4,6-Dichloro-5-methoxy­pyrimidine

Abstract

The mol­ecule of the title compound, C₅H₄Cl₂N₂O, is close to being planar (r.m.s. deviation = 0.013 Å), apart from the C atom of the meth­oxy group, which deviates by 1.082 (2) Å from the mean plane of the other atoms. In the crystal, short Cl⋯N contacts [3.0940 (15) and 3.1006 (17) Å] generate a three-dimensional framework.

Related literature

For background to the importance of pyrimidines and analogous compounds in pharmaceutical and biological fields, see: Townsend & Drach (2002a ▶,b ▶). For related structures, see: Bukhari et al. (2008 ▶, 2009 ▶); Fun et al. (2006 ▶, 2008 ▶)); Yathirajan et al. (2007 ▶); Zhao et al. (2009 ▶). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

• C₅H₄Cl₂N₂O

• M _r = 179.00

• Orthorhombic,

• a = 13.6545 (19) Å

• b = 3.9290 (6) Å

• c = 13.0275 (18) Å

• V = 698.91 (17) ų

• Z = 4

• Mo Kα radiation

• μ = 0.85 mm⁻¹

• T = 100 K

• 0.29 × 0.20 × 0.09 mm

Data collection

• Bruker APEX Duo CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.787, T _max = 0.926

• 4505 measured reflections

• 1520 independent reflections

• 1415 reflections with I > 2σ(I)

• R _int = 0.024

Refinement

• R[F ² > 2σ(F ²)] = 0.024

• wR(F ²) = 0.054

• S = 1.08

• 1520 reflections

• 92 parameters

• 1 restraint

• H-atom parameters constrained

• Δρ_max = 0.27 e Å⁻³

• Δρ_min = −0.19 e Å⁻³

• Absolute structure: Flack (1983 ▶), 459 Friedel pairs

• Flack parameter: −0.02 (6)

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

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

supplementary crystallographic information

Comment

The importance of pyrimidines and analogous compounds in pharmaceutical and biological fields is well known (Townsend et al., 2002a,b)). The crystal structures of 4-(4-bromophenyl)-6-(4-chlorophenyl)pyrimidin-2-ylamine (Bukhari et al., 2009), 4-(4-fluorophenyl)-6-(2-furyl)pyrimidin-2-amine (Bukhari et al., 2008), 2-amino-4,6-dichloropyrimidine (Fun et al., 2008), 4,6-diphenylpyrimidin-2-ylamine (Fun et al., 2006), 5-bromopyrimidin-2(1H)-one (Yathirajan et al., 2007) and 4-(4-chlorophenyl)-6-(methylsulfanyl)pyrimidin-2-amine (Zhao et al., 2009) have been reported. We now report the structure of the title compound, (I).

The geometrical parameters of the title compound (Fig. 1) are comparable to those related structures. In the crystal structure (Fig. 2), molecules are linked into chains by short Cl1···N2 interaction of 3.0940 (15) Å, symmetry code: -1/2 + x, 1/2 - y, z, along the a axis. The short Cl2···N1 interaction of 3.1006 (17) Å, symmetry code: 3/2 - x, 1/2 + y, -1/2 + z linked these chains into a three-dimensional framework.

Experimental

The title compound was obtained as a gift sample from R. L. Fine Chem., Bangalore, India. The compound was used without further purification. Colourless blocks of (I) were obtained from the slow evaporation of an acetonitrile solution (m.p.: 313–315 K).

Refinement

All hydrogen atoms were positioned geometrically with a riding model with C–H = 0.93–0.96 Å and U_iso(H) = 1.2 and 1.5 U_eq(C). A rotating-group model was applied for the methyl groups.

Figures

Fig. 1.

The molecular structure of (I) with 50% probability ellipsoids for non-H atoms.

Fig. 2.

The crystal packing of (I), viewed down the b axis, showing the short contacts (dashed lines) linking the molecules into a three-dimensional framework.

Crystal data

C5H4Cl2N2O	F(000) = 360
Mr = 179.00	Dx = 1.701 Mg m−3
Orthorhombic, Pna21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 1997 reflections
a = 13.6545 (19) Å	θ = 3.0–32.2°
b = 3.9290 (6) Å	µ = 0.85 mm−1
c = 13.0275 (18) Å	T = 100 K
V = 698.91 (17) Å3	Block, colourless
Z = 4	0.29 × 0.20 × 0.09 mm

Data collection

Bruker APEX Duo CCD diffractometer	1520 independent reflections
Radiation source: fine-focus sealed tube	1415 reflections with I > 2σ(I)
graphite	Rint = 0.024
φ and ω scans	θmax = 30.0°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −19→17
Tmin = 0.787, Tmax = 0.926	k = −5→4
4505 measured reflections	l = −18→13

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.024	H-atom parameters constrained
wR(F2) = 0.054	w = 1/[σ2(Fo2) + (0.0274P)2 + 0.0046P] where P = (Fo2 + 2Fc2)/3
S = 1.08	(Δ/σ)max = 0.001
1520 reflections	Δρmax = 0.27 e Å−3
92 parameters	Δρmin = −0.19 e Å−3
1 restraint	Absolute structure: Flack (1983), 459 Friedel pairs
Primary atom site location: structure-invariant direct methods	Flack parameter: −0.02 (6)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	1.00227 (3)	0.39313 (10)	0.31491 (4)	0.01880 (10)
Cl2	0.68657 (3)	−0.13063 (10)	0.50590 (3)	0.01823 (10)
O1	0.87265 (8)	0.2620 (3)	0.49779 (10)	0.0158 (2)
N1	0.85636 (12)	0.0895 (4)	0.22384 (12)	0.0173 (3)
N2	0.71682 (10)	−0.1454 (3)	0.30807 (13)	0.0164 (3)
C1	0.89051 (11)	0.1878 (4)	0.31413 (16)	0.0146 (3)
C2	0.77002 (14)	−0.0714 (5)	0.22517 (14)	0.0176 (4)
H2A	0.7446	−0.1382	0.1621	0.021*
C3	0.75310 (13)	−0.0416 (4)	0.39696 (13)	0.0134 (3)
C4	0.84177 (14)	0.1346 (4)	0.40704 (14)	0.0136 (3)
C5	0.94496 (15)	0.0608 (5)	0.55200 (16)	0.0225 (4)
H5A	0.9966	−0.0013	0.5057	0.034*
H5B	0.9147	−0.1413	0.5786	0.034*
H5C	0.9715	0.1917	0.6077	0.034*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.01301 (17)	0.02330 (19)	0.02010 (18)	−0.00290 (14)	0.00081 (16)	0.0021 (2)
Cl2	0.01565 (17)	0.02443 (19)	0.01463 (17)	−0.00177 (15)	0.00211 (17)	0.00248 (19)
O1	0.0159 (5)	0.0185 (5)	0.0130 (5)	0.0029 (4)	−0.0029 (6)	−0.0044 (6)
N1	0.0148 (7)	0.0222 (8)	0.0150 (7)	0.0019 (6)	−0.0012 (6)	−0.0009 (6)
N2	0.0152 (6)	0.0182 (7)	0.0159 (7)	0.0014 (5)	−0.0030 (7)	−0.0010 (6)
C1	0.0114 (6)	0.0150 (7)	0.0174 (7)	0.0020 (5)	0.0012 (8)	0.0010 (7)
C2	0.0172 (9)	0.0213 (10)	0.0145 (8)	0.0015 (7)	−0.0028 (7)	−0.0019 (7)
C3	0.0127 (8)	0.0144 (8)	0.0130 (7)	0.0017 (6)	0.0005 (7)	0.0016 (6)
C4	0.0133 (8)	0.0133 (7)	0.0142 (8)	0.0030 (5)	−0.0015 (6)	−0.0003 (6)
C5	0.0261 (10)	0.0243 (9)	0.0170 (8)	0.0052 (7)	−0.0097 (8)	−0.0013 (8)

Geometric parameters (Å, °)

Cl1—C1	1.7262 (16)	N2—C2	1.334 (2)
Cl2—C3	1.7210 (19)	C1—C4	1.397 (3)
O1—C4	1.351 (2)	C2—H2A	0.9300
O1—C5	1.449 (2)	C3—C4	1.401 (3)
N1—C1	1.323 (2)	C5—H5A	0.9600
N1—C2	1.338 (2)	C5—H5B	0.9600
N2—C3	1.324 (2)	C5—H5C	0.9600
C4—O1—C5	115.92 (13)	C4—C3—Cl2	118.65 (14)
C1—N1—C2	115.91 (16)	O1—C4—C1	123.64 (16)
C3—N2—C2	115.93 (14)	O1—C4—C3	122.32 (16)
N1—C1—C4	123.97 (15)	C1—C4—C3	113.86 (16)
N1—C1—Cl1	116.95 (14)	O1—C5—H5A	109.5
C4—C1—Cl1	119.08 (14)	O1—C5—H5B	109.5
N2—C2—N1	126.41 (17)	H5A—C5—H5B	109.5
N2—C2—H2A	116.8	O1—C5—H5C	109.5
N1—C2—H2A	116.8	H5A—C5—H5C	109.5
N2—C3—C4	123.89 (16)	H5B—C5—H5C	109.5
N2—C3—Cl2	117.46 (14)
C2—N1—C1—C4	−0.4 (2)	N1—C1—C4—O1	−173.85 (16)
C2—N1—C1—Cl1	179.51 (12)	Cl1—C1—C4—O1	6.2 (2)
C3—N2—C2—N1	1.5 (2)	N1—C1—C4—C3	1.4 (2)
C1—N1—C2—N2	−1.1 (3)	Cl1—C1—C4—C3	−178.53 (12)
C2—N2—C3—C4	−0.3 (2)	N2—C3—C4—O1	174.29 (15)
C2—N2—C3—Cl2	179.80 (13)	Cl2—C3—C4—O1	−5.8 (2)
C5—O1—C4—C1	−85.2 (2)	N2—C3—C4—C1	−1.0 (2)
C5—O1—C4—C3	99.96 (19)	Cl2—C3—C4—C1	178.89 (12)