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ISSN: 2056-9890

5-Bromo-2-chloro­pyrimidin-4-amine

aDepartment of Studies in Physics, Manasagangotri, University of Mysore, Mysore 570 006, India, bDepartment of Chemistry, Yuvarajas College, University of Mysore, Mysore 570 005, India, and cX-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India
*Correspondence e-mail: mas@physics.uni-mysore.ac.in

(Received 1 March 2013; accepted 16 March 2013; online 23 March 2013)

In the title compound, C4H3BrClN3, the pyrimidine ring is essentially planar (r.m.s. deviation from the plane = 0.087 Å). In the crystal, pairs of N—H⋯N hydrogen bonds connect the mol­ecules into inversion dimers; these are connected by further N—H⋯N hydrogen bonds into a two-dimensional framework parallel to the bc plane.

Related literature

For background to pyrimidine derivatives, see: Yu et al. (2007[Yu, Z. H., Niu, C. W., Ban, S. R., Wen, X. & Xi, Z. (2007). Chin. Sci. Bull. 52, 1929-1941.]). For related structures, see: van Albada et al. (2012[Albada, G. van, Ghazzali, M., Al-Farhan, K. & Reedijk, J. (2012). Acta Cryst. E68, o302.]); Yang et al. (2012[Yang, Q., Xu, N., Zhu, K., Lv, X. & Han, P. (2012). Acta Cryst. E68, o111.]).

[Scheme 1]

Experimental

Crystal data
  • C4H3BrClN3

  • Mr = 208.45

  • Monoclinic, P 21 /c

  • a = 6.0297 (1) Å

  • b = 8.1542 (2) Å

  • c = 13.4163 (3) Å

  • β = 90.491 (2)°

  • V = 659.62 (2) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 6.54 mm−1

  • T = 293 K

  • 0.3 × 0.2 × 0.1 mm

Data collection
  • Oxford Diffraction Xcalibur Sapphire3 diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.306, Tmax = 1.000

  • 43395 measured reflections

  • 1297 independent reflections

  • 1164 reflections with I > 2σ(I)

  • Rint = 0.046

Refinement
  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 0.058

  • S = 1.10

  • 1297 reflections

  • 90 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.28 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N7—H71⋯N1i 0.78 (3) 2.38 (3) 3.087 (3) 153 (3)
N7—H72⋯N3ii 0.91 (4) 2.19 (4) 3.088 (3) 171 (3)
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (ii) -x, -y+1, -z+1.

Data collection: CrysAlis PRO (Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis RED (Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); 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: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Some derivatives of pyrimidine are important chemical materials (Yu et al., 2007). Here in this article, the preparation and crystal structure of the title compound is presented. Bond lengths and angles in the title compound (Fig. 1) are comparable with the similar crystal structures (van Albada et al., 2012; Yang et al., 2012). The pyrimidine ring is essentially planar (r.m.s. deviation from the plane 0.087 Å). The atoms Br,Cl and N7 are coplanar with the pyrimidine ring. In the crystal, molecules are linked into dimers by N7—H72···N3 hydrogen bonds and these dimers are further connected by N7—H71···N1 hydrogen bonds, forming two dimensional supramolecular network in the bc plane (Fig.2, (Table 2).

Related literature top

For background to pyrimidine derivatives, see: Yu et al. (2007). For related structures, see: van Albada et al. (2012); Yang et al. (2012).

Experimental top

To a solution of stannous chloride dihydrate (2.8 ml, 0.012 mole) in hydrochloric acid (30 ml) cooled to 273K, 5-bromo-2-chloro-4-nitropyrimidine (2 g, 0.0083 mole) was added in portions while the suspension was vigorously stirred for 6 hrs. The mixture was then poured onto crushed ice, made alkaline with solid sodium hydroxide, and extracted three times with ethyl acetate (100 ml). The combined organic phase was dried over anhydrous sodium sulfate and the filtrate was evaporated to dryness. The compound was purified by successive recrystallization from acetonitrile (yield 90%, m. p. 460–461 K).

Refinement top

The N-bound H atoms were located in a difference Fourier map and freely refined. All other H atoms were positioned geometrically and were treated as riding on their parent C atoms, with C—H distances of 0.93 Å and with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis RED (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. ORTEP view of the molecule with the atom-labeling scheme. The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A molecular packing view of the title compound down the a axis, showing intermolecular interactions. The dotted lines show intermolecular N—H···N hydrogen bonds.
5-Bromo-2-chloropyrimidin-4-amine top
Crystal data top
C4H3BrClN3F(000) = 400
Mr = 208.45Dx = 2.099 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 20319 reflections
a = 6.0297 (1) Åθ = 3.7–29.0°
b = 8.1542 (2) ŵ = 6.54 mm1
c = 13.4163 (3) ÅT = 293 K
β = 90.491 (2)°Block, white
V = 659.62 (2) Å30.3 × 0.2 × 0.1 mm
Z = 4
Data collection top
Oxford Diffraction Xcalibur Sapphire3
diffractometer
1297 independent reflections
Radiation source: fine-focus sealed tube1164 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
Detector resolution: 16.1049 pixels mm-1θmax = 26.0°, θmin = 3.9°
ω scansh = 77
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
k = 1010
Tmin = 0.306, Tmax = 1.000l = 1616
43395 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)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.058H atoms treated by a mixture of independent and constrained refinement
S = 1.10 w = 1/[σ2(Fo2) + (0.0275P)2 + 0.4995P]
where P = (Fo2 + 2Fc2)/3
1297 reflections(Δ/σ)max < 0.001
90 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C4H3BrClN3V = 659.62 (2) Å3
Mr = 208.45Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.0297 (1) ŵ = 6.54 mm1
b = 8.1542 (2) ÅT = 293 K
c = 13.4163 (3) Å0.3 × 0.2 × 0.1 mm
β = 90.491 (2)°
Data collection top
Oxford Diffraction Xcalibur Sapphire3
diffractometer
1297 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
1164 reflections with I > 2σ(I)
Tmin = 0.306, Tmax = 1.000Rint = 0.046
43395 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0240 restraints
wR(F2) = 0.058H atoms treated by a mixture of independent and constrained refinement
S = 1.10Δρmax = 0.33 e Å3
1297 reflectionsΔρmin = 0.28 e Å3
90 parameters
Special details top

Experimental. CrysAlis PRO, Oxford Diffraction Ltd., Version 1.171.34.40 (release 27–08-2010 CrysAlis171. NET) (compiled Aug 27 2010,11:50:40) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Br10.69350 (4)0.17972 (4)0.48221 (2)0.04520 (12)
Cl10.00058 (12)0.44749 (10)0.78250 (5)0.04662 (19)
N10.3588 (4)0.2880 (3)0.74005 (15)0.0397 (5)
C20.1934 (4)0.3694 (3)0.69923 (17)0.0302 (5)
N30.1489 (3)0.4025 (3)0.60525 (14)0.0310 (4)
C40.2921 (4)0.3417 (3)0.53797 (17)0.0293 (5)
C50.4802 (4)0.2544 (3)0.57261 (17)0.0308 (5)
C60.5050 (4)0.2317 (4)0.67197 (19)0.0400 (6)
H60.62880.17440.69470.048*
N70.2498 (5)0.3721 (3)0.44228 (16)0.0413 (6)
H710.317 (5)0.329 (3)0.401 (2)0.037 (8)*
H720.125 (6)0.428 (4)0.425 (3)0.063 (10)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.03877 (18)0.05169 (19)0.04536 (18)0.00220 (12)0.01297 (12)0.00698 (12)
Cl10.0474 (4)0.0627 (5)0.0300 (3)0.0046 (3)0.0130 (3)0.0023 (3)
N10.0393 (12)0.0544 (14)0.0254 (10)0.0025 (10)0.0014 (9)0.0059 (9)
C20.0323 (13)0.0332 (12)0.0251 (11)0.0060 (10)0.0038 (9)0.0011 (9)
N30.0335 (11)0.0357 (11)0.0238 (9)0.0003 (9)0.0024 (8)0.0001 (8)
C40.0300 (12)0.0331 (13)0.0247 (11)0.0069 (10)0.0022 (9)0.0016 (9)
C50.0303 (13)0.0312 (12)0.0309 (12)0.0037 (10)0.0048 (10)0.0016 (10)
C60.0347 (14)0.0483 (16)0.0371 (13)0.0052 (12)0.0010 (11)0.0049 (12)
N70.0448 (14)0.0569 (15)0.0221 (11)0.0080 (12)0.0027 (10)0.0018 (10)
Geometric parameters (Å, º) top
Br1—C51.877 (2)C4—N71.330 (3)
Cl1—C21.744 (2)C4—C51.415 (3)
N1—C21.314 (3)C5—C61.353 (3)
N1—C61.355 (3)C6—H60.9300
C2—N31.315 (3)N7—H710.78 (3)
N3—C41.349 (3)N7—H720.91 (4)
C2—N1—C6112.7 (2)C6—C5—Br1121.5 (2)
N1—C2—N3130.6 (2)C4—C5—Br1120.20 (17)
N1—C2—Cl1115.35 (18)C5—C6—N1123.4 (2)
N3—C2—Cl1114.02 (18)C5—C6—H6118.3
C2—N3—C4116.1 (2)N1—C6—H6118.3
N7—C4—N3117.3 (2)C4—N7—H71121 (2)
N7—C4—C5123.9 (2)C4—N7—H72119 (2)
N3—C4—C5118.8 (2)H71—N7—H72119 (3)
C6—C5—C4118.3 (2)
C6—N1—C2—N30.5 (4)N3—C4—C5—C61.9 (4)
C6—N1—C2—Cl1179.43 (19)N7—C4—C5—Br12.1 (3)
N1—C2—N3—C41.4 (4)N3—C4—C5—Br1175.96 (17)
Cl1—C2—N3—C4178.71 (17)C4—C5—C6—N10.1 (4)
C2—N3—C4—N7179.4 (2)Br1—C5—C6—N1177.9 (2)
C2—N3—C4—C52.5 (3)C2—N1—C6—C51.2 (4)
N7—C4—C5—C6179.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N7—H71···N1i0.78 (3)2.38 (3)3.087 (3)153 (3)
N7—H72···N3ii0.91 (4)2.19 (4)3.088 (3)171 (3)
Symmetry codes: (i) x, y+1/2, z1/2; (ii) x, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC4H3BrClN3
Mr208.45
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)6.0297 (1), 8.1542 (2), 13.4163 (3)
β (°) 90.491 (2)
V3)659.62 (2)
Z4
Radiation typeMo Kα
µ (mm1)6.54
Crystal size (mm)0.3 × 0.2 × 0.1
Data collection
DiffractometerOxford Diffraction Xcalibur Sapphire3
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
Tmin, Tmax0.306, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
43395, 1297, 1164
Rint0.046
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.058, 1.10
No. of reflections1297
No. of parameters90
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.28

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), CrysAlis RED (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N7—H71···N1i0.78 (3)2.38 (3)3.087 (3)153 (3)
N7—H72···N3ii0.91 (4)2.19 (4)3.088 (3)171 (3)
Symmetry codes: (i) x, y+1/2, z1/2; (ii) x, y+1, z+1.
 

Acknowledgements

MK acknowledges the help of Bahubali College of Engineering, Shravanabelagola for his research work. RK acknowledges the Department of Science & Technology for the single-crystal X-ray diffractometer sanctioned as a National Facility under project No. SR/S2/CMP-47/2003.

References

First citationAlbada, G. van, Ghazzali, M., Al-Farhan, K. & Reedijk, J. (2012). Acta Cryst. E68, o302.  Web of Science CSD CrossRef IUCr Journals
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals
First citationOxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals
First citationYang, Q., Xu, N., Zhu, K., Lv, X. & Han, P. (2012). Acta Cryst. E68, o111.  Web of Science CSD CrossRef IUCr Journals
First citationYu, Z. H., Niu, C. W., Ban, S. R., Wen, X. & Xi, Z. (2007). Chin. Sci. Bull. 52, 1929–1941.  Web of Science CrossRef CAS

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ISSN: 2056-9890
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