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Acta Crystallogr Sect E Struct Rep Online. 2009 February 1; 65(Pt 2): o309.
Published online 2009 January 14. doi:  10.1107/S1600536809001251
PMCID: PMC2968226

N-Cyclo­hexyl-3-(4-hydr­oxy-6-oxo-1,6-dihydro­pyrimidin-5-yl)-3-p-tolyl­propanamide

Abstract

In the mol­ecule of the title compound, C20H25N3O3, the aromatic rings are oriented at a dihedral angle of 88.36 (3)°. The cyclo­hexane ring adopts a chair conformation. In the crystal structure, inter­molecular N—H(...)O and O—H(...)N hydrogen bonds link the mol­ecules. C—H(...)π inter­actions are also present.

Related literature

For general background, see: Johar et al. (2005 [triangle]); Janeba et al. (2005 [triangle]); Soloducho et al. (2003 [triangle]); Mathews & Asokan (2007 [triangle]); Lagoja (2005 [triangle]); Michael (2005 [triangle]); Erian (1993 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For ring-puckering parameters, see: Cremer & Pople (1975 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o309-scheme1.jpg

Experimental

Crystal data

  • C20H25N3O3
  • M r = 355.43
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o309-efi1.jpg
  • a = 7.1563 (12) Å
  • b = 19.637 (2) Å
  • c = 13.2746 (18) Å
  • β = 101.740 (2)°
  • V = 1826.5 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 298 (2) K
  • 0.23 × 0.16 × 0.14 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1998 [triangle]) T min = 0.980, T max = 0.988
  • 9491 measured reflections
  • 3216 independent reflections
  • 1916 reflections with I > 2σ(I)
  • R int = 0.073

Refinement

  • R[F 2 > 2σ(F 2)] = 0.048
  • wR(F 2) = 0.104
  • S = 1.02
  • 3216 reflections
  • 235 parameters
  • H-atom parameters constrained
  • Δρmax = 0.16 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT (Bruker, 1998 [triangle]); data reduction: SAINT (Bruker, 1998 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Bruker, 1998 [triangle]); software used to prepare material for publication: SHELXTL (Bruker, 1998 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809001251/hk2610sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809001251/hk2610Isup2.hkl

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

Acknowledgments

We thank the Natural Science Foundation of China (grant No. 20672090) and Natural Science Foundation of Jiangsu Province (grant No. BK2006033).

supplementary crystallographic information

Comment

The pyrimidines and their derivatives as a class of extremely important heterocyclic compounds are used in a wide array of synthetic and industrial applications. Not only they are an integral part of the genetic materials, viz. DNA and RNA as nucleotides and nucleosides but also play critical roles especially in pharmaceutical fields (Johar et al., 2005; Janeba et al., 2005). Some pyrimidine derivatives can give stable and good quality nanomaterials having many important electrical and optical properties (Soloducho et al., 2003; Mathews & Asokan, 2007), and also used as functional materials (Lagoja, 2005; Michael, 2005; Erian, 1993). We report herein the crystal structure of the title compound.

In the molecule of the title compound (Fig 1), the bond lengths (Allen et al., 1987) and angles are within normal ranges. Rings A (N1/N2/C1-C4) and B (C8-C13) are, of course, planar, and they are oriented at a dihedral angle of 88.36 (3)°. The cyclohexane ring C (C15-C20), having total puckering amplitude, QT, of 0.565 (3) Å, chair conformation [[var phi] = -30.33 (3)° and θ = 4.00 (3)°] (Cremer & Pople, 1975).

In the crystal structure, intermolecular N-H···O and O-H···N hydrogen bonds (Table 1) link the molecules, in which they may be effective in the stabilization of the structure. There also exist C–H···π interactions (Table 1).

Experimental

The title compound was prepared by the reaction of p-tolylidene-Meldrum's acid (1 mmol) with 6-hydroxypyrimidin-4(3H)-one (1 mmol) and cyclohexanamine (1 mmol) at 373 K in glacial acetic acid under microwave irradiation (maximum power 250 W, initial power 100 W) for 18 min (yield; 83%, m.p. 534–536 K). Crystals suitable for X-ray analysis were obtained from an ethanol solution by slow evaporation.

Refinement

H atoms were positioned geometrically, with O-H = 0.82 Å (for OH), N-H = 0.86 Å (for NH) and C-H = 0.93, 0.98, 0.97 and 0.96 Å for aromatic, methine, methylene and methyl H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = xUeq(C,N,O), where x = 1.5 for methyl and OH H and x = 1.2 for all other H atoms.

Figures

Fig. 1.
The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C20H25N3O3F(000) = 760
Mr = 355.43Dx = 1.293 Mg m3
Monoclinic, P21/nMelting point = 534–536 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 7.1563 (12) ÅCell parameters from 1921 reflections
b = 19.637 (2) Åθ = 2.6–27.7°
c = 13.2746 (18) ŵ = 0.09 mm1
β = 101.740 (2)°T = 298 K
V = 1826.5 (4) Å3Block, colorless
Z = 40.23 × 0.16 × 0.14 mm

Data collection

Bruker SMART CCD area-detector diffractometer3216 independent reflections
Radiation source: fine-focus sealed tube1916 reflections with I > 2σ(I)
graphiteRint = 0.073
[var phi] and ω scansθmax = 25.0°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 1998)h = −8→8
Tmin = 0.980, Tmax = 0.988k = −23→21
9491 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.104H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0354P)2] where P = (Fo2 + 2Fc2)/3
3216 reflections(Δ/σ)max = 0.001
235 parametersΔρmax = 0.16 e Å3
0 restraintsΔρmin = −0.19 e Å3

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.

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

xyzUiso*/Ueq
O10.8327 (2)1.04303 (8)0.89288 (11)0.0456 (5)
H1A0.85981.02970.95260.068*
O21.1335 (2)1.04358 (9)0.60752 (11)0.0511 (5)
O30.5892 (2)0.93937 (8)0.69802 (11)0.0447 (4)
N11.2782 (3)1.00038 (10)0.76292 (14)0.0387 (5)
H11.37860.99090.73940.046*
N21.1340 (3)0.99789 (9)0.90587 (13)0.0367 (5)
N30.7956 (3)0.91122 (9)0.59665 (13)0.0378 (5)
H30.85140.92510.54880.045*
C11.2753 (3)0.98462 (12)0.86043 (17)0.0396 (6)
H1B1.38150.96260.89870.048*
C20.9778 (3)1.02944 (11)0.84599 (16)0.0316 (5)
C30.9650 (3)1.04690 (10)0.74467 (15)0.0290 (5)
C41.1234 (3)1.03189 (11)0.69730 (17)0.0346 (6)
C50.6857 (3)0.95565 (11)0.63376 (16)0.0329 (6)
C60.6872 (3)1.02749 (11)0.59477 (16)0.0350 (6)
H6A0.55721.04220.56790.042*
H6B0.75631.02910.53910.042*
C70.7820 (3)1.07626 (11)0.68124 (15)0.0317 (6)
H70.69311.07950.72830.038*
C80.8005 (3)1.14835 (11)0.64204 (16)0.0302 (5)
C90.6815 (3)1.17248 (12)0.55327 (17)0.0366 (6)
H90.60221.14210.51080.044*
C100.6781 (3)1.24068 (12)0.52658 (18)0.0400 (6)
H100.59521.25530.46720.048*
C110.7955 (4)1.28759 (12)0.58638 (19)0.0393 (6)
C120.9218 (4)1.26311 (12)0.67173 (19)0.0412 (6)
H121.00681.29310.71150.049*
C130.9251 (3)1.19530 (12)0.69940 (17)0.0367 (6)
H131.01181.18060.75730.044*
C140.7807 (4)1.36269 (12)0.5595 (2)0.0587 (8)
H14A0.86431.37310.51350.088*
H14B0.81681.38920.62120.088*
H14C0.65171.37340.52690.088*
C150.8280 (3)0.84081 (11)0.63122 (17)0.0367 (6)
H150.72000.82660.66140.044*
C161.0092 (4)0.83383 (13)0.71338 (18)0.0488 (7)
H16A0.99990.86270.77140.059*
H16B1.11740.84920.68570.059*
C171.0429 (4)0.76056 (13)0.75025 (19)0.0532 (7)
H17A1.16490.75760.79790.064*
H17B0.94420.74730.78680.064*
C181.0418 (4)0.71171 (14)0.6614 (2)0.0593 (8)
H18A1.15380.71980.63240.071*
H18B1.04830.66530.68690.071*
C190.8642 (4)0.72005 (12)0.5780 (2)0.0556 (8)
H19A0.75360.70570.60430.067*
H19B0.87380.69100.52020.067*
C200.8367 (4)0.79365 (12)0.54125 (18)0.0435 (6)
H20A0.94180.80700.50950.052*
H20B0.71950.79750.49000.052*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0413 (10)0.0669 (13)0.0301 (9)0.0186 (9)0.0109 (8)0.0084 (8)
O20.0557 (12)0.0680 (13)0.0339 (10)0.0139 (10)0.0193 (9)0.0113 (8)
O30.0467 (11)0.0426 (10)0.0503 (10)0.0067 (8)0.0227 (9)0.0080 (8)
N10.0312 (12)0.0497 (13)0.0373 (11)0.0088 (10)0.0120 (10)0.0044 (10)
N20.0357 (12)0.0444 (13)0.0295 (11)0.0122 (10)0.0057 (9)0.0041 (9)
N30.0432 (13)0.0354 (12)0.0390 (11)0.0032 (10)0.0185 (10)0.0063 (9)
C10.0356 (15)0.0456 (15)0.0353 (14)0.0085 (12)0.0020 (12)0.0041 (11)
C20.0292 (13)0.0365 (14)0.0286 (13)0.0043 (11)0.0047 (11)−0.0004 (10)
C30.0301 (13)0.0301 (13)0.0257 (12)0.0031 (11)0.0030 (10)0.0007 (10)
C40.0371 (15)0.0360 (14)0.0304 (13)0.0042 (12)0.0061 (12)0.0026 (11)
C50.0296 (14)0.0373 (15)0.0302 (13)−0.0008 (11)0.0024 (11)0.0011 (11)
C60.0363 (15)0.0344 (14)0.0319 (13)0.0028 (11)0.0016 (11)0.0038 (10)
C70.0340 (14)0.0347 (14)0.0263 (12)0.0042 (11)0.0059 (11)0.0018 (10)
C80.0277 (13)0.0324 (14)0.0305 (13)0.0052 (11)0.0063 (11)0.0021 (11)
C90.0315 (14)0.0359 (15)0.0403 (14)−0.0024 (11)0.0020 (12)0.0036 (11)
C100.0372 (15)0.0397 (15)0.0420 (15)0.0012 (13)0.0053 (12)0.0081 (12)
C110.0348 (15)0.0356 (15)0.0493 (16)0.0008 (12)0.0130 (13)0.0031 (12)
C120.0328 (15)0.0378 (15)0.0537 (17)−0.0081 (12)0.0104 (13)−0.0084 (12)
C130.0292 (14)0.0418 (15)0.0376 (14)0.0014 (12)0.0034 (12)−0.0012 (11)
C140.066 (2)0.0381 (17)0.0760 (19)0.0006 (14)0.0241 (16)0.0061 (14)
C150.0355 (15)0.0356 (15)0.0413 (14)0.0049 (11)0.0132 (12)0.0074 (11)
C160.0460 (17)0.0539 (17)0.0462 (16)0.0012 (14)0.0090 (14)0.0077 (13)
C170.0423 (17)0.0642 (19)0.0551 (17)0.0101 (14)0.0148 (14)0.0224 (15)
C180.0567 (19)0.0523 (19)0.075 (2)0.0196 (15)0.0281 (17)0.0207 (15)
C190.059 (2)0.0414 (17)0.071 (2)0.0062 (14)0.0233 (17)−0.0026 (14)
C200.0406 (16)0.0427 (16)0.0477 (15)0.0063 (13)0.0099 (13)−0.0021 (12)

Geometric parameters (Å, °)

N1—C11.335 (3)C10—H100.9300
N1—C41.406 (3)C11—C121.384 (3)
N1—H10.8600C11—C141.516 (3)
N2—C11.305 (3)C12—C131.380 (3)
N2—C21.380 (3)C12—H120.9300
N3—C51.334 (3)C13—H130.9300
N3—C151.460 (3)C14—H14A0.9600
N3—H30.8600C14—H14B0.9600
O1—C21.341 (2)C14—H14C0.9600
O1—H1A0.8200C15—C161.522 (3)
O2—C41.230 (2)C15—C201.523 (3)
O3—C51.244 (2)C15—H150.9800
C1—H1B0.9300C16—C171.523 (3)
C2—C31.373 (3)C16—H16A0.9700
C3—C41.435 (3)C16—H16B0.9700
C3—C71.519 (3)C17—C181.519 (4)
C5—C61.504 (3)C17—H17A0.9700
C6—C71.542 (3)C17—H17B0.9700
C6—H6A0.9700C18—C191.515 (4)
C6—H6B0.9700C18—H18A0.9700
C7—C81.523 (3)C18—H18B0.9700
C7—H70.9800C19—C201.525 (3)
C8—C91.390 (3)C19—H19A0.9700
C8—C131.396 (3)C19—H19B0.9700
C9—C101.384 (3)C20—H20A0.9700
C9—H90.9300C20—H20B0.9700
C10—C111.383 (3)
C1—N1—C4122.5 (2)C13—C12—H12119.1
C1—N1—H1118.8C11—C12—H12119.1
C4—N1—H1118.8C12—C13—C8121.2 (2)
C1—N2—C2115.89 (18)C12—C13—H13119.4
C5—N3—C15124.82 (18)C8—C13—H13119.4
C5—N3—H3117.6C11—C14—H14A109.5
C15—N3—H3117.6C11—C14—H14B109.5
C2—O1—H1A109.5H14A—C14—H14B109.5
N2—C1—N1124.6 (2)C11—C14—H14C109.5
N2—C1—H1B117.7H14A—C14—H14C109.5
N1—C1—H1B117.7H14B—C14—H14C109.5
O1—C2—C3120.1 (2)N3—C15—C16111.59 (19)
O1—C2—N2115.78 (18)N3—C15—C20111.02 (18)
C3—C2—N2124.1 (2)C16—C15—C20110.01 (19)
C2—C3—C4118.5 (2)N3—C15—H15108.0
C2—C3—C7121.06 (19)C16—C15—H15108.0
C4—C3—C7120.26 (18)C20—C15—H15108.0
O2—C4—N1119.2 (2)C15—C16—C17111.8 (2)
O2—C4—C3126.4 (2)C15—C16—H16A109.3
N1—C4—C3114.34 (18)C17—C16—H16A109.3
O3—C5—N3122.4 (2)C15—C16—H16B109.3
O3—C5—C6121.4 (2)C17—C16—H16B109.3
N3—C5—C6116.14 (19)H16A—C16—H16B107.9
C5—C6—C7111.05 (17)C18—C17—C16111.8 (2)
C5—C6—H6A109.4C18—C17—H17A109.3
C7—C6—H6A109.4C16—C17—H17A109.3
C5—C6—H6B109.4C18—C17—H17B109.3
C7—C6—H6B109.4C16—C17—H17B109.3
H6A—C6—H6B108.0H17A—C17—H17B107.9
C3—C7—C8114.65 (18)C19—C18—C17111.7 (2)
C3—C7—C6112.09 (17)C19—C18—H18A109.3
C8—C7—C6112.24 (17)C17—C18—H18A109.3
C3—C7—H7105.7C19—C18—H18B109.3
C8—C7—H7105.7C17—C18—H18B109.3
C6—C7—H7105.7H18A—C18—H18B107.9
C9—C8—C13116.8 (2)C18—C19—C20111.7 (2)
C9—C8—C7121.7 (2)C18—C19—H19A109.3
C13—C8—C7121.2 (2)C20—C19—H19A109.3
C10—C9—C8121.5 (2)C18—C19—H19B109.3
C10—C9—H9119.2C20—C19—H19B109.3
C8—C9—H9119.2H19A—C19—H19B107.9
C11—C10—C9121.4 (2)C15—C20—C19110.4 (2)
C11—C10—H10119.3C15—C20—H20A109.6
C9—C10—H10119.3C19—C20—H20A109.6
C10—C11—C12117.3 (2)C15—C20—H20B109.6
C10—C11—C14120.5 (2)C19—C20—H20B109.6
C12—C11—C14122.2 (2)H20A—C20—H20B108.1
C13—C12—C11121.7 (2)
C2—N2—C1—N11.1 (3)C3—C7—C8—C9153.35 (19)
C4—N1—C1—N2−1.8 (4)C6—C7—C8—C924.0 (3)
C1—N2—C2—O1180.0 (2)C3—C7—C8—C13−33.2 (3)
C1—N2—C2—C3−0.1 (3)C6—C7—C8—C13−162.62 (19)
O1—C2—C3—C4179.7 (2)C13—C8—C9—C10−4.0 (3)
N2—C2—C3—C4−0.3 (3)C7—C8—C9—C10169.7 (2)
O1—C2—C3—C7−5.2 (3)C8—C9—C10—C111.0 (3)
N2—C2—C3—C7174.9 (2)C9—C10—C11—C122.5 (3)
C1—N1—C4—O2−178.3 (2)C9—C10—C11—C14−176.1 (2)
C1—N1—C4—C31.3 (3)C10—C11—C12—C13−3.1 (3)
C2—C3—C4—O2179.2 (2)C14—C11—C12—C13175.5 (2)
C7—C3—C4—O24.0 (4)C11—C12—C13—C80.1 (3)
C2—C3—C4—N1−0.3 (3)C9—C8—C13—C123.4 (3)
C7—C3—C4—N1−175.56 (18)C7—C8—C13—C12−170.3 (2)
C15—N3—C5—O3−4.8 (3)C5—N3—C15—C16−94.9 (3)
C15—N3—C5—C6174.2 (2)C5—N3—C15—C20142.0 (2)
O3—C5—C6—C766.6 (3)N3—C15—C16—C17179.60 (18)
N3—C5—C6—C7−112.4 (2)C20—C15—C16—C17−56.7 (3)
C2—C3—C7—C8117.4 (2)C15—C16—C17—C1854.0 (3)
C4—C3—C7—C8−67.5 (3)C16—C17—C18—C19−52.2 (3)
C2—C3—C7—C6−113.1 (2)C17—C18—C19—C2054.0 (3)
C4—C3—C7—C662.0 (3)N3—C15—C20—C19−178.2 (2)
C5—C6—C7—C344.5 (2)C16—C15—C20—C1957.8 (3)
C5—C6—C7—C8175.24 (18)C18—C19—C20—C15−57.0 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.861.982.813 (3)162
O1—H1A···N2ii0.821.952.753 (3)168
N3—H3···O2iii0.862.192.992 (4)155
C17—H17B···Cg2iv0.972.473.440 (3)177
C20—H20A···Cg2v0.972.743.629 (3)152

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HK2610).

References

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