organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

aKey Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, People's Republic of China, and bInstitute of Applied Chemistry, Guizhou University, Guiyang 550025, People's Republic of China
*Correspondence e-mail: sci.yqzhang@gzu.edu.cn

(Received 30 May 2008; accepted 7 July 2008; online 16 July 2008)

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[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 et al., (2005[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.]).

[Scheme 1]

Experimental

Crystal data
  • C6H8N2O·CH4N2O·H2O

  • Mr = 202.22

  • Triclinic, [P \overline 1]

  • 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[Bruker, (2005). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]) Tmin = 0.977, Tmax = 0.998

  • 5424 measured reflections

  • 1728 independent reflections

  • 1439 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.053

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯O2 0.92 (3) 1.87 (3) 2.779 (2) 172 (3)
N3—H3A⋯O1 0.87 (3) 2.09 (3) 2.953 (3) 169 (3)
N3—H3B⋯O1i 0.83 (3) 2.16 (3) 2.896 (3) 149 (3)
N4—H4A⋯O2ii 0.93 (3) 2.04 (3) 2.968 (3) 174 (3)
N4—H4B⋯O1Wi 0.83 (3) 2.12 (4) 2.948 (3) 175 (3)
O1W—H1WA⋯N1 0.850 (11) 2.121 (15) 2.930 (2) 159.1 (13)
O1W—H1WB⋯O1iii 0.850 (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.

Data collection: APEX2 (Bruker, 2005[Bruker, (2005). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker, (2005). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

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).

Related literature top

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

Experimental top

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 top

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).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. Packing diagram of I. H–bonds are shown as dashed lines.
4,6-Dimethylpyrimidin-2(1H)-one–urea–water (1/1/1) top
Crystal data top
C6H8N2O·CH4N2O·H2OZ = 2
Mr = 202.22F(000) = 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 = 2.6–25.1°
c = 8.9268 (9) ŵ = 0.11 mm1
α = 105.007 (3)°T = 293 K
β = 103.857 (3)°Prism, colourless
γ = 114.379 (2)°0.22 × 0.16 × 0.11 mm
V = 493.05 (7) Å3
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1728 independent reflections
Radiation source: Fine–focus sealed tube1439 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
ϕ and ω scansθmax = 25.1°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
h = 99
Tmin = 0.977, Tmax = 0.998k = 810
5424 measured reflectionsl = 1010
Refinement top
Refinement on F2Primary atom site location: Direct
Least-squares matrix: FullSecondary atom site location: Difmap
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: Geom
wR(F2) = 0.170H atoms treated by a mixture of independent and constrained refinement
S = 1.10 w = 1/[σ2(Fo2) + (0.0859P)2 + 0.3229P]
where P = (Fo2 + 2Fc2)/3
1728 reflections(Δ/σ)max < 0.001
143 parametersΔρmax = 0.45 e Å3
1 restraintΔρmin = 0.36 e Å3
Crystal data top
C6H8N2O·CH4N2O·H2Oγ = 114.379 (2)°
Mr = 202.22V = 493.05 (7) Å3
Triclinic, P1Z = 2
a = 8.1246 (5) ÅMo Kα radiation
b = 8.4062 (5) ŵ = 0.11 mm1
c = 8.9268 (9) ÅT = 293 K
α = 105.007 (3)°0.22 × 0.16 × 0.11 mm
β = 103.857 (3)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1728 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
1439 reflections with I > 2σ(I)
Tmin = 0.977, Tmax = 0.998Rint = 0.019
5424 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0531 restraint
wR(F2) = 0.170H atoms treated by a mixture of independent and constrained refinement
S = 1.10Δρmax = 0.45 e Å3
1728 reflectionsΔρmin = 0.36 e Å3
143 parameters
Special details top

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) top
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*
C70.0065 (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*
N30.0268 (4)0.1313 (3)0.6941 (3)0.0456 (6)
H3A0.067 (5)0.150 (4)0.657 (4)0.055*
H3B0.135 (5)0.035 (5)0.631 (4)0.055*
N40.1593 (3)0.2454 (3)0.8633 (3)0.0411 (5)
H4A0.151 (4)0.352 (5)0.938 (4)0.049*
H4B0.269 (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) top
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, º) top
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—C3179.4 (2)
C2—C3—C4—C5177.7 (2)N2—C1—N1—C30.3 (3)
C3—C4—C5—N20.8 (3)C4—C5—N2—C10.3 (3)
C3—C4—C5—C6178.9 (2)C6—C5—N2—C1179.4 (2)
C4—C3—N1—C10.8 (3)O1—C1—N2—C5179.7 (2)
C2—C3—N1—C1178.0 (2)N1—C1—N2—C50.1 (3)
Hydrogen-bond geometry (Å, º) top
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.

Experimental details

Crystal data
Chemical formulaC6H8N2O·CH4N2O·H2O
Mr202.22
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)8.1246 (5), 8.4062 (5), 8.9268 (9)
α, β, γ (°)105.007 (3), 103.857 (3), 114.379 (2)
V3)493.05 (7)
Z2
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.22 × 0.16 × 0.11
Data collection
DiffractometerBruker APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.977, 0.998
No. of measured, independent and
observed [I > 2σ(I)] reflections
5424, 1728, 1439
Rint0.019
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.053, 0.170, 1.10
No. of reflections1728
No. of parameters143
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.45, 0.36

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
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.
 

Acknowledgements

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

References

First citationBruker, (2005). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZhao, 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.  Web of Science CSD CrossRef CAS Google Scholar
First citationZheng, 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.  CAS Google Scholar

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