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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2109
https://doi.org/10.1107/S1600536812026220

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

Shi-Hong Shen,a Kui Hu,b Li Sun,b Xiao-Long Fanb and Hong Daic,b*

aJiangsu Rugao Middle School, Rugao 226500, People's Republic of China, bCollege of Chemistry and Chemical Engineering, Nantong University, Nantong 226019, People's Republic of China, and cCollege of Xinglin, Nantong University, Nantong 226019, People's Republic of China
*Correspondence e-mail: gaofz2005@yahoo.com.cn

(Received 15 May 2012; accepted 10 June 2012; online 16 June 2012)

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[Amin, K. M., Awadalla, F. M., Eissa, A. A. M., Abou-Seri, S. M. & Hassan, G. S. (2011). Bioorg. Med. Chem. 19, 6087-6097.]); Chen et al. (2009[Chen, C. N., Lv, L. L., Ji, F. Q., Chen, Q., Xu, H., Niu, C. W., Xi, Z. & Yang, G. F. (2009). Bioorg. Med. Chem. 17, 3011-3017.]); Popova et al. (1999[Popova, L. M., Trishina, A. U., Vershilov, S. V., Ginak, A. I. & Maksimov, B. N. (1999). J. Fluorine Chem. 96, 51-56.]); Sagi et al. (2011[Sagi, V. N., Liu, T. Y., Lu, X. Y., Bartfai, T. & Roberts, E. (2011). Bioorg. Med. Chem. Lett. 21, 7210-7215.]); Stec et al. (2008[Stec, M. M., Bo, Y. X., Chakrabarti, P. P., Liao, L., Ncube, M., Tamayo, N., Tamir, R., Gavva, N. R., Treanor, J. J. S. & Norman, M. H. (2008). Bioorg. Med. Chem. Lett. 18, 5118-5122.]). For related structures of 2-phen­oxy­pyrimidines, see: Shah Bakhtiar et al. (2009a[Shah Bakhtiar, N., Abdullah, Z. & Ng, S. W. (2009a). Acta Cryst. E65, o114.],b[Shah Bakhtiar, N., Abdullah, Z. & Ng, S. W. (2009b). Acta Cryst. E65, o1858.]). For standard bond lengths, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]).

[Scheme 1]

Experimental

Crystal data

  • C13H13ClN2O3

  • Mr = 280.70

  • Monoclinic, P 21 /c

  • a = 8.3998 (17) Å

  • b = 23.145 (5) Å

  • c = 7.7967 (16) Å

  • β = 117.28 (3)°

  • V = 1347.2 (6) Å3

  • 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[Rigaku (2008). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.912, Tmax = 0.942

  • 11307 measured reflections

  • 2358 independent reflections

  • 1899 reflections with I > 2σ(I)

  • Rint = 0.039
Refinement

  • R[F2 > 2σ(F2)] = 0.054

  • wR(F2) = 0.134

  • S = 1.09

  • 2358 reflections

  • 174 parameters

  • H-atom parameters constrained

  • Δρmax = 0.62 e Å−3

  • Δρmin = −0.52 e Å−3

Data collection: CrystalClear (Rigaku, 2008[Rigaku (2008). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812026220/yk2059sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812026220/yk2059Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812026220/yk2059Isup3.cml

checkCIF report


Comment top

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.

Related literature top

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 top

[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 top

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 Uiso(H) = 1.2Ueq(C).

Structure description top

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.

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).

Computing details top

Data collection: CrystalClear (Rigaku, 2008); cell refinement: CrystalClear (Rigaku, 2008); data reduction: CrystalClear (Rigaku, 2008); 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 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. View of the title compound showing atom labelling scheme. Thermal ellipsoids drawn at the 30% probability level.
2-[4-(Chloromethyl)phenoxy]-4,6-dimethoxypyrimidine top
Crystal data top
C13H13ClN2O3F(000) = 584
Mr = 280.70Dx = 1.384 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 11126 reflections
a = 8.3998 (17) Åθ = 3.1–27.6°
b = 23.145 (5) ŵ = 0.29 mm−1
c = 7.7967 (16) ÅT = 113 K
β = 117.28 (3)°Prism, colourless
V = 1347.2 (6) Å30.30 × 0.25 × 0.20 mm
Z = 4
Data collection top
Rigaku SCXmini
diffractometer		2358 independent reflections
Radiation source: fine-focus sealed tube1899 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.039
Detector resolution: 14.22 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω and φ scansh = −9→9
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2008)		k = −27→27
Tmin = 0.912, Tmax = 0.942l = −9→9
11307 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134H-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 parametersΔρmax = 0.62 e Å−3
0 restraintsΔρmin = −0.52 e Å−3
Crystal data top
C13H13ClN2O3V = 1347.2 (6) Å3
Mr = 280.70Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.3998 (17) ŵ = 0.29 mm−1
b = 23.145 (5) ÅT = 113 K
c = 7.7967 (16) Å0.30 × 0.25 × 0.20 mm
β = 117.28 (3)°
Data collection top
Rigaku SCXmini
diffractometer		2358 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2008)		1899 reflections with I > 2σ(I)
Tmin = 0.912, Tmax = 0.942Rint = 0.039
11307 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.134H-atom parameters constrained
S = 1.09Δρmax = 0.62 e Å−3
2358 reflectionsΔρmin = −0.52 e Å−3
174 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 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
xyzUiso*/Ueq
C11.0641 (3)0.96956 (10)0.2361 (4)0.0471 (6)
C21.2474 (3)0.97248 (11)0.3080 (4)0.0517 (6)
H21.31381.00400.37850.062*
C31.3259 (3)0.92547 (10)0.2683 (3)0.0446 (6)
C41.5903 (4)0.87913 (13)0.2908 (5)0.0638 (8)
H4A1.54720.84340.31660.096*
H4B1.71770.88150.36890.096*
H4C1.56240.88070.15690.096*
C50.7922 (4)1.01267 (13)0.2028 (5)0.0692 (8)
H5A0.73390.99710.07440.104*
H5B0.74701.05070.20320.104*
H5C0.76890.98820.28820.104*
C61.0600 (3)0.88216 (10)0.1124 (3)0.0437 (6)
C70.7881 (3)0.82754 (10)−0.0485 (4)0.0454 (6)
C80.7325 (3)0.78267 (11)0.0275 (4)0.0524 (6)
H80.81580.75930.12410.063*
C90.5507 (4)0.77293 (11)−0.0426 (4)0.0509 (6)
H90.51230.74250.00720.061*
C100.4246 (3)0.80752 (11)−0.1854 (3)0.0448 (6)
C110.4845 (3)0.85228 (11)−0.2603 (4)0.0507 (6)
H110.40170.8758−0.35650.061*
C120.6662 (4)0.86220 (11)−0.1929 (4)0.0520 (6)
H120.70540.8919−0.24460.062*
C130.2290 (4)0.79504 (14)−0.2462 (4)0.0653 (8)
H13A0.20130.8076−0.14420.078*
H13B0.21040.7536−0.26020.078*
Cl10.07844 (11)0.82848 (5)−0.46320 (16)0.1037 (4)
N10.9659 (3)0.92397 (8)0.1384 (3)0.0452 (5)
N21.2352 (2)0.87930 (9)0.1678 (3)0.0450 (5)
O10.9816 (3)1.01557 (8)0.2666 (3)0.0647 (6)
O21.5055 (2)0.92689 (8)0.3357 (3)0.0565 (5)
O30.9740 (2)0.83341 (7)0.0165 (3)0.0576 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0597 (15)0.0372 (13)0.0493 (14)0.0004 (11)0.0293 (13)−0.0034 (11)
C20.0567 (15)0.0407 (14)0.0558 (15)−0.0089 (11)0.0242 (13)−0.0105 (12)
C30.0450 (13)0.0441 (14)0.0448 (14)−0.0059 (11)0.0206 (11)−0.0004 (11)
C40.0492 (15)0.0636 (18)0.079 (2)0.0021 (13)0.0293 (15)−0.0057 (15)
C50.073 (2)0.0577 (18)0.091 (2)0.0119 (15)0.0504 (18)−0.0029 (16)
C60.0476 (13)0.0373 (13)0.0476 (14)−0.0038 (10)0.0232 (11)−0.0047 (10)
C70.0420 (12)0.0390 (13)0.0553 (15)−0.0055 (10)0.0223 (11)−0.0138 (11)
C80.0535 (15)0.0410 (14)0.0590 (16)0.0046 (11)0.0227 (13)0.0017 (12)
C90.0594 (15)0.0390 (14)0.0620 (16)−0.0044 (11)0.0345 (14)0.0017 (12)
C100.0468 (13)0.0457 (14)0.0438 (13)−0.0065 (11)0.0224 (11)−0.0096 (11)
C110.0515 (14)0.0496 (15)0.0443 (14)−0.0016 (11)0.0163 (12)0.0027 (11)
C120.0577 (15)0.0454 (15)0.0546 (15)−0.0115 (12)0.0271 (13)−0.0012 (12)
C130.0529 (16)0.077 (2)0.0670 (18)−0.0118 (14)0.0280 (14)−0.0035 (16)
Cl10.0508 (5)0.1230 (9)0.1064 (8)−0.0071 (5)0.0095 (5)0.0305 (6)
N10.0478 (11)0.0396 (11)0.0497 (12)0.0002 (9)0.0236 (10)−0.0043 (9)
N20.0444 (11)0.0408 (11)0.0518 (12)−0.0035 (9)0.0238 (10)−0.0049 (9)
O10.0698 (12)0.0451 (11)0.0882 (15)0.0026 (9)0.0442 (11)−0.0150 (10)
O20.0443 (9)0.0555 (11)0.0666 (12)−0.0082 (8)0.0227 (9)−0.0125 (9)
O30.0451 (10)0.0445 (10)0.0826 (13)−0.0061 (8)0.0288 (9)−0.0208 (9)
Geometric parameters (Å, º) top
C1—N11.341 (3)C6—O31.363 (3)
C1—O11.350 (3)C7—C121.379 (4)
C1—C21.378 (4)C7—C81.378 (4)
C2—C31.379 (3)C7—O31.410 (3)
C2—H20.9300C8—C91.385 (4)
C3—N21.337 (3)C8—H80.9300
C3—O21.351 (3)C9—C101.386 (4)
C4—O21.442 (3)C9—H90.9300
C4—H4A0.9600C10—C111.391 (3)
C4—H4B0.9600C10—C131.514 (3)
C4—H4C0.9600C11—C121.387 (4)
C5—O11.435 (3)C11—H110.9300
C5—H5A0.9600C12—H120.9300
C5—H5B0.9600C13—Cl11.760 (3)
C5—H5C0.9600C13—H13A0.9700
C6—N11.322 (3)C13—H13B0.9700
C6—N21.332 (3)
N1—C1—O1119.3 (2)C7—C8—C9118.8 (2)
N1—C1—C2123.4 (2)C7—C8—H8120.6
O1—C1—C2117.2 (2)C9—C8—H8120.6
C1—C2—C3115.5 (2)C8—C9—C10121.4 (2)
C1—C2—H2122.3C8—C9—H9119.3
C3—C2—H2122.3C10—C9—H9119.3
N2—C3—O2118.8 (2)C9—C10—C11118.5 (2)
N2—C3—C2124.0 (2)C9—C10—C13117.5 (2)
O2—C3—C2117.2 (2)C11—C10—C13124.0 (2)
O2—C4—H4A109.5C12—C11—C10120.7 (2)
O2—C4—H4B109.5C12—C11—H11119.6
H4A—C4—H4B109.5C10—C11—H11119.6
O2—C4—H4C109.5C7—C12—C11119.3 (2)
H4A—C4—H4C109.5C7—C12—H12120.4
H4B—C4—H4C109.5C11—C12—H12120.4
O1—C5—H5A109.5C10—C13—Cl1114.6 (2)
O1—C5—H5B109.5C10—C13—H13A108.6
H5A—C5—H5B109.5Cl1—C13—H13A108.6
O1—C5—H5C109.5C10—C13—H13B108.6
H5A—C5—H5C109.5Cl1—C13—H13B108.6
H5B—C5—H5C109.5H13A—C13—H13B107.6
N1—C6—N2129.5 (2)C6—N1—C1114.1 (2)
N1—C6—O3119.1 (2)C6—N2—C3113.5 (2)
N2—C6—O3111.5 (2)C1—O1—C5118.6 (2)
C12—C7—C8121.2 (2)C3—O2—C4118.3 (2)
C12—C7—O3121.5 (2)C6—O3—C7119.87 (18)
C8—C7—O3117.1 (2)

Experimental details

Crystal data
Chemical formulaC13H13ClN2O3
Mr280.70
Crystal system, space groupMonoclinic, P21/c
Temperature (K)113
a, b, c (Å)8.3998 (17), 23.145 (5), 7.7967 (16)
β (°) 117.28 (3)
V (Å3)1347.2 (6)
Z4
Radiation typeMo Kα
µ (mm−1)0.29
Crystal size (mm)0.30 × 0.25 × 0.20
Data collection
DiffractometerRigaku SCXmini
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2008)
Tmin, Tmax0.912, 0.942
No. of measured, independent and
observed [I > 2σ(I)] reflections		11307, 2358, 1899
Rint0.039
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.054, 0.134, 1.09
No. of reflections2358
No. of parameters174
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.62, −0.52

Computer programs: CrystalClear (Rigaku, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

Acknowledgements

This work was supported by the Science Foundation of Nantong University Xinglin College (grant No. 2010 K132) and the Scientific Research Foundation for Talent Introduction of Nantong University.

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CSD CrossRef Web of Science Google Scholar
 First citationAmin, K. M., Awadalla, F. M., Eissa, A. A. M., Abou-Seri, S. M. & Hassan, G. S. (2011). Bioorg. Med. Chem. 19, 6087–6097.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationChen, C. N., Lv, L. L., Ji, F. Q., Chen, Q., Xu, H., Niu, C. W., Xi, Z. & Yang, G. F. (2009). Bioorg. Med. Chem. 17, 3011–3017.  Web of Science CSD CrossRef PubMed CAS Google Scholar
 First citationPopova, L. M., Trishina, A. U., Vershilov, S. V., Ginak, A. I. & Maksimov, B. N. (1999). J. Fluorine Chem. 96, 51–56.  Web of Science CrossRef CAS Google Scholar
 First citationRigaku (2008). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
 First citationSagi, V. N., Liu, T. Y., Lu, X. Y., Bartfai, T. & Roberts, E. (2011). Bioorg. Med. Chem. Lett. 21, 7210–7215.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationShah Bakhtiar, N., Abdullah, Z. & Ng, S. W. (2009a). Acta Cryst. E65, o114.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationShah Bakhtiar, N., Abdullah, Z. & Ng, S. W. (2009b). Acta Cryst. E65, o1858.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationStec, M. M., Bo, Y. X., Chakrabarti, P. P., Liao, L., Ncube, M., Tamayo, N., Tamir, R., Gavva, N. R., Treanor, J. J. S. & Norman, M. H. (2008). Bioorg. Med. Chem. Lett. 18, 5118–5122.  Web of Science CrossRef PubMed CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2109
https://doi.org/10.1107/S1600536812026220
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