4-Chloro-1H-pyrrolo­[2,3-d]pyrimidine

Abstract

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,

• a = 10.8810 (19) Å

• b = 5.2783 (9) Å

• c = 12.751 (2) Å

• β = 114.333 (3)°

• V = 667.3 (2) ų

• 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[F ² > 2σ(F ²)] = 0.052

• wR(F ²) = 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

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.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536812034095/su2492Isup3.cml

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

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) ; (ii) .

supplementary crystallographic information

Comment

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).

Experimental

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

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 U_iso(H) = 1.2U_eq(N,C).

Figures

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].

Crystal data

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

Data collection

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

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

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 (Ų)

	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)

Atomic displacement parameters (Ų)

	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)

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)

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.