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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1858.
Published online 2010 June 30. doi:  10.1107/S1600536810024815
PMCID: PMC3006881

1,3-Bis(4-meth­oxy­benz­yl)-6-methyl­pyrimidine-2,4(1H,3H)-dione

Abstract

The title compound, C21H22N2O4, was prepared by reaction of 6-methyl­pyrimidine-2,4(1H,3H)-dione and 1-chloro­methyl-4-meth­oxy­benzene. In the title mol­ecule, the central pyrimidine ring forms dihedral angles of 62.16 (4) and 69.77 (3)° with the two benzene rings. In the crystal, weak inter­molecular C—H(...)O hydrogen bonds link the mol­ecules into chains.

Related literature

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993 [triangle]); as agrochemicals, see: Maeno et al. (1990 [triangle]); as anti­viral agents, see: Gilchrist (1997 [triangle]); as herbicides, see: Selby et al. (2002 [triangle]); Zhu et al. (2007 [triangle]). For a related structure, see: Yang & Li (2006 [triangle]).

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Object name is e-66-o1858-scheme1.jpg

Experimental

Crystal data

  • C21H22N2O4
  • M r = 366.41
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1858-efi1.jpg
  • a = 8.4133 (9) Å
  • b = 9.929 (1) Å
  • c = 21.407 (3) Å
  • β = 91.614 (4)°
  • V = 1787.5 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 113 K
  • 0.26 × 0.24 × 0.22 mm

Data collection

  • Rigaku Saturn724 CCD diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009 [triangle]) T min = 0.976, T max = 0.979
  • 17394 measured reflections
  • 4250 independent reflections
  • 3035 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.096
  • S = 0.98
  • 4250 reflections
  • 247 parameters
  • H-atom parameters constrained
  • Δρmax = 0.29 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2009 [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: CrystalStructure (Rigaku/MSC, 2009 [triangle]); software used to prepare material for publication: CrystalStructure.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810024815/pk2250sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810024815/pk2250Isup2.hkl

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

Acknowledgments

This work was supported by the Program for New Century Excellent Talents at the University of Henan Province (No. 2005HANCET-17), 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

Pyrimidine derivatives are very important molecules in biology and have many applications in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely used anti-AIDS drug (Gilchrist, 1997). Recently, a new series of highly active herbicides of substituted pyrimidines were reported (Selby et al., 2002); (Zhu et al., 2007), and we have previously reported a related structure (Yang & Li 2006). As part of our goal to discover further biologically active pyrimidine compounds, the title compound was synthesized and its crystal structure determined (Fig. 1).

In the title molecule, the central pyrimidine ring forms dihedral angles of 62.16 (4) and 69.77 (3)° with the two benzene rings. In the crystal, weak intermolecular C—H···O hydrogen bonds link molecules.

Experimental

6-methylpyrimidine-2,4(1H,3H)-dione (0.63 g, 5 mmol) and anhydrous potassium carbonate (0.84 g, 6 mmol) were mixed in dimethylformamide (20 ml). A solution of 1-(chloromethyl)-4-methoxybenzene (0.79 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 recrystallized from ethanol and single crystals were obtained by slow evaporation.

Refinement

All H atoms were placed in calculated positions, with C—H = 0.95 Å, 0.98 Å or 0.99 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The asymmetric unit of the title compound, with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A packing diagram of the title compound viewed down the a axis. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C21H22N2O4F(000) = 776
Mr = 366.41Dx = 1.361 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ynCell parameters from 5810 reflections
a = 8.4133 (9) Åθ = 1.9–28.0°
b = 9.929 (1) ŵ = 0.10 mm1
c = 21.407 (3) ÅT = 113 K
β = 91.614 (4)°Prism, colorless
V = 1787.5 (3) Å30.26 × 0.24 × 0.22 mm
Z = 4

Data collection

Rigaku Saturn724 CCD diffractometer4250 independent reflections
Radiation source: fine-focus sealed tube3035 reflections with I > 2σ(I)
graphiteRint = 0.037
Detector resolution: 14.222 pixels mm-1θmax = 27.9°, θmin = 1.9°
ω scansh = −9→11
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009)k = −12→13
Tmin = 0.976, Tmax = 0.979l = −28→28
17394 measured reflections

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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H-atom parameters constrained
S = 0.98w = 1/[σ2(Fo2) + (0.0556P)2] where P = (Fo2 + 2Fc2)/3
4250 reflections(Δ/σ)max = 0.001
247 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = −0.16 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
O10.77270 (10)−0.03179 (8)0.39409 (4)0.0326 (2)
O21.05849 (10)0.35414 (9)0.42566 (4)0.0349 (2)
O30.38155 (9)0.43800 (8)0.57937 (3)0.0258 (2)
O41.17640 (10)−0.48075 (8)0.20574 (4)0.0286 (2)
N10.91553 (10)0.16121 (9)0.41019 (4)0.0235 (2)
N20.87518 (10)0.07201 (9)0.30901 (4)0.0231 (2)
C10.84910 (13)0.06125 (12)0.37267 (5)0.0244 (3)
C21.00559 (13)0.27014 (12)0.38848 (5)0.0257 (3)
C31.02826 (13)0.27076 (12)0.32258 (5)0.0257 (3)
H31.08930.34080.30490.031*
C40.96571 (13)0.17502 (11)0.28489 (5)0.0234 (2)
C50.99072 (15)0.17657 (13)0.21620 (5)0.0304 (3)
H5A1.06460.24920.20610.037*
H5B0.88880.19150.19400.037*
H5C1.03530.09000.20340.037*
C60.89544 (14)0.14901 (13)0.47867 (5)0.0275 (3)
H6A0.99400.18080.50030.033*
H6B0.88200.05260.48910.033*
C70.75633 (13)0.22666 (12)0.50352 (5)0.0229 (3)
C80.77921 (13)0.34760 (12)0.53566 (5)0.0244 (3)
H80.88330.38380.54060.029*
C90.65212 (13)0.41528 (12)0.56044 (5)0.0240 (3)
H90.66920.49720.58250.029*
C100.49895 (13)0.36351 (11)0.55308 (5)0.0213 (2)
C110.47377 (14)0.24358 (12)0.52095 (5)0.0250 (3)
H110.36940.20800.51560.030*
C120.60341 (13)0.17605 (12)0.49672 (5)0.0248 (3)
H120.58660.09350.47510.030*
C130.22263 (13)0.38888 (13)0.57144 (6)0.0292 (3)
H13A0.19320.38670.52680.035*
H13B0.14970.44850.59330.035*
H13C0.21600.29780.58880.035*
C140.79638 (13)−0.02957 (12)0.26809 (6)0.0263 (3)
H14A0.75760.01530.22930.032*
H14B0.7027−0.06560.28950.032*
C150.90264 (13)−0.14602 (11)0.25073 (5)0.0224 (2)
C160.97928 (13)−0.22551 (12)0.29611 (5)0.0236 (3)
H160.9686−0.20360.33900.028*
C171.06997 (13)−0.33503 (12)0.28015 (5)0.0243 (3)
H171.1212−0.38760.31180.029*
C181.08652 (13)−0.36866 (11)0.21741 (5)0.0224 (2)
C191.01334 (13)−0.28976 (12)0.17146 (5)0.0251 (3)
H191.0255−0.31070.12860.030*
C200.92206 (13)−0.17982 (12)0.18864 (5)0.0249 (3)
H200.8717−0.12650.15700.030*
C211.18686 (15)−0.52057 (13)0.14183 (5)0.0324 (3)
H21A1.0798−0.53590.12410.039*
H21B1.2489−0.60380.13930.039*
H21C1.2391−0.44930.11830.039*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0372 (5)0.0225 (5)0.0387 (5)−0.0028 (4)0.0125 (4)−0.0013 (4)
O20.0361 (5)0.0325 (5)0.0360 (5)−0.0066 (4)−0.0008 (4)−0.0107 (4)
O30.0232 (4)0.0286 (5)0.0256 (4)0.0020 (3)0.0020 (3)−0.0037 (3)
O40.0340 (5)0.0237 (5)0.0280 (4)0.0067 (4)0.0025 (3)−0.0041 (3)
N10.0242 (5)0.0204 (5)0.0259 (5)0.0032 (4)0.0031 (4)−0.0023 (4)
N20.0226 (5)0.0181 (5)0.0287 (5)0.0000 (4)0.0040 (4)−0.0044 (4)
C10.0224 (6)0.0187 (6)0.0322 (6)0.0036 (5)0.0054 (5)−0.0008 (5)
C20.0213 (6)0.0224 (6)0.0334 (6)0.0026 (5)0.0004 (5)−0.0041 (5)
C30.0240 (6)0.0204 (6)0.0328 (6)−0.0003 (5)0.0053 (5)−0.0014 (5)
C40.0197 (6)0.0202 (6)0.0305 (6)0.0034 (5)0.0037 (4)0.0000 (5)
C50.0354 (7)0.0269 (7)0.0292 (6)−0.0024 (5)0.0058 (5)−0.0024 (5)
C60.0286 (6)0.0266 (7)0.0274 (6)0.0056 (5)0.0003 (5)0.0015 (5)
C70.0267 (6)0.0223 (6)0.0197 (5)0.0022 (5)0.0012 (4)0.0043 (4)
C80.0225 (6)0.0276 (7)0.0229 (6)−0.0012 (5)−0.0011 (4)0.0016 (5)
C90.0285 (6)0.0222 (6)0.0212 (6)−0.0012 (5)−0.0009 (4)−0.0016 (4)
C100.0252 (6)0.0232 (6)0.0158 (5)0.0029 (5)0.0022 (4)0.0025 (4)
C110.0238 (6)0.0279 (7)0.0233 (6)−0.0039 (5)0.0012 (4)0.0000 (5)
C120.0317 (6)0.0214 (6)0.0214 (5)−0.0007 (5)0.0024 (5)−0.0005 (5)
C130.0234 (6)0.0330 (7)0.0316 (6)0.0002 (5)0.0049 (5)0.0002 (5)
C140.0236 (6)0.0220 (6)0.0334 (6)−0.0016 (5)0.0003 (5)−0.0049 (5)
C150.0196 (6)0.0174 (6)0.0303 (6)−0.0033 (4)0.0022 (4)−0.0034 (5)
C160.0257 (6)0.0228 (6)0.0225 (5)−0.0043 (5)0.0036 (4)−0.0023 (5)
C170.0264 (6)0.0226 (6)0.0237 (6)−0.0017 (5)−0.0008 (4)0.0015 (5)
C180.0223 (6)0.0173 (6)0.0277 (6)−0.0022 (5)0.0027 (4)−0.0023 (5)
C190.0301 (6)0.0234 (6)0.0217 (6)−0.0025 (5)0.0010 (4)−0.0031 (5)
C200.0278 (6)0.0209 (6)0.0260 (6)−0.0004 (5)−0.0029 (4)0.0016 (5)
C210.0394 (7)0.0273 (7)0.0309 (7)0.0042 (6)0.0067 (5)−0.0069 (5)

Geometric parameters (Å, °)

O1—C11.2220 (13)C9—C101.3922 (15)
O2—C21.2276 (14)C9—H90.9500
O3—C101.3677 (13)C10—C111.3886 (16)
O3—C131.4288 (13)C11—C121.3929 (15)
O4—C181.3723 (13)C11—H110.9500
O4—C211.4292 (14)C12—H120.9500
N1—C11.3848 (15)C13—H13A0.9800
N1—C21.4070 (15)C13—H13B0.9800
N1—C61.4853 (14)C13—H13C0.9800
N2—C41.3838 (14)C14—C151.5142 (15)
N2—C11.3904 (14)C14—H14A0.9900
N2—C141.4803 (14)C14—H14B0.9900
C2—C31.4290 (15)C15—C201.3850 (15)
C3—C41.3444 (16)C15—C161.3954 (16)
C3—H30.9500C16—C171.3770 (16)
C4—C51.4914 (15)C16—H160.9500
C5—H5A0.9800C17—C181.3949 (15)
C5—H5B0.9800C17—H170.9500
C5—H5C0.9800C18—C191.3879 (16)
C6—C71.5108 (15)C19—C201.3901 (16)
C6—H6A0.9900C19—H190.9500
C6—H6B0.9900C20—H200.9500
C7—C121.3850 (15)C21—H21A0.9800
C7—C81.3946 (16)C21—H21B0.9800
C8—C91.3814 (15)C21—H21C0.9800
C8—H80.9500
C10—O3—C13116.79 (9)C11—C10—C9120.04 (10)
C18—O4—C21116.59 (9)C10—C11—C12119.15 (11)
C1—N1—C2124.87 (9)C10—C11—H11120.4
C1—N1—C6117.30 (9)C12—C11—H11120.4
C2—N1—C6117.78 (9)C7—C12—C11121.40 (11)
C4—N2—C1121.75 (9)C7—C12—H12119.3
C4—N2—C14121.65 (9)C11—C12—H12119.3
C1—N2—C14116.56 (9)O3—C13—H13A109.5
O1—C1—N1122.15 (11)O3—C13—H13B109.5
O1—C1—N2121.67 (10)H13A—C13—H13B109.5
N1—C1—N2116.18 (10)O3—C13—H13C109.5
O2—C2—N1119.80 (10)H13A—C13—H13C109.5
O2—C2—C3125.52 (11)H13B—C13—H13C109.5
N1—C2—C3114.68 (10)N2—C14—C15114.07 (9)
C4—C3—C2121.90 (11)N2—C14—H14A108.7
C4—C3—H3119.0C15—C14—H14A108.7
C2—C3—H3119.0N2—C14—H14B108.7
C3—C4—N2120.60 (10)C15—C14—H14B108.7
C3—C4—C5121.37 (11)H14A—C14—H14B107.6
N2—C4—C5118.03 (10)C20—C15—C16117.80 (10)
C4—C5—H5A109.5C20—C15—C14120.46 (10)
C4—C5—H5B109.5C16—C15—C14121.70 (10)
H5A—C5—H5B109.5C17—C16—C15121.49 (10)
C4—C5—H5C109.5C17—C16—H16119.3
H5A—C5—H5C109.5C15—C16—H16119.3
H5B—C5—H5C109.5C16—C17—C18119.94 (10)
N1—C6—C7114.63 (9)C16—C17—H17120.0
N1—C6—H6A108.6C18—C17—H17120.0
C7—C6—H6A108.6O4—C18—C19124.37 (10)
N1—C6—H6B108.6O4—C18—C17116.09 (10)
C7—C6—H6B108.6C19—C18—C17119.54 (10)
H6A—C6—H6B107.6C18—C19—C20119.54 (10)
C12—C7—C8118.64 (10)C18—C19—H19120.2
C12—C7—C6120.28 (11)C20—C19—H19120.2
C8—C7—C6121.04 (10)C15—C20—C19121.68 (10)
C9—C8—C7120.71 (11)C15—C20—H20119.2
C9—C8—H8119.6C19—C20—H20119.2
C7—C8—H8119.6O4—C21—H21A109.5
C8—C9—C10120.06 (11)O4—C21—H21B109.5
C8—C9—H9120.0H21A—C21—H21B109.5
C10—C9—H9120.0O4—C21—H21C109.5
O3—C10—C11124.45 (10)H21A—C21—H21C109.5
O3—C10—C9115.51 (10)H21B—C21—H21C109.5
C2—N1—C1—O1179.48 (10)C7—C8—C9—C10−0.49 (16)
C6—N1—C1—O12.11 (16)C13—O3—C10—C11−1.51 (15)
C2—N1—C1—N2−0.05 (15)C13—O3—C10—C9178.71 (9)
C6—N1—C1—N2−177.43 (9)C8—C9—C10—O3179.95 (9)
C4—N2—C1—O1−178.01 (10)C8—C9—C10—C110.15 (16)
C14—N2—C1—O14.12 (15)O3—C10—C11—C12−179.39 (10)
C4—N2—C1—N11.53 (15)C9—C10—C11—C120.38 (16)
C14—N2—C1—N1−176.34 (9)C8—C7—C12—C110.28 (16)
C1—N1—C2—O2179.50 (10)C6—C7—C12—C11177.94 (10)
C6—N1—C2—O2−3.13 (15)C10—C11—C12—C7−0.60 (16)
C1—N1—C2—C3−1.11 (15)C4—N2—C14—C1584.38 (13)
C6—N1—C2—C3176.25 (9)C1—N2—C14—C15−97.75 (11)
O2—C2—C3—C4−179.76 (12)N2—C14—C15—C20−126.06 (11)
N1—C2—C3—C40.89 (16)N2—C14—C15—C1656.27 (14)
C2—C3—C4—N20.48 (17)C20—C15—C16—C17−0.72 (16)
C2—C3—C4—C5−179.79 (10)C14—C15—C16—C17177.00 (10)
C1—N2—C4—C3−1.78 (16)C15—C16—C17—C18−0.11 (16)
C14—N2—C4—C3175.98 (10)C21—O4—C18—C19−3.25 (15)
C1—N2—C4—C5178.48 (10)C21—O4—C18—C17176.61 (10)
C14—N2—C4—C5−3.75 (15)C16—C17—C18—O4−178.78 (9)
C1—N1—C6—C7−95.32 (12)C16—C17—C18—C191.09 (16)
C2—N1—C6—C787.11 (12)O4—C18—C19—C20178.63 (10)
N1—C6—C7—C1278.75 (13)C17—C18—C19—C20−1.22 (16)
N1—C6—C7—C8−103.65 (12)C16—C15—C20—C190.58 (16)
C12—C7—C8—C90.27 (16)C14—C15—C20—C19−177.17 (10)
C6—C7—C8—C9−177.37 (10)C18—C19—C20—C150.38 (17)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C20—H20···O3i0.952.513.3627 (14)150

Symmetry codes: (i) x+1/2, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PK2250).

References

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