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Acta Crystallogr Sect E Struct Rep Online. 2008 August 1; 64(Pt 8): o1451.
Published online 2008 July 9. doi:  10.1107/S1600536808019430
PMCID: PMC2962082

1,3-Dicyclo­hexyl-1-isonicotinoylurea monohydrate

Abstract

The title organic compound, C19H27N3O2·H2O, was synthesized from methyl­ene dicyclo­hexyl­amine, 4-pyridine­carboxylic acid and N,N′-dicyclo­hexyl­carbodiimide. The water molecule is involved in inter­molecular hydrogen bonds, linking symmetry-related urea mol­ecules into a two-dimensional supra­molecular ladder-like structure.

Related literature

For related literature, see: Iyer et al. (1971 [triangle]); Jew et al. (2003 [triangle]); Li et al. (2006 [triangle]); Mu & Qin (2003 [triangle]); Wachter et al. (1998 [triangle]).

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Object name is e-64-o1451-scheme1.jpg

Experimental

Crystal data

  • C19H27N3O2·H2O
  • M r = 347.45
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1451-efi1.jpg
  • a = 6.6694 (13) Å
  • b = 11.106 (2) Å
  • c = 13.248 (3) Å
  • α = 98.55 (3)°
  • β = 94.11 (3)°
  • γ = 97.49 (3)°
  • V = 958.0 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 298 (2) K
  • 0.40 × 0.33 × 0.28 mm

Data collection

  • Bruker SMART APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.968, T max = 0.977
  • 9385 measured reflections
  • 4284 independent reflections
  • 2948 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.119
  • S = 1.04
  • 4284 reflections
  • 342 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.14 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: APEX2 (Bruker, 2003 [triangle]); cell refinement: SAINT (Bruker, 2003 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808019430/cs2080sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808019430/cs2080Isup2.hkl

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

Acknowledgments

The authors are grateful to the K. C. Wong Magna Fund of Ningbo University.

supplementary crystallographic information

Comment

Pyridine derivatives are important intermediates widely used in the synthesis of drugs (Wachter et al., 1998; Jew et al., 2003) and pesticides (Li et al., 2006; Mu & Qin, 2003). The title organic compound, 1,3-dicyclohexyl-1-isonicotinoyl-urea, is an intermediate for the synthesis of an anti-tuberculosis drug (Iyer et al., 1971). We report here its synthesis and the crystal structure of its hydrate.

The title compound was synthesized from methylene dicyclohexylamine, 4-pyridinecarboxylic acid and N,N'-dicyclohexylcarbodiimide. Asymmetric unit of the crystal structure consists of the organic molecule and one H2O molecule, C19H27N3O2.H2O. As shown in Fig. 1 and Table 1, the cyclohexyl groups display chair-type conformation. Interestingly, there are some strong intermolecular hydrogen bonds between the organic molecules and the crystal water. Thus each water effectively links two molecules as O–H···O donor to their O=C groups and accepts one N–H···O hydrogen bridge from a third molecule into a novel two-dimensional supramolecular ladder-like structure through both O—H···O and N—H···O hydrogen bonds (Fig.2 and Table 2).

Experimental

Methylene dicyclohexylamine (0.21 g, 1 mmol), 4-pyridinecarboxylic acid (0.12 g, 1 mmol) and N,N'-dicyclohexylcarbodiimide (0.25 g, 1.2 mmol) were added to a 50 ml round bottom flask, then added dichloromethane (25 ml). The mixture was stirred for 12 h at 298 K, after that the reaction mixture was washed with water (10 ml × 3). The organic layer was dried with anhydrous Na2SO4 and evaporated in vacuo to give a residue. The crude product was purified by column chromatography (SiO2–EtOAc and hexane, 1:10) to afford the title compound as a colorless solid (yield 69%). 1H NMR (400 MHz, CDCl3): d 8.57 (d, J = 5.6 Hz, 2 H), 7.37 (d, J = 5.6 Hz, 2 H), 4.16–4.11 (m, 1 H), 3.27–3.22 (m, 1 H), 1.81–1.64 (m, 8 H), 1.60–1.57 (m, 2 H), 1.51–1.22 (m, 4 H), 1.17–1.08 (m, 2 H), 1.00–0.94 (m, 2 H), 0.85–0.76 (m, 2 H).

Refinement

All H atoms were located in difference Fourier maps and refined independently with isotropic displacement parameters.

Figures

Fig. 1.
Perspective view of the title complex with the atom-numbering scheme. Atomic displacement ellipsoids are shown at the 30% probability level.
Fig. 2.
View of the two-dimensional hydrogen-bonded supramolecular structure.

Crystal data

C19H27N3O2·H2OZ = 2
Mr = 347.45F000 = 376
Triclinic, P1Dx = 1.205 Mg m3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 6.6694 (13) ÅCell parameters from 3059 reflections
b = 11.106 (2) Åθ = 3.1–27.5º
c = 13.248 (3) ŵ = 0.08 mm1
α = 98.55 (3)ºT = 298 (2) K
β = 94.11 (3)ºBlock, colorless
γ = 97.49 (3)º0.40 × 0.33 × 0.28 mm
V = 958.0 (3) Å3

Data collection

Bruker SMART CCD APEXII diffractometer4284 independent reflections
Radiation source: fine-focus sealed tube2948 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.029
Detector resolution: 8.40 pixels mm-1θmax = 27.5º
T = 298(2) Kθmin = 3.1º
ω scansh = −8→7
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)k = −14→14
Tmin = 0.968, Tmax = 0.977l = −17→17
9385 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.119  w = 1/[σ2(Fo2) + (0.054P)2 + 0.1047P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
4284 reflectionsΔρmax = 0.14 e Å3
342 parametersΔρmin = −0.19 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O10.25983 (16)0.03443 (9)0.01466 (8)0.0451 (3)
O20.57498 (15)0.02624 (10)0.32408 (8)0.0437 (3)
O30.11137 (18)−0.00473 (13)−0.19210 (11)0.0546 (3)
N10.2456 (3)−0.40235 (13)0.05844 (13)0.0635 (4)
N20.23694 (19)−0.04403 (11)0.29989 (9)0.0357 (3)
N30.38649 (17)0.06272 (10)0.18085 (8)0.0325 (3)
C10.6570 (4)0.39594 (16)0.21113 (19)0.0636 (5)
C20.3121 (3)0.39686 (17)0.2711 (2)0.0667 (6)
C30.0813 (4)−0.32783 (19)0.47794 (19)0.0731 (6)
C4−0.0296 (4)−0.2166 (2)0.48890 (18)0.0690 (6)
C50.0909 (3)−0.34257 (17)0.03668 (17)0.0650 (5)
C60.5319 (3)0.45402 (16)0.29056 (16)0.0602 (5)
C70.2898 (3)0.25718 (15)0.26796 (16)0.0536 (5)
C80.6370 (3)0.25617 (14)0.20801 (17)0.0513 (4)
C90.3026 (3)−0.29165 (18)0.46441 (15)0.0593 (5)
C100.4223 (3)−0.33354 (15)0.09157 (14)0.0524 (4)
C110.1057 (3)−0.21635 (15)0.04690 (14)0.0498 (4)
C12−0.0014 (3)−0.1451 (2)0.40009 (15)0.0539 (4)
C130.3287 (3)−0.22376 (17)0.37377 (14)0.0505 (4)
C140.4515 (3)−0.20672 (14)0.10728 (12)0.0414 (4)
C150.2219 (2)−0.11014 (14)0.38727 (11)0.0371 (3)
C160.4161 (2)0.19968 (12)0.18824 (12)0.0376 (3)
C170.4089 (2)0.01254 (12)0.27488 (10)0.0326 (3)
C180.2898 (2)−0.14614 (12)0.08435 (10)0.0351 (3)
C190.3093 (2)−0.00917 (12)0.09085 (10)0.0324 (3)
H10.289 (2)−0.0558 (14)0.4476 (12)0.039 (4)*
H20.365 (2)0.2150 (14)0.1216 (13)0.045 (4)*
H30.579 (3)−0.1618 (15)0.1334 (12)0.047 (4)*
H4−0.010 (3)−0.1756 (17)0.0266 (14)0.064 (5)*
H50.260 (3)−0.2770 (17)0.3092 (15)0.063 (5)*
H60.153 (4)−0.014 (2)−0.128 (2)0.093 (8)*
H7−0.061 (3)−0.1957 (18)0.3374 (16)0.064 (6)*
H80.341 (3)0.2358 (16)0.3374 (15)0.060 (5)*
H90.542 (3)0.5415 (19)0.2889 (15)0.074 (6)*
H100.118 (3)−0.0381 (17)0.2633 (15)0.063 (5)*
H110.686 (3)0.2370 (19)0.2787 (17)0.078 (6)*
H120.212 (4)−0.019 (2)−0.2310 (18)0.084 (7)*
H130.538 (3)−0.3773 (17)0.1074 (14)0.063 (5)*
H140.599 (3)0.4149 (19)0.1418 (19)0.084 (7)*
H150.373 (3)−0.2369 (19)0.5286 (17)0.075 (6)*
H160.706 (3)0.2202 (18)0.1530 (16)0.072 (6)*
H170.473 (3)−0.1978 (17)0.3659 (14)0.065 (6)*
H180.587 (3)0.4396 (17)0.3617 (16)0.067 (6)*
H190.015 (3)−0.387 (2)0.4148 (18)0.086 (7)*
H20−0.041 (3)−0.3951 (19)0.0133 (16)0.078 (6)*
H210.258 (3)0.4170 (19)0.2025 (18)0.079 (7)*
H220.150 (3)0.2190 (17)0.2552 (14)0.066 (6)*
H230.067 (3)−0.369 (2)0.5385 (18)0.087 (7)*
H240.018 (4)−0.160 (2)0.554 (2)0.094 (8)*
H250.379 (3)−0.3669 (19)0.4574 (15)0.072 (6)*
H260.235 (3)0.431 (2)0.3277 (19)0.093 (7)*
H27−0.064 (3)−0.0673 (19)0.4108 (15)0.071 (6)*
H28−0.174 (4)−0.239 (2)0.4927 (19)0.099 (8)*
H290.800 (4)0.430 (2)0.2219 (18)0.091 (7)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0575 (7)0.0422 (6)0.0340 (6)0.0022 (5)−0.0074 (5)0.0113 (5)
O20.0385 (6)0.0526 (6)0.0395 (6)0.0011 (5)−0.0045 (5)0.0143 (5)
O30.0408 (6)0.0825 (9)0.0413 (7)0.0172 (6)−0.0019 (5)0.0078 (6)
N10.0736 (11)0.0339 (7)0.0786 (11)−0.0003 (8)0.0038 (9)0.0040 (7)
N20.0354 (7)0.0420 (7)0.0322 (6)0.0058 (5)0.0029 (5)0.0134 (5)
N30.0406 (7)0.0281 (6)0.0287 (6)0.0027 (5)0.0015 (5)0.0066 (4)
C10.0734 (14)0.0375 (9)0.0786 (15)−0.0047 (9)0.0201 (11)0.0097 (9)
C20.0732 (14)0.0413 (10)0.0859 (16)0.0170 (10)0.0152 (12)−0.0004 (10)
C30.1100 (19)0.0512 (11)0.0591 (13)−0.0050 (12)0.0115 (12)0.0254 (10)
C40.0696 (14)0.0793 (15)0.0660 (14)0.0037 (12)0.0264 (11)0.0335 (12)
C50.0594 (12)0.0423 (10)0.0837 (14)−0.0081 (9)−0.0013 (10)−0.0042 (9)
C60.0873 (15)0.0319 (9)0.0589 (12)0.0045 (9)0.0076 (10)0.0019 (8)
C70.0506 (11)0.0397 (9)0.0706 (13)0.0082 (8)0.0159 (9)0.0022 (8)
C80.0533 (10)0.0342 (8)0.0661 (12)−0.0008 (7)0.0210 (9)0.0059 (8)
C90.0894 (15)0.0476 (10)0.0478 (11)0.0204 (10)0.0105 (10)0.0192 (8)
C100.0619 (11)0.0392 (9)0.0578 (11)0.0116 (9)0.0042 (9)0.0102 (8)
C110.0461 (9)0.0397 (9)0.0580 (11)−0.0006 (8)−0.0036 (8)−0.0007 (7)
C120.0492 (10)0.0645 (12)0.0537 (11)0.0056 (9)0.0152 (9)0.0253 (9)
C130.0656 (12)0.0488 (9)0.0435 (10)0.0182 (9)0.0106 (9)0.0172 (8)
C140.0468 (9)0.0357 (8)0.0411 (8)0.0023 (7)0.0018 (7)0.0082 (6)
C150.0449 (8)0.0391 (8)0.0289 (7)0.0050 (7)0.0041 (6)0.0108 (6)
C160.0530 (9)0.0272 (7)0.0323 (8)0.0048 (6)0.0011 (6)0.0064 (6)
C170.0387 (8)0.0289 (7)0.0302 (7)0.0056 (6)0.0026 (6)0.0049 (5)
C180.0427 (8)0.0320 (7)0.0291 (7)0.0006 (6)0.0047 (6)0.0039 (5)
C190.0321 (7)0.0336 (7)0.0309 (7)0.0013 (6)0.0026 (6)0.0067 (6)

Geometric parameters (Å, °)

O1—C191.2253 (16)C5—H200.99 (2)
O2—C171.2239 (17)C6—H90.97 (2)
O3—H60.89 (3)C6—H181.03 (2)
O3—H120.89 (2)C7—C161.516 (2)
N1—C101.325 (2)C7—H81.030 (19)
N1—C51.335 (3)C7—H220.96 (2)
N2—C171.3222 (19)C8—C161.513 (2)
N2—C151.4628 (18)C8—H111.03 (2)
N2—H100.91 (2)C8—H160.95 (2)
N3—C191.3587 (18)C9—C131.518 (2)
N3—C171.4443 (17)C9—H151.01 (2)
N3—C161.4957 (17)C9—H251.03 (2)
C1—C61.511 (3)C10—C141.379 (2)
C1—C81.535 (2)C10—H130.988 (19)
C1—H141.03 (2)C11—C181.382 (2)
C1—H290.97 (2)C11—H40.98 (2)
C2—C61.508 (3)C12—C151.518 (2)
C2—C71.533 (2)C12—H70.96 (2)
C2—H211.02 (2)C12—H271.00 (2)
C2—H260.99 (2)C13—C151.522 (2)
C3—C91.509 (3)C13—H51.008 (19)
C3—C41.515 (3)C13—H170.98 (2)
C3—H191.02 (2)C14—C181.382 (2)
C3—H230.99 (2)C14—H30.943 (17)
C4—C121.523 (3)C15—H10.969 (16)
C4—H240.99 (3)C16—H20.970 (17)
C4—H280.97 (3)C18—C191.4988 (19)
C5—C111.378 (2)
H6—O3—H12107 (2)C1—C8—H16109.9 (12)
C10—N1—C5116.45 (15)H11—C8—H16114.0 (16)
C17—N2—C15124.07 (13)C3—C9—C13111.55 (18)
C17—N2—H10118.8 (12)C3—C9—H15110.0 (12)
C15—N2—H10117.0 (12)C13—C9—H15108.9 (12)
C19—N3—C17121.70 (11)C3—C9—H25111.3 (11)
C19—N3—C16119.75 (11)C13—C9—H25110.8 (11)
C17—N3—C16117.70 (11)H15—C9—H25104.0 (16)
C6—C1—C8111.14 (16)N1—C10—C14124.03 (17)
C6—C1—H14105.6 (12)N1—C10—H13116.8 (11)
C8—C1—H14109.7 (12)C14—C10—H13119.1 (11)
C6—C1—H29113.1 (14)C5—C11—C18118.67 (17)
C8—C1—H29108.9 (14)C5—C11—H4121.7 (11)
H14—C1—H29108.3 (19)C18—C11—H4119.6 (11)
C6—C2—C7111.16 (17)C15—C12—C4111.31 (16)
C6—C2—H21107.2 (12)C15—C12—H7106.9 (12)
C7—C2—H21110.3 (12)C4—C12—H7109.6 (12)
C6—C2—H26109.6 (13)C15—C12—H27107.6 (11)
C7—C2—H26107.3 (13)C4—C12—H27111.5 (11)
H21—C2—H26111.3 (18)H7—C12—H27109.9 (16)
C9—C3—C4111.04 (17)C9—C13—C15110.16 (14)
C9—C3—H19109.2 (13)C9—C13—H5109.9 (11)
C4—C3—H19107.8 (12)C15—C13—H5105.7 (10)
C9—C3—H23110.5 (13)C9—C13—H17111.8 (11)
C4—C3—H23109.8 (13)C15—C13—H17108.5 (11)
H19—C3—H23108.4 (18)H5—C13—H17110.5 (16)
C3—C4—C12111.67 (18)C10—C14—C18118.81 (16)
C3—C4—H24111.1 (14)C10—C14—H3120.8 (10)
C12—C4—H24108.5 (14)C18—C14—H3120.3 (10)
C3—C4—H28112.3 (14)N2—C15—C12108.20 (13)
C12—C4—H28108.1 (15)N2—C15—C13112.09 (12)
H24—C4—H28105 (2)C12—C15—C13110.68 (15)
N1—C5—C11123.98 (18)N2—C15—H1108.0 (9)
N1—C5—H20115.5 (11)C12—C15—H1110.7 (9)
C11—C5—H20120.5 (12)C13—C15—H1107.1 (9)
C2—C6—C1110.99 (17)N3—C16—C8112.88 (13)
C2—C6—H9109.3 (12)N3—C16—C7110.71 (13)
C1—C6—H9109.7 (12)C8—C16—C7111.38 (14)
C2—C6—H18108.5 (11)N3—C16—H2105.2 (9)
C1—C6—H18108.6 (11)C8—C16—H2108.1 (9)
H9—C6—H18109.8 (16)C7—C16—H2108.2 (9)
C16—C7—C2110.43 (16)O2—C17—N2126.20 (13)
C16—C7—H8107.0 (10)O2—C17—N3120.23 (13)
C2—C7—H8111.0 (10)N2—C17—N3113.55 (12)
C16—C7—H22110.3 (11)C11—C18—C14118.01 (14)
C2—C7—H22112.4 (11)C11—C18—C19118.81 (14)
H8—C7—H22105.5 (15)C14—C18—C19123.02 (13)
C16—C8—C1110.19 (16)O1—C19—N3122.14 (13)
C16—C8—H11105.7 (12)O1—C19—C18119.26 (12)
C1—C8—H11109.8 (12)N3—C19—C18118.59 (12)
C16—C8—H16107.1 (12)
C9—C3—C4—C1254.2 (3)C1—C8—C16—N3178.11 (14)
C10—N1—C5—C11−0.1 (3)C1—C8—C16—C7−56.6 (2)
C7—C2—C6—C156.2 (3)C2—C7—C16—N3−177.01 (16)
C8—C1—C6—C2−56.5 (3)C2—C7—C16—C856.5 (2)
C6—C2—C7—C16−56.0 (3)C15—N2—C17—O2−6.0 (2)
C6—C1—C8—C1656.4 (2)C15—N2—C17—N3175.33 (11)
C4—C3—C9—C13−56.0 (2)C19—N3—C17—O2123.81 (15)
C5—N1—C10—C142.1 (3)C16—N3—C17—O2−66.79 (17)
N1—C5—C11—C18−1.7 (3)C19—N3—C17—N2−57.40 (17)
C3—C4—C12—C15−54.4 (3)C16—N3—C17—N2111.99 (14)
C3—C9—C13—C1557.5 (2)C5—C11—C18—C141.6 (2)
N1—C10—C14—C18−2.2 (3)C5—C11—C18—C19177.11 (16)
C17—N2—C15—C12171.48 (14)C10—C14—C18—C110.2 (2)
C17—N2—C15—C13−66.20 (19)C10—C14—C18—C19−175.11 (14)
C4—C12—C15—N2179.01 (16)C17—N3—C19—O1168.24 (12)
C4—C12—C15—C1355.8 (2)C16—N3—C19—O1−0.9 (2)
C9—C13—C15—N2−178.00 (15)C17—N3—C19—C18−13.44 (19)
C9—C13—C15—C12−57.1 (2)C16—N3—C19—C18177.38 (12)
C19—N3—C16—C8−115.27 (16)C11—C18—C19—O1−52.43 (19)
C17—N3—C16—C875.12 (17)C14—C18—C19—O1122.84 (16)
C19—N3—C16—C7119.10 (16)C11—C18—C19—N3129.19 (15)
C17—N3—C16—C7−50.51 (18)C14—C18—C19—N3−55.53 (19)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H6···O10.89 (3)1.95 (3)2.7959 (18)158 (2)
N2—H10···O3i0.91 (2)1.89 (2)2.7949 (19)170 (2)
O3—H12···O2ii0.89 (2)1.95 (3)2.8319 (19)171 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CS2080).

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