Hexagonal packing of cis,cis-cyclo-hexane-1,3,5-tricarboxamide

Article abstract of DOI:10.1107/S0108270107040048

The title compound, C9H15N3O3, which has crystallographically imposed threefold symmetry, crystallizes as a hexa-gonal columnar structure. The crystal structure is stabilized by a less common amide-amide synthon, where one amide group is hydrogen bonded t

Full text of DOI:10.1107/S0108270107040048

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
forming the usual amide dimer tape, the amide group is linked
to four other amide groups via strong NÐHÁ Á ÁO hydrogen
bonds using two NÐH donors and the bifurcated C
O
ISSN 0108-2701
acceptor (Fig. 2). The hydrogen-bond geometry is listed in
Table 1. This type of synthon is not very common for amide
functional groups. The trigonal molecules are bonded via
amide±amide hydrogen bonds to form a three-dimensional
network, where the two-dimensional layer contains hexagonal
arrays surrounded by six amide groups (Fig. 3) and these six
amide groups form a cylic hexamer via six NÐHÁ Á ÁO
hydrogen bonds. The remaining six NH groups form NÐ
HÁ Á ÁO hydrogen bonds with adjacent layers. The hexagonal
arrays are partially occupied by cyclohexyl rings from neigh-
Hexagonal packing of cis,cis-cyclo-
hexane-1,3,5-tricarboxamide
Binoy K. Saha
Department of Chemistry, Pondicherry University, Puducherry 605 014, India
Correspondence e-mail: binoypu@yahoo.co.in
Received 19 July 2007
Accepted 12 August 2007
Online 22 September 2007
The title compound, C9H15N3O3, which has crystallographi-
cally imposed threefold symmetry, crystallizes as a hexagonal
columnar structure. The crystal structure is stabilized by a less
common amide±amide synthon, where one amide group is
hydrogen bonded to four others. The amide groups form cyclic
amide±amide hexamers via NÐHÁ Á ÁO hydrogen bonds.
Comment
Acid and primary amide functional groups have been well
studied in organic supramolecular chemistry. They generally
form a centrosymmetric dimer synthon in the absence of other
strong hydrogen-bonding functional groups. The strong and
directional nature of the hydrogen bonds formed by these
functional groups has made them useful in crystal engineering.
Figure 1
A view of the title molecule, showing the atom-numbering scheme.
Displacement ellipsoids for non-H atoms are drawn at the 50%
probability level. [Symmetry codes: (A) y ‡ 1; x y; z; (B) x ‡ y ‡ 1,
x ‡ 1; z.]
Ê
Very often, the primary amide dimers form 5.1 A tapes
(Palmore & MacDonald, 2000; Saha et al., 2005) via NÐHÁ Á ÁO
hydrogen bonds, which are perpendicular to the amide dimer
motif. The trigonal molecule trimesic acid forms the expected
acid dimer but crystallizes in the C2/c space group instead of
crystallizing with trigonal symmetry (Duchamp & Marsh,
1969). cis,cis-Cyclohexane-1,3,5-tricarboxylic acid forms a
hydrate and also crystallizes in the C2/c space group (Bhogala
et al., 2002). The crystal structure of trimesic carboxamide has
not been reported so far. However, cis,cis-cyclohexane-1,3,5-
tris(ꢀ-picoloin-6-yl)tricarboxamide, (I), crystallizes in the R3c
space group (Fan et al., 1995). The solid-state architecture of
cis,cis-cyclohexane-1,3,5-tricarboxamide, (II), is described
here.
The compound crystallizes in the R3 space group with the
molecule lying about a threefold axis. The molecular geometry
and atom numbering of (II) are shown in Fig. 1. Instead of
Figure 2
One amide group is bonded to four other amide groups via NÐHÁ Á ÁO
hydrogen bonds (dashed lines).
Acta Cryst. (2007). C63, o591±o593
DOI: 10.1107/S0108270107040048
# 2007 International Union of Crystallography o591

organic compounds
boring layers and form a hexagonal close-packed structure.
The cyclohexyl rings are stacked along the c axis and form a
Piedfort unit of C3i symmetry (C3i-PU; Thalladi et al., 1998;
Saha & Nangia, 2007), as shown in Fig. 4, but they are not
packed ef®ciently along c (Fig. 5). The plane of each amide
group is tilted by 48.6ꢀ with respect to the mean plane of the
cyclohexyl ring, and the distances between the mean planes of
Figure 5
The packing along the c axis, shown in a space-®ll model. Note that the
molecules are not packed ef®ciently.
Ê
two consecutive rings are 5.13 and 5.66 A (at 100 K). The
consecutive two-dimensional layers are linked via strong NÐ
HÁ Á ÁO hydrogen bonds to form the three-dimensional
network. By comparison, the distance between the mean
Ê
planes of the cyclohexyl rings is only 4.85 A in the crystal
structure of (I).
The Cambridge Structural Database (CSD, Version 5.28 of
November 2006; Allen, 2002) was searched to check the
frequency of the amide±amide interaction pattern present in
the crystal structure of (II). The criteria used for this search
Ê
were a 2.0±3.0 A cutoff for NÁ Á ÁO distance, three-dimensional
coordinates determined, R ꢁ 0.1, no disorder, no errors, not
polymeric, no ions, no powder structures, and only organic
compounds. There are 889 hits where primary amide groups
are present and 312 hits contain the usual cyclic dimer pattern.
There are only 16 crystal structures (excluding multiple hits,
see supplementary information for CSD refcodes) where one
amide group is linked to four other amide groups via NÐ
HÁ Á ÁO hydrogen bonds and no cyclic dimer pattern is present.
Among these 16 crystal structures, acetamide (refcode
ACEMID01; Denne & Small, 1971) and 3,30,300-nitrilo-
tripropionamide (JALHIN01; Hahn et al., 1990) form similar
cyclic amide hexamers but the pattern is different from the
hexamer pattern (Fig. 3) found in (II). Therefore, the amide
hexamer pattern in the crystal structure of (II) is unique.
The cyclohexyl groups in the crystal structure of (II) stack
to form columns of cyclohexyl rings similar to the crystal
structure (I), but the hydrogen-bonding pattern is completely
different. The molecular symmetry and the three amide
functional groups play an important role in driving the hexa-
gonal crystal structure and the amide±amide synthon.
Currently, the synthesis and crystallization of different types
of anilide derivatives of cis,cis-cyclohexane-1,3,5-tricarboxylic
acid are underway.
Figure 3
The packing of the two-dimensional layer, showing a hexagonal array
surrounded by a cyclic amide hexamer bonded via NÐHÁ Á ÁO hydrogen
bonds.
Experimental
Figure 4
Two molecules are stacked to form a Piedfort unit of C3i symmetry
(C3i-PU).
cis,cis-Cyclohexane-1,3,5-tricarboxylic acid (639 mg, 3 mmol) was
re¯uxed in thionyl chloride (2 ml) for half an hour and then evapo-
ꢂ
o592 Binoy K. Saha C9H15N3O3
Acta Cryst. (2007). C63, o591±o593

organic compounds
rated to dryness under vacuum. Aqueous ammonia (10 ml) was
added to the solid mass at 273 K and stirred overnight. The material
was precipitated by addition of water (100 ml) and then the solid was
washed with methanol. Diffraction quality block-shaped crystals were
obtained from dimethyl sulfoxide (DMSO). 1H NMR (DMSO-d6): ꢁ
Data collection: SMART (Bruker, 1997); cell re®nement: SAINT
(Bruker, 1997); data reduction: SAINT; program(s) used to solve
structure: SHELXS97 (Sheldrick, 1997); program(s) used to re®ne
structure: SHELXL97 (Sheldrick, 1997); molecular graphics:
SHELXTL (Bruker, 2001); software used to prepare material for
publication: SHELXTL.
7.21 (s, 3H), 6.72 (s, 3H), 2.13 (t, 12 Hz, 3H), 1.77 (d, 12 Hz, 3H), 1.35
1
(q, 12 Hz, 3H). IR (KBr): 3342, 3192, 1676, 1622 cm
.
The author thanks Professor Ashwini Nangia, University of
Hyderabad, for providing laboratory facilities and for X-ray
data collection.
Crystal data
C9H15N3O3
Z = 6
Mo Kꢀ radiation
ꢂ = 0.11 mm
T = 100 (2) K
Mr = 213.24
Hexagonal, R3
a = 12.8094 (8) A
c = 10.7854 (13) A
Ê
V = 1532.6 (2) A
1
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SF3051). Services for accessing these data are
described at the back of the journal.
Ê
Ê
0.20 Â 0.20 Â 0.16 mm
3
Data collection
References
Bruker SMART CCD area-detector
diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.968, Tmax = 0.985
1881 measured re¯ections
672 independent re¯ections
608 re¯ections with I > 2ꢃ(I)
Rint = 0.016
Allen, F. H. (2002). Acta Cryst. B58, 380±388.
Bhogala, B. R., Vishweshwar, P. & Nangia, A. (2002). Cryst. Growth Des. 2,
325±328.
Bruker (1997). SMART (Version 5.054) and SAINT (Version 6.02). Bruker
AXS Inc., Madison, Wisconsin, USA.
Bruker (2001). SHELXTL. Version 6.12. Bruker AXS Inc., Madison,
Wisconsin, USA.
Denne, W. A. & Small, R. W. H. (1971). Acta Cryst. B27, 1094±1098.
Duchamp, D. J. & Marsh, R. E. (1969). Acta Cryst. B25, 5±19.
Fan, E., Yang, J., Stoner, T. C., Hopkins, M. D. & Hamilton, A. D. (1995). J.
Chem. Soc. Chem. Commun. pp. 1251±1252.
Re®nement
R[F2 > 2ꢃ(F2)] = 0.035
wR(F2) = 0.098
S = 1.10
66 parameters
All H-atom parameters re®ned
3
Ê
Áꢄmax = 0.25 e A
3
Ê
0.21 e A
672 re¯ections
Áꢄmin
=
Hahn, F. E., Tamm, M., Weimann, R. & Pickardt, J. (1990). Acta Cryst. C46,
1567±1569.
Table 1
Hydrogen-bond geometry (A, ).
Palmore, G. T. R. & MacDonald, J. C. (2000). The Amide Linkage: Selected
Structural Aspects in Chemistry, Biochemistry, and Materials Science, edited
by A. Greenberg, C. M. Breneman & J. F. Liebman, pp. 291±336. Chichester:
John Wiley.
Saha, B. K. & Nangia, A. (2007). Cryst. Growth Des. 7, 393±401.
Â
Saha, B. K., Nangia, A. & Jaskolski, M. (2005). CrystEngComm, 7, 355±358.
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N1ÐH1BÁ Á ÁO1i
0.893 (17)
0.897 (18)
1.975 (18)
2.030 (18)
2.8615 (14)
2.8834 (14)
171.2 (14)
158.4 (13)
N1ÐH1AÁ Á ÁO1ii
È
Gottingen, Germany.
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Gottingen,
Symmetry codes: (i) y ‡ 13; x
y
13; z 13; (ii) x
y
13; x
;
z ‡ 13.
2
3
È
Germany.
Thalladi, V. R., Brasselet, S., Weiss, H.-C., Blaser, D., Katz, A. K., Carrell, H. L.,
Boese, R., Zyss, J., Nangia, A. & Desiraju, G. R. (1998). J. Am. Chem. Soc.
120, 2563±2577.
È
H-atom parameters were re®ned freely, giving CÐH distances in
Ê
the range 0.986 (14)±0.991 (14) A.
ꢂ
Acta Cryst. (2007). C63, o591±o593
Binoy K. Saha C9H15N3O3 o593