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Acta Cryst. (2012). E68, o111    [ doi:10.1107/S1600536811051531 ]

5-Bromo-N-methylpyrimidin-2-amine

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

Abstract top

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.

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.

Refinement top

H atoms were positioned geometrically, with N—H = 0.86 Å and C—H = 0.93 and 0.96 Å for aryl and methyl H atoms, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(N/C-aryl) or 1.5Ueq(C-methyl).

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
[Figure 1] Fig. 1. The molecular structure of the title compound showing atom-numbering scheme and displacement ellipsoids plotted at 30% probability level.
[Figure 2] 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
C5H6BrN3Z = 2
Mr = 188.04F(000) = 184
Triclinic, P1Dx = 1.814 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 3.9900 (8) ÅCell parameters from 25 reflections
b = 9.862 (2) Åθ = 9–14°
c = 10.006 (2) ŵ = 5.88 mm1
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 tubeRint = 0.089
graphiteθmax = 25.4°, θmin = 2.3°
ω/2θ scansh = 04
Absorption correction: ψ scan
(North et al., 1968)
k = 1111
Tmin = 0.591, Tmax = 0.758l = 1111
1454 measured reflections3 standard reflections every 200 reflections
1260 independent reflections intensity decay: 1%
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)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.100H-atom parameters constrained
S = 1.00 w = 1/[σ2(Fo2) + (0.0385P)2]
where P = (Fo2 + 2Fc2)/3
1260 reflections(Δ/σ)max < 0.001
82 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = 0.39 e Å3
Crystal data top
C5H6BrN3γ = 87.45 (3)°
Mr = 188.04V = 344.24 (16) Å3
Triclinic, P1Z = 2
a = 3.9900 (8) ÅMo Kα radiation
b = 9.862 (2) ŵ = 5.88 mm1
c = 10.006 (2) ÅT = 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)
Rint = 0.089
Tmin = 0.591, Tmax = 0.758θmax = 25.4°
1454 measured reflections3 standard reflections every 200 reflections
1260 independent reflections intensity decay: 1%
Refinement top
R[F2 > 2σ(F2)] = 0.056H-atom parameters constrained
wR(F2) = 0.100Δρmax = 0.40 e Å3
S = 1.00Δρmin = 0.39 e Å3
1260 reflectionsAbsolute structure: ?
82 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
Br0.15554 (17)0.32133 (9)0.25400 (8)0.0790 (4)
N10.2779 (12)0.9216 (6)0.1902 (5)0.0673 (15)
H1A0.22011.00180.10480.081*
C10.4717 (15)0.9457 (7)0.3050 (7)0.080 (2)
H1B0.51571.05380.26630.120*
H1C0.34890.90940.39300.120*
H1D0.68140.89030.33300.120*
N20.0176 (11)0.7834 (5)0.0874 (5)0.0545 (13)
C20.1772 (14)0.7836 (7)0.2042 (7)0.0494 (15)
N30.2888 (11)0.6545 (6)0.3321 (5)0.0549 (13)
C30.1196 (13)0.6469 (7)0.1010 (7)0.0592 (16)
H3A0.26050.64070.02390.071*
C40.0086 (14)0.5125 (7)0.2352 (7)0.0535 (16)
C50.1934 (14)0.5251 (7)0.3455 (7)0.0574 (17)
H5A0.26480.43600.43400.069*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br0.0629 (5)0.0737 (5)0.0811 (6)0.0023 (3)0.0026 (3)0.0229 (4)
N10.059 (3)0.064 (4)0.049 (3)0.015 (3)0.015 (3)0.006 (3)
C10.082 (5)0.050 (4)0.077 (5)0.001 (3)0.037 (4)0.015 (4)
N20.048 (3)0.061 (3)0.042 (3)0.003 (2)0.015 (2)0.019 (3)
C20.049 (4)0.060 (4)0.042 (4)0.000 (3)0.009 (3)0.025 (3)
N30.048 (3)0.049 (3)0.041 (3)0.013 (2)0.013 (2)0.002 (3)
C30.039 (3)0.074 (4)0.058 (4)0.001 (3)0.013 (3)0.028 (4)
C40.046 (4)0.061 (4)0.047 (4)0.004 (3)0.006 (3)0.020 (3)
C50.054 (4)0.044 (4)0.053 (4)0.010 (3)0.006 (3)0.005 (3)
Geometric parameters (Å, °) top
Br—C41.876 (6)N2—C31.336 (7)
N1—C21.347 (7)C2—N31.354 (7)
N1—C11.424 (7)N3—C51.264 (7)
N1—H1A0.8600C3—C41.409 (8)
C1—H1B0.9600C3—H3A0.9300
C1—H1C0.9600C4—C51.347 (8)
C1—H1D0.9600C5—H5A0.9300
N2—C21.333 (7)
C2—N1—C1125.5 (5)N1—C2—N3118.5 (5)
C2—N1—H1A117.2C5—N3—C2118.5 (5)
C1—N1—H1A117.2N2—C3—C4118.4 (6)
N1—C1—H1B109.5N2—C3—H3A120.8
N1—C1—H1C109.5C4—C3—H3A120.8
H1B—C1—H1C109.5C5—C4—C3119.4 (6)
N1—C1—H1D109.5C5—C4—Br122.4 (5)
H1B—C1—H1D109.5C3—C4—Br118.1 (5)
H1C—C1—H1D109.5N3—C5—C4121.9 (5)
C2—N2—C3117.5 (5)N3—C5—H5A119.1
N2—C2—N1117.3 (5)C4—C5—H5A119.1
N2—C2—N3124.2 (6)
C3—N2—C2—N1179.6 (5)C2—N2—C3—C41.7 (8)
C3—N2—C2—N32.9 (8)N2—C3—C4—C50.5 (9)
C1—N1—C2—N2176.7 (6)N2—C3—C4—Br179.6 (4)
C1—N1—C2—N35.7 (8)C2—N3—C5—C41.4 (9)
N2—C2—N3—C52.8 (8)C3—C4—C5—N30.4 (9)
N1—C2—N3—C5179.7 (5)Br—C4—C5—N3179.4 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N2i0.862.193.035 (7)169.
C1—H1B···Brii0.962.853.751 (8)157.
C5—H5A···N3iii0.932.593.357 (7)140.
Symmetry codes: (i) −x, −y+2, −z; (ii) x−1, y+1, z; (iii) −x−1, −y+1, −z+1.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N2i0.862.193.035 (7)169.
C1—H1B···Brii0.962.853.751 (8)157.
C5—H5A···N3iii0.932.593.357 (7)140.
Symmetry codes: (i) −x, −y+2, −z; (ii) x−1, y+1, z; (iii) −x−1, −y+1, −z+1.
Acknowledgements top

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
References top

Aakeroey, C. B., Desper, J., Elisabeth, E., Helfrich, B. A., Levin, B. & Urbina, J. F. (2005). Z. Kristallogr. 220, 325–332.

Enraf–Nonius (1989). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.

Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.

North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Yu, Z. H., Niu, C. W., Ban, S. R., Wen, X. & Xi, Z. (2007). Chin. Sci. Bull. 52, 1929–1941.