organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

5-Bromo-N-methyl­pyrimidin-2-amine

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[Yu, Z. H., Niu, C. W., Ban, S. R., Wen, X. & Xi, Z. (2007). Chin. Sci. Bull. 52, 1929-1941.]). For a related structure, see: Aakeroey et al. (2005[Aakeroey, C. B., Desper, J., Elisabeth, E., Helfrich, B. A., Levin, B. & Urbina, J. F. (2005). Z. Kristallogr. 220, 325-332.]).

[Scheme 1]

Experimental

Crystal data
  • C5H6BrN3

  • Mr = 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[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.591, Tmax = 0.758

  • 1454 measured reflections

  • 1260 independent reflections

  • 714 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.40 e Å−3

  • Δρmin = −0.39 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Enraf-Nonius (1989). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); 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: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL97.

Supporting information


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
Graphite monochromatorθmax = 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 = 0.7583 standard reflections every 200 reflections
1454 measured reflections intensity decay: 1%
1260 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0560 restraints
wR(F2) = 0.100H-atom parameters constrained
S = 1.00Δρmax = 0.40 e Å3
1260 reflectionsΔρmin = 0.39 e Å3
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
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, º) 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, º) 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) x1, y+1, z; (iii) x1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC5H6BrN3
Mr188.04
Crystal system, space groupTriclinic, 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)
V3)344.24 (16)
Z2
Radiation typeMo Kα
µ (mm1)5.88
Crystal size (mm)0.10 × 0.05 × 0.05
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.591, 0.758
No. of measured, independent and
observed [I > 2σ(I)] reflections
1454, 1260, 714
Rint0.089
(sin θ/λ)max1)0.603
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.056, 0.100, 1.00
No. of reflections1260
No. of parameters82
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1A···N2i0.86002.19003.035 (7)169.00
C1—H1B···Brii0.96002.85003.751 (8)157.00
C5—H5A···N3iii0.93002.59003.357 (7)140.00
Symmetry codes: (i) x, y+2, z; (ii) x1, y+1, z; (iii) x1, 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

First citationAakeroey, C. B., Desper, J., Elisabeth, E., Helfrich, B. A., Levin, B. & Urbina, J. F. (2005). Z. Kristallogr. 220, 325–332.  CAS
First citationEnraf–Nonius (1989). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.
First citationNorth, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.  CrossRef IUCr Journals Web of Science
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 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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COMMUNICATIONS
ISSN: 2056-9890
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