5-Bromo-2-chloro­pyrimidin-4-amine

Kumar, M.; Mallikarjunaswamy, C.; Sridhar, M.A.; Bhadregowda, D.G.; Kapoor, K.; Gupta, V.K.; Kant, R.

doi:10.1107/S1600536813007228

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 69| Part 4| April 2013| Page o583

doi:10.1107/S1600536813007228

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5-Bromo-2-chloropyrimidin-4-amine

Mohan Kumar,^a C. Mallikarjunaswamy,^b M. A. Sridhar,^a ^* D. G. Bhadregowda,^b Kamini Kapoor,^c Vivek K. Gupta ^c and Rajni Kant ^c

^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 ). For related structures, see: van Albada et al. (2012 ); Yang et al. (2012 ).

Experimental

Crystal data

C₄H₃BrClN₃
M_r = 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 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ) T_min = 0.306, T_max = 1.000
43395 measured reflections
1297 independent reflections
1164 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); 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 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813007228/gk2560sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813007228/gk2560Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813007228/gk2560Isup3.cml

checkCIF report

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).

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

	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.
	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

C₄H₃BrClN₃	F(000) = 400
M_r = 208.45	D_x = 2.099 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 20319 reflections
a = 6.0297 (1) Å	θ = 3.7–29.0°
b = 8.1542 (2) Å	µ = 6.54 mm⁻¹
c = 13.4163 (3) Å	T = 293 K
β = 90.491 (2)°	Block, white
V = 659.62 (2) Å³	0.3 × 0.2 × 0.1 mm
Z = 4

Data collection top

Oxford Diffraction Xcalibur Sapphire3 diffractometer	1297 independent reflections
Radiation source: fine-focus sealed tube	1164 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
Detector resolution: 16.1049 pixels mm^-1	θ_max = 26.0°, θ_min = 3.9°
ω scans	h = −7→7
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)	k = −10→10
T_min = 0.306, T_max = 1.000	l = −16→16
43395 measured reflections

Refinement top

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)] = 0.024	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.058	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0275P)² + 0.4995P] where P = (F_o² + 2F_c²)/3
1297 reflections	(Δ/σ)_max < 0.001
90 parameters	Δρ_max = 0.33 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³

Crystal data top

C₄H₃BrClN₃	V = 659.62 (2) Å³
M_r = 208.45	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.0297 (1) Å	µ = 6.54 mm⁻¹
b = 8.1542 (2) Å	T = 293 K
c = 13.4163 (3) Å	0.3 × 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)
T_min = 0.306, T_max = 1.000	R_int = 0.046
43395 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.024	0 restraints
wR(F²) = 0.058	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.33 e Å⁻³
1297 reflections	Δρ_min = −0.28 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Br1	0.69350 (4)	0.17972 (4)	0.48221 (2)	0.04520 (12)
Cl1	−0.00058 (12)	0.44749 (10)	0.78250 (5)	0.04662 (19)
N1	0.3588 (4)	0.2880 (3)	0.74005 (15)	0.0397 (5)
C2	0.1934 (4)	0.3694 (3)	0.69923 (17)	0.0302 (5)
N3	0.1489 (3)	0.4025 (3)	0.60525 (14)	0.0310 (4)
C4	0.2921 (4)	0.3417 (3)	0.53797 (17)	0.0293 (5)
C5	0.4802 (4)	0.2544 (3)	0.57261 (17)	0.0308 (5)
C6	0.5050 (4)	0.2317 (4)	0.67197 (19)	0.0400 (6)
H6	0.6288	0.1744	0.6947	0.048*
N7	0.2498 (5)	0.3721 (3)	0.44228 (16)	0.0413 (6)
H71	0.317 (5)	0.329 (3)	0.401 (2)	0.037 (8)*
H72	0.125 (6)	0.428 (4)	0.425 (3)	0.063 (10)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.03877 (18)	0.05169 (19)	0.04536 (18)	0.00220 (12)	0.01297 (12)	−0.00698 (12)
Cl1	0.0474 (4)	0.0627 (5)	0.0300 (3)	0.0046 (3)	0.0130 (3)	−0.0023 (3)
N1	0.0393 (12)	0.0544 (14)	0.0254 (10)	0.0025 (10)	0.0014 (9)	0.0059 (9)
C2	0.0323 (13)	0.0332 (12)	0.0251 (11)	−0.0060 (10)	0.0038 (9)	−0.0011 (9)
N3	0.0335 (11)	0.0357 (11)	0.0238 (9)	−0.0003 (9)	0.0024 (8)	−0.0001 (8)
C4	0.0300 (12)	0.0331 (13)	0.0247 (11)	−0.0069 (10)	0.0022 (9)	−0.0016 (9)
C5	0.0303 (13)	0.0312 (12)	0.0309 (12)	−0.0037 (10)	0.0048 (10)	−0.0016 (10)
C6	0.0347 (14)	0.0483 (16)	0.0371 (13)	0.0052 (12)	−0.0010 (11)	0.0049 (12)
N7	0.0448 (14)	0.0569 (15)	0.0221 (11)	0.0080 (12)	0.0027 (10)	−0.0018 (10)

Geometric parameters (Å, º) top

Br1—C5	1.877 (2)	C4—N7	1.330 (3)
Cl1—C2	1.744 (2)	C4—C5	1.415 (3)
N1—C2	1.314 (3)	C5—C6	1.353 (3)
N1—C6	1.355 (3)	C6—H6	0.9300
C2—N3	1.315 (3)	N7—H71	0.78 (3)
N3—C4	1.349 (3)	N7—H72	0.91 (4)

C2—N1—C6	112.7 (2)	C6—C5—Br1	121.5 (2)
N1—C2—N3	130.6 (2)	C4—C5—Br1	120.20 (17)
N1—C2—Cl1	115.35 (18)	C5—C6—N1	123.4 (2)
N3—C2—Cl1	114.02 (18)	C5—C6—H6	118.3
C2—N3—C4	116.1 (2)	N1—C6—H6	118.3
N7—C4—N3	117.3 (2)	C4—N7—H71	121 (2)
N7—C4—C5	123.9 (2)	C4—N7—H72	119 (2)
N3—C4—C5	118.8 (2)	H71—N7—H72	119 (3)
C6—C5—C4	118.3 (2)

C6—N1—C2—N3	0.5 (4)	N3—C4—C5—C6	1.9 (4)
C6—N1—C2—Cl1	−179.43 (19)	N7—C4—C5—Br1	2.1 (3)
N1—C2—N3—C4	1.4 (4)	N3—C4—C5—Br1	−175.96 (17)
Cl1—C2—N3—C4	−178.71 (17)	C4—C5—C6—N1	0.1 (4)
C2—N3—C4—N7	179.4 (2)	Br1—C5—C6—N1	177.9 (2)
C2—N3—C4—C5	−2.5 (3)	C2—N1—C6—C5	−1.2 (4)
N7—C4—C5—C6	179.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, z−1/2; (ii) −x, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₄H₃BrClN₃
M_r	208.45
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	6.0297 (1), 8.1542 (2), 13.4163 (3)
β (°)	90.491 (2)
V (Å³)	659.62 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	6.54
Crystal size (mm)	0.3 × 0.2 × 0.1

Data collection
Diffractometer	Oxford Diffraction Xcalibur Sapphire3 diffractometer
Absorption correction	Multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)
T_min, T_max	0.306, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	43395, 1297, 1164
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.024, 0.058, 1.10
No. of reflections	1297
No. of parameters	90
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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+1/2, z−1/2; (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

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