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Acta Crystallogr Sect E Struct Rep Online. 2008 August 1; 64(Pt 8): o1488.
Published online 2008 July 16. doi:  10.1107/S1600536808020928
PMCID: PMC2961918

4,6-Dimethyl­pyrimidin-2(1H)-one–urea–water (1/1/1)

Abstract

In the crystal structure of the title compound, C6H8N2O·CH4N2O·H2O, mol­ecules are linked via N—H(...)O, O—H(...)N and O—H(...)O hydrogen bonds, forming a three–dimensional framework.

Related literature

For general background, see: Zhao et al., (2004 [triangle]); Zheng et al., (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1488-scheme1.jpg

Experimental

Crystal data

  • C6H8N2O·CH4N2O·H2O
  • M r = 202.22
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1488-efi1.jpg
  • a = 8.1246 (5) Å
  • b = 8.4062 (5) Å
  • c = 8.9268 (9) Å
  • α = 105.007 (3)°
  • β = 103.857 (3)°
  • γ = 114.379 (2)°
  • V = 493.05 (7) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 293 (2) K
  • 0.22 × 0.16 × 0.11 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.977, T max = 0.998
  • 5424 measured reflections
  • 1728 independent reflections
  • 1439 reflections with I > 2σ(I)
  • R int = 0.019

Refinement

  • R[F 2 > 2σ(F 2)] = 0.053
  • wR(F 2) = 0.170
  • S = 1.10
  • 1728 reflections
  • 143 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.45 e Å−3
  • Δρmin = −0.36 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [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: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808020928/rk2094sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808020928/rk2094Isup2.hkl

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

Acknowledgments

We acknowledge the support of the National Natural Science Foundation of China (No. 20662003) and the Foundation of the Governor of Guizhou Province, China.

supplementary crystallographic information

Comment

Recent years, we used different alkyl–substituted glycolurils as the building blocks to synthesize the partly alkyl substituted cucurbit[n]urils (Zhao et al., 2004; Zheng et al., 2005). In this work, we further report the crystal structure of a pyrimidine–substituted semi–glycoluril.

The crystal structure of the title compound C6H8N2O.CH4N2O.H2O, I, consists from 4,6–dimethylpyrimidin molecule, a urea molecule and a lattice water molecule. These molecules are linked via N—H···O, O—H···N and O—H···O hydrogen bonds forming a three–dimensional framework (Fig. 2).

Experimental

In a 3–neck flask fitted with water knockout trap and the thermometer, (36 g, 0.6 mol) of urea dissolved in 100 ml of toluene, stirred vigorously, at room temperature. At the same time, (24 g, 0.24 mol) of acetylacetone was added into flask in one portion. The 1.5 ml of trifluoroacetic acid was added too in order to make the value of pH of the solvent is around 4. The reaction mixture was stired and heated and maintained at reflux for 4 h. After cooling to room temperature, the reaction mixture was filtered. The filtrate was concentrated by rotary evaporation at 318–323 K and then maintained overnight at room temperature and crystals of I appear (yield: 4.5 g, 0.036 mol, 15%)

Refinement

Water H atoms and H atoms of amino group were located in a difference Fourier map and refined freely with Uiso(H) = 1.2Ueq(O, N). All H atoms based on C were placed in calculated positions and refined as riding, with C—H = 0.930–0.960Å with Uiso(H) = 1.2–1.5 Ueq(C).

Figures

Fig. 1.
The molecular structure of I showing the atom–labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are presented as a small spheres of arbitrary radius.
Fig. 2.
Packing diagram of I. H–bonds are shown as dashed lines.

Crystal data

C6H8N2O·CH4N2O·H2OZ = 2
Mr = 202.22F000 = 216
Triclinic, P1Dx = 1.362 Mg m3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 8.1246 (5) ÅCell parameters from 1728 reflections
b = 8.4062 (5) Åθ = 2.6–25.1º
c = 8.9268 (9) ŵ = 0.11 mm1
α = 105.007 (3)ºT = 293 (2) K
β = 103.857 (3)ºPrism, colourless
γ = 114.379 (2)º0.22 × 0.16 × 0.11 mm
V = 493.05 (7) Å3

Data collection

Bruker APEXII CCD area-detector diffractometer1728 independent reflections
Radiation source: Fine–focus sealed tube1439 reflections with I > 2σ(I)
Monochromator: GraphiteRint = 0.019
T = 293(2) Kθmax = 25.1º
[var phi] and ω scansθmin = 2.6º
Absorption correction: multi-scan(SADABS; Bruker, 2005)h = −9→9
Tmin = 0.977, Tmax = 0.998k = −8→10
5424 measured reflectionsl = −10→10

Refinement

Refinement on F2Secondary atom site location: Difmap
Least-squares matrix: FullHydrogen site location: Geom
R[F2 > 2σ(F2)] = 0.053H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.170  w = 1/[σ2(Fo2) + (0.0859P)2 + 0.3229P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
1728 reflectionsΔρmax = 0.45 e Å3
143 parametersΔρmin = −0.36 e Å3
1 restraintExtinction correction: None
Primary atom site location: Direct

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted < i>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
C10.4613 (3)0.3670 (3)0.6702 (3)0.0323 (5)
C20.9295 (4)0.6340 (4)0.6375 (4)0.0479 (7)
H2A0.90520.51820.55600.072*
H2B1.04770.68500.73410.072*
H2C0.94430.72540.58830.072*
C30.7605 (3)0.5927 (3)0.6906 (3)0.0343 (5)
C40.7602 (3)0.7390 (3)0.8094 (3)0.0342 (5)
H40.86310.86440.85380.041*
C50.6073 (3)0.6940 (3)0.8582 (3)0.0304 (5)
C60.5869 (4)0.8321 (3)0.9851 (3)0.0393 (6)
H6A0.46640.76580.99830.059*
H6B0.58530.92870.94730.059*
H6C0.69580.89071.09130.059*
C7−0.0065 (3)0.2768 (3)0.8185 (3)0.0326 (5)
N10.6150 (3)0.4123 (3)0.6221 (2)0.0345 (5)
N20.4613 (3)0.5103 (3)0.7881 (2)0.0305 (5)
H20.361 (5)0.477 (4)0.825 (4)0.037*
N3−0.0268 (4)0.1313 (3)0.6941 (3)0.0456 (6)
H3A0.067 (5)0.150 (4)0.657 (4)0.055*
H3B−0.135 (5)0.035 (5)0.631 (4)0.055*
N4−0.1593 (3)0.2454 (3)0.8633 (3)0.0411 (5)
H4A−0.151 (4)0.352 (5)0.938 (4)0.049*
H4B−0.269 (5)0.148 (5)0.801 (4)0.049*
O10.3211 (2)0.2007 (2)0.6121 (2)0.0431 (5)
O20.1517 (2)0.4327 (2)0.8930 (2)0.0383 (5)
O1W0.5570 (3)0.0847 (2)0.3512 (2)0.0459 (5)
H1WA0.5959 (10)0.175 (2)0.445 (2)0.055*
H1WB0.6047 (12)0.0249 (14)0.3918 (11)0.055*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0355 (12)0.0298 (12)0.0289 (11)0.0177 (10)0.0113 (9)0.0074 (9)
C20.0432 (14)0.0535 (16)0.0554 (16)0.0269 (13)0.0298 (13)0.0205 (13)
C30.0341 (12)0.0401 (13)0.0342 (12)0.0221 (11)0.0143 (10)0.0162 (10)
C40.0327 (12)0.0300 (12)0.0364 (12)0.0140 (10)0.0135 (10)0.0117 (10)
C50.0341 (11)0.0292 (11)0.0289 (11)0.0173 (10)0.0116 (9)0.0117 (9)
C60.0460 (14)0.0297 (12)0.0414 (13)0.0186 (11)0.0216 (11)0.0103 (10)
C70.0318 (11)0.0287 (12)0.0343 (12)0.0133 (10)0.0123 (10)0.0128 (9)
N10.0366 (10)0.0378 (11)0.0332 (10)0.0227 (9)0.0160 (8)0.0113 (9)
N20.0304 (10)0.0294 (10)0.0310 (10)0.0156 (9)0.0135 (8)0.0093 (8)
N30.0370 (12)0.0340 (12)0.0463 (13)0.0084 (10)0.0188 (10)0.0023 (10)
N40.0302 (10)0.0337 (11)0.0488 (13)0.0114 (9)0.0167 (10)0.0085 (10)
O10.0404 (10)0.0296 (9)0.0449 (10)0.0129 (8)0.0169 (8)0.0025 (7)
O20.0328 (9)0.0305 (9)0.0433 (10)0.0113 (7)0.0184 (7)0.0078 (7)
O1W0.0477 (10)0.0437 (10)0.0396 (10)0.0248 (9)0.0124 (8)0.0091 (8)

Geometric parameters (Å, °)

C1—O11.244 (3)C6—H6A0.9600
C1—N11.356 (3)C6—H6B0.9600
C1—N21.379 (3)C6—H6C0.9600
C2—C31.495 (3)C7—O21.249 (3)
C2—H2A0.9600C7—N41.339 (3)
C2—H2B0.9600C7—N31.341 (3)
C2—H2C0.9600N2—H20.92 (3)
C3—N11.329 (3)N3—H3A0.87 (3)
C3—C41.401 (3)N3—H3B0.83 (3)
C4—C51.354 (3)N4—H4A0.93 (3)
C4—H40.9300N4—H4B0.83 (3)
C5—N21.347 (3)O1W—H1WA0.850 (11)
C5—C61.492 (3)O1W—H1WB0.850 (11)
O1—C1—N1122.19 (19)C5—C6—H6B109.5
O1—C1—N2119.09 (19)H6A—C6—H6B109.5
N1—C1—N2118.7 (2)C5—C6—H6C109.5
C3—C2—H2A109.5H6A—C6—H6C109.5
C3—C2—H2B109.5H6B—C6—H6C109.5
H2A—C2—H2B109.5O2—C7—N4121.7 (2)
C3—C2—H2C109.5O2—C7—N3120.9 (2)
H2A—C2—H2C109.5N4—C7—N3117.3 (2)
H2B—C2—H2C109.5C3—N1—C1118.88 (19)
N1—C3—C4122.5 (2)C5—N2—C1123.10 (19)
N1—C3—C2116.8 (2)C5—N2—H2118.8 (19)
C4—C3—C2120.7 (2)C1—N2—H2117.9 (19)
C5—C4—C3118.7 (2)C7—N3—H3A119 (2)
C5—C4—H4120.6C7—N3—H3B122 (2)
C3—C4—H4120.6H3A—N3—H3B116 (3)
N2—C5—C4118.0 (2)C7—N4—H4A116.4 (19)
N2—C5—C6116.75 (19)C7—N4—H4B119 (2)
C4—C5—C6125.2 (2)H4A—N4—H4B120 (3)
C5—C6—H6A109.5H1WA—O1W—H1WB96.3 (12)
N1—C3—C4—C51.1 (4)O1—C1—N1—C3−179.4 (2)
C2—C3—C4—C5−177.7 (2)N2—C1—N1—C30.3 (3)
C3—C4—C5—N2−0.8 (3)C4—C5—N2—C10.3 (3)
C3—C4—C5—C6178.9 (2)C6—C5—N2—C1−179.4 (2)
C4—C3—N1—C1−0.8 (3)O1—C1—N2—C5179.7 (2)
C2—C3—N1—C1178.0 (2)N1—C1—N2—C5−0.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···O20.92 (3)1.87 (3)2.779 (2)172 (3)
N3—H3A···O10.87 (3)2.09 (3)2.953 (3)169 (3)
N3—H3B···O1i0.83 (3)2.16 (3)2.896 (3)149 (3)
N4—H4A···O2ii0.93 (3)2.04 (3)2.968 (3)174 (3)
N4—H4B···O1Wi0.83 (3)2.12 (4)2.948 (3)175 (3)
O1W—H1WA···N10.850 (11)2.121 (15)2.930 (2)159.1 (13)
O1W—H1WB···O1iii0.850 (11)2.209 (11)3.009 (3)156.9 (3)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RK2094).

References

  • Bruker, (2005). APEX2, SAINT and SADABS Bruker AXS, Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zhao, Y. J., Xue, S. F., Zhu, Q. J., Tao, Z., Zhang, J. X., Wei, Z. B., Long, L. S., Hu, M. L., Xiao, H. P. & Day, A. I. (2004). Chin. Sci. Bull.49, 1111–1116.
  • Zheng, L. M., Zhu, J. N., Zhang, Y. Q., Tao, Z., Xue, S. F., Zhu, Q. J., Wei, Z. B. & Long, L. S. (2005). Chin. J. Inorg. Chem.21, 1583–1588.

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