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

Fun, H.-K.; Chantrapromma, S.; Jana, S.; Chakrabarty, R.; Goswami, S.

doi:10.1107/S1600536808023714

organic compounds

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ISSN: 2056-9890

Volume 64| Part 9| September 2008| Pages o1659-o1660

doi:10.1107/S1600536808023714

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

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

^aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, ^bCrystal Materials Research Unit, Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90112, Thailand, and ^cDepartment of Chemistry, Bengal Engineering and Science University', Shibpur, Howrah, India 711 103
^*Correspondence e-mail: hkfun@usm.my

(Received 25 July 2008; accepted 27 July 2008; online 6 August 2008)

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 R²₂(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, C 2/c
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[F² > 2σ(F²)] = 0.040
wR(F²) = 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

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)
Symmetry codes: (i) -x+1, -y+2, -z+1; (ii) $[-x+{\script{3\over 2}}, -y+{\script{3\over 2}}, -z+1]$ .

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 ).

Supporting information

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

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

checkCIF report

Comment top

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.

Related literature top

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 top

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.

Computing details top

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

Figures top

	Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atomic numbering.
	Fig. 2. The crystal packing of (I), viewed approximately along the b axis showing one-dimensional chains along the a axis. Hydrogen bonds were shown as dashed lines.

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

Crystal data top

C₄H₃Cl₂N₃	F(000) = 1312
M_r = 163.99	D_x = 1.716 Mg m⁻³
Monoclinic, C2/c	Melting point = 492–494 K
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 32.060 (4) Å	Cell parameters from 2886 reflections
b = 3.8045 (6) Å	θ = 1.3–27.5°
c = 21.302 (3) Å	µ = 0.92 mm⁻¹
β = 102.193 (7)°	T = 296 K
V = 2539.6 (6) Å³	Block, colorless
Z = 16	0.57 × 0.14 × 0.02 mm

Data collection top

Bruker SMART APEX2 CCD area-detector diffractometer	2886 independent reflections
Radiation source: fine-focus sealed tube	1875 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.051
Detector resolution: 8.33 pixels mm^-1	θ_max = 27.5°, θ_min = 1.3°
ω scans	h = −40→40
Absorption correction: multi-scan (SADABS; Bruker, 2005)	k = −4→4
T_min = 0.620, T_max = 0.985	l = −27→27
12772 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.098	All H-atom parameters refined
S = 1.02	w = 1/[σ²(F_o²) + (0.0403P)²] where P = (F_o² + 2F_c²)/3
2886 reflections	(Δ/σ)_max = 0.001
187 parameters	Δρ_max = 0.22 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₄H₃Cl₂N₃	V = 2539.6 (6) Å³
M_r = 163.99	Z = 16
Monoclinic, C2/c	Mo Kα radiation
a = 32.060 (4) Å	µ = 0.92 mm⁻¹
b = 3.8045 (6) Å	T = 296 K
c = 21.302 (3) Å	0.57 × 0.14 × 0.02 mm
β = 102.193 (7)°

Data collection top

Bruker SMART APEX2 CCD area-detector diffractometer	2886 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	1875 reflections with I > 2σ(I)
T_min = 0.620, T_max = 0.985	R_int = 0.051
12772 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	0 restraints
wR(F²) = 0.098	All H-atom parameters refined
S = 1.02	Δρ_max = 0.22 e Å⁻³
2886 reflections	Δρ_min = −0.24 e Å⁻³
187 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

	x	y	z	U_iso*/U_eq
Cl1A	0.330814 (19)	0.45738 (18)	0.35093 (3)	0.0475 (2)
Cl2A	0.49584 (2)	0.5271 (2)	0.33992 (4)	0.0572 (2)
N1A	0.46421 (6)	0.7708 (5)	0.43348 (9)	0.0371 (5)
N2A	0.38986 (6)	0.7401 (5)	0.43849 (9)	0.0349 (5)
N3A	0.43941 (8)	0.9927 (7)	0.51907 (11)	0.0490 (6)
H2NA	0.4619 (8)	1.056 (7)	0.5293 (12)	0.033 (8)*
H1NA	0.4174 (9)	1.026 (7)	0.5366 (14)	0.057 (9)*
C1A	0.38306 (7)	0.5786 (6)	0.38271 (11)	0.0338 (6)
C2A	0.41389 (8)	0.5008 (7)	0.34867 (12)	0.0377 (6)
H2A	0.4102 (7)	0.386 (6)	0.3120 (11)	0.034 (7)*
C3A	0.45423 (7)	0.6088 (7)	0.37766 (11)	0.0353 (6)
C4A	0.43110 (7)	0.8296 (7)	0.46279 (11)	0.0350 (6)
Cl1B	0.58263 (2)	1.02542 (19)	0.31034 (3)	0.0510 (2)
Cl2B	0.73894 (2)	0.50031 (18)	0.32094 (3)	0.0474 (2)
N1B	0.71199 (6)	0.7404 (6)	0.41918 (9)	0.0389 (5)
N2B	0.64127 (6)	0.9690 (6)	0.41463 (9)	0.0406 (5)
N3B	0.69119 (9)	0.9534 (8)	0.50908 (11)	0.0589 (7)
H1NB	0.6706 (10)	1.049 (8)	0.5237 (16)	0.080 (12)*
H2NB	0.7156 (10)	0.881 (9)	0.5264 (16)	0.075 (11)*
C1B	0.63348 (7)	0.9103 (6)	0.35235 (12)	0.0364 (6)
C2B	0.66172 (7)	0.7709 (7)	0.31888 (11)	0.0374 (6)
H2B	0.6550 (7)	0.753 (7)	0.2743 (12)	0.047 (7)*
C3B	0.70066 (7)	0.6887 (7)	0.35702 (11)	0.0361 (6)
C4B	0.68134 (8)	0.8851 (7)	0.44634 (11)	0.0403 (6)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1A	0.0320 (3)	0.0586 (5)	0.0491 (4)	−0.0065 (3)	0.0027 (3)	−0.0029 (3)
Cl2A	0.0442 (4)	0.0698 (5)	0.0658 (5)	−0.0003 (4)	0.0298 (3)	−0.0132 (4)
N1A	0.0293 (10)	0.0422 (13)	0.0402 (11)	0.0003 (10)	0.0086 (9)	−0.0014 (11)
N2A	0.0295 (10)	0.0416 (13)	0.0339 (10)	0.0028 (10)	0.0073 (8)	−0.0013 (10)
N3A	0.0351 (14)	0.0707 (19)	0.0418 (13)	−0.0073 (14)	0.0093 (11)	−0.0161 (13)
C1A	0.0293 (12)	0.0320 (14)	0.0385 (13)	−0.0009 (11)	0.0040 (10)	0.0039 (11)
C2A	0.0378 (14)	0.0402 (16)	0.0355 (13)	−0.0012 (13)	0.0087 (11)	−0.0057 (13)
C3A	0.0338 (13)	0.0354 (14)	0.0396 (13)	0.0033 (12)	0.0141 (10)	0.0001 (12)
C4A	0.0327 (13)	0.0404 (15)	0.0315 (12)	−0.0020 (12)	0.0060 (10)	0.0013 (12)
Cl1B	0.0344 (4)	0.0669 (5)	0.0514 (4)	0.0072 (4)	0.0083 (3)	0.0056 (4)
Cl2B	0.0358 (3)	0.0566 (4)	0.0546 (4)	−0.0001 (3)	0.0204 (3)	−0.0103 (3)
N1B	0.0355 (11)	0.0438 (13)	0.0386 (11)	0.0036 (11)	0.0109 (9)	0.0016 (10)
N2B	0.0388 (12)	0.0481 (14)	0.0377 (11)	0.0044 (11)	0.0143 (9)	0.0001 (11)
N3B	0.0534 (17)	0.087 (2)	0.0368 (13)	0.0187 (16)	0.0102 (12)	−0.0034 (13)
C1B	0.0315 (13)	0.0386 (15)	0.0407 (13)	0.0001 (12)	0.0112 (10)	0.0014 (12)
C2B	0.0352 (14)	0.0465 (17)	0.0328 (13)	−0.0025 (13)	0.0123 (11)	−0.0036 (13)
C3B	0.0329 (13)	0.0369 (15)	0.0416 (14)	−0.0031 (12)	0.0151 (11)	−0.0009 (12)
C4B	0.0398 (15)	0.0477 (16)	0.0352 (13)	0.0043 (13)	0.0122 (11)	0.0023 (12)

Geometric parameters (Å, º) top

Cl1A—C1A	1.731 (2)	Cl1B—C1B	1.742 (2)
Cl2A—C3A	1.725 (2)	Cl2B—C3B	1.735 (2)
N1A—C3A	1.317 (3)	N1B—C3B	1.312 (3)
N1A—C4A	1.359 (3)	N1B—C4B	1.358 (3)
N2A—C1A	1.314 (3)	N2B—C1B	1.316 (3)
N2A—C4A	1.357 (3)	N2B—C4B	1.357 (3)
N3A—C4A	1.326 (3)	N3B—C4B	1.332 (3)
N3A—H2NA	0.75 (2)	N3B—H1NB	0.87 (3)
N3A—H1NA	0.87 (3)	N3B—H2NB	0.84 (3)
C1A—C2A	1.376 (3)	C1B—C2B	1.372 (3)
C2A—C3A	1.373 (3)	C2B—C3B	1.374 (3)
C2A—H2A	0.88 (2)	C2B—H2B	0.93 (2)

C3A—N1A—C4A	115.3 (2)	C3B—N1B—C4B	114.8 (2)
C1A—N2A—C4A	115.11 (19)	C1B—N2B—C4B	114.9 (2)
C4A—N3A—H2NA	114 (2)	C4B—N3B—H1NB	114 (2)
C4A—N3A—H1NA	115.4 (19)	C4B—N3B—H2NB	112 (2)
H2NA—N3A—H1NA	130 (3)	H1NB—N3B—H2NB	134 (3)
N2A—C1A—C2A	125.2 (2)	N2B—C1B—C2B	125.7 (2)
N2A—C1A—Cl1A	116.12 (18)	N2B—C1B—Cl1B	115.67 (18)
C2A—C1A—Cl1A	118.68 (19)	C2B—C1B—Cl1B	118.62 (19)
C3A—C2A—C1A	114.3 (2)	C1B—C2B—C3B	113.4 (2)
C3A—C2A—H2A	118.9 (14)	C1B—C2B—H2B	121.6 (15)
C1A—C2A—H2A	126.7 (15)	C3B—C2B—H2B	124.8 (14)
N1A—C3A—C2A	124.9 (2)	N1B—C3B—C2B	125.9 (2)
N1A—C3A—Cl2A	116.14 (18)	N1B—C3B—Cl2B	115.99 (17)
C2A—C3A—Cl2A	118.95 (19)	C2B—C3B—Cl2B	118.12 (18)
N3A—C4A—N2A	117.1 (2)	N3B—C4B—N2B	116.9 (2)
N3A—C4A—N1A	117.7 (2)	N3B—C4B—N1B	117.8 (2)
N2A—C4A—N1A	125.2 (2)	N2B—C4B—N1B	125.3 (2)

Hydrogen-bond geometry (Å, º) top

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)

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

Experimental details

Crystal data
Chemical formula	C₄H₃Cl₂N₃
M_r	163.99
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	296
a, b, c (Å)	32.060 (4), 3.8045 (6), 21.302 (3)
β (°)	102.193 (7)
V (Å³)	2539.6 (6)
Z	16
Radiation type	Mo Kα
µ (mm⁻¹)	0.92
Crystal size (mm)	0.57 × 0.14 × 0.02

Data collection
Diffractometer	Bruker SMART APEX2 CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.620, 0.985
No. of measured, independent and observed [I > 2σ(I)] reflections	12772, 2886, 1875
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.098, 1.02
No. of reflections	2886
No. of parameters	187
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.24

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008), SHELXTL and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

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)

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

Footnotes

‡Additional correspondence author, email: suchada.c@psu.ac.th.

Acknowledgements

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.

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