2-[4-(Chloro­meth­yl)phen­oxy]-4,6-dimeth­oxy­pyrimidine

Abstract

The title compound, C₁₃H₁₃ClN₂O₃, was synthesized in the course of the search for novel bioactive pyrimidine derivatives. The C—O—C angle at the phen­oxy O atom is widened to 119.87 (18)°. The dihedral angle between the pyrimidine and benzene rings is 64.2 (3)°.

Related literature  

For the biological activity of pyrimidine derivatives, see: Amin et al. (2011 ▶); Chen et al. (2009 ▶); Popova et al. (1999 ▶); Sagi et al. (2011 ▶); Stec et al. (2008 ▶). For related structures of 2-phen­oxy­pyrimidines, see: Shah Bakhtiar et al. (2009a ▶,b ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental  

Crystal data  

• C₁₃H₁₃ClN₂O₃

• M _r = 280.70

• Monoclinic,

• a = 8.3998 (17) Å

• b = 23.145 (5) Å

• c = 7.7967 (16) Å

• β = 117.28 (3)°

• V = 1347.2 (6) ų

• Z = 4

• Mo Kα radiation

• μ = 0.29 mm⁻¹

• T = 113 K

• 0.30 × 0.25 × 0.20 mm

Data collection  

• Rigaku SCXmini diffractometer

• Absorption correction: multi-scan (CrystalClear; Rigaku, 2008 ▶) T _min = 0.912, T _max = 0.942

• 11307 measured reflections

• 2358 independent reflections

• 1899 reflections with I > 2σ(I)

• R _int = 0.039

Refinement  

• R[F ² > 2σ(F ²)] = 0.054

• wR(F ²) = 0.134

• S = 1.09

• 2358 reflections

• 174 parameters

• H-atom parameters constrained

• Δρ_max = 0.62 e Å⁻³

• Δρ_min = −0.52 e Å⁻³

Data collection: CrystalClear (Rigaku, 2008 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536812026220/yk2059Isup3.cml

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

supplementary crystallographic information

Comment

In the past few years, many pyrimidine derivatives have drawn much attention in agrochemical and medicinal research because of their diverse bioactivities such as fungicidal, herbicidal and pharmacological activities (Popova et al., 1999; Stec et al., 2008; Chen et al., 2009; Amin et al., 2011; Sagi et al., 2011). In the search of novel biologically active molecules, we have synthesized new pyrimidines. We report here the crystal structure of the target compound. It contains two planar groups, the benzene ring (C7/C8/C9/C10/C11/C12), and the substituted pyrimidine ring (N1/C1/C2/C3/N2/C6) (Fig.1). All bond lengths and angles in the title compound lie within normal ranges (Allen et al., 1987) and are similar to those observed in the related 2-phenoxypyrimidines (Shah Bakhtiar et al., 2009a,b). The plane of pyrimidine ring makes a dihedral angle of 64.2 (3)° with the plane of benzene ring.

Experimental

[4-(4,6-dimethoxypyrimidin-2-yloxy)phenyl]methanol (5 mmol) was dissolved in 50 ml of CH₂Cl₂. Thionyl chloride (5.5 mmol) was then added dropwise, while cooling on an ice bath. The resulting solution was heated to 298 K for 3 h, and the mixture was poured into 50 ml of ice water. The organic layer was washed with saturated brine(3 x 30 ml) and dried over anhydrous sodium sulfate. The solvent was evaporated under reduced pressure, and the residue was recrystallized from a mixture of petroleum ether/ethyl acetate to obtain colourless crystals. Mp: 354–356 K.

Refinement

All H atoms were placed in calculated positions, with C—H = 0.93, 0.96 and 0.97Å for CH, CH₃ and CH₂ groups, respectively, and included in the final cycles of refinement using a riding model, with U_iso(H) = 1.2U_eq(C).

Figures

Fig. 1.

View of the title compound showing atom labelling scheme. Thermal ellipsoids drawn at the 30% probability level.

Crystal data

C13H13ClN2O3	F(000) = 584
Mr = 280.70	Dx = 1.384 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 11126 reflections
a = 8.3998 (17) Å	θ = 3.1–27.6°
b = 23.145 (5) Å	µ = 0.29 mm−1
c = 7.7967 (16) Å	T = 113 K
β = 117.28 (3)°	Prism, colourless
V = 1347.2 (6) Å3	0.30 × 0.25 × 0.20 mm
Z = 4

Data collection

Rigaku SCXmini diffractometer	2358 independent reflections
Radiation source: fine-focus sealed tube	1899 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.039
Detector resolution: 14.22 pixels mm-1	θmax = 25.0°, θmin = 3.1°
ω and φ scans	h = −9→9
Absorption correction: multi-scan (CrystalClear; Rigaku, 2008)	k = −27→27
Tmin = 0.912, Tmax = 0.942	l = −9→9
11307 measured reflections

Refinement

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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134	H-atom parameters constrained
S = 1.09	w = 1/[σ2(Fo2) + (0.0495P)2 + 0.8134P] where P = (Fo2 + 2Fc2)/3
2358 reflections	(Δ/σ)max < 0.001
174 parameters	Δρmax = 0.62 e Å−3
0 restraints	Δρmin = −0.52 e Å−3

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 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	1.0641 (3)	0.96956 (10)	0.2361 (4)	0.0471 (6)
C2	1.2474 (3)	0.97248 (11)	0.3080 (4)	0.0517 (6)
H2	1.3138	1.0040	0.3785	0.062*
C3	1.3259 (3)	0.92547 (10)	0.2683 (3)	0.0446 (6)
C4	1.5903 (4)	0.87913 (13)	0.2908 (5)	0.0638 (8)
H4A	1.5472	0.8434	0.3166	0.096*
H4B	1.7177	0.8815	0.3689	0.096*
H4C	1.5624	0.8807	0.1569	0.096*
C5	0.7922 (4)	1.01267 (13)	0.2028 (5)	0.0692 (8)
H5A	0.7339	0.9971	0.0744	0.104*
H5B	0.7470	1.0507	0.2032	0.104*
H5C	0.7689	0.9882	0.2882	0.104*
C6	1.0600 (3)	0.88216 (10)	0.1124 (3)	0.0437 (6)
C7	0.7881 (3)	0.82754 (10)	−0.0485 (4)	0.0454 (6)
C8	0.7325 (3)	0.78267 (11)	0.0275 (4)	0.0524 (6)
H8	0.8158	0.7593	0.1241	0.063*
C9	0.5507 (4)	0.77293 (11)	−0.0426 (4)	0.0509 (6)
H9	0.5123	0.7425	0.0072	0.061*
C10	0.4246 (3)	0.80752 (11)	−0.1854 (3)	0.0448 (6)
C11	0.4845 (3)	0.85228 (11)	−0.2603 (4)	0.0507 (6)
H11	0.4017	0.8758	−0.3565	0.061*
C12	0.6662 (4)	0.86220 (11)	−0.1929 (4)	0.0520 (6)
H12	0.7054	0.8919	−0.2446	0.062*
C13	0.2290 (4)	0.79504 (14)	−0.2462 (4)	0.0653 (8)
H13A	0.2013	0.8076	−0.1442	0.078*
H13B	0.2104	0.7536	−0.2602	0.078*
Cl1	0.07844 (11)	0.82848 (5)	−0.46320 (16)	0.1037 (4)
N1	0.9659 (3)	0.92397 (8)	0.1384 (3)	0.0452 (5)
N2	1.2352 (2)	0.87930 (9)	0.1678 (3)	0.0450 (5)
O1	0.9816 (3)	1.01557 (8)	0.2666 (3)	0.0647 (6)
O2	1.5055 (2)	0.92689 (8)	0.3357 (3)	0.0565 (5)
O3	0.9740 (2)	0.83341 (7)	0.0165 (3)	0.0576 (5)

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0597 (15)	0.0372 (13)	0.0493 (14)	0.0004 (11)	0.0293 (13)	−0.0034 (11)
C2	0.0567 (15)	0.0407 (14)	0.0558 (15)	−0.0089 (11)	0.0242 (13)	−0.0105 (12)
C3	0.0450 (13)	0.0441 (14)	0.0448 (14)	−0.0059 (11)	0.0206 (11)	−0.0004 (11)
C4	0.0492 (15)	0.0636 (18)	0.079 (2)	0.0021 (13)	0.0293 (15)	−0.0057 (15)
C5	0.073 (2)	0.0577 (18)	0.091 (2)	0.0119 (15)	0.0504 (18)	−0.0029 (16)
C6	0.0476 (13)	0.0373 (13)	0.0476 (14)	−0.0038 (10)	0.0232 (11)	−0.0047 (10)
C7	0.0420 (12)	0.0390 (13)	0.0553 (15)	−0.0055 (10)	0.0223 (11)	−0.0138 (11)
C8	0.0535 (15)	0.0410 (14)	0.0590 (16)	0.0046 (11)	0.0227 (13)	0.0017 (12)
C9	0.0594 (15)	0.0390 (14)	0.0620 (16)	−0.0044 (11)	0.0345 (14)	0.0017 (12)
C10	0.0468 (13)	0.0457 (14)	0.0438 (13)	−0.0065 (11)	0.0224 (11)	−0.0096 (11)
C11	0.0515 (14)	0.0496 (15)	0.0443 (14)	−0.0016 (11)	0.0163 (12)	0.0027 (11)
C12	0.0577 (15)	0.0454 (15)	0.0546 (15)	−0.0115 (12)	0.0271 (13)	−0.0012 (12)
C13	0.0529 (16)	0.077 (2)	0.0670 (18)	−0.0118 (14)	0.0280 (14)	−0.0035 (16)
Cl1	0.0508 (5)	0.1230 (9)	0.1064 (8)	−0.0071 (5)	0.0095 (5)	0.0305 (6)
N1	0.0478 (11)	0.0396 (11)	0.0497 (12)	0.0002 (9)	0.0236 (10)	−0.0043 (9)
N2	0.0444 (11)	0.0408 (11)	0.0518 (12)	−0.0035 (9)	0.0238 (10)	−0.0049 (9)
O1	0.0698 (12)	0.0451 (11)	0.0882 (15)	0.0026 (9)	0.0442 (11)	−0.0150 (10)
O2	0.0443 (9)	0.0555 (11)	0.0666 (12)	−0.0082 (8)	0.0227 (9)	−0.0125 (9)
O3	0.0451 (10)	0.0445 (10)	0.0826 (13)	−0.0061 (8)	0.0288 (9)	−0.0208 (9)

Geometric parameters (Å, º)

C1—N1	1.341 (3)	C6—O3	1.363 (3)
C1—O1	1.350 (3)	C7—C12	1.379 (4)
C1—C2	1.378 (4)	C7—C8	1.378 (4)
C2—C3	1.379 (3)	C7—O3	1.410 (3)
C2—H2	0.9300	C8—C9	1.385 (4)
C3—N2	1.337 (3)	C8—H8	0.9300
C3—O2	1.351 (3)	C9—C10	1.386 (4)
C4—O2	1.442 (3)	C9—H9	0.9300
C4—H4A	0.9600	C10—C11	1.391 (3)
C4—H4B	0.9600	C10—C13	1.514 (3)
C4—H4C	0.9600	C11—C12	1.387 (4)
C5—O1	1.435 (3)	C11—H11	0.9300
C5—H5A	0.9600	C12—H12	0.9300
C5—H5B	0.9600	C13—Cl1	1.760 (3)
C5—H5C	0.9600	C13—H13A	0.9700
C6—N1	1.322 (3)	C13—H13B	0.9700
C6—N2	1.332 (3)
N1—C1—O1	119.3 (2)	C7—C8—C9	118.8 (2)
N1—C1—C2	123.4 (2)	C7—C8—H8	120.6
O1—C1—C2	117.2 (2)	C9—C8—H8	120.6
C1—C2—C3	115.5 (2)	C8—C9—C10	121.4 (2)
C1—C2—H2	122.3	C8—C9—H9	119.3
C3—C2—H2	122.3	C10—C9—H9	119.3
N2—C3—O2	118.8 (2)	C9—C10—C11	118.5 (2)
N2—C3—C2	124.0 (2)	C9—C10—C13	117.5 (2)
O2—C3—C2	117.2 (2)	C11—C10—C13	124.0 (2)
O2—C4—H4A	109.5	C12—C11—C10	120.7 (2)
O2—C4—H4B	109.5	C12—C11—H11	119.6
H4A—C4—H4B	109.5	C10—C11—H11	119.6
O2—C4—H4C	109.5	C7—C12—C11	119.3 (2)
H4A—C4—H4C	109.5	C7—C12—H12	120.4
H4B—C4—H4C	109.5	C11—C12—H12	120.4
O1—C5—H5A	109.5	C10—C13—Cl1	114.6 (2)
O1—C5—H5B	109.5	C10—C13—H13A	108.6
H5A—C5—H5B	109.5	Cl1—C13—H13A	108.6
O1—C5—H5C	109.5	C10—C13—H13B	108.6
H5A—C5—H5C	109.5	Cl1—C13—H13B	108.6
H5B—C5—H5C	109.5	H13A—C13—H13B	107.6
N1—C6—N2	129.5 (2)	C6—N1—C1	114.1 (2)
N1—C6—O3	119.1 (2)	C6—N2—C3	113.5 (2)
N2—C6—O3	111.5 (2)	C1—O1—C5	118.6 (2)
C12—C7—C8	121.2 (2)	C3—O2—C4	118.3 (2)
C12—C7—O3	121.5 (2)	C6—O3—C7	119.87 (18)
C8—C7—O3	117.1 (2)