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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1659–o1660.
Published online 2008 August 6. doi:  10.1107/S1600536808023714
PMCID: PMC2960503

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

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

An external file that holds a picture, illustration, etc.
Object name is e-64-o1659-scheme1.jpg

Experimental

Crystal data

  • C4H3Cl2N3
  • M r = 163.99
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1659-efi1.jpg
  • 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 [triangle]) 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
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.24 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

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

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.

Refinement

All H atoms were located in a difference map and freely refined isotropically. The highest residual electron density peak is located at 1.00 Å from N2A and the deepest hole is located at 0.81 Å from H2NA.

Figures

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.

Crystal data

C4H3Cl2N3F000 = 1312
Mr = 163.99Dx = 1.716 Mg m3
Monoclinic, C2/cMelting point = 492–494 K
Hall symbol: -C 2ycMo Kα radiation λ = 0.71073 Å
a = 32.060 (4) ÅCell parameters from 2886 reflections
b = 3.8045 (6) Åθ = 1.3–27.5º
c = 21.302 (3) ŵ = 0.92 mm1
β = 102.193 (7)ºT = 296 (2) K
V = 2539.6 (6) Å3Block, colorless
Z = 160.57 × 0.14 × 0.02 mm

Data collection

Bruker SMART APEX2 CCD area-detector diffractometer2886 independent reflections
Radiation source: fine-focus sealed tube1875 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.051
Detector resolution: 8.33 pixels mm-1θmax = 27.5º
T = 296(2) Kθmin = 1.3º
ω scansh = −40→40
Absorption correction: multi-scan(SADABS; Bruker, 2005)k = −4→4
Tmin = 0.620, Tmax = 0.985l = −27→27
12772 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040All H-atom parameters refined
wR(F2) = 0.098  w = 1/[σ2(Fo2) + (0.0403P)2] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
2886 reflectionsΔρmax = 0.22 e Å3
187 parametersΔρmin = −0.24 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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)

xyzUiso*/Ueq
Cl1A0.330814 (19)0.45738 (18)0.35093 (3)0.0475 (2)
Cl2A0.49584 (2)0.5271 (2)0.33992 (4)0.0572 (2)
N1A0.46421 (6)0.7708 (5)0.43348 (9)0.0371 (5)
N2A0.38986 (6)0.7401 (5)0.43849 (9)0.0349 (5)
N3A0.43941 (8)0.9927 (7)0.51907 (11)0.0490 (6)
H2NA0.4619 (8)1.056 (7)0.5293 (12)0.033 (8)*
H1NA0.4174 (9)1.026 (7)0.5366 (14)0.057 (9)*
C1A0.38306 (7)0.5786 (6)0.38271 (11)0.0338 (6)
C2A0.41389 (8)0.5008 (7)0.34867 (12)0.0377 (6)
H2A0.4102 (7)0.386 (6)0.3120 (11)0.034 (7)*
C3A0.45423 (7)0.6088 (7)0.37766 (11)0.0353 (6)
C4A0.43110 (7)0.8296 (7)0.46279 (11)0.0350 (6)
Cl1B0.58263 (2)1.02542 (19)0.31034 (3)0.0510 (2)
Cl2B0.73894 (2)0.50031 (18)0.32094 (3)0.0474 (2)
N1B0.71199 (6)0.7404 (6)0.41918 (9)0.0389 (5)
N2B0.64127 (6)0.9690 (6)0.41463 (9)0.0406 (5)
N3B0.69119 (9)0.9534 (8)0.50908 (11)0.0589 (7)
H1NB0.6706 (10)1.049 (8)0.5237 (16)0.080 (12)*
H2NB0.7156 (10)0.881 (9)0.5264 (16)0.075 (11)*
C1B0.63348 (7)0.9103 (6)0.35235 (12)0.0364 (6)
C2B0.66172 (7)0.7709 (7)0.31888 (11)0.0374 (6)
H2B0.6550 (7)0.753 (7)0.2743 (12)0.047 (7)*
C3B0.70066 (7)0.6887 (7)0.35702 (11)0.0361 (6)
C4B0.68134 (8)0.8851 (7)0.44634 (11)0.0403 (6)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl1A0.0320 (3)0.0586 (5)0.0491 (4)−0.0065 (3)0.0027 (3)−0.0029 (3)
Cl2A0.0442 (4)0.0698 (5)0.0658 (5)−0.0003 (4)0.0298 (3)−0.0132 (4)
N1A0.0293 (10)0.0422 (13)0.0402 (11)0.0003 (10)0.0086 (9)−0.0014 (11)
N2A0.0295 (10)0.0416 (13)0.0339 (10)0.0028 (10)0.0073 (8)−0.0013 (10)
N3A0.0351 (14)0.0707 (19)0.0418 (13)−0.0073 (14)0.0093 (11)−0.0161 (13)
C1A0.0293 (12)0.0320 (14)0.0385 (13)−0.0009 (11)0.0040 (10)0.0039 (11)
C2A0.0378 (14)0.0402 (16)0.0355 (13)−0.0012 (13)0.0087 (11)−0.0057 (13)
C3A0.0338 (13)0.0354 (14)0.0396 (13)0.0033 (12)0.0141 (10)0.0001 (12)
C4A0.0327 (13)0.0404 (15)0.0315 (12)−0.0020 (12)0.0060 (10)0.0013 (12)
Cl1B0.0344 (4)0.0669 (5)0.0514 (4)0.0072 (4)0.0083 (3)0.0056 (4)
Cl2B0.0358 (3)0.0566 (4)0.0546 (4)−0.0001 (3)0.0204 (3)−0.0103 (3)
N1B0.0355 (11)0.0438 (13)0.0386 (11)0.0036 (11)0.0109 (9)0.0016 (10)
N2B0.0388 (12)0.0481 (14)0.0377 (11)0.0044 (11)0.0143 (9)0.0001 (11)
N3B0.0534 (17)0.087 (2)0.0368 (13)0.0187 (16)0.0102 (12)−0.0034 (13)
C1B0.0315 (13)0.0386 (15)0.0407 (13)0.0001 (12)0.0112 (10)0.0014 (12)
C2B0.0352 (14)0.0465 (17)0.0328 (13)−0.0025 (13)0.0123 (11)−0.0036 (13)
C3B0.0329 (13)0.0369 (15)0.0416 (14)−0.0031 (12)0.0151 (11)−0.0009 (12)
C4B0.0398 (15)0.0477 (16)0.0352 (13)0.0043 (13)0.0122 (11)0.0023 (12)

Geometric parameters (Å, °)

Cl1A—C1A1.731 (2)Cl1B—C1B1.742 (2)
Cl2A—C3A1.725 (2)Cl2B—C3B1.735 (2)
N1A—C3A1.317 (3)N1B—C3B1.312 (3)
N1A—C4A1.359 (3)N1B—C4B1.358 (3)
N2A—C1A1.314 (3)N2B—C1B1.316 (3)
N2A—C4A1.357 (3)N2B—C4B1.357 (3)
N3A—C4A1.326 (3)N3B—C4B1.332 (3)
N3A—H2NA0.75 (2)N3B—H1NB0.87 (3)
N3A—H1NA0.87 (3)N3B—H2NB0.84 (3)
C1A—C2A1.376 (3)C1B—C2B1.372 (3)
C2A—C3A1.373 (3)C2B—C3B1.374 (3)
C2A—H2A0.88 (2)C2B—H2B0.93 (2)
C3A—N1A—C4A115.3 (2)C3B—N1B—C4B114.8 (2)
C1A—N2A—C4A115.11 (19)C1B—N2B—C4B114.9 (2)
C4A—N3A—H2NA114 (2)C4B—N3B—H1NB114 (2)
C4A—N3A—H1NA115.4 (19)C4B—N3B—H2NB112 (2)
H2NA—N3A—H1NA130 (3)H1NB—N3B—H2NB134 (3)
N2A—C1A—C2A125.2 (2)N2B—C1B—C2B125.7 (2)
N2A—C1A—Cl1A116.12 (18)N2B—C1B—Cl1B115.67 (18)
C2A—C1A—Cl1A118.68 (19)C2B—C1B—Cl1B118.62 (19)
C3A—C2A—C1A114.3 (2)C1B—C2B—C3B113.4 (2)
C3A—C2A—H2A118.9 (14)C1B—C2B—H2B121.6 (15)
C1A—C2A—H2A126.7 (15)C3B—C2B—H2B124.8 (14)
N1A—C3A—C2A124.9 (2)N1B—C3B—C2B125.9 (2)
N1A—C3A—Cl2A116.14 (18)N1B—C3B—Cl2B115.99 (17)
C2A—C3A—Cl2A118.95 (19)C2B—C3B—Cl2B118.12 (18)
N3A—C4A—N2A117.1 (2)N3B—C4B—N2B116.9 (2)
N3A—C4A—N1A117.7 (2)N3B—C4B—N1B117.8 (2)
N2A—C4A—N1A125.2 (2)N2B—C4B—N1B125.3 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3A—H2NA···N1Ai0.75 (3)2.43 (3)3.172 (3)176 (2)
N3A—H1NA···N2Bi0.87 (3)2.33 (3)3.201 (3)172 (2)
N3B—H1NB···N2Ai0.87 (3)2.39 (3)3.253 (4)174 (3)
N3B—H2NB···N1Bii0.84 (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

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2524).

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–S19.
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Blackburn, G. M. & Gait, M. J. (1996). Nucleic Acids in Chemistry and Biology Editors. Oxford University Press.
  • Brown, D. J. (1988). Fused Pyrimidines The Chemistry of Heterocyclic Compounds, Vol. 24, pt. 3. New York: John Wiley & Sons.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Clews, C. J. B. & Cochran, W. (1948). Acta Cryst.1, 4–11.
  • Goswami, S., Jana, S., Das, N. K., Fun, H.-K. & Chantrapromma, S. (2008a). J. Mol. Struct 876, 313–321.
  • Goswami, S., Jana, S., Hazra, A., Fun, H.-K. & Chantrapromma, S. (2008b). Supramol. Chem 20, 495–500.
  • Hurst, D. T. (1980). Chemistry and Biochemistry of Pyrimidines, Purines, Pteridines Chichester: Wiley.
  • Ligthart, G. B. W. L., Ohkawa, H., Sijbesma, R. P. & Meijer, E. W. (2005). J. Am. Chem. Soc 127, 810–811. [PubMed]
  • Low, J. N., Quesada, A., Marchal, A., Melguizo, M., Nogueras, M. & Glidewell, C. (2002). Acta Cryst. C58, o289–o294. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Sherrington, D. C. & Taskinen, K. A. (2001). Chem. Soc. Rev 30, 83–93.
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.

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