4-Chloro-1H-pyrrolo­[2,3-d]pyrimidine

Dong, S.-L.; Cheng, X.

doi:10.1107/S1600536812034095

organic compounds

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ISSN: 2056-9890

Volume 68| Part 9| September 2012| Page o2666

doi:10.1107/S1600536812034095

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4-Chloro-1H-pyrrolo[2,3-d]pyrimidine

Su-Lan Dong ^a ^* and Xiaochun Cheng ^a

^aCollege of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaiyin 223003, Jiangsu, People's Republic of China
^*Correspondence e-mail: dsl710221@163.com

(Received 30 July 2012; accepted 31 July 2012; online 8 August 2012)

The title compound, C₆H₄ClN₃, is essentially planar with the pyrrole and pyrimidine rings inclined to one another by 0.79 (15)°. In the crystal, molecules are connected via pairs of N—H⋯N hydrogen bonds, forming inversion dimers. These dimers are linked via C—H⋯N interactions, forming a two-dimensional network parallel to (10-1).

Related literature

The title compound is an important organic intermediate in the synthesis of a drug which shows promising activity against HCV replication, see: Chang et al. (2010 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₆H₄ClN₃
M_r = 153.57
Monoclinic, P 2₁ /n
a = 10.8810 (19) Å
b = 5.2783 (9) Å
c = 12.751 (2) Å
β = 114.333 (3)°
V = 667.3 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.49 mm⁻¹
T = 296 K
0.18 × 0.16 × 0.10 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
Absorption correction: ψ scan (North et al., 1968 ) T_min = 0.918, T_max = 0.953
3597 measured reflections
1273 independent reflections
1166 reflections with I > 2σ(I)
R_int = 0.017
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.052
wR(F²) = 0.145
S = 1.00
1273 reflections
91 parameters
H-atom parameters constrained
Δρ_max = 0.58 e Å⁻³
Δρ_min = −0.43 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯N1ⁱ	0.86	2.07	2.927 (3)	174
C6—H6⋯N3ⁱⁱ	0.93	2.57	3.315 (3)	137
Symmetry codes: (i) -x+2, -y+2, -z+1; (ii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CAD-4 Software (Enraf–Nonius, 1985 ); cell refinement: CAD-4 Software; 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: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812034095/su2492sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812034095/su2492Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812034095/su2492Isup3.cml

checkCIF report

Comment top

The title compound is an important organic intermediate that has been used to synthesis a drug which has shown promising activity against HCV replication (Chang et al., 2010).

The molecular structure of the title molecule is shown in Fig. 1. The bond lengths (Allen et al., 1987) and angles are within normal ranges. The molecule is planar with the pyrrole ring (N1/C2-C5) and pyrimidine ring (N2/N3/C1/C2/C5/C6) being inclined to one another by only 0.79 (15)°.

In the crystal, molecules are connected via a pair of N-H···N hydrogen bonds to form inversion dimers, which are further linked via C-H···N interactions (Table 1 and Fig. 2). This results in the formation of a two-dimensional network parallel to (1 0 -1).

Related literature top

The title compound is an important organic intermediate in the synthesis of a drug which shows promising activity against HCV replication, see: Chang et al. (2010). For bond-length data, see: Allen et al. (1987).

Experimental top

The title compound was prepared by a method reported in the literature (Chang et al., 2010). A solution of phosphoryl trichloride (22.7 g, 158 mmol) in dichloromethane (50 ml) was added slowly to a solution of 3H-pyrrolo[2,3-d]pyrimidin-4(4aH)-one (10 g, 74 mmol). After being stirred for 6 h at reflux temperature, the solvent was filtered and the organic phase was evaporated on a rotary evaporator and gave the title compound. Colourless block-like crystals, suitable for X-ray diffraction analysis, were obtained by dissolving the solid (0.5 g, 3.26 mmol) in ethanol (25 ml) and evaporating the solvent slowly at room temperature for about 7d.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell refinement: CAD-4 Software (Enraf–Nonius, 1985); 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: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title molecule, with atom numbering. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A view along the a axis of the crystal packing of the title compound. The N-H···N and C-H···N hydrogen bonds are shown as dashed lines (see Table 1 for details].

4-Chloro-1H-pyrrolo[2,3-d]pyrimidine top

Crystal data top

C₆H₄ClN₃	F(000) = 312
M_r = 153.57	D_x = 1.529 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 4634 reflections
a = 10.8810 (19) Å	θ = 6.4–60.4°
b = 5.2783 (9) Å	µ = 0.49 mm⁻¹
c = 12.751 (2) Å	T = 296 K
β = 114.333 (3)°	Block, colourless
V = 667.3 (2) Å³	0.18 × 0.16 × 0.10 mm
Z = 4

Data collection top

Enraf–Nonius CAD-4 diffractometer	1166 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.017
Graphite monochromator	θ_max = 26.0°, θ_min = 3.2°
ω/2θ scans	h = −13→11
Absorption correction: ψ scan (North et al., 1968)	k = −6→6
T_min = 0.918, T_max = 0.953	l = −14→15
3597 measured reflections	3 standard reflections every 200 reflections
1273 independent reflections	intensity decay: 1%

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.145	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0781P)² + 0.6149P] where P = (F_o² + 2F_c²)/3
1273 reflections	(Δ/σ)_max < 0.001
91 parameters	Δρ_max = 0.58 e Å⁻³
0 restraints	Δρ_min = −0.43 e Å⁻³

Crystal data top

C₆H₄ClN₃	V = 667.3 (2) Å³
M_r = 153.57	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 10.8810 (19) Å	µ = 0.49 mm⁻¹
b = 5.2783 (9) Å	T = 296 K
c = 12.751 (2) Å	0.18 × 0.16 × 0.10 mm
β = 114.333 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	1166 reflections with I > 2σ(I)
Absorption correction: ψ scan (North et al., 1968)	R_int = 0.017
T_min = 0.918, T_max = 0.953	3 standard reflections every 200 reflections
3597 measured reflections	intensity decay: 1%
1273 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	0 restraints
wR(F²) = 0.145	H-atom parameters constrained
S = 1.00	Δρ_max = 0.58 e Å⁻³
1273 reflections	Δρ_min = −0.43 e Å⁻³
91 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
Cl1	0.62621 (8)	0.17642 (16)	0.50664 (6)	0.0659 (3)
C1	0.7287 (2)	0.3943 (4)	0.4803 (2)	0.0401 (5)
C2	0.8091 (2)	0.5538 (5)	0.56688 (18)	0.0385 (5)
C3	0.8403 (3)	0.6051 (6)	0.6845 (2)	0.0533 (7)
H3	0.8069	0.5213	0.7315	0.064*
C4	0.9284 (3)	0.8009 (6)	0.7143 (2)	0.0581 (7)
H4	0.9656	0.8744	0.7870	0.070*
C5	0.8835 (2)	0.7273 (4)	0.53211 (19)	0.0365 (5)
C6	0.8026 (3)	0.5695 (5)	0.3549 (2)	0.0448 (6)
H6	0.8000	0.5698	0.2810	0.054*
N1	0.9559 (2)	0.8772 (4)	0.62302 (18)	0.0470 (5)
N2	0.8820 (2)	0.7376 (4)	0.42666 (16)	0.0411 (5)
H2	0.9289	0.8447	0.4077	0.049*
N3	0.7247 (2)	0.3972 (4)	0.37545 (17)	0.0461 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0695 (5)	0.0685 (5)	0.0662 (5)	−0.0334 (4)	0.0343 (4)	−0.0032 (3)
C1	0.0408 (11)	0.0391 (11)	0.0427 (12)	−0.0039 (9)	0.0195 (9)	0.0030 (9)
C2	0.0379 (10)	0.0418 (12)	0.0393 (11)	−0.0043 (9)	0.0193 (9)	0.0025 (9)
C3	0.0585 (15)	0.0679 (17)	0.0406 (12)	−0.0180 (13)	0.0276 (11)	−0.0020 (12)
C4	0.0618 (16)	0.0768 (19)	0.0407 (13)	−0.0208 (14)	0.0261 (12)	−0.0115 (13)
C5	0.0357 (10)	0.0374 (11)	0.0386 (11)	−0.0018 (9)	0.0175 (9)	0.0019 (9)
C6	0.0557 (13)	0.0454 (13)	0.0373 (11)	−0.0035 (11)	0.0233 (10)	0.0020 (10)
N1	0.0476 (11)	0.0521 (12)	0.0452 (11)	−0.0138 (9)	0.0230 (9)	−0.0071 (9)
N2	0.0474 (11)	0.0397 (10)	0.0433 (10)	−0.0046 (8)	0.0260 (9)	0.0040 (8)
N3	0.0529 (12)	0.0441 (11)	0.0418 (10)	−0.0085 (9)	0.0201 (9)	−0.0025 (8)

Geometric parameters (Å, º) top

Cl1—C1	1.728 (2)	C4—H4	0.9300
C1—N3	1.319 (3)	C5—N2	1.339 (3)
C1—C2	1.378 (3)	C5—N1	1.356 (3)
C2—C5	1.409 (3)	C6—N2	1.312 (3)
C2—C3	1.421 (3)	C6—N3	1.341 (3)
C3—C4	1.353 (4)	C6—H6	0.9300
C3—H3	0.9300	N2—H2	0.8600
C4—N1	1.376 (3)

N3—C1—C2	123.4 (2)	N2—C5—N1	126.6 (2)
N3—C1—Cl1	116.75 (18)	N2—C5—C2	124.9 (2)
C2—C1—Cl1	119.89 (17)	N1—C5—C2	108.5 (2)
C1—C2—C5	113.7 (2)	N2—C6—N3	127.6 (2)
C1—C2—C3	139.4 (2)	N2—C6—H6	116.2
C5—C2—C3	106.9 (2)	N3—C6—H6	116.2
C4—C3—C2	105.9 (2)	C5—N1—C4	107.4 (2)
C4—C3—H3	127.0	C6—N2—C5	113.9 (2)
C2—C3—H3	127.0	C6—N2—H2	123.0
C3—C4—N1	111.3 (2)	C5—N2—H2	123.0
C3—C4—H4	124.4	C1—N3—C6	116.5 (2)
N1—C4—H4	124.4

N3—C1—C2—C5	2.1 (4)	C3—C2—C5—N1	−0.2 (3)
Cl1—C1—C2—C5	−177.86 (17)	N2—C5—N1—C4	−179.5 (3)
N3—C1—C2—C3	−179.7 (3)	C2—C5—N1—C4	0.0 (3)
Cl1—C1—C2—C3	0.3 (4)	C3—C4—N1—C5	0.1 (4)
C1—C2—C3—C4	−178.0 (3)	N3—C6—N2—C5	0.8 (4)
C5—C2—C3—C4	0.3 (3)	N1—C5—N2—C6	180.0 (2)
C2—C3—C4—N1	−0.2 (4)	C2—C5—N2—C6	0.5 (3)
C1—C2—C5—N2	−1.9 (3)	C2—C1—N3—C6	−1.1 (4)
C3—C2—C5—N2	179.4 (2)	Cl1—C1—N3—C6	178.90 (18)
C1—C2—C5—N1	178.6 (2)	N2—C6—N3—C1	−0.5 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.86	2.07	2.927 (3)	174
C6—H6···N3ⁱⁱ	0.93	2.57	3.315 (3)	137

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

Experimental details

Crystal data
Chemical formula	C₆H₄ClN₃
M_r	153.57
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	296
a, b, c (Å)	10.8810 (19), 5.2783 (9), 12.751 (2)
β (°)	114.333 (3)
V (Å³)	667.3 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.49
Crystal size (mm)	0.18 × 0.16 × 0.10

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	ψ scan (North et al., 1968)
T_min, T_max	0.918, 0.953
No. of measured, independent and observed [I > 2σ(I)] reflections	3597, 1273, 1166
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.052, 0.145, 1.00
No. of reflections	1273
No. of parameters	91
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.58, −0.43

Computer programs: CAD-4 Software (Enraf–Nonius, 1985), XCAD4 (Harms & Wocadlo,1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.86	2.07	2.927 (3)	174
C6—H6···N3ⁱⁱ	0.93	2.57	3.315 (3)	137

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

Acknowledgements

The authors thank the Center of Testing and Analysis, Nanjing University, for the data collection.

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. CrossRef Web of Science Google Scholar
Chang, J. B., Hu, W. D., Song, C. J., Pan, Z. L., Wang, Q., Guo, X. C., Yu, X. J., Shen, Z. H. & Wang, S. Y. (2010). Bioorg. Med. Chem. Lett. 20, 7297–7298. Web of Science CrossRef PubMed Google Scholar
Enraf–Nonius (1985). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands. 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