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

Wu, F.; Zhang, Y.-Q.; Zhu, Q.-J.; Xue, S.-F.; Tao, Z.

doi:10.1107/S1600536808020928

organic compounds

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Volume 64| Part 8| August 2008| Page o1488

doi:10.1107/S1600536808020928

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

Feng Wu,^a Yun-Qian Zhang,^a Qian-Jiang Zhu,^a ^* Sai-Feng Xue ^a and Zhu Tao ^b

^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 ); Zheng et al., (2005 ).

Experimental

Crystal data

C₆H₈N₂O·CH₄N₂O·H₂O
M_r = 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 ) 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[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
Δρ_max = 0.45 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; 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 ).

Supporting information

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

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

checkCIF report

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%)

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

	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.

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

Crystal data top

C₆H₈N₂O·CH₄N₂O·H₂O	Z = 2
M_r = 202.22	F(000) = 216
Triclinic, P1	D_x = 1.362 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.1246 (5) Å	Cell parameters from 1728 reflections
b = 8.4062 (5) Å	θ = 2.6–25.1°
c = 8.9268 (9) Å	µ = 0.11 mm⁻¹
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 tube	1439 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.019
ϕ and ω scans	θ_max = 25.1°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −9→9
T_min = 0.977, T_max = 0.998	k = −8→10
5424 measured reflections	l = −10→10

Refinement top

Refinement on F²	Primary atom site location: Direct
Least-squares matrix: Full	Secondary atom site location: Difmap
R[F² > 2σ(F²)] = 0.053	Hydrogen site location: Geom
wR(F²) = 0.170	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0859P)² + 0.3229P] where P = (F_o² + 2F_c²)/3
1728 reflections	(Δ/σ)_max < 0.001
143 parameters	Δρ_max = 0.45 e Å⁻³
1 restraint	Δρ_min = −0.36 e Å⁻³

Crystal data top

C₆H₈N₂O·CH₄N₂O·H₂O	γ = 114.379 (2)°
M_r = 202.22	V = 493.05 (7) Å³
Triclinic, P1	Z = 2
a = 8.1246 (5) Å	Mo Kα radiation
b = 8.4062 (5) Å	µ = 0.11 mm⁻¹
c = 8.9268 (9) Å	T = 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)
T_min = 0.977, T_max = 0.998	R_int = 0.019
5424 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.053	1 restraint
wR(F²) = 0.170	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.45 e Å⁻³
1728 reflections	Δρ_min = −0.36 e Å⁻³
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

	x	y	z	U_iso*/U_eq
C1	0.4613 (3)	0.3670 (3)	0.6702 (3)	0.0323 (5)
C2	0.9295 (4)	0.6340 (4)	0.6375 (4)	0.0479 (7)
H2A	0.9052	0.5182	0.5560	0.072*
H2B	1.0477	0.6850	0.7341	0.072*
H2C	0.9443	0.7254	0.5883	0.072*
C3	0.7605 (3)	0.5927 (3)	0.6906 (3)	0.0343 (5)
C4	0.7602 (3)	0.7390 (3)	0.8094 (3)	0.0342 (5)
H4	0.8631	0.8644	0.8538	0.041*
C5	0.6073 (3)	0.6940 (3)	0.8582 (3)	0.0304 (5)
C6	0.5869 (4)	0.8321 (3)	0.9851 (3)	0.0393 (6)
H6A	0.4664	0.7658	0.9983	0.059*
H6B	0.5853	0.9287	0.9473	0.059*
H6C	0.6958	0.8907	1.0913	0.059*
C7	−0.0065 (3)	0.2768 (3)	0.8185 (3)	0.0326 (5)
N1	0.6150 (3)	0.4123 (3)	0.6221 (2)	0.0345 (5)
N2	0.4613 (3)	0.5103 (3)	0.7881 (2)	0.0305 (5)
H2	0.361 (5)	0.477 (4)	0.825 (4)	0.037*
N3	−0.0268 (4)	0.1313 (3)	0.6941 (3)	0.0456 (6)
H3A	0.067 (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*
O1	0.3211 (2)	0.2007 (2)	0.6121 (2)	0.0431 (5)
O2	0.1517 (2)	0.4327 (2)	0.8930 (2)	0.0383 (5)
O1W	0.5570 (3)	0.0847 (2)	0.3512 (2)	0.0459 (5)
H1WA	0.5959 (10)	0.175 (2)	0.445 (2)	0.055*
H1WB	0.6047 (12)	0.0249 (14)	0.3918 (11)	0.055*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0355 (12)	0.0298 (12)	0.0289 (11)	0.0177 (10)	0.0113 (9)	0.0074 (9)
C2	0.0432 (14)	0.0535 (16)	0.0554 (16)	0.0269 (13)	0.0298 (13)	0.0205 (13)
C3	0.0341 (12)	0.0401 (13)	0.0342 (12)	0.0221 (11)	0.0143 (10)	0.0162 (10)
C4	0.0327 (12)	0.0300 (12)	0.0364 (12)	0.0140 (10)	0.0135 (10)	0.0117 (10)
C5	0.0341 (11)	0.0292 (11)	0.0289 (11)	0.0173 (10)	0.0116 (9)	0.0117 (9)
C6	0.0460 (14)	0.0297 (12)	0.0414 (13)	0.0186 (11)	0.0216 (11)	0.0103 (10)
C7	0.0318 (11)	0.0287 (12)	0.0343 (12)	0.0133 (10)	0.0123 (10)	0.0128 (9)
N1	0.0366 (10)	0.0378 (11)	0.0332 (10)	0.0227 (9)	0.0160 (8)	0.0113 (9)
N2	0.0304 (10)	0.0294 (10)	0.0310 (10)	0.0156 (9)	0.0135 (8)	0.0093 (8)
N3	0.0370 (12)	0.0340 (12)	0.0463 (13)	0.0084 (10)	0.0188 (10)	0.0023 (10)
N4	0.0302 (10)	0.0337 (11)	0.0488 (13)	0.0114 (9)	0.0167 (10)	0.0085 (10)
O1	0.0404 (10)	0.0296 (9)	0.0449 (10)	0.0129 (8)	0.0169 (8)	0.0025 (7)
O2	0.0328 (9)	0.0305 (9)	0.0433 (10)	0.0113 (7)	0.0184 (7)	0.0078 (7)
O1W	0.0477 (10)	0.0437 (10)	0.0396 (10)	0.0248 (9)	0.0124 (8)	0.0091 (8)

Geometric parameters (Å, º) top

C1—O1	1.244 (3)	C6—H6A	0.9600
C1—N1	1.356 (3)	C6—H6B	0.9600
C1—N2	1.379 (3)	C6—H6C	0.9600
C2—C3	1.495 (3)	C7—O2	1.249 (3)
C2—H2A	0.9600	C7—N4	1.339 (3)
C2—H2B	0.9600	C7—N3	1.341 (3)
C2—H2C	0.9600	N2—H2	0.92 (3)
C3—N1	1.329 (3)	N3—H3A	0.87 (3)
C3—C4	1.401 (3)	N3—H3B	0.83 (3)
C4—C5	1.354 (3)	N4—H4A	0.93 (3)
C4—H4	0.9300	N4—H4B	0.83 (3)
C5—N2	1.347 (3)	O1W—H1WA	0.850 (11)
C5—C6	1.492 (3)	O1W—H1WB	0.850 (11)

O1—C1—N1	122.19 (19)	C5—C6—H6B	109.5
O1—C1—N2	119.09 (19)	H6A—C6—H6B	109.5
N1—C1—N2	118.7 (2)	C5—C6—H6C	109.5
C3—C2—H2A	109.5	H6A—C6—H6C	109.5
C3—C2—H2B	109.5	H6B—C6—H6C	109.5
H2A—C2—H2B	109.5	O2—C7—N4	121.7 (2)
C3—C2—H2C	109.5	O2—C7—N3	120.9 (2)
H2A—C2—H2C	109.5	N4—C7—N3	117.3 (2)
H2B—C2—H2C	109.5	C3—N1—C1	118.88 (19)
N1—C3—C4	122.5 (2)	C5—N2—C1	123.10 (19)
N1—C3—C2	116.8 (2)	C5—N2—H2	118.8 (19)
C4—C3—C2	120.7 (2)	C1—N2—H2	117.9 (19)
C5—C4—C3	118.7 (2)	C7—N3—H3A	119 (2)
C5—C4—H4	120.6	C7—N3—H3B	122 (2)
C3—C4—H4	120.6	H3A—N3—H3B	116 (3)
N2—C5—C4	118.0 (2)	C7—N4—H4A	116.4 (19)
N2—C5—C6	116.75 (19)	C7—N4—H4B	119 (2)
C4—C5—C6	125.2 (2)	H4A—N4—H4B	120 (3)
C5—C6—H6A	109.5	H1WA—O1W—H1WB	96.3 (12)

N1—C3—C4—C5	1.1 (4)	O1—C1—N1—C3	−179.4 (2)
C2—C3—C4—C5	−177.7 (2)	N2—C1—N1—C3	0.3 (3)
C3—C4—C5—N2	−0.8 (3)	C4—C5—N2—C1	0.3 (3)
C3—C4—C5—C6	178.9 (2)	C6—C5—N2—C1	−179.4 (2)
C4—C3—N1—C1	−0.8 (3)	O1—C1—N2—C5	179.7 (2)
C2—C3—N1—C1	178.0 (2)	N1—C1—N2—C5	−0.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₆H₈N₂O·CH₄N₂O·H₂O
M_r	202.22
Crystal system, space group	Triclinic, 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)
V (Å³)	493.05 (7)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.22 × 0.16 × 0.11

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.977, 0.998
No. of measured, independent and observed [I > 2σ(I)] reflections	5424, 1728, 1439
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.597

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.170, 1.10
No. of reflections	1728
No. of parameters	143
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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.

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

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