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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2863.
Published online 2009 October 28. doi:  10.1107/S1600536809043645
PMCID: PMC2971243

5-Chloro­pyrimidin-2-amine

Abstract

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 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

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Object name is e-65-o2863-scheme1.jpg

Experimental

Crystal data

  • C4H4ClN3
  • M r = 129.55
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2863-efi1.jpg
  • 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 [triangle]) T min = 0.844, T max = 0.944
  • 1047 measured reflections
  • 534 independent reflections
  • 462 reflections with I > 2˘I)
  • R int = 0.020
  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 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

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 [triangle]); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809043645/hb5158sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809043645/hb5158Isup2.hkl

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

supplementary crystallographic information

Experimental

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

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).

Figures

Fig. 1.
The molecular structure of (I) showing 50% displacement ellipsoids.

Crystal data

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

Enraf–Nonius CAD-4 diffractometer462 reflections with I > 2˘I)
Radiation source: fine-focus sealed tubeRint = 0.020
graphiteθmax = 25.3°, θmin = 2.4°
ω/2θ scansh = 0→9
Absorption correction: ψ scan (North et al., 1968)k = 0→9
Tmin = 0.844, Tmax = 0.944l = −20→20
1047 measured reflections3 standard reflections every 200 reflections
534 independent reflections intensity decay: 1%

Refinement

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) = 0.116w = 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)

Special details

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)

xyzUiso*/Ueq
Cl0.50000.22728 (9)0.27440 (4)0.0527 (4)
N10.65713 (16)−0.11849 (18)0.41923 (8)0.0360 (5)
C30.5000−0.1761 (3)0.44284 (14)0.0319 (6)
N20.5000−0.3014 (3)0.49308 (15)0.0432 (7)
H2A0.6021−0.34340.50990.052*
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)

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)0.0000.000−0.0039 (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, °)

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—N1i−0.8 (4)N1—C2—C1—Cl179.28 (14)
C3—N1—C2—C1−0.1 (3)

Symmetry codes: (i) −x+1, y, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···N1ii0.902.223.087 (2)161

Symmetry codes: (ii) −x+3/2, −y−1/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5158).

References

  • 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.
  • Enraf–Nonius (1994). CAD-4 EXPRESS Enraf–Nonius, Delft, The Netherlands.
  • Hannouta, I. B. & Johnson, A. (1982). Dyes Pigments, 3, 173–182.
  • 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. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography