Two-dimensional hydrogen-bonded networks in two novel glycoluril derivatives

Article abstract of DOI:10.1107/S0108270107067108

Two new glycoluril derivatives, namely diethyl 6-ethyl-1,4-dioxo-1,2,2a,3, 4,6,7,7b-octa-hydro-5H-2,3,4a,6,7a-penta-aza-cyclo-penta-[cd]indene-2a, 7b-dicarboxyl-ate, C₁₄H₂₁N₅O₆, (I), and 6-ethyl-2a,7b-diphenyl-1

Full text of DOI:10.1107/S0108270107067108

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
between sulfamides and ureas linking adjacent hydrogen-
bonded ribbons (Johnson et al., 2002, 2003). Isaacs and co-
workers have reported similar hydrogen-bonded ribbons in a
related syn-protected glycoluril derivative (Wu et al., 2002).
One of our laboratory interests is to develop a robust supra-
molecular synthon based on glycoluril for crystal engineering
(Wang et al., 2006; Chen et al., 2007). As part of our research
programme aimed at the study of hydrogen-bonding inter-
actions involving glycoluril, the present work has been
undertaken. We report here the two-dimensional hydrogen-
bonded networks formed by two novel glycoluril derivatives,
(I) and (II), that adopt an unusual twisted conformation in the
solid state (Matta et al., 2000; Li et al., 1994; Duspara et al.,
2001).
ISSN 0108-2701
Two-dimensional hydrogen-bonded
networks in two novel glycoluril
derivatives
Li-Ping Cao,* Xiang-Gao Meng, Meng Gao, Neng-Fang
She and An-Xin Wu
Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, People's
Republic of China
Correspondence e-mail: chlpcao@mails.ccnu.edu.cn
Received 28 November 2007
Accepted 15 December 2007
Online 22 January 2008
Two new glycoluril derivatives, namely diethyl 6-ethyl-1,4-di-
oxo-1,2,2a,3,4,6,7,7b-octahydro-5H-2,3,4a,6,7a-pentaazacyclo-
penta[cd]indene-2a,7b-dicarboxylate, C14H21N5O6, (I), and
6-ethyl-2a,7b-diphenyl-1,2,2a,3,4,6,7,7b-octahydro-5H-2,3,4a,-
6,7a-pentaazacyclopenta[cd]indene-1,4-dione, C20H21N5O2,
(II), both bearing two free syn-urea NH groups and two
ureidyl C O groups, assemble the same one-dimensional
chains in the solid state running parallel to the [010] direction
via NÐHÁ Á ÁO hydrogen bonds. Furthermore, the chains of (I)
are linked together into two-dimensional networks via CÐ
HÁ Á ÁO hydrogen bonds.
Comment
Glycoluril, a biurea compound known for about 130 years, has
established an impressive career as a building block for mol-
ecular and supramolecular chemistry during the past two
decades. For example, glycoluril derivatives have been used in
a variety of applications, including polymer crosslinking
(Jacobs et al., 1996), explosives (Yinon et al., 1994), the
stabilization of organic compounds against photodegradation
(Krause et al., 1997), textile waste stream puri®cation (Karcher
et al., 1999) and combinatorial chemistry, and furthermore in
the ®elds of cucurbituril chemistry (Freeman et al., 1981; Kim
et al., 2000; Pryor & Rebek, 1999; Lee et al., 2003; Burnett et
al., 2003) and anion sensors (Kang et al., 2004; Kang & Kim,
2005). The intriguing structural feature in a number of
glycoluril derivatives is the twisting observed about the
bridgehead dihedral angle, and the rigid and nonplanar
glycoluril skeleton, with well de®ned geometry, is more
favourable for constructing a three-dimensional structure,
which suggests that glycoluril derivatives have signi®cant
potential as building blocks in crystal engineering studies.
Rebek and co-workers have reported that achiral glycolurils
form chiral hydrogen-bonded ribbons in the solid state, and
subsequently observed four complementary hydrogen bonds
The molecular structures of (I) and (II) (Fig. 1) are built up
from three fused rings, namely two nearly planar imidazole
®ve-membered rings that adopt envelope conformations, with
the C O groups at the ¯ap positions, and one six-membered
triazacyclohexane ring that adopts a chair conformation.
These rings bear two CO2Et groups in (I) and two Ph groups in
(II) on their `convex' faces. The bond lengths and angles in
both compounds are similar to those reported previously
(Johnson et al., 2002, 2003; Wu et al., 2002; Wang et al., 2006;
Ê
Chen et al., 2007). The OÁ Á ÁO distances are 5.657 (2) A in
2
(I) and 5.691 (2) A in (II). All Csp ÐN and Csp ÐN distances
3
Ê
Ê
lie in the ranges 1.349 (4)±1.381 (4) and 1.442 (3)±1.478 (4) A,
respectively. Obviously, the NÐC(carbonyl) bond distances
are much shorter than the other NÐC bond distances in the
three fused rings, indicating some electron delocalization
within these rings. Again, the cis-fused ®ve-membered rings
bearing CO2Et or Ph groups enforce their cup-shaped
geometry. The angle between the mean planes de®ned by the
Acta Cryst. (2008). C64, o69±o72
DOI: 10.1107/S0108270107067108
# 2008 International Union of Crystallography o69

organic compounds
1
2
®ve-membered rings is 115.1 (1)ꢀ in (I) and 112.9 (1)ꢀ in (II).
The glycoluril units are both almost coplanar, which is indi-
cated by the key torsion angles [(I): N1ÐC3ÐC7ÐN3 =
2.9 (3)ꢀ and C4ÐC3ÐC7ÐC8 = 9.6 (3)ꢀ; (II): N1ÐC1ÐC8Ð
N3 = 4.7 (2)ꢀ and C2ÐC1ÐC8ÐC9 = 5.1 (3)ꢀ]. These
slight differences are thought to be due to the different
substituents on the `convex' faces.
In their supramolecular structures formed via NÐHÁ Á ÁO
and CÐHÁ Á ÁO hydrogen bonds, the molecules of both (I) and
(II) are linked into two-dimensional networks. In (I), the
crystal packing can be easily analysed in terms of two simple
substructures. In the ®rst substructure, amide atoms N1 and
N2 in the molecule at (x, y, z) act as hydrogen-bond donors,
via atoms H1 and H2, respectively, to carboxyl atom O2 in the
molecule at ( x + 12, y + 21, z + 21) and atom O1 at ( x + 12, y
,
z + 12), both producing one-dimensional chains running
parallel to the [010] direction generated by the 21 screw axis at
(14, y, 14). These two types of [010] chains are interlinked by an
approximately centrosymmetric R22(8) (Bernstein et al. 1995)
hydrogen-bonding motif centred at (0.257, 0.295, 0.249),
forming a one-dimensional chain structure along the [010]
direction (Fig. 2 and Table 1). Four chains of this type pass
through each unit cell; two of these, running along the (14, y, 41)
and (34, y, ) directions, respectively, are antiparallel to the
3
4
other two, which run along the (34, y, 41) and (41, y, 34) directions,
respectively. As reported by Wu et al. (2002), if all the CO2Et
groups were located on one side of the molecule, this would
lead to cyclic structures for these analogues. We did not
observe these cyclic structures in the solid state of (I), which
may be due to the unfavourable entropy associated with the
formation of cyclic structures. In the second substructure,
ethyl atom C13 in the molecule at (x, y, z) acts as a hydrogen-
bond donor, via atom H13B, to carboxyl atom O3 in the
1
2
molecule at (x, y, z + ), forming another one-dimensional
chain along the [001] direction generated by a c-glide plane at
y = 0, which suf®ces to link the [010] chains into a two-
dimensional network (Fig. 3) running parallel to the (100)
direction. No direction-speci®c interactions between adjacent
two-dimensional networks are observed.
Similar to compound (I), molecules in compound (II) also
form one-dimensional hydrogen-bonded tapes in the solid
state along the [010] direction (Fig. 4 and Table 2). Structure
(II) can also be easily analysed in terms of two one-dimen-
sional substructures. In the ®rst substructure, two amide
atoms, N1 and N2, in the molecule at (x, y, z) act as hydrogen-
bond donors, via atoms H1 and H2, respectively, to carboxyl
atom O2 in the molecule at ( x + 32, y + 21, z + 21) and atom O1
Figure 1
3
1
1
The molecular structures of compounds (I) (left) and (II) (right), showing
the atom-numbering schemes. In both cases, displacement ellipsoids are
drawn at the 30% probability level and H atoms are shown as small
spheres of arbitrary radii.
at ( x + , y
,
z + ), both producing one-dimensional
2
2
2
Figure 2
Figure 3
The packing of (I), showing the formation of a one-dimensional
hydrogen-bonded R22(8) chain along the b axis involving syn-NH atoms
and C O groups. Hydrogen bonds are drawn as dashed lines. [Symmetry
Part of the crystal structure of (I), showing the formation of the two-
dimensional network linked by CÐHÁ Á ÁO hydrogen bonds along the
[100] direction. Hydrogen bonds are shown as dashed lines. [Symmetry
codes: (ii) x ‡ 12 ; y ‡ 21 ; z ‡ 21; (iv) x ‡ 21 ; y ‡ 12 ; z ‡ 1.]
1
1
1
1
1
codes: (i) x + , y
,
z + ; (ii) x + , y + 12, z + .]
2
2
2 2 2
ꢁ
o70 Cao et al. C14H21N5O6 and C20H21N5O2
Acta Cryst. (2008). C64, o69±o72

organic compounds
Compound (I)
Crystal data
3
Ê
V = 3475.2 (5) A
C14H21N5O6
Mr = 355.36
Z = 8
Mo Kꢁ radiation
Monoclinic, C2=c
1
Ê
a = 23.898 (2) A
ꢂ = 0.11 mm
T = 296 (2) K
Ê
b = 10.4791 (9) A
Ê
c = 15.9302 (13) A
ꢀ = 119.4120 (10)ꢀ
0.20 Â 0.20 Â 0.10 mm
Data collection
Bruker SMART APEX CCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.979, Tmax = 0.989
10973 measured re¯ections
3061 independent re¯ections
2206 re¯ections with I > 2ꢃ(I)
Rint = 0.046
Figure 4
Re®nement
The packing of (II), showing the formation of a one-dimensional
hydrogen-bonded R22(8) chain along the b axis involving syn-NH atoms
and C O groups. Hydrogen bonds are drawn as dashed lines. [Symmetry
R[F2 > 2ꢃ(F2)] = 0.069
wR(F2) = 0.172
S = 1.07
3061 re¯ections
236 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
3
2
1
2
1
3
1
codes: (i) x + , y
,
z + ; (ii) x + , y + 12, z + .]
2 2 2
3
Ê
Áꢄmax = 0.22 e A
3
Ê
0.41 e A
Áꢄmin
=
chains running parallel to the [010] direction generated by the
Table 1
Hydrogen-bond geometry (A, ) for (I).
3
21 screw axis at (34, y, ). These two type [010] chains are
ꢀ
Ê
4
interlinked by the approximately centrosymmetric R22(8)
(Bernstein et al. 1995) hydrogen-bonding motif centred at
(0.966, 0.400, 0.279), forming a one-dimensional chain struc-
ture along the [010] direction. In comparison with the
formation of the four chains in each unit cell in compound (I),
only two one-dimensional chains pass through each unit cell in
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N2ÐH2Á Á ÁO1i
0.93 (3)
0.91 (3)
0.97
1.98 (4)
1.89 (4)
2.45
2.886 (3)
2.786 (3)
3.342 (4)
166 (3)
170 (3)
153
N1ÐH1Á Á ÁO2ii
C13ÐH13BÁ Á ÁO3iii
Symmetry codes: (i) x ‡ 12; y
;
z ‡ 12; (ii) x ‡ 21; y ‡ 21; z ‡ 21; (iii) x; y; z ‡ 12.
1
2
1
3
(II); these two chains run along the (34, y, ) and (41, y, )
4
4
directions, respectively.
As noted above, the same one-dimensional hydrogen-
bonded chains along the [010] direction are found here for (I)
and (II). This may be ascribed to the same motifs of these two
novel glycoluril derivatives, which both bear two free syn-urea
NH groups and two ureidyl C O groups. The CÐHÁ Á ÁO
hydrogen bonds [along the [001] direction in (I) and along the
[100] direction in (II)] link these one-dimensional helical
chains into two-dimensional networks.
Compound (II)
Crystal data
3
Ê
V = 1778.16 (19) A
C20H21N5O2
Mr = 363.42
Z = 4
Mo Kꢁ radiation
Monoclinic, P21=n
1
Ê
a = 8.0724 (5) A
ꢂ = 0.09 mm
T = 295 (2) K
Ê
b = 11.6462 (7) A
Ê
c = 19.2338 (12) A
0.20 Â 0.20 Â 0.10 mm
ꢀ = 100.462 (1)ꢀ
Data collection
Experimental
Bruker SMART APEX CCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.982, Tmax = 0.991
16184 measured re¯ections
3860 independent re¯ections
2581 re¯ections with I > 2ꢃ(I)
Rint = 0.058
The preparation of the glycoluril monomers (I) and (II) followed a
well established methodology (Yin et al., 2006; Li et al., 2006), but
ethanol was used as
a solvent. When diethoxycarbonyl- or
diphenylglycoluril are combined with equivalent ethylamines in the
presence of anhydrous formaldehyde in ethanol under re¯ux, the
expected compounds, the new glycolurils, were obtained in good
yields. EtOH and the ethylamines were freshly distilled. A suspension
of diethoxycarbonylglycoluril (1.43 g, 5 mmol) or diphenylglycoluril
(1.47 g, 5 mmol) in anhydrous formaldehyde (0.3 g, 10 mmol) and
EtOH (50 ml) was brought to re¯ux under magnetic stirring. A
solution of ethylamine (5 mmol) in EtOH (10 ml) was added drop-
wise (over 1 h) to the mixture. Re¯uxing was continued for 10±12 h
and the reactions were monitored by thin-layer chromatography. The
solvent was removed under reduced pressure and the products were
separated by column chromatography (silica gel) in 80 and 50%
isolated yields, respectively. Crystals of (I) and (II) suitable for X-ray
data collection were obtained by slow evaporation of dichloro-
ethane±methanol solutions (4:1 v/v) at 293 K.
Re®nement
R[F2 > 2ꢃ(F2)] = 0.063
wR(F2) = 0.159
S = 1.03
3860 re¯ections
251 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
3
Ê
Áꢄmax = 0.28 e A
3
Ê
0.21 e A
Áꢄmin
=
Table 2
Hydrogen-bond geometry (A, ) for (II).
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N2ÐH2Á Á ÁO1i
0.89 (3)
0.93 (3)
2.20 (3)
1.96 (3)
3.043 (3)
2.873 (3)
158 (2)
168 (2)
N1ÐH1Á Á ÁO2ii
Symmetry codes: (i) x ‡ 32; y
;
z ‡ 12; (ii) x ‡ 32; y ‡ 21; z ‡ 12.
1
2
ꢁ
Acta Cryst. (2008). C64, o69±o72
Cao et al. C14H21N5O6 and C20H21N5O2 o71

organic compounds
Duspara, P. A., Matta, C. F., Jenkins, S. I. & Harrison, P. H. M. (2001). Org.
Lett. 3, 495±498.
Freeman, W. A., Mock, W. L. & Shih, N. Y. (1981). J. Am. Chem. Soc. 103,
7367±7368.
For both (I) and (II), all H atoms bonded to C atoms were initially
located in difference Fourier maps and then constrained to their ideal
Ê
geometry positions, with CÐH = 0.96 (methyl) or 0.97 A (methyl-
ene), and with Uiso(H) = 1.5Ueq(methyl C) or 1.2Ueq(methylene C). H
atoms bonded to N atoms were found in difference maps; the NÐH
Jacobs, W., Foster, D., Sansur, S. & Lees, R. G. (1996). Prog. Org. Coat. 29, 127±
138.
Ê
distances were re®ned freely [0.89 (3)±0.93 (3) A] and Uiso(H) values
were set at 1.2Ueq(N).
Johnson, D. W., Hof, F., Palmer, L. C., Martin, T., Obst, U. & Rebek, J. (2003).
Chem. Commun. pp. 1638±1639.
Johnson, D. W., Palmer, L. C., Hof, F., Iovine, P. M. & Rebek, J. (2002). Chem.
Commun. pp. 2228±2229.
Kang, J., Jo, J. H. & In, S. (2004). Tetrahedron Lett. 45, 5225±5228.
Kang, J. & Kim, J. (2005). Tetrahedron Lett. 46, 1759±1762.
Karcher, S., Kornmuller, A. & Jekel, M. (1999). Water Sci. Technol. 40, 425±
433.
Kim, J., Jung, I. S., Kim, S. Y., Lee, E., Kang, J. K., Sakanoto, S., Yamaguchi, K.
& Kim, K. (2000). J. Am. Chem. Soc. 122, 540±541.
Krause, A., Aumueller, A., Korona, E. & Trauth, H. (1997). US Patent No.
5670613.
For both compounds, data collection: SMART (Bruker, 2001); cell
re®nement: SMART; data reduction: SAINT-Plus (Bruker, 2001);
program(s) used to solve structure: SHELXS97 (Sheldrick, 1997);
program(s) used to re®ne structure: SHELXL97 (Sheldrick, 1997);
molecular graphics: PLATON (Spek, 2003); software used to prepare
material for publication: PLATON.
The authors thank the National Natural Science Foundation
of China (grant No. 20672042).
Lee, J. W., Samal, S., Selvapalam, N., Kim, H. J. & Kim, K. (2003). Acc. Chem.
Res. 36, 621±630.
Li, N., Maluendes, S., Blessing, R. H., Dupuis, M., Moss, G. R. & de Titta, G. T.
(1994). J. Am. Chem. Soc. 116, 6494±6507.
Li, Y., Yin, G., Zhou, B. & Wu, A. (2006). Synthesis, 17, 2897±2902.
Matta, C. F., Cow, C. C., Sun, S., Britten, J. F. & Harrison, P. H. M. (2000). J.
Mol. Struct. 523, 241±255.
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: AV3132). Services for accessing these data are
described at the back of the journal.
Pryor, K. E. & Rebek, J. (1999). Org. Lett. 1, 39±42.
È
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Got-
tingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
Sheldrick, G. M. (1996). SADABS. University of Gottingen, Germany.
References
È
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555±1573.
Bruker (2001). SMART (Version 5.628) and SAINT-Plus (Version 6.45).
Bruker AXS Inc., Madison, Wisconsin, USA.
Wang, Z., Zhou, B., Chen, Y., Yin, G., Li, Y., Wu, A. & Isaacs, L. (2006). J. Org.
Chem. 71, 4502±4508.
Burnett, C. A., Lagona, J., Wu, A., Shaw, J. A., Coady, D., Fettinger, J. A., Day,
A. I. & Isaacs, L. (2003). Tetrahedron, 59, 1961±1970.
Chen, Y., She, N., Meng, X., Yin, G., Wu, A. & Isaacs, L. (2007). Org. Lett. 9,
1899±1902.
Wu, A., Fettinger, J. C. & Isaacs, L. (2002). Tetrahedron, 58, 9769±9777.
Yin, G., Wang, Z., Chen, Y., Wu, A. & Pan, Y. (2006). Synlett, 1, 49±52.
Yinon, J., Bulusu, S., Axenrod, T. & Yazdekhasti, H. (1994). Org. Mass
Spectrom. 29, 625±631.
ꢁ
o72 Cao et al. C14H21N5O6 and C20H21N5O2
Acta Cryst. (2008). C64, o69±o72