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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1921–o1922.
Published online 2009 July 18. doi:  10.1107/S160053680902769X
PMCID: PMC2977098

Methyl 4-(3-eth­oxy-4-hydroxy­phen­yl)-6-methyl-2-oxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate monohydrate

Abstract

In the title compound, C15H18N2O5·H2O, the pyrimidine ring adopts a flattened-boat conformation. The eth­oxy group attached to the benzene ring is in an extended conformation. The oxopyrimidine mol­ecules are linked into centrosymmetric R 2 2(20) dimers by O—H(...)O hydrogen bonds. The dimers are linked by N—H(...)O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. Adjacent networks are cross-linked via N—H(...)O and O—H(...)O hydrogen bonds involving the water mol­ecules.

Related literature

For the biological properties of pyrimidine compounds, see: Kidwai et al. (2003 [triangle]). For C=O bond-length data, see: Litvinov et al. (1992 [triangle]). For hybridization, see: Beddoes et al. (1986 [triangle]). For ring conformational analysis, see: Cremer & Pople (1975 [triangle]); Nardelli (1983 [triangle]). For graph-set analysis, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1921-scheme1.jpg

Experimental

Crystal data

  • C15H18N2O5·H2O
  • M r = 324.33
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1921-efi1.jpg
  • a = 11.4927 (6) Å
  • b = 15.3756 (8) Å
  • c = 8.9240 (5) Å
  • β = 95.932 (2)°
  • V = 1568.49 (15) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 293 K
  • 0.25 × 0.20 × 0.20 mm

Data collection

  • Bruker Kappa APEXII area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2001 [triangle]) T min = 0.977, T max = 0.981
  • 20671 measured reflections
  • 4719 independent reflections
  • 3292 reflections with I > 2σ(I)
  • R int = 0.025

Refinement

  • R[F 2 > 2σ(F 2)] = 0.048
  • wR(F 2) = 0.140
  • S = 1.04
  • 4719 reflections
  • 231 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.31 e Å−3
  • Δρmin = −0.25 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR92 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXS97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008 [triangle]) and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680902769X/ci2843sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680902769X/ci2843Isup2.hkl

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

Acknowledgments

MT thanks the University of Madras for a University Research Fellowship.

supplementary crystallographic information

Comment

Pyrimidines are considered to be important not only they form an integral part of the genetic material (viz. DNA and RNA), but also impart numerous biological activities such as bactericides, fungicides, viricides, insecticides and meticides. They have also found applications in agricultural and industrial chemicals (Kidwai et al., 2003).

The pyrimidine ring assumes a flattened-boat conformation with puckering parameters (Cremer & Pople, 1975) q2 = 0.241 (1) Å, q3 = 0.077 (1) Å and [var phi]= 12.5 (3)°, and the asymmetry parameter (Nardelli, 1983) Δs(N1,C4) = 8.4 (2)°. The hydroxyphenyl ring is almost perpendicular to the C2/N3/C5/C6 plane, with a dihedral angle of 85.13 (7)°. The ethoxy [C14—C13—O3—C11 = -177.41 (13)°] and carboxylate [C5—C15—O4—C16 = 179.32 (14)°] groups attached to the pyrimidine ring exhibit extented conformations. The sum of the bond angles around atom N1 [357.4°] of the pyrimidine ring is in accordance with sp2 hybridization (Beddoes et al., 1986). The C2═O1 bond length of 1.2420 (18) Å is close to the expected value of 1.225 Å for a free, unbridged bond (Litvinov et al., 1992).

The molecules are linked into centrosymmetric R22(20) dimers by O—H···O hydrogen bonds and the dimers are linked by N—H···O hydrogen bonds to form a two-dimensional network parallel to the bc plane. The adjacent networks are cross-linked via N—H···O and O—H···O hydrogen bonds involving the water molecules.

Experimental

A mixture of 3-ethoxy-4-hydroxy benzaldehyde (10 mmol), methylacetoacetate (12 mmol), urea (15 mmol) and 1 ml of conc. HCl was placed in a round bottom flask containing 30 ml of acetonitrile. The reaction mixture was refluxed for 5 h at 348-353 K. After completion of the reaction (checked by TLC), the reaction mixture was poured in ice cooled water. The separated solid was filtered, dried and recrystallized with methanol.

Refinement

O- and N-bound H atoms were located in a difference map and refined freely. C-bound H atoms were positioned geometrically (C-H = 0.93–0.98 Å) and allowed to ride on their parent atoms, with Uiso(H) = 1.2–1.5(methyl) Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound, showing 30% probability displacement ellipsoids. The dashed line indicates a hydrogen bond.
Fig. 2.
Part of the crystal packing of the title compound, showing hydrogen-bonded (dashed lines) dimers.

Crystal data

C15H18N2O5·H2OF(000) = 688
Mr = 324.33Dx = 1.373 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4719 reflections
a = 11.4927 (6) Åθ = 1.8–30.3°
b = 15.3756 (8) ŵ = 0.11 mm1
c = 8.9240 (5) ÅT = 293 K
β = 95.932 (2)°Block, yellow
V = 1568.49 (15) Å30.25 × 0.20 × 0.20 mm
Z = 4

Data collection

Bruker Kappa APEXII area-detector diffractometer4719 independent reflections
Radiation source: fine-focus sealed tube3292 reflections with I > 2σ(I)
graphiteRint = 0.025
ω and [var phi] scansθmax = 30.3°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)h = −16→16
Tmin = 0.977, Tmax = 0.981k = −21→21
20671 measured reflectionsl = −12→12

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) = 0.140H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0643P)2 + 0.381P] where P = (Fo2 + 2Fc2)/3
4719 reflections(Δ/σ)max = 0.001
231 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = −0.25 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
C20.35042 (12)0.17029 (9)0.52062 (17)0.0356 (3)
C40.30165 (12)0.07826 (8)0.29487 (15)0.0323 (3)
H40.34470.07200.20630.039*
C50.33233 (11)0.00144 (8)0.39770 (15)0.0318 (3)
C60.35124 (11)0.01266 (8)0.54780 (16)0.0321 (3)
C70.17205 (12)0.08179 (8)0.24074 (15)0.0314 (3)
C80.08815 (12)0.06691 (10)0.33778 (15)0.0372 (3)
H80.11090.05430.43850.045*
C9−0.02997 (13)0.07060 (10)0.28638 (16)0.0394 (3)
H9−0.08580.06060.35280.047*
C10−0.06474 (12)0.08894 (9)0.13824 (15)0.0347 (3)
C110.01924 (12)0.10656 (9)0.03979 (15)0.0329 (3)
C120.13663 (12)0.10213 (9)0.09088 (15)0.0337 (3)
H120.19250.11280.02480.040*
C130.05268 (15)0.15592 (11)−0.20597 (17)0.0458 (4)
H13A0.10740.1099−0.22330.055*
H13B0.09660.2062−0.16640.055*
C14−0.01997 (19)0.17865 (13)−0.34907 (19)0.0579 (5)
H14A−0.06420.1287−0.38570.087*
H14B0.03010.1968−0.42290.087*
H14C−0.07250.2251−0.33060.087*
C150.33489 (12)−0.08120 (9)0.31629 (17)0.0373 (3)
C160.3448 (2)−0.23424 (11)0.3223 (3)0.0685 (6)
H16A0.2807−0.23580.24420.103*
H16B0.3372−0.28130.39130.103*
H16C0.4172−0.24000.27830.103*
C170.37615 (14)−0.05489 (10)0.66793 (17)0.0422 (3)
H17A0.3058−0.08660.68030.063*
H17B0.4037−0.02710.76120.063*
H17C0.4348−0.09420.63920.063*
N10.34801 (11)0.09613 (8)0.60651 (15)0.0381 (3)
N30.34091 (11)0.15896 (8)0.37262 (14)0.0371 (3)
O10.36409 (10)0.24219 (7)0.58341 (13)0.0474 (3)
O2−0.18113 (9)0.09133 (9)0.09076 (14)0.0498 (3)
O3−0.02656 (9)0.12778 (8)−0.10273 (11)0.0444 (3)
O40.34354 (12)−0.15218 (7)0.40215 (14)0.0555 (3)
O50.32921 (11)−0.08496 (8)0.18008 (13)0.0521 (3)
O60.43101 (15)0.11524 (11)0.92163 (16)0.0654 (4)
H10.3666 (16)0.1039 (11)0.703 (2)0.045 (5)*
H2−0.193 (2)0.0937 (15)−0.010 (3)0.077 (7)*
H30.3418 (15)0.2040 (12)0.317 (2)0.048 (5)*
H6A0.418 (2)0.1623 (17)0.981 (3)0.086 (8)*
H6B0.508 (3)0.109 (2)0.921 (4)0.136 (13)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C20.0302 (7)0.0344 (6)0.0417 (8)−0.0002 (5)0.0015 (6)−0.0002 (5)
C40.0312 (6)0.0350 (6)0.0301 (7)−0.0004 (5)0.0001 (5)0.0019 (5)
C50.0280 (6)0.0315 (6)0.0353 (7)0.0000 (5)0.0006 (5)0.0025 (5)
C60.0263 (6)0.0343 (6)0.0360 (7)0.0002 (5)0.0043 (5)0.0037 (5)
C70.0310 (6)0.0325 (6)0.0301 (6)0.0003 (5)0.0013 (5)0.0003 (5)
C80.0363 (7)0.0490 (8)0.0259 (6)0.0012 (6)0.0015 (5)0.0037 (5)
C90.0342 (7)0.0546 (8)0.0304 (7)−0.0001 (6)0.0079 (5)0.0020 (6)
C100.0288 (7)0.0439 (7)0.0313 (7)0.0014 (5)0.0028 (5)−0.0031 (5)
C110.0350 (7)0.0379 (7)0.0254 (6)0.0002 (5)0.0010 (5)0.0012 (5)
C120.0322 (7)0.0400 (7)0.0294 (6)−0.0016 (5)0.0055 (5)0.0021 (5)
C130.0518 (9)0.0531 (9)0.0332 (8)−0.0040 (7)0.0082 (7)0.0053 (6)
C140.0819 (14)0.0552 (10)0.0366 (9)0.0059 (9)0.0054 (9)0.0085 (7)
C150.0290 (7)0.0372 (7)0.0445 (8)0.0001 (5)−0.0020 (6)−0.0031 (6)
C160.0751 (13)0.0344 (8)0.0933 (16)−0.0003 (8)−0.0045 (11)−0.0136 (9)
C170.0440 (8)0.0438 (8)0.0388 (8)0.0028 (6)0.0050 (6)0.0113 (6)
N10.0443 (7)0.0375 (6)0.0323 (6)0.0001 (5)0.0028 (5)0.0002 (5)
N30.0406 (7)0.0319 (6)0.0373 (6)−0.0047 (5)−0.0026 (5)0.0063 (5)
O10.0557 (7)0.0356 (5)0.0501 (7)−0.0013 (5)0.0018 (5)−0.0059 (4)
O20.0289 (5)0.0835 (9)0.0366 (6)0.0018 (5)0.0019 (4)−0.0008 (6)
O30.0380 (6)0.0664 (7)0.0281 (5)−0.0014 (5)0.0005 (4)0.0087 (5)
O40.0748 (9)0.0310 (5)0.0591 (8)0.0006 (5)−0.0011 (6)−0.0010 (5)
O50.0593 (7)0.0524 (7)0.0431 (7)0.0062 (5)−0.0016 (5)−0.0114 (5)
O60.0703 (10)0.0753 (9)0.0500 (8)0.0054 (8)0.0034 (7)−0.0158 (7)

Geometric parameters (Å, °)

C2—O11.2421 (16)C13—O31.4279 (19)
C2—N31.3255 (19)C13—C141.493 (2)
C2—N11.3758 (18)C13—H13A0.97
C4—N31.4696 (17)C13—H13B0.97
C4—C51.5149 (18)C14—H14A0.96
C4—C71.5186 (18)C14—H14B0.96
C4—H40.98C14—H14C0.96
C5—C61.3457 (19)C15—O51.2119 (18)
C5—C151.4654 (19)C15—O41.3314 (18)
C6—N11.3881 (18)C16—O41.450 (2)
C6—C171.4988 (19)C16—H16A0.96
C7—C81.3801 (19)C16—H16B0.96
C7—C121.3926 (18)C16—H16C0.96
C8—C91.388 (2)C17—H17A0.96
C8—H80.93C17—H17B0.96
C9—C101.370 (2)C17—H17C0.96
C9—H90.93N1—H10.877 (19)
C10—O21.3613 (17)N3—H30.852 (19)
C10—C111.3972 (19)O2—H20.90 (2)
C11—O31.3648 (16)O6—H6A0.92 (3)
C11—C121.3804 (19)O6—H6B0.89 (4)
C12—H120.93
O1—C2—N3124.06 (13)C14—C13—H13A110.4
O1—C2—N1119.69 (14)O3—C13—H13B110.4
N3—C2—N1116.23 (12)C14—C13—H13B110.4
N3—C4—C5109.36 (11)H13A—C13—H13B108.6
N3—C4—C7111.30 (11)C13—C14—H14A109.5
C5—C4—C7112.32 (11)C13—C14—H14B109.5
N3—C4—H4107.9H14A—C14—H14B109.5
C5—C4—H4107.9C13—C14—H14C109.5
C7—C4—H4107.9H14A—C14—H14C109.5
C6—C5—C15126.53 (12)H14B—C14—H14C109.5
C6—C5—C4120.43 (12)O5—C15—O4122.09 (13)
C15—C5—C4113.02 (12)O5—C15—C5122.48 (13)
C5—C6—N1119.10 (12)O4—C15—C5115.44 (13)
C5—C6—C17128.48 (13)O4—C16—H16A109.5
N1—C6—C17112.41 (12)O4—C16—H16B109.5
C8—C7—C12119.08 (12)H16A—C16—H16B109.5
C8—C7—C4121.36 (12)O4—C16—H16C109.5
C12—C7—C4119.55 (12)H16A—C16—H16C109.5
C7—C8—C9120.57 (13)H16B—C16—H16C109.5
C7—C8—H8119.7C6—C17—H17A109.5
C9—C8—H8119.7C6—C17—H17B109.5
C10—C9—C8120.32 (13)H17A—C17—H17B109.5
C10—C9—H9119.8C6—C17—H17C109.5
C8—C9—H9119.8H17A—C17—H17C109.5
O2—C10—C9119.01 (13)H17B—C17—H17C109.5
O2—C10—C11121.30 (12)C2—N1—C6123.58 (13)
C9—C10—C11119.67 (13)C2—N1—H1114.8 (12)
O3—C11—C12126.10 (12)C6—N1—H1119.0 (12)
O3—C11—C10114.04 (12)C2—N3—C4124.82 (12)
C12—C11—C10119.86 (12)C2—N3—H3118.0 (12)
C11—C12—C7120.46 (12)C4—N3—H3115.6 (12)
C11—C12—H12119.8C10—O2—H2111.0 (15)
C7—C12—H12119.8C11—O3—C13117.61 (12)
O3—C13—C14106.57 (14)C15—O4—C16115.74 (14)
O3—C13—H13A110.4H6A—O6—H6B108 (3)
N3—C4—C5—C621.65 (17)O3—C11—C12—C7178.32 (13)
C7—C4—C5—C6−102.44 (14)C10—C11—C12—C7−1.2 (2)
N3—C4—C5—C15−159.91 (11)C8—C7—C12—C11−0.6 (2)
C7—C4—C5—C1576.00 (14)C4—C7—C12—C11−179.32 (12)
C15—C5—C6—N1178.59 (12)C6—C5—C15—O5−171.98 (14)
C4—C5—C6—N1−3.19 (19)C4—C5—C15—O59.7 (2)
C15—C5—C6—C17−1.7 (2)C6—C5—C15—O48.2 (2)
C4—C5—C6—C17176.53 (13)C4—C5—C15—O4−170.10 (12)
N3—C4—C7—C8−79.50 (16)O1—C2—N1—C6−169.74 (13)
C5—C4—C7—C843.50 (17)N3—C2—N1—C68.4 (2)
N3—C4—C7—C1299.20 (14)C5—C6—N1—C2−13.8 (2)
C5—C4—C7—C12−137.80 (13)C17—C6—N1—C2166.38 (13)
C12—C7—C8—C91.1 (2)O1—C2—N3—C4−167.13 (14)
C4—C7—C8—C9179.85 (13)N1—C2—N3—C414.8 (2)
C7—C8—C9—C100.1 (2)C5—C4—N3—C2−28.53 (18)
C8—C9—C10—O2179.40 (14)C7—C4—N3—C296.16 (15)
C8—C9—C10—C11−1.9 (2)C12—C11—O3—C13−6.2 (2)
O2—C10—C11—O31.5 (2)C10—C11—O3—C13173.34 (13)
C9—C10—C11—O3−177.11 (13)C14—C13—O3—C11−177.41 (13)
O2—C10—C11—C12−178.89 (13)O5—C15—O4—C16−0.5 (2)
C9—C10—C11—C122.5 (2)C5—C15—O4—C16179.32 (14)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O60.87 (2)2.02 (2)2.890 (2)172 (2)
N3—H3···O1i0.85 (2)2.28 (2)3.031 (2)147 (2)
O2—H2···O5ii0.90 (2)2.07 (2)2.810 (2)139 (2)
O6—H6A···O1iii0.92 (3)1.87 (3)2.777 (2)170 (2)
O6—H6B···O5iv0.89 (3)2.19 (3)3.025 (2)156 (3)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2843).

References

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