5-Bromo-2-chloro­pyrimidin-4-amine

Abstract

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,

• a = 6.0297 (1) Å

• b = 8.1542 (2) Å

• c = 13.4163 (3) Å

• β = 90.491 (2)°

• V = 659.62 (2) ų

• 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 ▶) 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[F ² > 2σ(F ²)] = 0.024

• wR(F ²) = 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

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; 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 ▶).

Supplementary Material

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

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) ; (ii) .

supplementary crystallographic information

Comment

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).

Experimental

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

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 U_iso(H) = 1.2U_eq(C).

Figures

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.

Crystal data

C4H3BrClN3	F(000) = 400
Mr = 208.45	Dx = 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

Oxford Diffraction Xcalibur Sapphire3 diffractometer	1297 independent reflections
Radiation source: fine-focus sealed tube	1164 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.046
Detector resolution: 16.1049 pixels mm-1	θmax = 26.0°, θmin = 3.9°
ω scans	h = −7→7
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)	k = −10→10
Tmin = 0.306, Tmax = 1.000	l = −16→16
43395 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)] = 0.024	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(Fo2) + (0.0275P)2 + 0.4995P] where P = (Fo2 + 2Fc2)/3
1297 reflections	(Δ/σ)max < 0.001
90 parameters	Δρmax = 0.33 e Å−3
0 restraints	Δρmin = −0.28 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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)

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)

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.