with S-shaped diureas by H-bonding to furnish an interpenetrated fishnet-type crystal structure.
generation of folding structures in crystal engineering, we
prepared S-shaped phenylenediurea dibenzoic acids 1, 2, 3, and
5, and an amide derivative 4.
INTRODUCTION
■
Folding structures are commonly observed in nature, and they
play important roles in the construction of biological
architectures. To mimic these architectures, numerous folding
structures named foldamers1 have been synthesized artificially,
and their physicochemical properties have been studied.2
Among these foldamers, urea-,3 imide-,4 and guanidium-
based5 aromatic foldamers have special features. Owing to the
nature of the linkers, these aromatic foldamers possess helically
zigzag folding structures, which can create piling of aromatic
moieties to furnish columns of aromatics. We are interested in
creating such columns in a supramoleclular way. In our
previous work, we prepared U-shaped aromatic urea dicarbox-
ylic acid derivatives as building blocks and applied them to the
fabrication of cocrystals with dipyridyl derivatives as H-bonding
acceptors.6 Depending on the structures of the acceptors,
cocrystals comprising zigzag and triple helices were obtained.
To develop further these bent-type building blocks for the
Substitution with a methyl, ethyl, or propyl group at the urea
nitrogen atom ensures the U-shaped cis,cis-conformation of the
urea.7 Therefore, a combination of two U-shaped units could
afford an S-shaped structure. There are two possible ways of
folding in the S-shaped structure owing to a twisted
conformation of the ureylene linker. If the first and the second
ureylene linkers have an opposite direction of twisting, a meso-
conformer is derived. In contrast, the same direction of twisting
for both urea linkers can furnish a helical-conformer (Figure 1).
This kind of conformational diversity was previously observed
in the S-shaped aromatic foldamers with imide linkers.8 We
Received: November 22, 2013
Revised: March 13, 2014
Published: March 18, 2014
© 2014 American Chemical Society
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Figure 1. Chemical structures of the S-shaped diurea derivatives 1−5 and their two possible conformations, meso and helical.
4,4′-(((1,4-Phenylenebis(ethylazanediyl))bis(carbonyl))bis-
(ethylazanediyl))dibenzoic Acid (2). Mp > 300 °C; IR (KBr) 3422
(br. w), 2983 (m), 1719 (s), 1597 (s), 1514 (m), 1229 (m) cm−1; 1H
NMR (300 MHz, (CD3)2SO) δ 7.55 (d, J = 8.5 Hz, 4H), 6.82 (d, J =
8.5 Hz, 4H), 6.50 (s, 4H), 3.50 (q, J = 7.5 Hz, 4H), 0.97 (t, J = 7.0 Hz,
6H), 0.88 (t, J = 7.0 Hz, 6H), the peak corresponding to one of the
methylene protons of ethyl group was overlapped with the residual
water peak; HRMS (APCI) Calcd. for C30H35O6N4 [M + H]+
547.2551, found 547.2545.
consider that the S-shaped phenylenediureas can transfer their
folding nature via H-bonding with H-bonding acceptors to
afford unique folding structures similar to the creation of
folding structures by the U-shaped urea dibenzoic acids. Also,
H-bonding among the S-shaped phenylenediurea dicarboxylic
acids themselves can furnish folding structures as well. The
present S-shaped molecules can possibly transfer not only
folding but also a twisting nature to generate aromatic helical
columns.
In this paper, we report on the crystal structures of the S-
shaped phenylenediurea dibenzoic acids and application of their
unique structures to the creation of cocrystals with extra-
ordinary crystal structures. An unusual tape of H-bonded
melamine network with a zigzag structure was generated in the
cocrystals with melamine.
4,4′-(((1,4-Phenylenebis(propylazanediyl))bis(carbonyl))bis-
(propylazanediyl))dibenzoic Acid (3). Mp >300 °C; IR (KBr) 3438
(br. w), 2967 (w), 1721 (m), 1601 (s), 1512 (m), 1400 (m), 1235 (m)
1
cm−1; H NMR (300 MHz, (CD3)2SO) δ 7.52 (d, J = 8.6 Hz, 4H),
6.78 (d, J = 8.6 Hz, 4H), 6.48 (s, 4H), 1.40 (sextet, J = 7.4 Hz, 4H),
1.22 (sixt, J = 7.4 Hz, 4H), 0.77 (t, J = 7.2 Hz, 6H), 0.76 (t, J = 7.2 Hz,
6H); one of the triplet methylene peak of propyl group was
overlapped with the residual water peak; 13C NMR (75 MHz,
(CD3)2SO) δ 166.8, 158.5, 147.8, 139.1, 129.6, 126.1, 125.6, 124.1,
51.8, 51.6, 21.1, 20.4, 11.2, 11.1; HRMS (APCI) Calcd. for
C34H43O6N4 [M + H]+ 603.3177, found 603.3172.
EXPERIMENTAL SECTION
■
Materials and Methods. All the reagents and solvents employed
4,4′-(((1,4-Phenylenebis(ethylazanediyl))bis(carbonyl))bis-
(ethylazanediyl))bis(N-methylbenzamide) (4). Phenylenediurea 2
(0.100 g, 0.18 mmol) was dissolved in a mixed solution of DMF (2
mL) and 40% aqueous methylamine solution (0.09 mL, 1.10 mmol).
To this solultion, DMT-MM (4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-
methylmorpholinium chloride, 0.122 g, 0.44 mmol) was added, and
the resulting solution was stirred for 24 h at room temperature. The
reaction was quenched by the addition of water to give a precipitate.
Filtration gave 4 (0.105 mg, 100%) as a pure form. Mp 248−252 °C;
were commercially available and used as received without further
1
purification. H and 13C NMR spectra were recorded for samples in
CDCl3 with Me4Si as an internal standard.
Synthesis. Synthesis of S-shaped diureas 1−3 was carried out in
the following way. Reaction of ethyl 4-aminobenzoate (1.20 g, 7.2
mmol) and 1,4-diisocyanatobenzene (0.48 g, 3.0 mmol) was carried
out in DMF (10 mL) with triethylamine (2.1 mL) at 90 °C for 24 h.
The reaction was quenched by the addition of aqueous 1 M HCl
solution. The resulting precipitate was filtered, washed with water, and
dried to give a diurea derivative (1.18 g, 80%). In the case of 5, 3-
aminobenzoate was reacted with 1,3-diisocyanatobenzene in a similar
manner as for the synthesis of 1−3 to give the corresponding diurea
(89%). The diureas were converted to the corresponding N-alkylated
derivatives by the reactions with alkyl halides. For example,
methylation for the synthesis of 1 was carried out with methyl iodide
(1.2 mL, 19.2 mmol) in dichloromethane (20 mL) with sodium
hydride (0.74 g, 19.2 mmol) at 0 °C for 24 h. After evaporation of the
solvent, the residue was extracted with ethyl acetate and purified with
column chromatography on silica gel to give an N-methylated diurea
derivative (0.54 g, 41%). Saponification of the N-methylated disurea
derivative (0.71 g, 13.0 mmol) was carried out in aqueous ethanol
solution (30 mL) with potassium hydroxide (0.59 g, 10.4 mmol) for
24 h under reflux. The resulting mixture was neutralized with aqueous
1 M HCl solution. The resulting precipitate was filtered and dried to
give 1 (0.64 g) in a yield of 85%.
1
IR (KBr); 2975 (w), 635 (s), 1606 (m), 1510 (m) cm−1; H NMR
(300 MHz, CDCl3) δ 7.45 (d, J = 8.7 Hz, 4H), 6.78 (d, J = 8.7 Hz,
4H), 6.46 (s, 4H), 6.33 (br. q, J = 4.8 Hz, 2H), 3.63 (q, J = 7.2 Hz,
4H), 3.49 (q, J = 7.2 Hz, 4H), 2.97 (d, J = 4.8 Hz, 6H), 1.12 (t, J = 7.2
Hz, 6H), 0.98 (t, J = 7.2 Hz, 6H); 13C NMR (75 MHz, CDCl3) δ
159.8, 157.6, 146.9, 140.2, 130.9, 127.6, 126.9, 126.0, 46.3, 46.1, 26.9,
13.7, 13.2; HRMS (ESI) Calcd. for C32H41O4N6 [M + H]+ 573.3184,
found 573.3177.
3,3′-(((1,3-Phenylenebis(methylazanediyl))bis(carbonyl))bis-
(methylazanediyl))dibenzoic Acid (5). Mp 284−288 °C; IR (KBr)
1
2930 (s), 1695 (s), 1660 (s), 1595 (s), 1585 (s), 1490 (m) cm−1; H
NMR (300 MHz, (CD3)2SO) δ 7.46 (d, J = 7.8 Hz, 2H), 7.29 (s, 2H),
7.18 (t, J = 7.8 Hz, 2H), 7.08 (d, J = 8.6 Hz, 2H), 6.80 (t, J = 7.8 Hz,
1H), 6.44 (dd, J = 8.0, 1.8 Hz, 2H), 6.23 (s, 1H), 3.03 (s, 6H), 2.93 (s,
6H); HRMS (ESI) Calcd. For C26H27O6N4 [M + H]+ 491.1925, found
491.1930.
Crystallization Procedure. Single crystals for X-ray analysis were
obtained by recrystallization at room temperature with a vapor
diffusion method after a sample stood for several days. The vessel
containing a sample (3−10 mg) dissolved in a good solvent (3−6 mL)
was placed in a jar in which a poor solvent to be vaporized was added.
The following combination of solvents (good solvent/poor solvent)
was employed: DMF/H2O for 1 and 3, DMF/CH3OH for 2,
CH3CN/H2O for 4, and CH3OH/H2O for 5. Approximately 30−50%
of single crystals were obtained. In a similar way, cocrystals of 1 and 2
4,4′-(((1,4-Phenylenebis(methylazanediyl))bis(carbonyl))bis-
(methylazanediyl))dibenzoic Acid (1). Mp > 300 °C; IR (KBr) 3420
(br. m), 2930 (m), 1710 (s), 1600 (s), 1515 (m), 1372 (m), 1250 (m)
1
cm−1; H NMR (300 MHz, (CD3)2SO) δ 7.70 (d, J = 8.7 Hz, 4H),
7.01 (d, J = 8.7 Hz, 4H), 6.83 (s, 4H), 3.09 (s, 6H), 2.88 (s, 6H); 13C
NMR (75 MHz) δ 166.9, 159.0, 148.6, 141.2, 130.0, 124.9, 124.7,
121.1, 38.4, 37.2; HRMS (APCI) Calcd. for C26H27O6N4 [M + H]+
491.1925, found 491.1915.
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Table 1. Crystallographic Data for Phenylenediurea Dibenzoic Acids 1, 2, 3, and 5, Amide 4, and Cocrystals of 1 and 2 with
Melamine
compound
formula
1·(DMF)2
2
3
4·(H2O)6
5
a
C32H40N6O8
triclinic
C30H34N4O6
monoclinic
P21/n
C34H42N4O6
monoclinic
P21/c
C32H40N6O10
monoclinic
P21/c
C26H26H4O6
triclinic
crystal system
space group
a (Å)
P1
P1
̅
̅
6.638(11)
11.0651(13)
12.2752(14)
11.2974(13)
90.00
7.9720(6)
14.4455(11)
13.8272(10)
90.00
12.539(2)
13.016(2)
12.101(2)
90.00
7.089(3)
10.960(4)
16.368(6)
87.243(5)
88.814(5)
74.4450(4)
1223.7(7)
1.331
b (Å)
8.963(14)
c (Å)
14.27(2)
α (°)
β (°)
γ (°)
V (Å3)
95.39(2)
95.30(2)
116.2630(10)
90.00
96.5010(10)
90.00
115.409(2)
90.00
101.83(2)
822(2)
1376.1(3)
1.319
1582.1(2)
1.265
1783.9(5)
1.245
Dc (Mg m−3
)
1.286
Z
1
2
2
2
2
T (K)
173
173
173
173
173
R1, [I > 2σ(I)]
wR2 [I > 2σ(I)]
0.0619
0.0458
0.0439
0.0491
0.0642
0.1375
0.1036
0.1097
0.1535
0.1646
1·(melamine)2·ethyl acetate·DMF
2·(melamine)2·(DMF)2
C39H53N17O9
monoclinic
C2/c
C42H60N18O8
monoclinic
C2/c
32.338(2)
8.9444(6)
18.5257(13)
90.00
32.348(3)
9.4691(7)
18.4136(14)
90.00
120.9760(10)
90.00
121.8120(10)
90.00
4594.3(6)
1.307
4792.9(6)
1.310
4
4
173
173
0.0492
0.0586
0.1380
0.1940
a
Hydrogen atoms of water molecules are not included.
with melamine were obtained from DMF/ethyl acetate and DMF/
H2O, respectively.
Carboxylic acids are known to form solvates with DMF via H-
bonding. Eighty examples of such DMF solvates of non-
organometallic compounds are recorded in the CSD (Cam-
bridge Structural Database, Ver. 5.34). A majority of them (55
examples) involve H-bonding (O−H···O and CO···H−C)
between the carboxy and the formyl groups.11 Thirty-five of
them include the O−H···O hydrogen bonding as the sole
interaction observed between the carboxy and the formyl
group.12 In some cases (10 examples), one formyl group
interacts with two carboxy groups.13 Figure 2a,b shows the
molecular structure of 1, front and top views, respectively. The
molecule has an S-shaped structure with meso conformation.
The molecule of 1 is located on a center of inversion.
Therefore, a torsion angle of 38.06(17)° between the
phenylene and phenyl rings is accompanied by −38.06(17)°
(Figure 2a). The distance between the centroids of the adjacent
phenylene and phenyl rings is 3.618(6) Å. This indicates that
these two rings are overlapped closely. Figure 2c shows a sheet-
like structure created by the array of 1 and DMF. The formyl
group of DMF interacts with the carboxy group by H-bonding
with the oxygen−oxygen atomic distance of 2.614(5) Å and H-
bonding (CH···O) with the carbon−oxygen atomic distance of
3.183(7) Å. A DMF molecule is associated at both tails of 1.
The resulting S-shaped 1·(DMF)2 units interact with each
other by H-bonding (CH···O) between the urea carbonyl and
the neighboring hydrogen atom of the phenylene moiety with a
X-ray Crystallographic Analysis. Single crystal X-ray diffraction
data of the crystals were collected on a CCD diffractometer with
graphite monochromated Mo Kα (λ = 0.71073 Å) radiation. The
crystal structure was solved by direct methods SHELXS-97 and refined
by full-matrix least-squares SHELXL-97.9 All non-hydrogen atoms
were refined anisotropically. Positions of hydrogen atoms except those
included in water molecules in the cocrystal of 1 with melamine were
calculated with constraints based on geometrical adequacy by “HFIX”
of SHELXL program. The geometrical parameters of intermolecular
hydrogen bonds in the crystals (Tables S1−S7, Supporting
Information) are calculated by PLATON program.10
RESULTS AND DISCUSSION
■
The S-shaped phenylenediurea dibenzoic acids 1−3 are
insoluble in most of organic solvents except DMF and
1
DMSO. The H NMR analysis of the solvated cocrystal of 1
showed that it consisted of 1, melamine, ethyl acetate, and
DMF in a ratio of 1:2:1:1. The optimized results from X-ray
analysis were obtained with this composite ratio: 1·
(melamine)2·ethyl acetate·DMF. The cocrystal of 2 with
melamine was obtained as a DMF solvate, 2·(melamine)2·
(DMF)2. The same composite ratio was confirmed by 1H NMR
analysis. Their crystal data are summarized in Table 1.
Single crystal X-ray analysis of 1 showed that the crystal
contained DMF molecule in a molar ratio 1:2 (1/DMF).
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Figure 3. Crystal structure of 2. (a) Arrays of ladders in which H-
bonding is indicated by blue dotted lines. (b) Schematic
representation of the packing of ladders. Ladders of the same
orientation are colored the same. (c) Front and (d) side views of the
packing of ethyl groups in the cavity of the ladder. Ethyl groups to be
packed in the cavity are presented by a space-filling model, and the
molecules bearing these ethyl groups are colored green.
ladders is schematically represented in Figure 3b in which
ladders of the same orientation are colored the same. The
reason the single crystal of 2 does not contain DMF molecules
is because of the size of the N-substituent. The size of the ethyl
group can just fit into the cavity of the ladder. This is shown in
Figure 3c,d in which ethyl groups to be packed in the cavity are
presented by a space-filling model, and the molecules bearing
these ethyl groups are colored green. It is interesting that just a
small difference in the size of N-substituent can bring about a
large difference in the crystal packing.
The molecular structure of 3 elucidated by single crystal X-
ray analysis was similar to those of 1 and 2 with meso-
conformation but with a smaller torsion angle, 26.85(7)°,
between its phenylene and phenyl rings. A network of the S-
shaped molecules is created by H-bonding between the urea
carbonyl and the adjacent hydroxy group with the oxygen−
oxygen atomic distance of 2.6590(13) Å. A sheet-like structure
is created (Figure 4a). Figure 4b shows multiple H-bonding
(CH···O) among the sheets. They are indicated by blue dotted
lines. The interactions take place between the urea carbonyl
oxygen atom and the two adjacent hydrogen atoms of the
phenyl moieties and between the hydroxy oxygen atom of the
carboxy group and the adjacent hydrogen atom of the
phenylene moiety. The carbon−oxygen atomic distances for
the former two and the latter are 3.2661(15) and 3.3341(16) Å,
and 3.3517(16) Å, respectively.
Since the para-substituted diureas 1−3 afforded meso-
conformation in their crystal structures, we prepared the
meta-substituted diurea 5 to examine the effect of substitution
pattern on the conformation of the S-shaped diurea. Some
reports showed the creation of helical-conformation derived
from meta-substituted oligoureas.14 The molecular shape of 5
was found to be helical with torsion angles of 48.5(2) and
50.1(2)° between the phenylene and phenyl rings (Figure
5a,b). The distances between the centroids of the phenylene
and phenyl rings are 3.795(2) and 3.849(2) Å. The molecule
has a well-stacked S-shaped conformation. The S-shaped
molecules pile up to create helical columns (Figure 5c). Within
Figure 2. Crystal structure of 1·(DMF)2. (a) Front and (b) top views
of the molecular structure of 1. (c) A sheet-like structure created by
the array of 1 and DMF. (d) H-bonding between the sheets indicated
by blue dotted lines.
carbon−oxygen atomic distance of 3.356(6) Å and the carbonyl
of the carboxylic acid and one of the methyl hydrogen atoms of
DMF with the carbon−oxygen atomic distance of 3.443(7) Å.
Accordingly, a sheet-like structure is furnished. Figure 2d
exhibits intermolecular interactions between the sheets. H-
bonding (CH···O) exists between the urea carbonyl and one of
the hydrogen atoms of the phenylene moiety in the adjacent
sheet with a carbon−oxygen atomic distance of 3.340(6) Å.
Unlike urea 1, single crystals of 2 did not contain DMF
molecules. Figure 3 shows its crystal structure. The molecule
has an S-shaped structure with meso-conformation which is
almost identical to that of 1. The torsion angle between the
phenylene and phenyl rings is 36.35(10)°. These agree with
those of 1. Even though the molecular shape is almost the
same, its packing structure is rather different from that of 1.
Assembling 2 via H-bonding between the carboxy and the urea
carbonyl (the oxygen−oxygen atomic distance of 2.626(2) Å)
created a ladder structure. There are two orientations of
ladders. Each neighboring ladder is rotated 90°. The piling of
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Figure 4. Crystal structure of 3. (a) A sheet-like structure viewed along
the crystallographic c-axis. (b) Intermolecular H-bonding (CH···O)
between the sheets viewed along the crystallographic b-axis indicated
by blue dotted lines.
the column, helicities of the piling molecules are the same. The
columns of the opposite helicity are arranged alternately. The
distance between the centroids of the phenyl rings of two
adjacent molecules is 4.106(3) Å. One of the carboxy groups of
5 is involved in the formation of an H-bonded dimer of
carboxylic acid and the other interacts with the urea oxygen
atom via H-bonding (CH···O). It is obvious that the
substitution pattern of the phenylene ring is the key to
differentiate the conformation of the S-shaped diurea
molecules.
To develop analogous S-shaped molecules with H-bonding
sites at their molecular termini, we prepared amide derivative 4
whose single crystals were obtained as hydrates 4·(H2O)6
recrystallized from acetonitrile/H2O. It has an S-shaped
meso-conformation similar to that of the corresponding
dicarboxylic acid 2. Torsion angles between the phenylene
and phenyl rings are almost identical to those of 2. Six water
molecules are associated per a molecule of 4 as a water cluster
of cyclic hexamer.15 Figure 6a shows its packing structure. The
generated cyclic water hexamer possesses a chair-shaped
conformation. The water molecules are H-bonded with the
neighboring carbonyl oxygen and amide hydrogen atoms
(Figure 6b). The way of its crystal packing is almost identical
to that of 2 except the involvement of water clusters. A ladder-
like structure is created, and the ethyl groups are located in its
cavity.
Figure 5. Crystal structure of 5. (a) Front and (b) top views of the
molecular structure of 5. (c) Intermolecular H-bonding (blue dotted
lines) between the stacked helical columns. Numbers in the figure
indicate the distance between the centroids of the adjacent phenylene
and phenyl rings and between those of the phenyl and phenyl rings in
Å.
Out of these hetero aromatics, melamine afforded cocrystals
with 1 and 2. Cocrystals were obtained by recrystallization from
DMF with dispersion of ethyl acetate vapor for 1 and water
vapor for 2, respectively. The X-ray structure of the cocrystal of
1 was solved as an ethyl acetate/DMF solvate with the molar
ratio 1/melamine/ethyl acetate/DMF as 1:2:1:1. For this
cocrystal, solvated ethyl acetate and DMF molecules occupied
the same (overlapped) location in the asymmetric unit of the
crystal (Figures S6 and S9a in Supporting Information). The
atoms of the molecules were disordered considerably. To refine
the disordered structure, restraints on displacement parameters
were used. The anisotropic displacement parameters of the
atoms were fitted into acceptable values by the DELU and
SIMU restraints in the SHELEXL-97 program. The molecule of
1 is located on the inversion center, and there is no molecular
species on the 2-fold rotation axis. An urea/melamine/DMF
ratio of 1:2:2 was found for the cocrystal of 2 with inclusion of
DMF molecules. Solvated DMF molecules were located in
almost the same manner as in the cocrystal of 1 (Figure S9b in
Supporting Information). The S-shaped molecular structures of
diureas 1 and 2 in the cocrystals are almost identical to those
found in their own crystal structures. The torsion angles
between the phenylene and phenyl rings in the cocrystals are
38.07(11)° and 40.70(11)° for 1 and 2, respectively. Figure
It is well-known that carboxylic acids gave cocrystals with
hetero aromatics containing nitrogen atoms as H-bonding
acceptors.16 Combination of dicarboxylic acids with those
hetero aromatics possessing two H-bonding sites can create
infinite H-bonding networks.17 We have investigated the
cocrystallization of our S-shaped phenylenediurea dibenzoic
acids with bipyridyl, 2-aminopyrimidine, and melamine. These
bases are known to afford cocrystals with carboxylic acids.18
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S10 in Supporting Information). Owing to its structure, a
melamine molecule can create three cyclic H-bonding motifs,
19
2
graph set R2 (8). In the cocrystals, two of them are utilized
for H-bonding between the neighboring melamine molecules,
and the rest is provided for H-bonding between the adjacent
carboxy group. Two molecules of melamine are H-bonded
planarly to create a cyclic dimer. There is no torsion between
the two H-bonds in this cyclic dimer. The planarly cyclic dimers
of melamine are alternately arranged via H-bonding in an
orthogonal way to create a zigzag tape of H-bonded melamine
network. The angle between them is 98°. A similar angle (96°)
is observed for the cocrystal of 2. This is an unusual angle for
the H-bonding network of melamine in the crystal structures of
cocrystals, salts, and metal complexes involving melamine. The
carboxylic functions of 1 and 2 are H-bonded via the cyclic
motif with the remaining H-bonding sites of melamine. Thus,
zigzag tapes of melamine molecules are bridged with the S-
shaped phenylenediureas 1 and 2 affording fishnet-type
structures. Figure 8a shows a portion of the fishnet for the
Figure 6. Crystal structure of 4. (a) Ladder-like packing structure
including cyclic water hexamers. Water oxygen atoms are indicated by
spheres of an arbitrary size colored blue. (b) A schematic
representation of the chair-shaped cyclic water hexamer H-bonded
with surrounding carbonyl oxygen and amide hydrogen atoms. The
positions of hydrogen atoms included in the water molecules were not
calculated.
7a,b shows H-bonding between 1 and melamine and the zigzag
tape of melamine, respectively. An almost identical H-bonding
pattern to that of 1 was observed for the cocrystal of 2 (Figure
Figure 8. Crystal structures of 1·(melamine)2·ethyl acetate·DMF. (a)
H-bonding network and (b) an interpenetrating fishnet structure
presented by a space-filling model viewed along the crystallographic b
and a axes, respectively. For clarity, solvated ethyl acetate and DMF
molecules are omitted. H-bonding is indicated by blue dotted lines.
cocrystal of 1 in which H-bonding is indicated by blue dotted
lines. Fishnets are interpenetrated with each other because of
the large cavity size to create a 3D structure of the cocrystal
(Figure 8b).
To demonstrate the unusualness of the H-bonded network
structure of melamine found in the cocrystal, we searched the
patterns of H-bonded infinite melamine networks on CSD
(Ver. 5.34). The following five patterns of H-bonded melamine
networks were found in the cocrystals, salts, and metal
complexes involving melamine (Figure 9). In most cases of
cocrystals of melamine with acids, melamine was protonated by
acids and it was found as melaminium in cocrystals. Types A−C
Figure 7. H-bonding interactions (blue dotted lines) found in
cocrystals of 1 with melamine. (a) H-bonding between 1 and
melamine dimer. (b) H-bonding network of melamine. H-bonding
distances, a, 3.008(2); b, 2.864(2); c, 2.946(2); d, 2.872(3); e,
2.580(2); f, 3.014(2) Å.
2
are the H-bonding motifs with graph set R2 (8). Among these,
the examples of type C were very limited.20 In type B, an
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Figure 9. Five types of H-bonding networks of melamine and melaminium found in the cocrystals, salts, and metal complexes involving it. For types
A−D, a melamine model is presented as a representative one. Only melaminium was involved in type E.
Figure 10. CSD database search for the H-bonded network of melamine and melaminium found in the cocrystals, salts, and metal complexes
involving them. (a) A histogram of the number of structures in type A as a function of the AB angle. (b) The relation between angles AB and BA′ in
type B network in which the plots with the black circles indicate the present results of the cocrystals of 1 and 2 with melamine. Angles AB and BA′
are defined as the angles created by the two melamine ring planes between A and B, and B and A′, respectively.
interesting melamine sheet structure was created in which six
molecules of melamine were assembled in a cyclic way to give a
hexagonal unit.21 Several types of infinite H-bonding networks
including types B and C were found in the crystal structure of
melamine itself.22 Other than types A−C, only a few examples
showed type D23 and E24 H-bonding networks in which H-
Figure 10a shows a histogram of the number of structures in
type A as a function of the AB angle. The plots of angle BA′
against angle AB for type B pattern are presented in Figure 10b.
Both angles are rather small with a maximum value of 6°. Out
of 34 examples belonging to type B network, 16 examples show
0° for both angles. This does not necessarily mean that all
melamine molecules are on the same plane. In most cases, they
are on parallel planes. However, the distance between the
parallel planes is rather small. Most of them are less than 0.3 Å.
Therefore, the type B network has a flat tape structure in
general. In contrast to this characteristic feature of type B
network, our case is exceptional. The H-bonding networks of
the cocrystals of 1 and 2 with melamine belong to type B.
Angles BA′ in the cocrystals of 1 and 2 are 98 and 96°,
respectively. They are indicated by the black circles in Figure
10b. These values are exceptionally large compared with the
2
bonded melamine dimers (graph set R2 (8)) were arranged
3
orthogonally with graph sets D and R2 (8), respectively.
Evaluation of the H-bonding pattern of melamine (melami-
nium) in types A and B, the major patterns observed, was
achieved based on the angles created by the two melamine ring
planes between A and B (angle AB), and B and A′ (angle BA′).
For type A, 35 examples were found in the database. Most of
them have the same angle for AB and BA′. It ranges from 0 to
48°. It means that the networks undulate because of the
alternation of the opposite inclination of melamine ring planes.
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other examples (≤6°). The angles, AB and BA′, found in the
crystal structure of melamine itself for type B are 0°. All
melamine molecules are located on parallel planes in this H-
bonding network. The distances of 1.4 and 0.7 Å were observed
between the planes where the rings A and B, and A and B′ are
located, respectively. This kind of zigzag tape of the H-bonding
network of melamine observed in our cocrystals is
unprecedented.
CONCLUSION
■
By linking two units of U-shaped urea linkers, we prepared S-
shaped phenylenediurea dibenzoic acids. Their crystal
structures were elucidated by single crystal X-ray crystallo-
graphic analysis to possess meso-conformation. While N-methyl
and propyl derivatives, 1 and 3, provided sheet-like packing
structures, the N-ethyl derivative 2 afforded a ladder type
network. Phenylenediureas 1 and 2 afforded cocrystals with
melamine. An unprecedented zigzag H-bonded melamine
network is created in the cocrystals. The way of H-bonding is
very different from the known melamine H-bonded networks.
This uniqueness could be derived from the unique shape of the
phenylenediureas. The directions of H-bonding to be created
by two carboxylic functions of the S-shaped phenylendiureas
are opposite, but they are not on the same plane. They are
placed on approximately parallel planes whose distance is
almost equivalent to the molecular distance of H-bonded
melamine dimer. This could force to arrange melamine dimers
in the unprecedented zigzag H-bonded network. This idea can
possibly be applied to other H-bonded networks. The
directions of H-bonding can be adjusted by the substitution
pattern of phenylendiureas. Meta-substitued 5 afforded helical
conformation. Diurea 4 possessing amide groups as H-bonding
sites can also generate a similar H-bonding network.
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ASSOCIATED CONTENT
* Supporting Information
■
S
Tables of distances and angles of intermolecular hydrogen
bonds, ORTEP diagrams, X-ray crystallographic information
files (CIF) of compounds 1, 2, 3, 4, and 5 and cocrystals of 1
and 2 with melamine, and figures of the packing structures of
cocrystals of 1 and 2 with melamine and H-bonding
interactions in cocrystals of 2 with melamine are available
free of charge via the Internet at http://pubs.acs.org.
(8) Kohmoto, S.; Takeichi, H.; Kishikawa, K.; Masu, H.; Azumaya, I.
Tetrahedron Lett. 2008, 49, 1223−1227.
(9) A short history of SHELX. Sheldrick, G. M. Acta Crystallogr.
2008, A64, 112−122.
(10) Spek, A. L. J. Appl. Crystallogr. 2003, 36, 7−13.
(11) (a) Weber, E.; Hecker, M.; Koepp, E.; Orlia, W.; Czugler, M.;
Csoregh, I. J. Chem. Soc., Perkin Trans. 2 1988, 1251−1257.
̈
(b) Schleuss, T. W.; Abbel, R.; Gross, M.; Schollmeyer, D.; Frey,
H.; Maskos, M.; Berger, R.; Kilbinger, A. F. M. Angew. Chem., Int. Ed.
2006, 45, 2969−2975. (c) Jakobsen, S.; Wragg, D. S.; Lillerud, K. P.
Acta Crystallogr. 2010, E66, o2209. (d) Atkinson, M. B. J.; Halasz, I.;
AUTHOR INFORMATION
Corresponding Author
*E-mail: kohmoto@faculty.chiba-u.jp. Tel: +81-43-290-3420.
■
̌
Bucar, D.-K.; Dinnebier, R. E.; Mariappan, S. V. S.; Sokolov, A. N.;
Notes
MacGillivray, L. R. Chem. Commun. 2011, 47, 236−238. (e) Seetha-
Lekshmi, S.; Row, T. N. G. Cryst. Growth Des. 2012, 12, 4283−4289.
(12) (a) Ling, C.-S.; Wang, X.; Liu, Y.; Wu, Q. Acta Crystallogr. 2009,
E65, o2975. (b) Long, S.; Li, T. Cryst. Growth Des. 2010, 10, 2465−
2469.
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This research is supported in part by a Grant-in-Aid for
Scientific Research from Japan Society for the Promotion of
Science (JSPS) (No. 2541008). S.H. is grateful for JSPS
Research Fellowships for Young Scientists.
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