The R22(8) hydrogen-bonded supramolecular synthon in two novel glycoluril derivatives

Article abstract of DOI:10.1007/s10870-010-9963-8

Two new glycoluril derivatives, namely 6-phenyl-1,4-dioxo-2,2a,3,4,6,7- hexahydro-1H,5H-2,3,4a,6,7a-pentaazacyclopenta[cd]indene-2a,7b-dicarboxylate (1), and diethyl 6-(2,4-dichorophenyl)-1,4-dioxo-2,2a,3,4,6,7-hexahydro-1H,5H-2, 3,4a,6,7a-pentaazacyclopenta[cd]indene-2a,7b-dicarboxylate (2) have been synthesized and structurally determined by X-ray diffraction analysis. Compound 1 is, monoclinic, space group C2/c, with a = 20.0784(7), b = 9.0316(3), c = 23.0980(8) A, β = 98.3930(10), V = 4143.7(2) A³, with Z = 8 for d _calc = 1.338 Mg/m³. The analog 2 is, Triclinic, space group P-1, with a = 8.9353(18), b = 10.466(2), c = 14.679(3) A, β = 73.60(3), V = 1268.1(4) A³, with Z = 2 for d _calc = 1.533 Mg/m³. X-ray analysis reveals that both glycoluril derivatives bearing two free syn-urea NH groups and two ureidyl C=O, assemble the same one-dimensional chains in the solid-state running parallel to the [110], [1-10] and [010] directions via N-H·O hydrogen bonds.

Full text of DOI:10.1007/s10870-010-9963-8

J Chem Crystallogr (2011) 41:425–429
DOI 10.1007/s10870-010-9963-8
COMMUNICATION
The R22(8) Hydrogen-Bonded Supramolecular Synthon in Two
Novel Glycoluril Derivatives
•
Li-Ping Cao Xiang-Gao Meng Jiao-Yang Ding
•
•
•
Hai-Ling Xi An-Xin Wu
Received: 15 July 2009 / Accepted: 31 December 2010 / Published online: 18 January 2011
Ó Springer Science+Business Media, LLC 2011
Abstract Two new glycoluril derivatives, namely 6-phe-
nyl-1,4-dioxo-2,2a,3,4,6,7-hexahydro-1H,5H-2,3,4a,6,7a-
pentaazacyclopenta[cd]indene-2a,7b-dicarboxylate (1), and
diethyl 6-(2,4-dichorophenyl)-1,4-dioxo-2,2a,3,4,6,7-hexa-
hydro-1H,5H-2,3,4a,6,7a-pentaazacyclopenta[cd]indene-2a,
7b-dicarboxylate (2) have been synthesized and structurally
determined by X-ray diffraction analysis. Compound 1 is,
monoclinic, space group C2/c, with a = 20.0784(7), b =
Introduction
Glycoluril and its derivatives, due to their special precaved
structure and a richness of hydrogen-bonding sites, are
widely used as building blocks to construct a series of
compounds with more sophisticated structures [1, 2] and
anion sensors [3–5]. As a result of its curved but rigid
skeleton and its multiplicity of hydrogen bond donating
(NH) and accepting (ureidyl C=O) groups, glycoluril and
its derivatives have recently emerged as a versatile building
block for studies of crystal engineering [6–11]. In contin-
uation of our effort in hydrogen-bonding interactions in
crystal engineering using glycoluril derivatives as building
blocks [12–14], we report here the two-dimensional
hydrogen-bonded layer and three-dimensional hydrogen-
bonded network formed by the two novel glycoluril
derivatives 1 and 2, in which kernel of crystal structures is
the same supramolecular synthon [15].
˚
9.0316(3), c = 23.0980(8) A, b = 98.3930(10), V = 4143.
3
7(2) A , with Z = 8 for dcalc = 1.338 Mg/m3. The analog 2
˚
is, Triclinic, space group P-1, with a = 8.9353(18), b =
˚
10.466(2), c = 14.679(3) A, b = 73.60(3), V = 1268.1(4)
3
A , with Z = 2 for dcalc = 1.533 Mg/m3. X-ray analysis
˚
reveals that both glycoluril derivatives bearing two free syn-
urea NH groups and two ureidyl C=O, assemble the same
one-dimensional chains in the solid-state running parallel to
the [110], [1–10] and [010] directions via N–HÁÁÁO hydrogen
bonds.
Keywords Glycoluril Á Crystal structure Á Hydrogen
bonding
Experimental
X-ray Crystallography
Single of 1 and 2 suitable for X-ray diffraction were grown
from the CHCl3 or ClCH2CH2Cl and MeOH, respectively.
The intensities of 4078 and 4961 independent reflections
with I [ 2r(I) were measured on a Bruker Smart Apex
CCD area-detector and Rigaku R-axis Spider diffractom-
L.-P. Cao (&) Á X.-G. Meng Á J.-Y. Ding Á A.-X. Wu
Key Laboratory of Pesticide and Chemical Biology, Ministry
of Education, Central China Normal University,
Wuhan 430079, People’s Republic of China
e-mail: chlpcao@mails.ccnu.edu.cn
˚
eter with Mo-Ka radiation (k = 0.71073 A), respectively.
The structure was solved by direct methods and refined on
F2 using SHELXL-97 [16–18]. All the non-hydrogen
atoms were refined anisotropically. Carbon bound H-atoms
were located at the geometrical positions. The crystal
data, intensity collection, and structure refinement are
H.-L. Xi
6th Department, Research Institute of Chemical Defence,
Beijing 102205, People’s Republic of China
123

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J Chem Crystallogr (2011) 41:425–429
˚
Table 1 Crystal data and structure refinement
Table 2 Hydrogen-bonding geometry for 1 (A,°)
Compound
1
2
D–HÁÁÁA
D–H
HÁÁÁA
DÁÁÁA
D–HÁÁÁA
CCDC deposit no.
Color/shape
740030
740031
N2–H2ÁÁÁO2i
0.85(2)
0.87(2)
0.93(2)
2.05(2)
2.05(2)
2.49 (2)
2.876(2)
2.894(2)
3.417(3)
164(2)
165(2)
176(1)
Colorless/block
Colorless/block
N1–H1ÁÁÁO1ii
C17–H17ÁÁÁO1iii
Empirical formula
C19H23N5O6
C19H21Cl2N5O6Á
ClCH2CH2Cl
Symmetry code: (i) -x ? 1, -y ? 2, -z ? 1; (ii) -x ? 1/2,
-y ? 3/2, -z ? 1; (iii) x ? 1/2, y-1/2, z
Formula weight
Crystal system
Space group
417.42
585.26
Triclinic
P-1
Monoclinic
C2/c
˚
a (A)
20.0784(7)
9.0316(3)
23.0980(8)
90.00
8.9353(18)
10.466(2)
14.679(3)
74.74(3)
73.60(3)
89.01(3)
1268.1(4)
2
˚
Table 3 Hydrogen-bonding geometry of 2 (A,°)
˚
b (A)
D–HÁÁÁA
D–H
HÁÁÁA
DÁÁÁA
D–HÁÁÁA
˚
c (A)
N4–H4AÁÁÁO1i
N5–H5AÁÁÁO2ii
C19–H19ÁÁÁCl1iii
C14–H14BÁÁÁO1iii
C7–H7AÁÁÁO3iv
0.78(4
0.82(4)
0.96
2.07(4)
2.01(4)
2.65
2.845(3)
2.823(3)
3.137(15)
3.288(3)
3.337(3)
172(3)
170(3)
112(3)
133(3)
139(3)
a (°)
b (°)
c (°)
98.3930(10)
90.00
3
˚
V (A )
4143.7(2)
8
0.97
2.55
Z
0.97
2.54
Dc (Mg M-3
l(Mo Ka) (mm-1
)
1.338
1.533
Symmetry code: (i) -x, -y ? 2, -z; (ii) -x, -y ? 1, -z;
(iii) -x ? 1, -y ? 2, -z; (iv) -x ? 1, -y ? 1, -z
)
0.102
0.514
F(000)
1760
604
Absorption
correction
Multi-scan
Multi-scan
Tmin and Tmax
0.9770 and 0.9899
1.78 and 26.00
0.9041 and 0.9041
3.00 and 26.00
h Range for data
collection
Index ranges
-24 B h B 24,
-10 B k B 11,
-28 B l B 28
-11 B h B 11,
-12 B k B 12,
-17 B l B 18
Reflections collected
Unique reflections
Observed reflections
No. of parameters
16224
4078
3163
299
10981
4961
4537
334
Scheme 1 Synthesis of the title compounds 1 and 2
Goodness-of-fit on F2
1.105
1.061
diethoxycarbonyl glycoluril (1.43 g, 5 mmol) with anhy-
drous formaldehyde (0.3 g, 10 mmol) and EtOH (50 mL)
were brought to reflux under Ar. A solution of equivalent
phenyl or 2,4-dichorophenyl methanamine (5 mmol) in
EtOH (10 mL) was added, dropwise slowly (over 1 h) to
the mixture. Then refluxing was continued for 10–12 h,
monitored by TLC (the reaction time must be strictly
controlled at less 12 h). The solvent was removed under
reduced pressure and the products were separated by col-
umn chromatography (silica gel). Crystals of 1 and 2
suitable for X-ray data collection were obtained by slow
evaporation of a dichloroethane and methanol solution in
ratio of 4:1 (v:v) at 293 K. Compound 1: yield 79%; m.p.
180–181 °C; TLC (CHCl3/MeOH, 30:1) Rf 0.15; IR (KBr,
cm-1): 3217m, 3097m, 2985m, 2851m, 1864w, 1844w,
1755s, 1709s, 1653m, 1636m, 1475m, 1457m, 1421m,
1388m, 1339m, 1292s, 1276s, 1193w, 1151m, 1099m,
1048m, 1020m, 993m; 1H NMR (400 MHz, CDCl3):
7.33–7.27 (m, 5H), 6.56 (s, 2H), 4.81 (d, J = 13.6, 2H),
4.34 (d, J = 14.0, 2H), 4.30–4.24 (m, 4H), 3.66 (s, 2H),
Final R indices
[I [ 2r(I)]
R indices (all data)
R1 = 0.0650,
xR = 0.1348
R1 = 0.0477,
xR = 0.1336
R1 = 0.0874,
xR = 0.1452
R1 = 0.0511,
xR = 0.1364
summarized in Table 1; the hydrogen-bonding geometry is
listed in Tables 2 and 3, respectively.
Synthesis
The preparation of glycoluril monomers 1 and 2 followed
well established methodology [19, 20], as shown in
Scheme 1. When diethoxycarbonyl was combined with
equivalent phenyl or 2,4-dichorophenyl methanamine in
the presence of anhydrous formaldehyde in ethanol at
reflux, the expected compounds, the new glycolurils, were
obtained, respectively, in good yields. EtOH and the ethyl
amines had to be freshly distilled. A suspension of
123

J Chem Crystallogr (2011) 41:425–429
427
1.32–1.28 (m, 6H); 13C NMR(100 MHz, CDCl3): 166.0,
165.4, 158.1, 136.7, 129.3, 128.4, 127.6,78.4, 74.3, 63.6,
63.2, 59.6, 54.2, 13.9, 13.8. Compound 2: yield 83%; m.p.
145–146 °C; TLC (CHCl3/MeOH, 50:1) Rf 0.20; IR (KBr,
cm-1):3210m, 3096m, 2982w, 2936w, 2854w, 1844w,
1828w, 1764s, 1741s, 1693s, 1651m, 1636w, 1589w,
1474m, 1446m, 1425m, 1395m, 1369m, 1340m, 1308m,
1286m, 1262m, 1224m, 1188m, 1161m, 1082m, 1040m,
1
986m; H NMR (400 MHz, CDCl3):7.42 (d, J = 8.0, 1H),
7.38 (s, 1H), 7.23(d, J = 8.0, 1H),6.75 (s, 2H), 4.82(d,
J = 14.0, 2H), 4.33 (d, J = 14.0, 2H), 4.23–4.24 (m, 4H),
3.70(s, 2H), 1.32–1.29 (m, 6H); 13C NMR (100 MHz,
CDCl3): 165.9, 165.4, 158.3, 135.8, 134.2, 132.9, 132.1,
129.6, 127.0, 78.4, 74.5, 63.7, 63.3, 59.7, 51.2, 13.9, 13.8.
Result and Discussion
The molecular structures of 1 (Fig. 1) and 2 (Fig. 2) are
built up from three fused rings, namely two nearly planar
imidazole five-membered rings that adopt envelope con-
formations, with the ureidyl C=O groups at the flap posi-
tions, and one six-membered triazacyclohexane ring that
adopts a chair conformation. These rings bear two CO2Et
groups on their ‘convex’ faces. The bond lengths and bond
angles in both the compounds are similar to those reported
previously [7, 8, 6, 9, 10, 12]. The =OÁÁÁO= distances are
Fig. 1 The molecular structures of 1, showing 30% probability level
and H atoms are shown as small spheres of arbitrary radii. Atoms of
the minor disorder components has been omitted for clarity
˚
˚
5.652(2) A in (I) and 5.657(2) A in (II) and all of the
Csp2–N distances and Csp3–N distances lie in the range
˚
˚
1.347(3)–1.472(3) A and 1.444(3) 1.482(3) A, respec-
tively. Obviously, the N–C(carbonyl) bond distances are
much shorter than the other N–C bond distances in three
fused rings, indicating some electron delocalization within
these rings. Again, the cis-fused five-membered rings
bearing CO2Et groups enforce their cup shaped geometry.
The angle between the mean planes defined by the five-
membered rings amounts to 114.99(10)° in 1 and 114.
88(12)° in 2. The glycoluril units are both almost coplanar,
which are indicated by the key torsional angles [in 1: N1–
C1–C2–N3 0.64(2)°, C5–C1–C2–C8 4.5(2)°; in 2: N2–
C12–C16–N4-4.2(2)°, C13–C12–C16–C17-12.6(2)°].
In their supramolecular structures formed via N–HÁÁÁO
hydrogen bonds, the molecules of 1 and 2 are linked into
one-dimensional hydrogen-bonded chain (Scheme 2). In 1,
amide N1 and N2 atoms in molecule at (x, y, z) act
H-bonding donors, via H1 and H2, respectively, to car-
boxyl O1 in molecule at (1/2-x, 3/2-y, 1-z) and O2 at
(1-x, 2-y, 1-z), both producing one-dimensional chains
(Chain A, Fig. 3) running parallel to the [110] direction.
These two type [110] chains are interlinked by the
approximately centrosymmetric R22(8) [21] H-bonding
motif, forming a one-dimensional chain structure along the
[110] direction (Table 2). Interestingly, this chain produces
another different chain generated by the 21 screw axis at
(1/4, y, 1/4), running parallel to the [1–10] direction (Chain
B, Fig. 3). Four chains, including two chain A and two
chain B, pass through each unit cell. Some weak nonclas-
˚
sical hydrogen bonds, C17–H17ÁÁÁO2 [CÁÁÁO = 3.417(3) A]
(Table 2), further consolidate the supramolecular structure.
Similar to compound 1, molecules in compound 2 also
forms the similar one-dimensional hydrogen-bonded tapes
in the solid-state along the [010] direction (Fig. 4,
Table 3). In 2, two amide atoms, N4 and N5 in molecule at
(x, y, z) act as H-bonding donors, via H4 and H5, respec-
tively, to carboxyl O1 in molecule at (-x, 2-y, 2-z) and
O2 at (-x, 1-y, 2-z), both producing the one-dimensional
chains running parallel to the [010] direction. These two
type [010] chains are interlinked by the approximately
centrosymmetric R22(8) [21] H-bonding motif, forming the
one-dimensional chain structure along the [010] direction.
Furthermore, the second substructure is constructed by way
of C–HÁÁÁO and C–HÁÁÁCl hydrogen bonds: C14–H14BÁÁÁO1
˚
[CÁÁÁO = 3.288(3) A], C7–H7AÁÁÁO3 [CÁÁÁO = 3.337(3)
˚
˚
A] and C19–HÁÁÁCl1 [CÁÁÁCl = 3.137(2) A], forming
the other one-dimensional tapes along the [100] direc-
tion which suffices to link the [010] tapes into a
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J Chem Crystallogr (2011) 41:425–429
Fig. 3 Packing of 1, showing the formation of a one-dimensional
hydrogen-bonded R22(8) chain along the [110] (up) and [1–10] (down)
directions involving syn-NH atoms and C=O. Hydrogen bonds are
drawn as dashed lines
Fig. 2 The molecular structures of 2, showing 30% probability level
and H atoms are shown as small spheres of arbitrary radii. The solvent
molecule (ClCH2CH2Cl) has been omitted for clarity
Fig. 4 Packing of 2, showing the formation of a one-dimensional
hydrogen-bonded R22(8) chain along the [010] direction involving syn-
NH atoms and C=O. Hydrogen bonds are drawn as dashed lines
here for 1 and 2 (Scheme 2). This may be ascribed to the
same supramolecular synthon of the two novel glycoluril
derivatives, which both bear two free syn-urea NH groups
and two ureidyl C=O groups. The C–HÁÁÁO and C–HÁÁÁCl
hydrogen bonds link these one-dimensional chains into
hydrogen-bonded l network in 1 and 2, respectively.
Scheme 2 R22(8) hydrogen-bonded chain in 1 and 2
two-dimensional layer running parallel to the (001) direc-
tion (Table 3). There are no direction-specific interactions
between the adjacent three-dimensional networks, either.
Supplementary Material
CCDC 740030 and 740031 contain the supplementary crys-
tallographic data for this paper. These data can be obtained
free of charge via www.ccdc.cam.ac.uk/data_request/cif, by
e-mailing data_request@ccdc.cam.ac.uk, or by contacting
The Cambridge Crystallographic Data Centre, 12 Union
Road, Cambridge CB2 1EZ, UK; fax: ?44-1223-336033.
Conclusion
In summary, the same one-dimensional hydrogen-bonded
chains along [110], [1–10] and [010] directions are found
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11. She NF, Meng XG, Gao M, Wu AX, Isaacs L (2008) Chem
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