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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

4,6-Di­chloro-5-meth­oxy­pyrimidine

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India
*Correspondence e-mail: hkfun@usm.my

(Received 10 January 2010; accepted 13 January 2010; online 20 January 2010)

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[Townsend, L. B. & Drach, J. C. (2002a). Chem. Abstr. 136, 134778.],b[Townsend, L. B. & Drach, J. C. (2002b). US Patent 6 342 501.]). For related structures, see: Bukhari et al. (2008[Bukhari, M. H., Siddiqui, H. L., Chaudhary, M. A., Hussain, T. & Parvez, M. (2008). Acta Cryst. E64, o963.], 2009[Bukhari, M. H., Siddiqui, H. L., Ahmad, N., Siddiqui, W. A. & Parvez, M. (2009). Acta Cryst. E65, o390.]); Fun et al. (2006[Fun, H.-K., Goswami, S., Jana, S. & Chantrapromma, S. (2006). Acta Cryst. E62, o5332-o5334.], 2008[Fun, H.-K., Chantrapromma, S., Jana, S., Chakrabarty, R. & Goswami, S. (2008). Acta Cryst. E64, o1659-o1660.])); Yathirajan et al. (2007[Yathirajan, H. S., Narayana, B., Ashalatha, B. V., Sarojini, B. K. & Bolte, M. (2007). Acta Cryst. E63, o923-o924.]); Zhao et al. (2009[Zhao, Q.-H., Li, L.-N. & Wang, K.-M. (2009). Acta Cryst. E65, o1793.]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C5H4Cl2N2O

  • Mr = 179.00

  • Orthorhombic, P n a 21

  • a = 13.6545 (19) Å

  • b = 3.9290 (6) Å

  • c = 13.0275 (18) Å

  • V = 698.91 (17) Å3

  • 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[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.787, Tmax = 0.926

  • 4505 measured reflections

  • 1520 independent reflections

  • 1415 reflections with I > 2σ(I)

  • Rint = 0.024

Refinement
  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 0.054

  • S = 1.08

  • 1520 reflections

  • 92 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.19 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 459 Friedel pairs

  • Flack parameter: −0.02 (6)

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

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 top

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 top

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

Structure description top

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.

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with 50% probability ellipsoids for non-H atoms.
[Figure 2] 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.
4,6-Dichloro-5-methoxypyrimidine top
Crystal data top
C5H4Cl2N2OF(000) = 360
Mr = 179.00Dx = 1.701 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 1997 reflections
a = 13.6545 (19) Åθ = 3.0–32.2°
b = 3.9290 (6) ŵ = 0.85 mm1
c = 13.0275 (18) ÅT = 100 K
V = 698.91 (17) Å3Block, colourless
Z = 40.29 × 0.20 × 0.09 mm
Data collection top
Bruker APEX Duo CCD
diffractometer
1520 independent reflections
Radiation source: fine-focus sealed tube1415 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
φ and ω scansθmax = 30.0°, θmin = 3.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 1917
Tmin = 0.787, Tmax = 0.926k = 54
4505 measured reflectionsl = 1813
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.024H-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 reflectionsΔρmax = 0.27 e Å3
92 parametersΔρmin = 0.19 e Å3
1 restraintAbsolute structure: Flack (1983), 459 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (6)
Crystal data top
C5H4Cl2N2OV = 698.91 (17) Å3
Mr = 179.00Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 13.6545 (19) ŵ = 0.85 mm1
b = 3.9290 (6) ÅT = 100 K
c = 13.0275 (18) Å0.29 × 0.20 × 0.09 mm
Data collection top
Bruker APEX Duo CCD
diffractometer
1520 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
1415 reflections with I > 2σ(I)
Tmin = 0.787, Tmax = 0.926Rint = 0.024
4505 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.024H-atom parameters constrained
wR(F2) = 0.054Δρmax = 0.27 e Å3
S = 1.08Δρmin = 0.19 e Å3
1520 reflectionsAbsolute structure: Flack (1983), 459 Friedel pairs
92 parametersAbsolute structure parameter: 0.02 (6)
1 restraint
Special details top

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 (Å2) top
xyzUiso*/Ueq
Cl11.00227 (3)0.39313 (10)0.31491 (4)0.01880 (10)
Cl20.68657 (3)0.13063 (10)0.50590 (3)0.01823 (10)
O10.87265 (8)0.2620 (3)0.49779 (10)0.0158 (2)
N10.85636 (12)0.0895 (4)0.22384 (12)0.0173 (3)
N20.71682 (10)0.1454 (3)0.30807 (13)0.0164 (3)
C10.89051 (11)0.1878 (4)0.31413 (16)0.0146 (3)
C20.77002 (14)0.0714 (5)0.22517 (14)0.0176 (4)
H2A0.74460.13820.16210.021*
C30.75310 (13)0.0416 (4)0.39696 (13)0.0134 (3)
C40.84177 (14)0.1346 (4)0.40704 (14)0.0136 (3)
C50.94496 (15)0.0608 (5)0.55200 (16)0.0225 (4)
H5A0.99660.00130.50570.034*
H5B0.91470.14130.57860.034*
H5C0.97150.19170.60770.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01301 (17)0.02330 (19)0.02010 (18)0.00290 (14)0.00081 (16)0.0021 (2)
Cl20.01565 (17)0.02443 (19)0.01463 (17)0.00177 (15)0.00211 (17)0.00248 (19)
O10.0159 (5)0.0185 (5)0.0130 (5)0.0029 (4)0.0029 (6)0.0044 (6)
N10.0148 (7)0.0222 (8)0.0150 (7)0.0019 (6)0.0012 (6)0.0009 (6)
N20.0152 (6)0.0182 (7)0.0159 (7)0.0014 (5)0.0030 (7)0.0010 (6)
C10.0114 (6)0.0150 (7)0.0174 (7)0.0020 (5)0.0012 (8)0.0010 (7)
C20.0172 (9)0.0213 (10)0.0145 (8)0.0015 (7)0.0028 (7)0.0019 (7)
C30.0127 (8)0.0144 (8)0.0130 (7)0.0017 (6)0.0005 (7)0.0016 (6)
C40.0133 (8)0.0133 (7)0.0142 (8)0.0030 (5)0.0015 (6)0.0003 (6)
C50.0261 (10)0.0243 (9)0.0170 (8)0.0052 (7)0.0097 (8)0.0013 (8)
Geometric parameters (Å, º) top
Cl1—C11.7262 (16)N2—C21.334 (2)
Cl2—C31.7210 (19)C1—C41.397 (3)
O1—C41.351 (2)C2—H2A0.9300
O1—C51.449 (2)C3—C41.401 (3)
N1—C11.323 (2)C5—H5A0.9600
N1—C21.338 (2)C5—H5B0.9600
N2—C31.324 (2)C5—H5C0.9600
C4—O1—C5115.92 (13)C4—C3—Cl2118.65 (14)
C1—N1—C2115.91 (16)O1—C4—C1123.64 (16)
C3—N2—C2115.93 (14)O1—C4—C3122.32 (16)
N1—C1—C4123.97 (15)C1—C4—C3113.86 (16)
N1—C1—Cl1116.95 (14)O1—C5—H5A109.5
C4—C1—Cl1119.08 (14)O1—C5—H5B109.5
N2—C2—N1126.41 (17)H5A—C5—H5B109.5
N2—C2—H2A116.8O1—C5—H5C109.5
N1—C2—H2A116.8H5A—C5—H5C109.5
N2—C3—C4123.89 (16)H5B—C5—H5C109.5
N2—C3—Cl2117.46 (14)
C2—N1—C1—C40.4 (2)N1—C1—C4—O1173.85 (16)
C2—N1—C1—Cl1179.51 (12)Cl1—C1—C4—O16.2 (2)
C3—N2—C2—N11.5 (2)N1—C1—C4—C31.4 (2)
C1—N1—C2—N21.1 (3)Cl1—C1—C4—C3178.53 (12)
C2—N2—C3—C40.3 (2)N2—C3—C4—O1174.29 (15)
C2—N2—C3—Cl2179.80 (13)Cl2—C3—C4—O15.8 (2)
C5—O1—C4—C185.2 (2)N2—C3—C4—C11.0 (2)
C5—O1—C4—C399.96 (19)Cl2—C3—C4—C1178.89 (12)

Experimental details

Crystal data
Chemical formulaC5H4Cl2N2O
Mr179.00
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)100
a, b, c (Å)13.6545 (19), 3.9290 (6), 13.0275 (18)
V3)698.91 (17)
Z4
Radiation typeMo Kα
µ (mm1)0.85
Crystal size (mm)0.29 × 0.20 × 0.09
Data collection
DiffractometerBruker APEX Duo CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.787, 0.926
No. of measured, independent and
observed [I > 2σ(I)] reflections
4505, 1520, 1415
Rint0.024
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.054, 1.08
No. of reflections1520
No. of parameters92
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.27, 0.19
Absolute structureFlack (1983), 459 Friedel pairs
Absolute structure parameter0.02 (6)

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

 

Footnotes

Thomson Reuters ResearcherID: A-3561-2009.

§Thomson Reuters ResearcherID: A-5523-2009.

Acknowledgements

HKF thanks Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CSY thanks USM for the award of a USM Fellowship. CSC thanks the University of Mysore for research facilities.

References

First citationBruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBukhari, M. H., Siddiqui, H. L., Ahmad, N., Siddiqui, W. A. & Parvez, M. (2009). Acta Cryst. E65, o390.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationBukhari, M. H., Siddiqui, H. L., Chaudhary, M. A., Hussain, T. & Parvez, M. (2008). Acta Cryst. E64, o963.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationCosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFun, H.-K., Chantrapromma, S., Jana, S., Chakrabarty, R. & Goswami, S. (2008). Acta Cryst. E64, o1659–o1660.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationFun, H.-K., Goswami, S., Jana, S. & Chantrapromma, S. (2006). Acta Cryst. E62, o5332–o5334.  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 citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationTownsend, L. B. & Drach, J. C. (2002a). Chem. Abstr. 136, 134778.  Google Scholar
First citationTownsend, L. B. & Drach, J. C. (2002b). US Patent 6 342 501.  Google Scholar
First citationYathirajan, H. S., Narayana, B., Ashalatha, B. V., Sarojini, B. K. & Bolte, M. (2007). Acta Cryst. E63, o923–o924.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationZhao, Q.-H., Li, L.-N. & Wang, K.-M. (2009). Acta Cryst. E65, o1793.  Web of Science CSD CrossRef IUCr Journals 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
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds