A second monoclinic polymorph of 2-amino-4,6-dichloro­pyrimidine

Hoong-Kun Fun; Suchada Chantrapromma; Subrata Jana; Rinku Chakrabarty; Shyamaprosad Goswami

doi:10.1107/S1600536808023714

. 2008 Aug 6;64(Pt 9):o1659–o1660. doi: 10.1107/S1600536808023714

A second monoclinic polymorph of 2-amino-4,6-dichloropyrimidine

Hoong-Kun Fun ^a,^*, Suchada Chantrapromma ^b,^‡, Subrata Jana ^c, Rinku Chakrabarty ^c, Shyamaprosad Goswami ^c

PMCID: PMC2960503 PMID: 21201653

Abstract

The title chloro-substituted 2-aminopyrimidine, C₄H₃Cl₂N₃, is a second monoclinic polymorph of this compound which crystallizes in the space group C2/c. The structure was previously reported [Clews & Cochran (1948 ▶). Acta Cryst. 1, 4–11] in the space group P21/a. There are two crystallographically independent molecules in the asymmetric unit and each molecule is planar. The dihedral angle between the two pyrimidine rings is 30.71 (12)°. In the crystal structure, molecules are linked via N—H⋯N intermolecular hydrogen bonds, forming infinite one-dimensional chains along the a axis. These hydrogen bonds generate R ² ₂(8) ring motifs. The chains are stacked along the b axis.

Related literature

For bond-length data, see: Allen et al. (1987 ▶). For details of hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For related structures, see: the polymorph reported by Clews & Cochran (1948 ▶); Low et al. (2002 ▶). For applications of pyrimidine compounds and their supramolecular chemistry, see, for example: Blackburn & Gait (1996 ▶); Brown (1988 ▶); Hurst (1980 ▶); Goswami et al. (2008a ▶,b ▶); Ligthart et al. (2005 ▶); Sherrington & Taskinen (2001 ▶).

Experimental

Crystal data

C₄H₃Cl₂N₃
M _r = 163.99
Monoclinic,
a = 32.060 (4) Å
b = 3.8045 (6) Å
c = 21.302 (3) Å
β = 102.193 (7)°
V = 2539.6 (6) Å³
Z = 16
Mo Kα radiation
μ = 0.92 mm⁻¹
T = 296 (2) K
0.57 × 0.14 × 0.02 mm

Data collection

Bruker SMART APEX2 CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T _min = 0.620, T _max = 0.985
12772 measured reflections
2886 independent reflections
1875 reflections with I > 2σ(I)
R _int = 0.051

Refinement

R[F ² > 2σ(F ²)] = 0.040
wR(F ²) = 0.098
S = 1.02
2886 reflections
187 parameters
All H-atom parameters refined
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: APEX2; data reduction: SAINT (Bruker, 2005 ▶); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808023714/sj2524sup1.cif

e-64-o1659-sup1.cif^{(15.6KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808023714/sj2524Isup2.hkl

e-64-o1659-Isup2.hkl^{(141.7KB, hkl)}

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3A—H2NA⋯N1Aⁱ	0.75 (3)	2.43 (3)	3.172 (3)	176 (2)
N3A—H1NA⋯N2Bⁱ	0.87 (3)	2.33 (3)	3.201 (3)	172 (2)
N3B—H1NB⋯N2Aⁱ	0.87 (3)	2.39 (3)	3.253 (4)	174 (3)
N3B—H2NB⋯N1Bⁱⁱ	0.84 (3)	2.41 (3)	3.242 (3)	172 (3)

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

SJ, RC and SG acknowledge the DST [SR/S1/OC-13/2005] and CSIR [01(1913)/04/EMR-II], Government of India for financial support. SJ and RC thank the CSIR, Government of India, for research fellowships. The authors also thank Universiti Sains Malaysia for the Research University Golden Goose Grant No. 1001/PFIZIK/811012.

supplementary crystallographic information

Comment

Functionalized pyrimidines play a major role in the synthesis of different drug molecules and of naturally occurring pyrimidine bases (Blackburn & Gait, 1996; Brown, 1988; Hurst, 1980). Substituted pyrimidines are also very important for studies on multiple hydrogen bonding interactions in molecular recognition and supramolecular chemistry (Sherrington & Taskinen, 2001; Goswami et al., 2008a,b; Ligthart et al., 20050). In this work we report the crystal structure of the title compound, Fig 1, which is a second monoclinic polymorph of 2-amino-4,6-dichloropyrimidine.

The crystal structure of the title compound (I) was previously reported by Clews & Cochran (1948) in the monoclinic space group P21/a, with a = 16.447, b = 3.845, c = 10.283 Å, β = 107.58° and Z = 4. In the present work, the compound crystallized out in the monoclinic space group C2/c with Z = 16. There are two crystallographically independent molecules in the asymmetric unit, A and B, (see Fig. 1) with slightly different bond lengths and bond angles. Both molecules A and B are planar with maximum deviations of 0.005 (2) Å for atom N2A in A and 0.009 (2) Å for atom C2B in B. The dihedral angle between the two pyrimidine rings is 30.71 (12)°. The amino group acts as a double donor in N—H···N hydrogen bonds, while the two ring N atoms (N1 and N2) act as the acceptors. The molecules are linked via N—H···N intermolecular hydrogen bonds to form infinite one-dimensional chains along the a axis, Table 1. These hydrogen bonds generate R²₂(8) ring motifs (Bernstein at al., 1995) (Fig. 2). Interestingly, the Cl atoms do not form N—H···Cl hydrogen bonds. The closest Cl···Cl distance is 3.3635 (11) Å [3.37 Å in Clews & Cochran (1948)]. The bond lengths and angles in (I) are within normal ranges (Allen et al., 1987) and comparable to those found in related structures (Clews & Cochran, 1948; Low et al., 2002).

In the crystal packing shown in Fig. 2, the [1 0 0] molecular chains are stacked along the b axis.

Experimental

Phosphorus oxy-chloride (POCl₃) (25 ml) was added to anhydrous 2-amino-4,6-dioxopyrimidine (6 g) and the mixture refluxed at 383 K for 12 h. Excess POCl₃ was distilled off. The solid residue was neutralized using KOH solution in an ice bath and saturated NaHCO₃ solution was added. The solid residue was filtered off, extracted with CHCl₃ and the solution was dried over Na₂SO₄ and then concentrated under vacuum. The crude product was purified by column chromatography using 20% ethyl acetate in petroleum ether as eluent and the title compound (I) (4.29 g, 61%) was isolated. Single crystals were grown by slow evaporation of a CH₂Cl₂/ethanol (v/v 3:1) solution, Mp. 492–494 K.