5-Chloro­pyrimidin-2-amine

Wang, B.; Lu, R.-Z.; Han, L.-N.; Wei, W.-B.; Wang, H.-B.

doi:10.1107/S1600536809043645

organic compounds

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Volume 65| Part 11| November 2009| Page o2863

https://doi.org/10.1107/S1600536809043645

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5-Chloropyrimidin-2-amine

Bin Wang,^a,^b Ran-Zhe Lu,^a,^b Lu-Na Han,^a,^b Wen-Bin Wei ^a,^b and Hai-Bo Wang ^a ^*

^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 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₄H₄ClN₃
M_r = 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 ) 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[F² > 2σ(F²)] = 0.033
wR(F²) = 0.116
S = 0.92
534 reflections
44 parameters
H-atom parameters constrained
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: CAD-4 EXPRESS; 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 ).

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536809043645/hb5158Isup2.hkl

checkCIF report

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.

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

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

5-Chloropyrimidin-2-amine top

Crystal data top

C₄H₄ClN₃	D_x = 1.602 Mg m⁻³
M_r = 129.55	Melting point: 506 K
Orthorhombic, Cmca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2bc 2	Cell parameters from 25 reflections
a = 7.6380 (15) Å	θ = 10–13°
b = 8.2240 (16) Å	µ = 0.59 mm⁻¹
c = 17.100 (3) Å	T = 293 K
V = 1074.1 (4) Å³	Block, colourless
Z = 8	0.30 × 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 tube	R_int = 0.020
Graphite monochromator	θ_max = 25.3°, θ_min = 2.4°
ω/2θ scans	h = 0→9
Absorption correction: ψ scan (North et al., 1968)	k = 0→9
T_min = 0.844, T_max = 0.944	l = −20→20
1047 measured reflections	3 standard reflections every 200 reflections
534 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.033	H-atom parameters constrained
wR(F²) = 0.116	w = 1/[σ²(F_o²) + (0.1P)² + 0.2P] where P = (F_o² + 2F_c²)/3
S = 0.92	(Δ/σ)_max < 0.001
534 reflections	Δρ_max = 0.20 e Å⁻³
44 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.025 (4)

Crystal data top

C₄H₄ClN₃	V = 1074.1 (4) Å³
M_r = 129.55	Z = 8
Orthorhombic, Cmca	Mo Kα radiation
a = 7.6380 (15) Å	µ = 0.59 mm⁻¹
b = 8.2240 (16) Å	T = 293 K
c = 17.100 (3) Å	0.30 × 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)	R_int = 0.020
T_min = 0.844, T_max = 0.944	3 standard reflections every 200 reflections
1047 measured reflections	intensity decay: 1%
534 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	0 restraints
wR(F²) = 0.116	H-atom parameters constrained
S = 0.92	Δρ_max = 0.20 e Å⁻³
534 reflections	Δρ_min = −0.22 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Cl	0.5000	0.22728 (9)	0.27440 (4)	0.0527 (4)
N1	0.65713 (16)	−0.11849 (18)	0.41923 (8)	0.0360 (5)
C3	0.5000	−0.1761 (3)	0.44284 (14)	0.0319 (6)
N2	0.5000	−0.3014 (3)	0.49308 (15)	0.0432 (7)
H2A	0.6021	−0.3434	0.5099	0.052*
C2	0.6542 (2)	0.0027 (2)	0.36821 (10)	0.0364 (5)
H2C	0.7598	0.0457	0.3507	0.044*
C1	0.5000	0.0674 (3)	0.34019 (13)	0.0347 (6)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl	0.0488 (6)	0.0514 (6)	0.0580 (6)	0.000	0.000	0.0225 (3)
N1	0.0258 (9)	0.0398 (9)	0.0424 (9)	−0.0007 (6)	0.0004 (5)	0.0045 (6)
C3	0.0278 (12)	0.0325 (13)	0.0354 (12)	0.000	0.000	−0.0039 (11)
N2	0.0288 (11)	0.0450 (13)	0.0559 (14)	0.000	0.000	0.0179 (11)
C2	0.0296 (10)	0.0379 (10)	0.0418 (9)	−0.0033 (7)	0.0032 (7)	0.0013 (7)
C1	0.0353 (13)	0.0328 (13)	0.0359 (13)	0.000	0.000	0.0026 (10)

Geometric parameters (Å, º) top

Cl—C1	1.730 (2)	N2—H2A	0.9000
N1—C2	1.325 (2)	C2—C1	1.378 (2)
N1—C3	1.3519 (18)	C2—H2C	0.9300
C3—N2	1.341 (4)	C1—C2ⁱ	1.378 (2)
C3—N1ⁱ	1.3519 (18)

C2—N1—C3	116.44 (14)	N1—C2—H2C	118.9
N2—C3—N1ⁱ	117.41 (11)	C1—C2—H2C	118.9
N2—C3—N1	117.41 (11)	C2—C1—C2ⁱ	117.4 (2)
N1ⁱ—C3—N1	125.2 (2)	C2—C1—Cl	121.28 (11)
C3—N2—H2A	120.0	C2ⁱ—C1—Cl	121.28 (11)
N1—C2—C1	122.25 (15)

C2—N1—C3—N2	178.5 (2)	N1—C2—C1—C2ⁱ	1.0 (4)
C2—N1—C3—N1ⁱ	−0.8 (4)	N1—C2—C1—Cl	179.28 (14)
C3—N1—C2—C1	−0.1 (3)

Symmetry code: (i) −x+1, y, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱⁱ	0.90	2.22	3.087 (2)	161

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

Experimental details

Crystal data
Chemical formula	C₄H₄ClN₃
M_r	129.55
Crystal system, space group	Orthorhombic, Cmca
Temperature (K)	293
a, b, c (Å)	7.6380 (15), 8.2240 (16), 17.100 (3)
V (Å³)	1074.1 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.59
Crystal size (mm)	0.30 × 0.20 × 0.10

Data collection
Diffractometer	Enraf–Nonius CAD-4
Absorption correction	ψ scan (North et al., 1968)
T_min, T_max	0.844, 0.944
No. of measured, independent and observed [I > 2˘I)] reflections	1047, 534, 462
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.600

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.116, 0.92
No. of reflections	534
No. of parameters	44
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.90	2.22	3.087 (2)	161

Symmetry code: (i) −x+3/2, −y−1/2, −z+1.

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. CSD CrossRef Web of Science Google Scholar
Enraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Hannouta, I. B. & Johnson, A. (1982). Dyes Pigments, 3, 173–182. Google Scholar
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany. Google Scholar
North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359. CrossRef IUCr Journals Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 11| November 2009| Page o2863

https://doi.org/10.1107/S1600536809043645

Open

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