Hexagonal packing of cis,cis-cyclo­hexane-1,3,5-tricarboxamide

The title compound, C₉H₁₅N₃O₃, which has crystallographically 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 N-H...O hydrogen bonds.

S1. Comment

Acid and primary amide functional groups are 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. Very often, the primary amide dimers form 5.1 Å tapes (Palmore & MacDonald, 2000; Saha et al., 2005) via N—H···O hydrogen bonds, which are perpendicular to the amide dimer motif. The trigonal molecule trimesic acid forms the expected acid dimer but crystallizes in space group C2/c instead of crystallizing with trigonal symmetry (Duchamp & Marsh, 1969). cis,cis-Cyclohexane-1,3,5-tricarboxylic acid forms a hydrate and also crystallizes in space group C2/c (Bhogala et al., 2002). The crystal structure of trimesic carboxamide has not been reported so far. However, cis,cis-cyclohexane-1,3,5-tris(α-picoloin-6-yl)tricarboxamide, (I), crystallizes in space group R3c (Fan et al., 1995). The solid-state architecture of cis,cis-cyclohexane-1,3,5-tricarboxamide, (II), is described here.

The compound crystallizes in space group R3 with 0.33 molecules in the asymmetric unit. The molecular geometry and atom numbering of (II) are given in Fig. 1. Instead of forming the usual amide dimer tape, the amide group is linked to four other amide groups via strong N—H···O hydrogen bonds using two N—H donors and the bifurcated C═O 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 cavities surrounded by six amide groups (Fig. 3) and these six amide groups form a cylic hexamer via six N—H···O hydrogen bonds. The remaining six N—H groups form N—H···O hydrogen bonds with adjacent layers. The hexagonal cavities are partially occupied by cyclohexyl rings from neighboring 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 efficiently along c (Fig. 5). The plane of each amide group is tilted by 48.6° with respect to the mean plane of the cyclohexyl ring, and the distances between the mean planes of two consecutive rings are 5.13 and 5.66 Å (at 100 K). The consecutive two-dimensional layers are linked via strong N—H···O hydrogen bonds to form the three-dimensional network. By comparison, the distance between the mean planes of the cyclohexyl rings is only 4.85 Å in the crystal structure of (I).

The Cambridge Structural Datbase (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 are a 2.0–3.0 Å cutoff for N···O 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 [please provide this information]) where one amide group is linked to four other amide groups via N—H···O hydrogen bonds and no cyclic dimer pattern is present. Among these 16 crystal structures, acetamide (refcode ACEMID01) and 3,3',3''-nitrilotripropionamide (JALHIN01) 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 hexagonal 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.

Related literature

For related literature, see: Bhogala et al. (2002); Duchamp & Marsh (1969); Fan et al. (1995); Palmore & MacDonald (2000); Saha & Nangia (2007); Saha et al. (2005); Thalladi et al. (1998).

S2. Experimental

cis,cis-Cyclohexane-1,3,5-tricarboxylic acid (639 mg, 3 mmol) was refluxed in thionyl chloride (2 ml) for half an hour and then evaporated 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 DMSO. ¹H NMR (DMSO-d₆): δ 7.21 (s, 3H), 6.72 (s, 3H), 2.13 (t, 12 Hz, 3H), 1.77 (d, 12 Hz, 3H), 1.35 (q, 12 Hz, 3H). IR (KBr): 3342, 3192, 1676, 1622 cm⁻¹.

S3. Refinement

H-atom parameters were refined freely, giving C—H distances in the range 0.986 (14)–0.991 (14) Å.

Computing details

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2001); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures

	Fig. 1. A view of the title molecule with the atom-numbering scheme. Displacement ellipsoids for the non-H atoms are drawn at the 50% probability level.
	Fig. 2. One amide group is bonded to four other amide groups via N—H···O hydrogen bonds.
	Fig. 3. The packing of the two-dimensional layer, showing a hexagonal void surrounded by a cyclic amide hexamer bonded via N—H···O hydrogen bonds.
	Fig. 4. Two molecules are stacked to form a Piedfort unit of C3i symmetry (C3i—PU).
	Fig. 5. The packing along the c axis, shown in a space-fill model. Note that the molecules are not packed efficiently.

cis,cis-cyclohexane-1,3,5-tricarboxamide

Crystal data

C9H15N3O3	Dx = 1.386 Mg m^−3
Mr = 213.24	Mo Kα radiation, λ = 0.71073 Å
Hexagonal, R3	Cell parameters from 1281 reflections
Hall symbol: -R 3	θ = 2.6–25.9°
a = 12.8094 (8) Å	µ = 0.11 mm^−1
c = 10.7854 (13) Å	T = 100 K
V = 1532.6 (2) Å^3	Block, colourless
Z = 6	0.20 × 0.20 × 0.16 mm
F(000) = 684

Data collection

Bruker SMART CCD area-detector diffractometer	672 independent reflections
Radiation source: fine-focus sealed tube	608 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
ϕ and ω scans	θmax = 25.9°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −15→15
Tmin = 0.968, Tmax = 0.985	k = −15→15
1881 measured reflections	l = −13→7

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.098	All H-atom parameters refined
S = 1.10	w = 1/[σ^2(Fo^2) + (0.06P)^2 + 0.7155P] where P = (Fo^2 + 2Fc^2)/3
672 reflections	(Δ/σ)max < 0.001
66 parameters	Δρmax = 0.25 e Å^−3
0 restraints	Δρmin = −0.21 e Å^−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. H atoms were located in the difference Fourier map and freely refined.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.50231 (7)	0.03017 (7)	0.20612 (8)	0.0206 (3)
N1	0.37420 (10)	0.03312 (10)	0.06494 (10)	0.0190 (3)
C1	0.48113 (10)	0.08117 (10)	0.11991 (11)	0.0157 (3)
C3	0.70166 (10)	0.24104 (10)	0.11752 (12)	0.0165 (3)
C2	0.57507 (10)	0.20580 (10)	0.07383 (12)	0.0159 (3)
H1A	0.3123 (15)	−0.0347 (16)	0.0958 (15)	0.028 (4)*
H1B	0.3599 (14)	0.0727 (14)	0.0053 (15)	0.026 (4)*
H3B	0.7230 (12)	0.1817 (12)	0.0852 (12)	0.015 (3)*
H3A	0.7026 (12)	0.2383 (12)	0.2091 (14)	0.019 (4)*
H2	0.5714 (11)	0.2042 (11)	−0.0175 (13)	0.014 (3)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0170 (5)	0.0201 (5)	0.0252 (5)	0.0097 (4)	0.0018 (3)	0.0056 (4)
N1	0.0157 (6)	0.0149 (6)	0.0236 (6)	0.0055 (5)	−0.0012 (4)	0.0022 (4)
C1	0.0157 (6)	0.0154 (6)	0.0180 (6)	0.0093 (5)	0.0023 (5)	−0.0016 (4)
C3	0.0151 (6)	0.0139 (6)	0.0208 (7)	0.0075 (5)	0.0001 (5)	0.0002 (5)
C2	0.0156 (6)	0.0149 (6)	0.0171 (6)	0.0076 (5)	−0.0001 (4)	0.0004 (5)

Geometric parameters (Å, º)

O1—C1	1.2419 (15)	C3—C2	1.5241 (16)
N1—C1	1.3279 (16)	C3—H3B	0.991 (14)
N1—H1A	0.897 (18)	C3—H3A	0.988 (15)
N1—H1B	0.893 (17)	C2—H2	0.986 (14)
C1—C2	1.5240 (16)
C1—N1—H1A	119.4 (10)	C2—C3—H3A	109.2 (8)
C1—N1—H1B	121.0 (10)	C2^i—C3—H3A	109.0 (8)
H1A—N1—H1B	118.9 (13)	H3B—C3—H3A	108.2 (11)
O1—C1—N1	122.44 (11)	C1—C2—C3	112.05 (10)
O1—C1—C2	121.97 (10)	C1—C2—C3^ii	108.86 (9)
N1—C1—C2	115.55 (11)	C3—C2—C3^ii	110.99 (11)
C2—C3—C2^i	111.00 (11)	C1—C2—H2	107.4 (7)
C2—C3—H3B	108.9 (8)	C3—C2—H2	110.3 (8)
C2^i—C3—H3B	110.5 (8)	C3^ii—C2—H2	107.0 (8)

Symmetry codes: (i) −y+1, x−y, z; (ii) −x+y+1, −x+1, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1B···O1^iii	0.893 (17)	1.975 (18)	2.8615 (14)	171.2 (14)
N1—H1A···O1^iv	0.897 (18)	2.030 (18)	2.8834 (14)	158.4 (13)

Symmetry codes: (iii) −y+1/3, x−y−1/3, z−1/3; (iv) x−y−1/3, x−2/3, −z+1/3.