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ISSN: 2056-9890

4-Chloro-1H-pyrrolo­[2,3-d]pyrimidine

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

[Scheme 1]

Experimental

Crystal data
  • C6H4ClN3

  • Mr = 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[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.918, Tmax = 0.953

  • 3597 measured reflections

  • 1273 independent reflections

  • 1166 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.58 e Å−3

  • Δρmin = −0.43 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Enraf-Nonius (1985). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo,1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


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.

Refinement top

All the H atoms were positioned geometrically and constrained to ride on their parent: N-H = 0.86 Å, C—H = 0.93 Å with Uiso(H) = 1.2Ueq(N,C).

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
[Figure 1] Fig. 1. The molecular structure of the title molecule, with atom numbering. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] 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
C6H4ClN3F(000) = 312
Mr = 153.57Dx = 1.529 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4634 reflections
a = 10.8810 (19) Åθ = 6.4–60.4°
b = 5.2783 (9) ŵ = 0.49 mm1
c = 12.751 (2) ÅT = 296 K
β = 114.333 (3)°Block, colourless
V = 667.3 (2) Å30.18 × 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 tubeRint = 0.017
Graphite monochromatorθmax = 26.0°, θmin = 3.2°
ω/2θ scansh = 1311
Absorption correction: ψ scan
(North et al., 1968)
k = 66
Tmin = 0.918, Tmax = 0.953l = 1415
3597 measured reflections3 standard reflections every 200 reflections
1273 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.145H-atom parameters constrained
S = 1.00 w = 1/[σ2(Fo2) + (0.0781P)2 + 0.6149P]
where P = (Fo2 + 2Fc2)/3
1273 reflections(Δ/σ)max < 0.001
91 parametersΔρmax = 0.58 e Å3
0 restraintsΔρmin = 0.43 e Å3
Crystal data top
C6H4ClN3V = 667.3 (2) Å3
Mr = 153.57Z = 4
Monoclinic, P21/nMo Kα radiation
a = 10.8810 (19) ŵ = 0.49 mm1
b = 5.2783 (9) ÅT = 296 K
c = 12.751 (2) Å0.18 × 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)
Rint = 0.017
Tmin = 0.918, Tmax = 0.9533 standard reflections every 200 reflections
3597 measured reflections intensity decay: 1%
1273 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.145H-atom parameters constrained
S = 1.00Δρmax = 0.58 e Å3
1273 reflectionsΔρmin = 0.43 e Å3
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
xyzUiso*/Ueq
Cl10.62621 (8)0.17642 (16)0.50664 (6)0.0659 (3)
C10.7287 (2)0.3943 (4)0.4803 (2)0.0401 (5)
C20.8091 (2)0.5538 (5)0.56688 (18)0.0385 (5)
C30.8403 (3)0.6051 (6)0.6845 (2)0.0533 (7)
H30.80690.52130.73150.064*
C40.9284 (3)0.8009 (6)0.7143 (2)0.0581 (7)
H40.96560.87440.78700.070*
C50.8835 (2)0.7273 (4)0.53211 (19)0.0365 (5)
C60.8026 (3)0.5695 (5)0.3549 (2)0.0448 (6)
H60.80000.56980.28100.054*
N10.9559 (2)0.8772 (4)0.62302 (18)0.0470 (5)
N20.8820 (2)0.7376 (4)0.42666 (16)0.0411 (5)
H20.92890.84470.40770.049*
N30.7247 (2)0.3972 (4)0.37545 (17)0.0461 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0695 (5)0.0685 (5)0.0662 (5)0.0334 (4)0.0343 (4)0.0032 (3)
C10.0408 (11)0.0391 (11)0.0427 (12)0.0039 (9)0.0195 (9)0.0030 (9)
C20.0379 (10)0.0418 (12)0.0393 (11)0.0043 (9)0.0193 (9)0.0025 (9)
C30.0585 (15)0.0679 (17)0.0406 (12)0.0180 (13)0.0276 (11)0.0020 (12)
C40.0618 (16)0.0768 (19)0.0407 (13)0.0208 (14)0.0261 (12)0.0115 (13)
C50.0357 (10)0.0374 (11)0.0386 (11)0.0018 (9)0.0175 (9)0.0019 (9)
C60.0557 (13)0.0454 (13)0.0373 (11)0.0035 (11)0.0233 (10)0.0020 (10)
N10.0476 (11)0.0521 (12)0.0452 (11)0.0138 (9)0.0230 (9)0.0071 (9)
N20.0474 (11)0.0397 (10)0.0433 (10)0.0046 (8)0.0260 (9)0.0040 (8)
N30.0529 (12)0.0441 (11)0.0418 (10)0.0085 (9)0.0201 (9)0.0025 (8)
Geometric parameters (Å, º) top
Cl1—C11.728 (2)C4—H40.9300
C1—N31.319 (3)C5—N21.339 (3)
C1—C21.378 (3)C5—N11.356 (3)
C2—C51.409 (3)C6—N21.312 (3)
C2—C31.421 (3)C6—N31.341 (3)
C3—C41.353 (4)C6—H60.9300
C3—H30.9300N2—H20.8600
C4—N11.376 (3)
N3—C1—C2123.4 (2)N2—C5—N1126.6 (2)
N3—C1—Cl1116.75 (18)N2—C5—C2124.9 (2)
C2—C1—Cl1119.89 (17)N1—C5—C2108.5 (2)
C1—C2—C5113.7 (2)N2—C6—N3127.6 (2)
C1—C2—C3139.4 (2)N2—C6—H6116.2
C5—C2—C3106.9 (2)N3—C6—H6116.2
C4—C3—C2105.9 (2)C5—N1—C4107.4 (2)
C4—C3—H3127.0C6—N2—C5113.9 (2)
C2—C3—H3127.0C6—N2—H2123.0
C3—C4—N1111.3 (2)C5—N2—H2123.0
C3—C4—H4124.4C1—N3—C6116.5 (2)
N1—C4—H4124.4
N3—C1—C2—C52.1 (4)C3—C2—C5—N10.2 (3)
Cl1—C1—C2—C5177.86 (17)N2—C5—N1—C4179.5 (3)
N3—C1—C2—C3179.7 (3)C2—C5—N1—C40.0 (3)
Cl1—C1—C2—C30.3 (4)C3—C4—N1—C50.1 (4)
C1—C2—C3—C4178.0 (3)N3—C6—N2—C50.8 (4)
C5—C2—C3—C40.3 (3)N1—C5—N2—C6180.0 (2)
C2—C3—C4—N10.2 (4)C2—C5—N2—C60.5 (3)
C1—C2—C5—N21.9 (3)C2—C1—N3—C61.1 (4)
C3—C2—C5—N2179.4 (2)Cl1—C1—N3—C6178.90 (18)
C1—C2—C5—N1178.6 (2)N2—C6—N3—C10.5 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N1i0.862.072.927 (3)174
C6—H6···N3ii0.932.573.315 (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 formulaC6H4ClN3
Mr153.57
Crystal system, space groupMonoclinic, P21/n
Temperature (K)296
a, b, c (Å)10.8810 (19), 5.2783 (9), 12.751 (2)
β (°) 114.333 (3)
V3)667.3 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.49
Crystal size (mm)0.18 × 0.16 × 0.10
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.918, 0.953
No. of measured, independent and
observed [I > 2σ(I)] reflections
3597, 1273, 1166
Rint0.017
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.145, 1.00
No. of reflections1273
No. of parameters91
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N2—H2···N1i0.862.072.927 (3)174
C6—H6···N3ii0.932.573.315 (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

First citationAllen, 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
First citationChang, 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
First citationEnraf–Nonius (1985). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.
First citationNorth, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.  CrossRef IUCr Journals Web of Science
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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