5-Bromo-N-methyl­pyrimidin-2-amine

Yang, Q.; Xu, N.; Zhu, K.; Lv, X.; Han, P.

doi:10.1107/S1600536811051531

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o111

doi:10.1107/S1600536811051531

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5-Bromo-N-methylpyrimidin-2-amine

Qi Yang,^a Ning Xu,^b Kai Zhu,^a Xiaoping Lv ^a and Ping-fang Han ^a ^*

^aCollege of Life Science and Pharmaceutical Engineering, Nanjing University of Technology, Xinmofan Road No. 5 Nanjing, Nanjing 210009, People's Republic of China, and ^bCollege of Environment, Nanjing University of Technolgy, Xinmofan Road No. 5 Nanjing, Nanjing 210009, People's Republic of China
^*Correspondence e-mail: hpf@njut.edu.cn

(Received 15 November 2011; accepted 30 November 2011; online 14 December 2011)

In the title molecule, C₅H₆BrN₃, the pyrimidine ring is essentially planar, with an r.m.s. deviation of 0.007 Å. The Br and N atoms substituted to the pyrimidine ring are coplanar with the ring [displacements = 0.032 (1) and 0.009 (5) Å, respectively], while the methyl C atom lies 0.100 (15) Å from this plane with a dihedral angle between the pyrimidine ring and the methylamine group of 4.5 (3)°. In the crystal, C—H⋯N, C—H⋯Br and N—H⋯N hydrogen bonds link the molecules into a two-dimensional network in the (011) plane.

Related literature

Derivatives of pyrimidine are important chemical materials, see: Yu et al. (2007 ). For a related structure, see: Aakeroey et al. (2005 ).

Experimental

Crystal data

C₅H₆BrN₃
M_r = 188.04
Triclinic, $[P \overline 1]$
a = 3.9900 (8) Å
b = 9.862 (2) Å
c = 10.006 (2) Å
α = 61.57 (3)°
β = 83.84 (3)°
γ = 87.45 (3)°
V = 344.24 (16) Å³
Z = 2
Mo Kα radiation
μ = 5.88 mm⁻¹
T = 293 K
0.10 × 0.05 × 0.05 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
Absorption correction: ψ scan (North et al., 1968 ) T_min = 0.591, T_max = 0.758
1454 measured reflections
1260 independent reflections
714 reflections with I > 2σ(I)
R_int = 0.089
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.056
wR(F²) = 0.100
S = 1.00
1260 reflections
82 parameters
H-atom parameters constrained
Δρ_max = 0.40 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯N2ⁱ	0.86	2.19	3.035 (7)	169
C1—H1B⋯Brⁱⁱ	0.96	2.85	3.751 (8)	157
C5—H5A⋯N3ⁱⁱⁱ	0.93	2.59	3.357 (7)	140
Symmetry codes: (i) -x, -y+2, -z; (ii) x-1, y+1, z; (iii) -x-1, -y+1, -z+1.

Data collection: CAD-4 Software (Enraf–Nonius, 1989 ); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811051531/pv2488sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811051531/pv2488Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811051531/pv2488Isup3.cml

checkCIF report

Comment top

Some derivatives of pyrimidin are important chemical materials (Yu et al., 2007). Here in this article, the preparation and crystal structure of the title compound is presented. The pyrimidin ring is essentially planar with rms deviation 0.0071. The atoms Br and N1 are coplanar with the pyrimidin ring while C1 lies 0.100 (15) Å from this plane with a dihedral angle between the pyrimidin ring and the methylamine group 4.5 (3)°. In the crystal structure, intermolecular C—H···N, C—H···Br and N—H···N hydrogen bonding interactions link the molecules into a two dimensional cluster in (0 1 1) plane (Tab. 1 and Fig. 2).

Related literature top

Derivatives of pyrimidin are important chemical materials, see: Yu et al. (2007). For a related structure, see: Aakeroey et al. (2005).

Experimental top

5-Bromo-hexahydro-pyrimidine (2.06 g, 0.01 mol) and 1,3-propanediamine (1.48 g, 0.02 mol) were refluxed in 10 ml benzene for 18 h. After completion of the reaction (TLC control), the product was washed with cold toluene (2*15 ml), at room temperature, dried over sodium sulfate and yielded 2.43 g (69%) of the title compound which was further purified by crystallization from methanol. Crystals of the title compound suitable for X-ray crystallographic studies were obstained by slow evaporation of a methanol solution.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: CAD-4 Software (Enraf–Nonius, 1989); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound showing atom-numbering scheme and displacement ellipsoids plotted at 30% probability level.
	Fig. 2. A packing diagram of the title compound. The intermolecular hydrogen bonding interactions are shown as dashed lines.

5-Bromo-N-methylpyrimidin-2-amine top

Crystal data top

C₅H₆BrN₃	Z = 2
M_r = 188.04	F(000) = 184
Triclinic, P1	D_x = 1.814 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 3.9900 (8) Å	Cell parameters from 25 reflections
b = 9.862 (2) Å	θ = 9–14°
c = 10.006 (2) Å	µ = 5.88 mm⁻¹
α = 61.57 (3)°	T = 293 K
β = 83.84 (3)°	Block, colorless
γ = 87.45 (3)°	0.10 × 0.05 × 0.05 mm
V = 344.24 (16) Å³

Data collection top

Enraf–Nonius CAD-4 diffractometer	714 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.089
Graphite monochromator	θ_max = 25.4°, θ_min = 2.3°
ω/2θ scans	h = 0→4
Absorption correction: ψ scan (North et al., 1968)	k = −11→11
T_min = 0.591, T_max = 0.758	l = −11→11
1454 measured reflections	3 standard reflections every 200 reflections
1260 independent reflections	intensity decay: 1%

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)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.100	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0385P)²] where P = (F_o² + 2F_c²)/3
1260 reflections	(Δ/σ)_max < 0.001
82 parameters	Δρ_max = 0.40 e Å⁻³
0 restraints	Δρ_min = −0.39 e Å⁻³

Crystal data top

C₅H₆BrN₃	γ = 87.45 (3)°
M_r = 188.04	V = 344.24 (16) Å³
Triclinic, P1	Z = 2
a = 3.9900 (8) Å	Mo Kα radiation
b = 9.862 (2) Å	µ = 5.88 mm⁻¹
c = 10.006 (2) Å	T = 293 K
α = 61.57 (3)°	0.10 × 0.05 × 0.05 mm
β = 83.84 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	714 reflections with I > 2σ(I)
Absorption correction: ψ scan (North et al., 1968)	R_int = 0.089
T_min = 0.591, T_max = 0.758	3 standard reflections every 200 reflections
1454 measured reflections	intensity decay: 1%
1260 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	0 restraints
wR(F²) = 0.100	H-atom parameters constrained
S = 1.00	Δρ_max = 0.40 e Å⁻³
1260 reflections	Δρ_min = −0.39 e Å⁻³
82 parameters

Special details top

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

	x	y	z	U_iso*/U_eq
Br	0.15554 (17)	0.32133 (9)	0.25400 (8)	0.0790 (4)
N1	−0.2779 (12)	0.9216 (6)	0.1902 (5)	0.0673 (15)
H1A	−0.2201	1.0018	0.1048	0.081*
C1	−0.4717 (15)	0.9457 (7)	0.3050 (7)	0.080 (2)
H1B	−0.5157	1.0538	0.2663	0.120*
H1C	−0.3489	0.9094	0.3930	0.120*
H1D	−0.6814	0.8903	0.3330	0.120*
N2	0.0176 (11)	0.7834 (5)	0.0874 (5)	0.0545 (13)
C2	−0.1772 (14)	0.7836 (7)	0.2042 (7)	0.0494 (15)
N3	−0.2888 (11)	0.6545 (6)	0.3321 (5)	0.0549 (13)
C3	0.1196 (13)	0.6469 (7)	0.1010 (7)	0.0592 (16)
H3A	0.2605	0.6407	0.0239	0.071*
C4	0.0086 (14)	0.5125 (7)	0.2352 (7)	0.0535 (16)
C5	−0.1934 (14)	0.5251 (7)	0.3455 (7)	0.0574 (17)
H5A	−0.2648	0.4360	0.4340	0.069*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br	0.0629 (5)	0.0737 (5)	0.0811 (6)	−0.0023 (3)	0.0026 (3)	−0.0229 (4)
N1	0.059 (3)	0.064 (4)	0.049 (3)	−0.015 (3)	0.015 (3)	−0.006 (3)
C1	0.082 (5)	0.050 (4)	0.077 (5)	−0.001 (3)	0.037 (4)	−0.015 (4)
N2	0.048 (3)	0.061 (3)	0.042 (3)	0.003 (2)	0.015 (2)	−0.019 (3)
C2	0.049 (4)	0.060 (4)	0.042 (4)	0.000 (3)	−0.009 (3)	−0.025 (3)
N3	0.048 (3)	0.049 (3)	0.041 (3)	−0.013 (2)	0.013 (2)	−0.002 (3)
C3	0.039 (3)	0.074 (4)	0.058 (4)	−0.001 (3)	0.013 (3)	−0.028 (4)
C4	0.046 (4)	0.061 (4)	0.047 (4)	0.004 (3)	−0.006 (3)	−0.020 (3)
C5	0.054 (4)	0.044 (4)	0.053 (4)	−0.010 (3)	−0.006 (3)	−0.005 (3)

Geometric parameters (Å, º) top

Br—C4	1.876 (6)	N2—C3	1.336 (7)
N1—C2	1.347 (7)	C2—N3	1.354 (7)
N1—C1	1.424 (7)	N3—C5	1.264 (7)
N1—H1A	0.8600	C3—C4	1.409 (8)
C1—H1B	0.9600	C3—H3A	0.9300
C1—H1C	0.9600	C4—C5	1.347 (8)
C1—H1D	0.9600	C5—H5A	0.9300
N2—C2	1.333 (7)

C2—N1—C1	125.5 (5)	N1—C2—N3	118.5 (5)
C2—N1—H1A	117.2	C5—N3—C2	118.5 (5)
C1—N1—H1A	117.2	N2—C3—C4	118.4 (6)
N1—C1—H1B	109.5	N2—C3—H3A	120.8
N1—C1—H1C	109.5	C4—C3—H3A	120.8
H1B—C1—H1C	109.5	C5—C4—C3	119.4 (6)
N1—C1—H1D	109.5	C5—C4—Br	122.4 (5)
H1B—C1—H1D	109.5	C3—C4—Br	118.1 (5)
H1C—C1—H1D	109.5	N3—C5—C4	121.9 (5)
C2—N2—C3	117.5 (5)	N3—C5—H5A	119.1
N2—C2—N1	117.3 (5)	C4—C5—H5A	119.1
N2—C2—N3	124.2 (6)

C3—N2—C2—N1	179.6 (5)	C2—N2—C3—C4	1.7 (8)
C3—N2—C2—N3	−2.9 (8)	N2—C3—C4—C5	−0.5 (9)
C1—N1—C2—N2	−176.7 (6)	N2—C3—C4—Br	−179.6 (4)
C1—N1—C2—N3	5.7 (8)	C2—N3—C5—C4	−1.4 (9)
N2—C2—N3—C5	2.8 (8)	C3—C4—C5—N3	0.4 (9)
N1—C2—N3—C5	−179.7 (5)	Br—C4—C5—N3	179.4 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N2ⁱ	0.86	2.19	3.035 (7)	169
C1—H1B···Brⁱⁱ	0.96	2.85	3.751 (8)	157
C5—H5A···N3ⁱⁱⁱ	0.93	2.59	3.357 (7)	140

Symmetry codes: (i) −x, −y+2, −z; (ii) x−1, y+1, z; (iii) −x−1, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₅H₆BrN₃
M_r	188.04
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	3.9900 (8), 9.862 (2), 10.006 (2)
α, β, γ (°)	61.57 (3), 83.84 (3), 87.45 (3)
V (Å³)	344.24 (16)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	5.88
Crystal size (mm)	0.10 × 0.05 × 0.05

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	ψ scan (North et al., 1968)
T_min, T_max	0.591, 0.758
No. of measured, independent and observed [I > 2σ(I)] reflections	1454, 1260, 714
R_int	0.089
(sin θ/λ)_max (Å⁻¹)	0.603

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.100, 1.00
No. of reflections	1260
No. of parameters	82
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.40, −0.39

Computer programs: CAD-4 Software (Enraf–Nonius, 1989), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N2ⁱ	0.8600	2.1900	3.035 (7)	169.00
C1—H1B···Brⁱⁱ	0.9600	2.8500	3.751 (8)	157.00
C5—H5A···N3ⁱⁱⁱ	0.9300	2.5900	3.357 (7)	140.00

Symmetry codes: (i) −x, −y+2, −z; (ii) x−1, y+1, z; (iii) −x−1, −y+1, −z+1.

Acknowledgements

The authors thank Dr Bo-nian Liu from Nanjing University of Technology for useful discussions and the Center of Testing and Analysis, Nanjing University, for support.

References

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