1,3-Dicyclo­hexyl-3-[(pyridin-2-yl)carbon­yl]urea monohydrate from synchrotron radiation

Alessandra C Pinheiro; Marcus V N de Souza; James L Wardell; Solange M S V Wardell; Edward R T Tiekink

doi:10.1107/S1600536811037512

. 2011 Sep 17;67(Pt 10):o2676–o2677. doi: 10.1107/S1600536811037512

1,3-Dicyclohexyl-3-[(pyridin-2-yl)carbonyl]urea monohydrate from synchrotron radiation

Alessandra C Pinheiro ^a, Marcus V N de Souza ^a, James L Wardell ^b,^‡, Solange M S V Wardell ^c, Edward R T Tiekink ^d,^*

PMCID: PMC3201464 PMID: 22058785

Abstract

The title urea derivative crystallizes as a monohydrate, C₁₉H₂₇N₃O₂·H₂O. The central C₃N grouping is almost planar (r.m.s. deviation = 0.0092 Å), and the amide and pyridine groups are substantially twisted out this plane [dihedral angles = 62.80 (12) and 34.98 (10)°, respectively]. Supramolecular double chains propagating along the b-axis direction feature in the crystal packing whereby linear chains sustained by N—H⋯O hydrogen bonds formed between the amide groups are linked by helical chains of water molecules (linked by O—H⋯O hydrogen bonds). The H atom that participates in these water chains is disordered over two positions of equal occupancy. The double chains are connected into a two-dimensional array by C—H⋯O contacts and the layers stack along the a axis.

Related literature

For the preparation of N-(arenecarbonyl)-N,N′-dicyclohexylurea derivatives, see: Kaiser et al. (2008 ▶); Neves Filho et al. (2007 ▶); Schotman (1991 ▶). For the crystal structures of related N-(arenecarbonyl)-N,N′-dicyclohexylurea derivatives, see: Chérioux et al. (2002 ▶); Cai et al. (2009 ▶); Dhinaa et al. (2010 ▶); Orea Flores et al. (2006 ▶); Gallagher et al. (1999 ▶); Wang & Zhou (2008 ▶); Wu et al. (2006 ▶).

Experimental

Crystal data

C₁₉H₂₇N₃O₂·H₂O
M _r = 347.46
Monoclinic,
a = 18.639 (19) Å
b = 5.035 (5) Å
c = 21.59 (2) Å
β = 111.395 (9)°
V = 1887 (3) Å³
Z = 4
Synchrotron radiation
λ = 0.6905 Å
μ = 0.05 mm⁻¹
T = 120 K
0.25 × 0.08 × 0.02 mm

Data collection

Bruker SMART APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2007 ▶) T _min = 0.743, T _max = 1.000
13440 measured reflections
3810 independent reflections
3200 reflections with I > 2σ(I)
R _int = 0.043

Refinement

R[F ² > 2σ(F ²)] = 0.048
wR(F ²) = 0.126
S = 1.06
3810 reflections
238 parameters
7 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811037512/hb6408sup1.cif

e-67-o2676-sup1.cif^{(21.9KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811037512/hb6408Isup2.hkl

e-67-o2676-Isup2.hkl^{(183KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811037512/hb6408Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1n⋯O1ⁱ	0.88 (1)	2.07 (1)	2.908 (3)	160 (2)
O1w—H1w⋯O2	0.84 (2)	1.98 (2)	2.820 (3)	174 (2)
O1w—H2w⋯O1wⁱⁱ	0.84 (3)	1.97 (3)	2.773 (4)	162 (4)
O1w—H3w⋯O1wⁱⁱⁱ	0.84 (3)	1.98 (3)	2.799 (4)	167 (4)
C17—H17⋯O1w^iv	0.95	2.59	3.517 (4)	164
C18—H18⋯O2^v	0.95	2.47	3.367 (4)	157

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

We thank Professor W. Clegg and the synchrotron component, based at Daresbury, of the EPSRC National Crystallographic Service, University of Southampton, for the data collection. JLW acknowledges support from CAPES and FAPEMIG (Brazil).

supplementary crystallographic information

Comment

Reactions of arenecarboxylic acids with dicyclohexylcarbodiimide (DCC) in the presence of a catalyst, such as 1-hydroxybenzotriazole, HOBt, produce N-(arenecarbonyl)-N,N'-dicyclohexylureas (Kaiser et al., 2008; Neves Filho et al., 2007; Schotman, 1991). Several crystal structures of N-(arenecarbonyl)-N,N'-dicyclohexylurea derivatives have been reported (Chérioux et al., 2002; Cai et al., 2009; Dhinaa et al., 2010; Orea Flores et al., 2006; Gallagher et al., 1999; Wang et al., 2008; Wu et al., 2006). Herein, we now report the crystal structure of the monohydrate of N,N'-dicyclohexyl- N-(pyridine-2-carbonyl)urea, (I).

A molecule of N,N'-dicyclohexyl- N-(pyridine-2-carbonyl)urea and a water molecule of solvation comprise the asymmetric unit of (I). Two of the water bound H atoms are disordered and have been assigned site occupancy factors of 0.50. The disorder is accounted for in terms of the dictates of hydrogen bonding in the crystal structure, see below. The pyridine ring is twisted out of the central C₃N plane (r.m.s. deviation = 0.0092 Å) with the dihedral angle being 34.98 (10) °. The amide group is even more twisted out of the plane through the central ring forming a dihedral angle of 62.80 (12) °. Each of the cyclohexyl rings adopts a chair conformation.

Hydrogen bonding of the type O—H···O and N—H···O lead to the formation of supramolecular chains along the b axis, Table 1. The amide groups self-associate to form linear chains. Pairs of chains are linked by hydrogen bonding interactions involving the water molecules. Thus, the carbonyl-O2 atom is linked to the water molecule, and the remaining water-H atoms (each with site occupancy factor = 1/2) link water molecules into a helical chain, Fig. 2. The chains are linked into layers via C—H···O interactions, Table 1, which stack along the a direction.

Experimental

To a stirred solution of the pyridin-2-carboxylic acid (1 mmol) in anhydrous CH₂Cl₂ (25 ml) were added DCC (0.8 mmol, 1 equiv.) and HOBt (ca 10 mg). After leaving at room temperature for 2 h, the precipitate of N,N'-dicyclohexylurea was removed and the filtrate was poured into saturated aqueous NaHCO₃ solution (20 ml). The organic material was extracted into EtOAc (3 x 20 ml), the combined layers dried over MgSO₄, and rotary evaporated. The residue was chromatographed (10% to 50% EtOAc/hexanes) to give N-(pyridin-2-carbonyl)-N,N'-dicyclohexylurea. Yield: 60%, as a white solid. Recrystallization from moist EtOH gave the monohydrate as colourless laths.

¹H NMR (400 MHz, CDCl₃) δ: 8.57 (d, J = 3.6, 1H, H6), 7.78 (m, 1H, H4), 7.68 (d, J = 7.6, 1H, H3), 7.37 (m, 1H, H5), 6.09 (s, 1H, NH), 4.20 (m, 1H, NCH), 3.51 (m, 1H, NHCH), 0.8–2 (m, 20 H, cyclohexyl) p.p.m.. ¹³C NMR (100 MHz, CDCl₃) δ: 168.1 (CON), 154.0 (CONH), 153.9 (C2), 148.5 (C6), 137.0 (C4), 125.1, 122.9 (C3 and C5), 56.4 (NCH), 49.8 (NHCH), 33.9, 32.4, 30.7, 26.2, 25.6, 25.4, 25.3, 24.9, 24.6 (cyclohexyl) p.p.m.. M.pt.: 415 K. IR (cm^-1; KBr): 1710 (CONH) and 1680 (CON).