organic compounds
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
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
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Refinement
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Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell 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
10.1107/S1600536812034095/su2492sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812034095/su2492Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812034095/su2492Isup3.cml
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
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.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).
Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell
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).C6H4ClN3 | F(000) = 312 |
Mr = 153.57 | Dx = 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 |
Enraf–Nonius CAD-4 diffractometer | 1166 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.017 |
Graphite monochromator | θmax = 26.0°, θmin = 3.2° |
ω/2θ scans | h = −13→11 |
Absorption correction: ψ scan (North et al., 1968) | k = −6→6 |
Tmin = 0.918, Tmax = 0.953 | l = −14→15 |
3597 measured reflections | 3 standard reflections every 200 reflections |
1273 independent reflections | intensity decay: 1% |
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(Fo2) + (0.0781P)2 + 0.6149P] where P = (Fo2 + 2Fc2)/3 |
1273 reflections | (Δ/σ)max < 0.001 |
91 parameters | Δρmax = 0.58 e Å−3 |
0 restraints | Δρmin = −0.43 e Å−3 |
C6H4ClN3 | V = 667.3 (2) Å3 |
Mr = 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)° |
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 = 0.953 | 3 standard reflections every 200 reflections |
3597 measured reflections | intensity decay: 1% |
1273 independent reflections |
R[F2 > 2σ(F2)] = 0.052 | 0 restraints |
wR(F2) = 0.145 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.58 e Å−3 |
1273 reflections | Δρmin = −0.43 e Å−3 |
91 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
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) |
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) |
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) |
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 |
Mr | 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) |
Tmin, Tmax | 0.918, 0.953 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3597, 1273, 1166 |
Rint | 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 |
Δρmax, Δρmin (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).
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
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).