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 ▶); Zheng et al., (2005 ▶).

Experimental

Crystal data

• C₆H₈N₂O·CH₄N₂O·H₂O

• M _r = 202.22

• Triclinic,

• 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) ų

• 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[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

• Δρ_max = 0.45 e Å⁻³

• Δρ_min = −0.36 e Å⁻³

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 ▶).

Supplementary Material

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

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) ; (ii) ; (iii) .

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 U_iso(H) = 1.2U_eq(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 U_iso(H) = 1.2–1.5 U_eq(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·H2O	Z = 2
Mr = 202.22	F000 = 216
Triclinic, P1	Dx = 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 = 2.6–25.1º
c = 8.9268 (9) Å	µ = 0.11 mm−1
α = 105.007 (3)º	T = 293 (2) K
β = 103.857 (3)º	Prism, colourless
γ = 114.379 (2)º	0.22 × 0.16 × 0.11 mm
V = 493.05 (7) Å3

Data collection

Bruker APEXII CCD area-detector diffractometer	1728 independent reflections
Radiation source: Fine–focus sealed tube	1439 reflections with I > 2σ(I)
Monochromator: Graphite	Rint = 0.019
T = 293(2) K	θmax = 25.1º
φ and ω scans	θmin = 2.6º
Absorption correction: multi-scan(SADABS; Bruker, 2005)	h = −9→9
Tmin = 0.977, Tmax = 0.998	k = −8→10
5424 measured reflections	l = −10→10

Refinement

Refinement on F2	Secondary atom site location: Difmap
Least-squares matrix: Full	Hydrogen site location: Geom
R[F2 > 2σ(F2)] = 0.053	H 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 reflections	Δρmax = 0.45 e Å−3
143 parameters	Δρmin = −0.36 e Å−3
1 restraint	Extinction 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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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.