6-(Trifluoro­meth­yl)pyrimidine-2,4(1H,3H)-dione monohydrate

Li, G.-C.; Wang, H.-S.; Niu, Y.-J.; Yang, F.-L.

doi:10.1107/S1600536810022683

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 66| Part 7| July 2010| Page o1699

doi:10.1107/S1600536810022683

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6-(Trifluoromethyl)pyrimidine-2,4(1H,3H)-dione monohydrate

Gong-Chun Li,^a Hong-Sheng Wang,^a Yu-Jiao Niu ^a and Feng-Ling Yang ^a ^*

^aCollege of Chemistry and Chemical Engineering, Xuchang University, Xuchang, Henan Province 461000, People's Republic of China
^*Correspondence e-mail: actaeli@gmail.com

(Received 27 May 2010; accepted 13 June 2010; online 18 June 2010)

The title compound, C₅H₃F₃N₂O₂·H₂O, was prepared by the reaction of ethyl 4,4,4-trifluoro-3-oxobutanoate with urea. In the crystal, the 6-(trifluoromethyl)pyrimidine-2,4(1H,3H)-dione and water molecules are linked by N—H⋯O and O—H⋯O hydrogen bonds. A ring dimer structure is formed by additional intermolecular N—H⋯O hydrogen bonds.

Related literature

For applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993 ); as agrochemicals, see: Maeno et al. (1990 ); as antiviral agents, see: Gilchrist (1997 ); as herbicides, see: Selby et al. (2002 ).

Experimental

Crystal data

C₅H₃F₃N₂O₂·H₂O
M_r = 198.11
Monoclinic, P 2₁ /c
a = 5.0250 (8) Å
b = 7.046 (1) Å
c = 20.769 (2) Å
β = 91.300 (7)°
V = 735.16 (17) Å³
Z = 4
Mo Kα radiation
μ = 0.19 mm⁻¹
T = 113 K
0.24 × 0.20 × 0.18 mm

Data collection

Rigaku Saturn724 CCD diffractometer
Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku/MSC, 2009 ) T_min = 0.956, T_max = 0.966
6863 measured reflections
1747 independent reflections
1382 reflections with I > 2σ(I)
R_int = 0.029

Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.100
S = 1.07
1747 reflections
134 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.21 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3B⋯O1ⁱ	0.825 (17)	2.017 (18)	2.7815 (13)	153.9 (17)
O3—H3A⋯O2ⁱⁱ	0.86 (2)	1.95 (2)	2.8066 (13)	176.0 (17)
N2—H2⋯O3	0.896 (17)	1.824 (17)	2.7191 (14)	177.9 (16)
N1—H1⋯O1ⁱⁱⁱ	0.954 (17)	1.896 (18)	2.8490 (14)	176.4 (16)
Symmetry codes: (i) -x, -y+1, -z+1; (ii) x-1, y-1, z; (iii) -x+1, -y+2, -z+1.

Data collection: CrystalClear-SM Expert (Rigaku/MSC, 2009); cell refinement: CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810022683/fj2309sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536810022683/fj2309Isup2.hkl

checkCIF report

Comment top

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, shch as AZT, which is the most widely used anti-AIDS drug (Gilchrist, 1997). Recently, a new series of highly active herbicides of substituted azolylpyrimidines were reported (Selby et al., 2002). In order to discover further biologically active pyrimidine compounds, the title compound, (I), was synthesized and its crystal structure determined (Fig. 1).

In the crystal strucrure, The part of 6-(trifluoromethyl)pyrimidine-2,4(1H,3H)-dione and water molecule are linked by N—H···O and O—H···O hydrogen bonds. The ring dimer structure is formed by addition intermolecular N—H···O hydrogen bonds.

Related literature top

For applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993); as agrochemicals, see: Maeno et al. (1990); as antiviral agents, see: Gilchrist (1997); as herbicides, see: Selby et al. (2002).

Experimental top

To 35 ml absolute ethanol sodium (1.38 g, 60 mmol) was added. When sodium was dissppeared, ethyl 4,4,4-trifluoro-3-oxobutanoate(5.50 g, 30 mmol) and urea (1.80 g, 30 mmol) were added to the solution. The mixture was refluxed for 20 hr., The solvent was evaporated in vacuo and the residue was washed with water. The title compound was recrystallized from water and single crystals of (I) were obtained by slow evaporation.

Computing details top

Data collection: CrystalClear-SM Expert (Rigaku/MSC, 2009); cell refinement: CrystalClear-SM Expert (Rigaku/MSC, 2009); data reduction: CrystalClear-SM Expert (Rigaku/MSC, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2009).

Figures top

	Fig. 1. The asymmetric unit of the title compound, (I), with displacement ellipsoids drawn at the 30% probability level.
	Fig. 2. The packing diagram of the title compound. Intermolecular hydrogen bonds are shown as dashed line.

6-(Trifluoromethyl)pyrimidine-2,4(1H,3H)-dione monohydrate top

Crystal data top

C₅H₃F₃N₂O₂·H₂O	F(000) = 400
M_r = 198.11	D_x = 1.790 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71075 Å
a = 5.0250 (8) Å	Cell parameters from 2492 reflections
b = 7.046 (1) Å	θ = 2.0–27.9°
c = 20.769 (2) Å	µ = 0.19 mm⁻¹
β = 91.300 (7)°	T = 113 K
V = 735.16 (17) Å³	Prism, colorless
Z = 4	0.24 × 0.20 × 0.18 mm

Data collection top

Rigaku Saturn724 CCD diffractometer	1747 independent reflections
Radiation source: rotating anode	1382 reflections with I > 2σ(I)
Multilayer monochromator	R_int = 0.029
ω scans	θ_max = 27.9°, θ_min = 2.0°
Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku/MSC, 2009)	h = −6→6
T_min = 0.956, T_max = 0.966	k = −6→9
6863 measured reflections	l = −27→27

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.100	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0589P)² + 0.0166P] where P = (F_o² + 2F_c²)/3
1747 reflections	(Δ/σ)_max < 0.001
134 parameters	Δρ_max = 0.33 e Å⁻³
0 restraints	Δρ_min = −0.21 e Å⁻³

Crystal data top

C₅H₃F₃N₂O₂·H₂O	V = 735.16 (17) Å³
M_r = 198.11	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 5.0250 (8) Å	µ = 0.19 mm⁻¹
b = 7.046 (1) Å	T = 113 K
c = 20.769 (2) Å	0.24 × 0.20 × 0.18 mm
β = 91.300 (7)°

Data collection top

Rigaku Saturn724 CCD diffractometer	1747 independent reflections
Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku/MSC, 2009)	1382 reflections with I > 2σ(I)
T_min = 0.956, T_max = 0.966	R_int = 0.029
6863 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.100	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.33 e Å⁻³
1747 reflections	Δρ_min = −0.21 e Å⁻³
134 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
F1	0.74748 (17)	0.37877 (12)	0.26992 (4)	0.0431 (3)
F2	0.33139 (17)	0.43344 (12)	0.28202 (4)	0.0433 (3)
F3	0.54045 (16)	0.25207 (11)	0.34843 (4)	0.0359 (2)
O1	0.32964 (16)	0.78481 (12)	0.48978 (4)	0.0247 (2)
O2	1.03039 (17)	0.99065 (12)	0.37275 (4)	0.0261 (2)
O3	0.09114 (19)	0.33980 (15)	0.43644 (5)	0.0299 (3)
N1	0.67605 (19)	0.88773 (14)	0.42979 (5)	0.0199 (2)
N2	0.46193 (19)	0.60395 (14)	0.40583 (5)	0.0187 (2)
C1	0.4798 (2)	0.76007 (17)	0.44449 (5)	0.0191 (3)
C2	0.8566 (2)	0.87123 (17)	0.38039 (6)	0.0193 (3)
C3	0.8191 (2)	0.70430 (17)	0.34028 (6)	0.0196 (3)
H3	0.9296	0.6828	0.3045	0.023*
C4	0.6262 (2)	0.58089 (16)	0.35448 (5)	0.0183 (3)
C5	0.5641 (2)	0.40964 (18)	0.31352 (6)	0.0237 (3)
H1	0.681 (3)	0.999 (2)	0.4561 (9)	0.048 (5)*
H2	0.340 (3)	0.518 (2)	0.4169 (8)	0.041 (5)*
H3A	0.081 (3)	0.234 (3)	0.4166 (10)	0.049 (5)*
H3B	−0.024 (3)	0.336 (3)	0.4642 (8)	0.043 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0459 (5)	0.0380 (5)	0.0467 (5)	−0.0137 (4)	0.0277 (4)	−0.0219 (4)
F2	0.0400 (5)	0.0422 (6)	0.0467 (5)	0.0051 (4)	−0.0173 (4)	−0.0201 (4)
F3	0.0481 (5)	0.0177 (4)	0.0423 (5)	−0.0059 (4)	0.0095 (4)	−0.0025 (3)
O1	0.0267 (5)	0.0250 (5)	0.0229 (4)	−0.0091 (4)	0.0097 (4)	−0.0050 (3)
O2	0.0237 (5)	0.0225 (5)	0.0325 (5)	−0.0076 (4)	0.0092 (4)	−0.0012 (4)
O3	0.0307 (5)	0.0248 (6)	0.0347 (6)	−0.0110 (4)	0.0140 (4)	−0.0049 (4)
N1	0.0204 (5)	0.0192 (6)	0.0204 (5)	−0.0058 (4)	0.0042 (4)	−0.0025 (4)
N2	0.0191 (5)	0.0165 (5)	0.0208 (5)	−0.0046 (4)	0.0043 (4)	−0.0009 (4)
C1	0.0190 (6)	0.0193 (6)	0.0190 (5)	−0.0028 (4)	0.0014 (4)	0.0000 (5)
C2	0.0176 (5)	0.0187 (6)	0.0215 (6)	−0.0006 (5)	0.0023 (4)	0.0028 (4)
C3	0.0192 (6)	0.0195 (7)	0.0201 (6)	0.0010 (5)	0.0039 (4)	0.0010 (4)
C4	0.0185 (5)	0.0174 (6)	0.0191 (6)	0.0019 (4)	0.0013 (4)	0.0007 (5)
C5	0.0227 (6)	0.0216 (7)	0.0270 (6)	−0.0019 (5)	0.0064 (5)	−0.0038 (5)

Geometric parameters (Å, º) top

F1—C5	1.3245 (14)	N1—H1	0.954 (17)
F2—C5	1.3374 (15)	N2—C1	1.3636 (15)
F3—C5	1.3328 (15)	N2—C4	1.3729 (14)
O1—C1	1.2317 (14)	N2—H2	0.896 (17)
O2—C2	1.2255 (14)	C2—C3	1.4512 (17)
O3—H3A	0.86 (2)	C3—C4	1.3400 (17)
O3—H3B	0.825 (17)	C3—H3	0.9500
N1—C1	1.3742 (15)	C4—C5	1.5050 (17)
N1—C2	1.3898 (15)

H3A—O3—H3B	105.8 (17)	C4—C3—C2	119.01 (11)
C1—N1—C2	126.37 (10)	C4—C3—H3	120.5
C1—N1—H1	114.8 (11)	C2—C3—H3	120.5
C2—N1—H1	118.8 (11)	C3—C4—N2	123.00 (11)
C1—N2—C4	121.34 (10)	C3—C4—C5	122.52 (11)
C1—N2—H2	115.5 (11)	N2—C4—C5	114.42 (10)
C4—N2—H2	123.2 (11)	F1—C5—F3	107.89 (10)
O1—C1—N2	122.04 (10)	F1—C5—F2	107.48 (10)
O1—C1—N1	122.15 (11)	F3—C5—F2	106.44 (10)
N2—C1—N1	115.80 (10)	F1—C5—C4	112.30 (10)
O2—C2—N1	121.15 (11)	F3—C5—C4	112.34 (10)
O2—C2—C3	124.46 (11)	F2—C5—C4	110.10 (10)
N1—C2—C3	114.39 (10)

C4—N2—C1—O1	178.24 (10)	C2—C3—C4—C5	176.73 (10)
C4—N2—C1—N1	−1.87 (16)	C1—N2—C4—C3	2.53 (18)
C2—N1—C1—O1	179.13 (11)	C1—N2—C4—C5	−174.89 (10)
C2—N1—C1—N2	−0.76 (17)	C3—C4—C5—F1	10.94 (17)
C1—N1—C2—O2	−177.49 (11)	N2—C4—C5—F1	−171.62 (10)
C1—N1—C2—C3	2.59 (16)	C3—C4—C5—F3	132.78 (12)
O2—C2—C3—C4	178.20 (11)	N2—C4—C5—F3	−49.78 (14)
N1—C2—C3—C4	−1.88 (16)	C3—C4—C5—F2	−108.79 (13)
C2—C3—C4—N2	−0.49 (18)	N2—C4—C5—F2	68.65 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3B···O1ⁱ	0.825 (17)	2.017 (18)	2.7815 (13)	153.9 (17)
O3—H3A···O2ⁱⁱ	0.86 (2)	1.95 (2)	2.8066 (13)	176.0 (17)
N2—H2···O3	0.896 (17)	1.824 (17)	2.7191 (14)	177.9 (16)
N1—H1···O1ⁱⁱⁱ	0.954 (17)	1.896 (18)	2.8490 (14)	176.4 (16)

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

Experimental details

Crystal data
Chemical formula	C₅H₃F₃N₂O₂·H₂O
M_r	198.11
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	113
a, b, c (Å)	5.0250 (8), 7.046 (1), 20.769 (2)
β (°)	91.300 (7)
V (Å³)	735.16 (17)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.19
Crystal size (mm)	0.24 × 0.20 × 0.18

Data collection
Diffractometer	Rigaku Saturn724 CCD diffractometer
Absorption correction	Multi-scan (CrystalClear-SM Expert; Rigaku/MSC, 2009)
T_min, T_max	0.956, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections	6863, 1747, 1382
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.657

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.100, 1.07
No. of reflections	1747
No. of parameters	134
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.33, −0.21

Computer programs: CrystalClear-SM Expert (Rigaku/MSC, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), CrystalStructure (Rigaku/MSC, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3B···O1ⁱ	0.825 (17)	2.017 (18)	2.7815 (13)	153.9 (17)
O3—H3A···O2ⁱⁱ	0.86 (2)	1.95 (2)	2.8066 (13)	176.0 (17)
N2—H2···O3	0.896 (17)	1.824 (17)	2.7191 (14)	177.9 (16)
N1—H1···O1ⁱⁱⁱ	0.954 (17)	1.896 (18)	2.8490 (14)	176.4 (16)

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

Acknowledgements

This work was supported by the Program for New Century Excellent Talents in Universities of Henan Province (No. 2005HANCET-17), the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Eduation Department, China (grant No. 2007150036).

References

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Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman. Google Scholar
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