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ISSN: 2056-9890

5-Chloro­pyrimidin-2-amine

aCollege of Food Science and Light Industry, Nanjing University of Technology, Xinmofan Road No. 5 Nanjing, Nanjing 210009, People's Republic of China, and bCollege of Science, Nanjing University of Technology, Xinmofan Road No. 5 Nanjing, Nanjing 210009, People's Republic of China
*Correspondence e-mail: wanghaibo@njut.edu.cn

(Received 19 October 2009; accepted 22 October 2009; online 28 October 2009)

The complete mol­ecule of the title compound, C4H3ClN3, is generated by crystallographic mirror symmetry, with the Cl atom, one N atom and two C atoms lying on the reflecting plane. In the crystal structure, inter­molecular N—H⋯N hydrogen bonds link the mol­ecules into chains propagating in [100].

Related literature

For general background, see: Hannouta & Johnson (1982[Hannouta, I. B. & Johnson, A. (1982). Dyes Pigments, 3, 173-182.]). For bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]).

[Scheme 1]

Experimental

Crystal data
  • C4H4ClN3

  • Mr = 129.55

  • Orthorhombic, C m c a

  • a = 7.6380 (15) Å

  • b = 8.2240 (16) Å

  • c = 17.100 (3) Å

  • V = 1074.1 (4) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.59 mm−1

  • T = 293 K

  • 0.30 × 0.20 × 0.10 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 = 0.844, Tmax = 0.944

  • 1047 measured reflections

  • 534 independent reflections

  • 462 reflections with I > 2˘I)

  • Rint = 0.020

  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement
  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.116

  • S = 0.92

  • 534 reflections

  • 44 parameters

  • H-atom parameters constrained

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2A⋯N1i 0.90 2.22 3.087 (2) 161
Symmetry code: (i) [-x+{\script{3\over 2}}, -y-{\script{1\over 2}}, -z+1].

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994[Enraf-Nonius (1994). CAD-4 EXPRESS. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 EXPRESS; 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Related literature top

For general background, see: Hannouta & Johnson (1982). For bond-length data, see: Allen et al. (1987).

Experimental top

Guanidine (20 g) and 2-chloromalonaldehyde (16 g) were added to concentrated H2SO4 (50g) with cooling; the mixture was allowed to stand for two hours at room temperature, the product poured into ice water, neutralized with NH4OH, the precipitated filtered, made strongly alkaline with NH4OH, and the precipitate was recrystallized from alcohol or sublimed to give the title compound. Colourless blocks of (I) were obtained by slow evaporation of an methanol solution.

Refinement top

H atoms were positioned geometrically (N—H = 0.86 Å, C—H = 0.93–0.98Å) and refined as riding with Uiso(H) = 1.2Ueq(C,N) or 1.5Ueq(methyl C).

Structure description top

For general background, see: Hannouta & Johnson (1982). For bond-length data, see: Allen et al. (1987).

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); 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: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing 50% displacement ellipsoids.
5-Chloropyrimidin-2-amine top
Crystal data top
C4H4ClN3Dx = 1.602 Mg m3
Mr = 129.55Melting point: 506 K
Orthorhombic, CmcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2bc 2Cell parameters from 25 reflections
a = 7.6380 (15) Åθ = 10–13°
b = 8.2240 (16) ŵ = 0.59 mm1
c = 17.100 (3) ÅT = 293 K
V = 1074.1 (4) Å3Block, colourless
Z = 80.30 × 0.20 × 0.10 mm
F(000) = 528
Data collection top
Enraf–Nonius CAD-4
diffractometer
462 reflections with I > 2˘I)
Radiation source: fine-focus sealed tubeRint = 0.020
Graphite monochromatorθmax = 25.3°, θmin = 2.4°
ω/2θ scansh = 09
Absorption correction: ψ scan
(North et al., 1968)
k = 09
Tmin = 0.844, Tmax = 0.944l = 2020
1047 measured reflections3 standard reflections every 200 reflections
534 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.116 w = 1/[σ2(Fo2) + (0.1P)2 + 0.2P]
where P = (Fo2 + 2Fc2)/3
S = 0.92(Δ/σ)max < 0.001
534 reflectionsΔρmax = 0.20 e Å3
44 parametersΔρmin = 0.22 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.025 (4)
Crystal data top
C4H4ClN3V = 1074.1 (4) Å3
Mr = 129.55Z = 8
Orthorhombic, CmcaMo Kα radiation
a = 7.6380 (15) ŵ = 0.59 mm1
b = 8.2240 (16) ÅT = 293 K
c = 17.100 (3) Å0.30 × 0.20 × 0.10 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
462 reflections with I > 2˘I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.020
Tmin = 0.844, Tmax = 0.9443 standard reflections every 200 reflections
1047 measured reflections intensity decay: 1%
534 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0330 restraints
wR(F2) = 0.116H-atom parameters constrained
S = 0.92Δρmax = 0.20 e Å3
534 reflectionsΔρmin = 0.22 e Å3
44 parameters
Special details top

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 > 2sigma(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
Cl0.50000.22728 (9)0.27440 (4)0.0527 (4)
N10.65713 (16)0.11849 (18)0.41923 (8)0.0360 (5)
C30.50000.1761 (3)0.44284 (14)0.0319 (6)
N20.50000.3014 (3)0.49308 (15)0.0432 (7)
H2A0.60210.34340.50990.052*
C20.6542 (2)0.0027 (2)0.36821 (10)0.0364 (5)
H2C0.75980.04570.35070.044*
C10.50000.0674 (3)0.34019 (13)0.0347 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl0.0488 (6)0.0514 (6)0.0580 (6)0.0000.0000.0225 (3)
N10.0258 (9)0.0398 (9)0.0424 (9)0.0007 (6)0.0004 (5)0.0045 (6)
C30.0278 (12)0.0325 (13)0.0354 (12)0.0000.0000.0039 (11)
N20.0288 (11)0.0450 (13)0.0559 (14)0.0000.0000.0179 (11)
C20.0296 (10)0.0379 (10)0.0418 (9)0.0033 (7)0.0032 (7)0.0013 (7)
C10.0353 (13)0.0328 (13)0.0359 (13)0.0000.0000.0026 (10)
Geometric parameters (Å, º) top
Cl—C11.730 (2)N2—H2A0.9000
N1—C21.325 (2)C2—C11.378 (2)
N1—C31.3519 (18)C2—H2C0.9300
C3—N21.341 (4)C1—C2i1.378 (2)
C3—N1i1.3519 (18)
C2—N1—C3116.44 (14)N1—C2—H2C118.9
N2—C3—N1i117.41 (11)C1—C2—H2C118.9
N2—C3—N1117.41 (11)C2—C1—C2i117.4 (2)
N1i—C3—N1125.2 (2)C2—C1—Cl121.28 (11)
C3—N2—H2A120.0C2i—C1—Cl121.28 (11)
N1—C2—C1122.25 (15)
C2—N1—C3—N2178.5 (2)N1—C2—C1—C2i1.0 (4)
C2—N1—C3—N1i0.8 (4)N1—C2—C1—Cl179.28 (14)
C3—N1—C2—C10.1 (3)
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1ii0.902.223.087 (2)161
Symmetry code: (ii) x+3/2, y1/2, z+1.

Experimental details

Crystal data
Chemical formulaC4H4ClN3
Mr129.55
Crystal system, space groupOrthorhombic, Cmca
Temperature (K)293
a, b, c (Å)7.6380 (15), 8.2240 (16), 17.100 (3)
V3)1074.1 (4)
Z8
Radiation typeMo Kα
µ (mm1)0.59
Crystal size (mm)0.30 × 0.20 × 0.10
Data collection
DiffractometerEnraf–Nonius CAD-4
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.844, 0.944
No. of measured, independent and
observed [I > 2˘I)] reflections
1047, 534, 462
Rint0.020
(sin θ/λ)max1)0.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.116, 0.92
No. of reflections534
No. of parameters44
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.22

Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.902.223.087 (2)161
Symmetry code: (i) x+3/2, y1/2, z+1.
 

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CSD CrossRef Web of Science Google Scholar
First citationEnraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands.  Google Scholar
First citationHannouta, I. B. & Johnson, A. (1982). Dyes Pigments, 3, 173–182.  Google Scholar
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.  Google Scholar
First citationNorth, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.  CrossRef IUCr Journals Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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ISSN: 2056-9890
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