PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 January 1; 66(Pt 1): o193.
Published online 2009 December 19. doi:  10.1107/S1600536809053586
PMCID: PMC2980275

1,3-Bis(4-methyl­benz­yl)pyrimidine-2,4(1H,3H)-dione

Abstract

In the title mol­ecule, C20H20N2O2, the central pyrimidine ring forms dihedral angles of 71.9 (1) and 69.8 (1)° with the two benzene rings. In the crystal, weak inter­molecular C—H(...)O hydrogen bonds link mol­ecules into centrosymmetric dimers. The crystal packing exhibits also π–π inter­actions as indicated by short distances of 3.674 (2) Å between the centroids of the pyrimidine rings of neighbouring mol­ecules.

Related literature

For the crystal structure of 1,3-bis­(4-chloro­benz­yl)pyrimidine-2,4(1H,3H)-dione, see: Yang & Li (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o193-scheme1.jpg

Experimental

Crystal data

  • C20H20N2O2
  • M r = 320.38
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o193-efi1.jpg
  • a = 9.4182 (19) Å
  • b = 10.102 (2) Å
  • c = 10.448 (2) Å
  • α = 66.25 (3)°
  • β = 80.79 (3)°
  • γ = 71.18 (3)°
  • V = 860.7 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 293 K
  • 0.20 × 0.20 × 0.20 mm

Data collection

  • Rigaku Saturn CCD area-detector diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006 [triangle]) T min = 0.984, T max = 0.984
  • 8622 measured reflections
  • 3001 independent reflections
  • 2529 reflections with I > 2σ(I)
  • R int = 0.034

Refinement

  • R[F 2 > 2σ(F 2)] = 0.088
  • wR(F 2) = 0.161
  • S = 1.27
  • 3001 reflections
  • 219 parameters
  • H-atom parameters constrained
  • Δρmax = 0.14 e Å−3
  • Δρmin = −0.17 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2006 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; 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/S1600536809053586/cv2673sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809053586/cv2673Isup2.hkl

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

Acknowledgments

This work was supported by the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Education Department, China (grant No. 2007150036).

supplementary crystallographic information

Comment

In continuation of our search for new biologically active pyrimidine derivatives (Yang & Li, 2006), we present here the title compound (I).

In (I) (Fig. 1), all bond lengths and angles are normal and correspond to those observed in the related 1,3-bis(4-chlorobenzyl)pyrimidine-2,4(1H,3H)-dione (Yang & Li, 2006). The central pyrimidine ring forms dihedral angles of 71.9 (1)° and 69.8 (1)° with the two benzene rings, respectively. Weak intermolecular C—H···O hydrogen bonds (Table 1) link molecules into centrosymmetric dimers. The crystal packing exhibits also π-π interactions proved by short distances of 3.674 (2) Å between the centroids of pyrimidine rings from the neighbouring molecules.

Experimental

Uracil (0.56 g, 5 mmol) and anhydrous potassium carbonate (0.84 g, 6 mmol) were mixed in N,N-dimethylformamide (20 ml). A solution of 4-methyl-benzyl chloride (0.70 g, 5 mmol) in acetone (10 ml) was then added dropwise, with stirring, at room temperature, and the mixture was stirred for another 10 h and then refluxed for 4 h. The solvent was evaporated in vacuo and the residue was washed with water. The resulting white precipitate was filtered off and purified by column chromatography on silica gel (petroleum ether:ethyl acetate = 2:1). The title compound was recrystallized from ethanol and single crystals of (I) were obtained by slow evaporation.

Refinement

All H atoms were placed in calculated positions, with C—H = 0.93 - 0.97 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2–1.5 Ueq(C).

Figures

Fig. 1.
The molecular structure of (I), with displacement ellipsoids drawn at the 30% probability level. H atoms omitted for clarity.

Crystal data

C20H20N2O2Z = 2
Mr = 320.38F(000) = 340
Triclinic, P1Dx = 1.236 Mg m3
a = 9.4182 (19) ÅMo Kα radiation, λ = 0.71073 Å
b = 10.102 (2) ÅCell parameters from 2459 reflections
c = 10.448 (2) Åθ = 2.1–27.9°
α = 66.25 (3)°µ = 0.08 mm1
β = 80.79 (3)°T = 293 K
γ = 71.18 (3)°Prism, colourless
V = 860.7 (3) Å30.20 × 0.20 × 0.20 mm

Data collection

Rigaku Saturn CCD area-detector diffractometer3001 independent reflections
Radiation source: fine-focus sealed tube2529 reflections with I > 2σ(I)
graphiteRint = 0.034
Detector resolution: 28.5714 pixels mm-1θmax = 25.0°, θmin = 2.1°
phi and ω scansh = −11→11
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006)k = −11→12
Tmin = 0.984, Tmax = 0.984l = −12→12
8622 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)] = 0.088H-atom parameters constrained
wR(F2) = 0.161w = 1/[σ2(Fo2) + (0.0409P)2 + 0.3734P] where P = (Fo2 + 2Fc2)/3
S = 1.27(Δ/σ)max < 0.001
3001 reflectionsΔρmax = 0.14 e Å3
219 parametersΔρmin = −0.17 e Å3
Primary atom site location: structure-invariant direct methods

Special details

Experimental. Software + citation
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
O10.4982 (3)0.1871 (3)0.6026 (3)0.0711 (7)
O20.3392 (2)0.4909 (3)0.8542 (2)0.0661 (7)
N10.4156 (2)0.3369 (3)0.7299 (2)0.0452 (6)
N20.2678 (3)0.5867 (3)0.6284 (3)0.0491 (6)
C10.3407 (3)0.4728 (3)0.7458 (3)0.0483 (7)
C20.6580 (3)0.1972 (3)0.8500 (3)0.0431 (7)
C30.1828 (3)0.7346 (3)0.6372 (4)0.0596 (9)
H3A0.19600.81470.54940.072*
H3B0.22270.74670.71050.072*
C40.3402 (3)0.4340 (4)0.4937 (3)0.0562 (8)
H40.33700.42350.40990.067*
C50.2677 (3)0.5635 (4)0.5079 (3)0.0543 (8)
H50.21430.64220.43300.065*
C60.7652 (3)0.0843 (3)0.8165 (3)0.0529 (8)
H60.73580.01490.79730.064*
C70.4931 (3)0.2105 (3)0.8525 (3)0.0521 (8)
H7A0.48270.11700.85500.063*
H7B0.44510.22490.93720.063*
C8−0.2911 (3)0.7765 (3)0.7206 (3)0.0492 (8)
C90.4242 (3)0.3092 (4)0.6070 (3)0.0526 (8)
C10−0.0848 (4)0.8346 (4)0.5629 (3)0.0577 (8)
H10−0.05100.88440.47300.069*
C110.0171 (3)0.7490 (3)0.6673 (3)0.0473 (7)
C120.9150 (4)0.0739 (4)0.8113 (3)0.0614 (9)
H120.9854−0.00400.79010.074*
C13−0.0374 (4)0.6768 (4)0.7999 (3)0.0599 (9)
H130.02860.61890.87260.072*
C14−0.1891 (4)0.6899 (3)0.8254 (3)0.0582 (9)
H14−0.22310.63920.91500.070*
C150.9639 (4)0.1749 (4)0.8365 (3)0.0630 (10)
C16−0.4572 (3)0.7930 (4)0.7502 (4)0.0696 (10)
H16A−0.50290.87700.77870.104*
H16B−0.47120.70250.82350.104*
H16C−0.50300.80990.66710.104*
C170.7049 (4)0.2967 (4)0.8803 (3)0.0601 (9)
H170.63490.37140.90640.072*
C18−0.2361 (4)0.8480 (4)0.5894 (4)0.0610 (9)
H18−0.30220.90660.51680.073*
C190.8569 (4)0.2856 (4)0.8720 (4)0.0717 (11)
H190.88690.35480.89090.086*
C201.1291 (4)0.1673 (6)0.8239 (4)0.1041 (16)
H20A1.18840.06360.86010.156*
H20B1.14620.21950.87640.156*
H20C1.15720.21370.72740.156*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0713 (16)0.0577 (15)0.0837 (18)−0.0011 (12)−0.0192 (13)−0.0334 (13)
O20.0646 (15)0.0773 (16)0.0552 (14)−0.0105 (12)−0.0044 (11)−0.0303 (13)
N10.0379 (13)0.0480 (15)0.0434 (14)−0.0112 (11)−0.0041 (11)−0.0106 (12)
N20.0424 (14)0.0438 (14)0.0534 (16)−0.0082 (11)−0.0015 (12)−0.0138 (12)
C10.0381 (17)0.0513 (19)0.052 (2)−0.0148 (14)0.0023 (14)−0.0162 (16)
C20.0462 (17)0.0411 (16)0.0355 (15)−0.0103 (14)−0.0092 (13)−0.0066 (13)
C30.0519 (19)0.0480 (19)0.076 (2)−0.0136 (16)0.0004 (16)−0.0216 (17)
C40.053 (2)0.057 (2)0.058 (2)−0.0112 (17)−0.0080 (16)−0.0218 (17)
C50.0481 (19)0.058 (2)0.0452 (19)−0.0149 (16)−0.0077 (14)−0.0052 (16)
C60.055 (2)0.0476 (18)0.0524 (19)−0.0145 (15)−0.0082 (15)−0.0126 (15)
C70.0487 (18)0.0488 (18)0.0469 (18)−0.0157 (15)−0.0059 (14)−0.0032 (14)
C80.0509 (19)0.0464 (18)0.0543 (19)−0.0124 (15)0.0041 (15)−0.0262 (15)
C90.0415 (18)0.054 (2)0.062 (2)−0.0143 (16)−0.0056 (15)−0.0203 (17)
C100.059 (2)0.056 (2)0.0474 (19)−0.0160 (16)0.0000 (15)−0.0094 (16)
C110.0463 (17)0.0376 (16)0.0568 (19)−0.0090 (14)−0.0008 (15)−0.0192 (14)
C120.052 (2)0.060 (2)0.054 (2)−0.0038 (17)−0.0051 (16)−0.0103 (17)
C130.056 (2)0.060 (2)0.0489 (19)−0.0025 (16)−0.0081 (16)−0.0143 (16)
C140.060 (2)0.054 (2)0.0499 (19)−0.0094 (17)0.0092 (16)−0.0181 (16)
C150.050 (2)0.073 (2)0.047 (2)−0.0214 (19)−0.0100 (15)0.0015 (17)
C160.053 (2)0.081 (3)0.083 (3)−0.0202 (18)0.0078 (18)−0.042 (2)
C170.058 (2)0.056 (2)0.068 (2)−0.0105 (17)−0.0118 (17)−0.0254 (17)
C180.051 (2)0.070 (2)0.057 (2)−0.0112 (17)−0.0121 (16)−0.0191 (18)
C190.075 (3)0.072 (2)0.079 (3)−0.034 (2)−0.024 (2)−0.021 (2)
C200.055 (2)0.149 (4)0.084 (3)−0.042 (3)−0.010 (2)−0.007 (3)

Geometric parameters (Å, °)

O1—C91.221 (4)C8—C141.382 (4)
O2—C11.215 (3)C8—C161.513 (4)
N1—C11.390 (4)C10—C181.381 (4)
N1—C91.405 (4)C10—C111.378 (4)
N1—C71.478 (3)C10—H100.9300
N2—C51.370 (4)C11—C131.383 (4)
N2—C11.386 (4)C12—C151.371 (5)
N2—C31.482 (4)C12—H120.9300
C2—C171.376 (4)C13—C141.383 (4)
C2—C61.381 (4)C13—H130.9300
C2—C71.512 (4)C14—H140.9300
C3—C111.512 (4)C15—C191.375 (5)
C3—H3A0.9700C15—C201.520 (4)
C3—H3B0.9700C16—H16A0.9600
C4—C51.322 (4)C16—H16B0.9600
C4—C91.439 (4)C16—H16C0.9600
C4—H40.9300C17—C191.391 (4)
C5—H50.9300C17—H170.9300
C6—C121.375 (4)C18—H180.9300
C6—H60.9300C19—H190.9300
C7—H7A0.9700C20—H20A0.9600
C7—H7B0.9700C20—H20B0.9600
C8—C181.374 (4)C20—H20C0.9600
C1—N1—C9125.6 (3)C18—C10—C11121.3 (3)
C1—N1—C7117.3 (3)C18—C10—H10119.4
C9—N1—C7117.1 (3)C11—C10—H10119.4
C5—N2—C1121.7 (3)C10—C11—C13117.7 (3)
C5—N2—C3119.8 (3)C10—C11—C3120.8 (3)
C1—N2—C3118.5 (3)C13—C11—C3121.5 (3)
O2—C1—N2122.4 (3)C6—C12—C15122.0 (3)
O2—C1—N1122.7 (3)C6—C12—H12119.0
N2—C1—N1114.9 (3)C15—C12—H12119.0
C17—C2—C6118.5 (3)C14—C13—C11120.7 (3)
C17—C2—C7121.2 (3)C14—C13—H13119.6
C6—C2—C7120.3 (3)C11—C13—H13119.6
N2—C3—C11111.9 (2)C8—C14—C13121.5 (3)
N2—C3—H3A109.2C8—C14—H14119.3
C11—C3—H3A109.2C13—C14—H14119.3
N2—C3—H3B109.2C12—C15—C19117.3 (3)
C11—C3—H3B109.2C12—C15—C20121.7 (4)
H3A—C3—H3B107.9C19—C15—C20120.9 (4)
C5—C4—C9120.5 (3)C8—C16—H16A109.5
C5—C4—H4119.8C8—C16—H16B109.5
C9—C4—H4119.8H16A—C16—H16B109.5
C4—C5—N2122.8 (3)C8—C16—H16C109.5
C4—C5—H5118.6H16A—C16—H16C109.5
N2—C5—H5118.6H16B—C16—H16C109.5
C12—C6—C2120.5 (3)C2—C17—C19120.1 (3)
C12—C6—H6119.8C2—C17—H17120.0
C2—C6—H6119.8C19—C17—H17120.0
N1—C7—C2112.6 (2)C10—C18—C8121.4 (3)
N1—C7—H7A109.1C10—C18—H18119.3
C2—C7—H7A109.1C8—C18—H18119.3
N1—C7—H7B109.1C15—C19—C17121.6 (3)
C2—C7—H7B109.1C15—C19—H19119.2
H7A—C7—H7B107.8C17—C19—H19119.2
C18—C8—C14117.5 (3)C15—C20—H20A109.5
C18—C8—C16121.4 (3)C15—C20—H20B109.5
C14—C8—C16121.1 (3)H20A—C20—H20B109.5
O1—C9—N1120.2 (3)C15—C20—H20C109.5
O1—C9—C4125.3 (3)H20A—C20—H20C109.5
N1—C9—C4114.4 (3)H20B—C20—H20C109.5
C5—N2—C1—O2−178.4 (3)C5—C4—C9—O1−177.7 (3)
C3—N2—C1—O2−1.2 (4)C5—C4—C9—N12.5 (4)
C5—N2—C1—N11.6 (4)C18—C10—C11—C13−0.1 (5)
C3—N2—C1—N1178.9 (2)C18—C10—C11—C3179.8 (3)
C9—N1—C1—O2−178.8 (3)N2—C3—C11—C10−103.7 (3)
C7—N1—C1—O21.1 (4)N2—C3—C11—C1376.1 (4)
C9—N1—C1—N21.2 (4)C2—C6—C12—C15−1.1 (5)
C7—N1—C1—N2−178.9 (2)C10—C11—C13—C140.5 (5)
C5—N2—C3—C1180.2 (3)C3—C11—C13—C14−179.3 (3)
C1—N2—C3—C11−97.2 (3)C18—C8—C14—C130.8 (5)
C9—C4—C5—N20.0 (5)C16—C8—C14—C13−178.6 (3)
C1—N2—C5—C4−2.2 (4)C11—C13—C14—C8−0.9 (5)
C3—N2—C5—C4−179.5 (3)C6—C12—C15—C192.1 (5)
C17—C2—C6—C12−1.1 (4)C6—C12—C15—C20−177.1 (3)
C7—C2—C6—C12178.7 (3)C6—C2—C17—C192.3 (5)
C1—N1—C7—C2−95.8 (3)C7—C2—C17—C19−177.5 (3)
C9—N1—C7—C284.1 (3)C11—C10—C18—C80.0 (5)
C17—C2—C7—N174.8 (4)C14—C8—C18—C10−0.3 (5)
C6—C2—C7—N1−105.0 (3)C16—C8—C18—C10179.0 (3)
C1—N1—C9—O1177.0 (3)C12—C15—C19—C17−0.9 (5)
C7—N1—C9—O1−2.8 (4)C20—C15—C19—C17178.3 (3)
C1—N1—C9—C4−3.2 (4)C2—C17—C19—C15−1.3 (5)
C7—N1—C9—C4176.9 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C14—H14···O2i0.932.503.430 (4)174

Symmetry codes: (i) −x, −y+1, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2673).

References

  • Rigaku/MSC (2006). CrystalClear Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [PubMed]
  • Yang, F.-L. & Li, G.-C. (2006). Acta Cryst. E62, o3405–o3406.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography