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5-Bromo-1H-pyrrolo­[2,3-b]pyridine

aDepartment of Inorganic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, CZ-771 46 Olomouc, Czech Republic
*Correspondence e-mail: zdenek.travnicek@upol.cz

(Received 9 February 2013; accepted 11 February 2013; online 16 February 2013)

In the title compound, C7H5BrN2, fused six-membered pyridine and five-membered pyrrole rings form the essentially planar aza­indole skeleton (r.m.s. deviation = 0.017 Å). In the crystal, pairs of N—H⋯N hydrogen bonds connect the mol­ecules into inversion dimers.

Related literature

For the structure of 7-aza­indole (C7H6N2), see: Dufour et al. (1990[Dufour, P., Dartiguenave, Y., Dartiguenave, M., Dufour, N., Lebuis, A. M., Belanger-Gariepy, F. & Beauchamp, A. L. (1990). Can. J. Chem. 68, 193-202.]) and for the structure of 3-iodo-7-aza­indole (C7H5IN2), see: Chou et al. (2000[Chou, P. T., Liao, J. H., Wei, C. Y., Yang, C. Y., Yu, W. S. & Chou, Y. H. (2000). J. Am. Chem. Soc. 122, 986-987.]). For the utilization of the title compound as the N-donor carrier ligand of highly cytotoxic platinum(II) dichlorido complexes, see: Štarha et al. (2012[Štarha, P., Trávníček, Z., Popa, A., Popa, I., Muchová, T. & Brabec, V. (2012). J. Inorg. Biochem. 115, 57-63.]).

[Scheme 1]

Experimental

Crystal data
  • C7H5BrN2

  • Mr = 197.04

  • Monoclinic, P 21 /c

  • a = 8.9082 (4) Å

  • b = 13.3632 (6) Å

  • c = 5.8330 (3) Å

  • β = 103.403 (5)°

  • V = 675.47 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 6.00 mm−1

  • T = 100 K

  • 0.24 × 0.24 × 0.12 mm

Data collection
  • Oxford Diffraction Xcalibur Sapphire2 CCD diffractometer

  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.327, Tmax = 0.533

  • 3977 measured reflections

  • 1185 independent reflections

  • 1047 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.092

  • S = 1.13

  • 1185 reflections

  • 91 parameters

  • H-atom parameters constrained

  • Δρmax = 1.69 e Å−3

  • Δρmin = −0.33 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯N7i 0.88 2.12 2.960 (5) 159
Symmetry code: (i) -x+1, -y+1, -z+1.

Data collection: CrysAlis CCD (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); data reduction: CrysAlis RED; 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: DIAMOND (Brandenburg et al., 2011[Brandenburg, K. (2011). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

The title compound 5-bromo-7-azaindole (5BrHaza), which is commercially available, was recently used, together with 3-chloro-7-azaindole and 3-iodo-7-azaindole, for the preparation of the platinum(II) dichlorido and oxalato (ox) complexes of the general formula cis-[PtCl2(nHaza)2], and [Pt(ox)(nHaza)2], respectively (Štarha et al., 2012); nHaza stands for the above-mentioned 7-azaindole halogeno-derivatives. The prepared Pt(II)-dichlorido complexes were found to be highly cytotoxic against the osteosarcoma (HOS), breast carcinoma (MCF7) and prostate carcinoma (LNCaP) human cancer cell lines. Particularly cis-[PtCl2(5BrHaza)2] exceeded the clinically applied platinum-based anticancer drug cisplatin, (cis-[PtCl2(NH3)2]), since its IC50 values (the concentration lethal for 50% of the tested cancer cells) equaled 2.5 µM (HOS; 34.2 µM for cisplatin), 2.0 µM (MCF7; 19.6 µM for cisplatin) and 1.5 µM (LNCaP; 3.8 µM for cisplatin).

The discrete molecules (Fig. 1) of the title compound contain fused six-membered pyridine and five-membered pyrrole rings forming the 7-azaindole skeleton. The planes fitted through the atoms of both rings form a dihedral angle of 2.09 (14)° (Fig. 2). The most deviated atoms from the mentioned planes are C6 (-0.012 (4) Å) and C3 (-0.006 (4) Å), respectively, while the most deviated atom from the plane fitted through nonhydrogen atoms of the 7-azaindole moiety is C5 (0.025 (4) Å).

The crystal structure contains the N—H···N hydrogen bonds and C—H···C non-covalent contacts (Fig. 3). Two N1—H1···N7 hydrogen bonds (Table 1) bind together two 5BrHaza molecules into a centrosymmetric dimer. The dimers are connected by C4—H4···C4 and C4—H···C5 non-covalent contacts (see Hydrogen-bond geometry) with four other dimers, which results in the formation of a 2D supramolecular array (Fig. 4).

The molecular structure of the title compound resembles literature precedents: 7-azaindole (Dufour et al., 1990) and 3-iodo-7-azaindole (Chou et al., 2000).

Related literature top

For the structure of 7-azaindole (C7H6N2), see: Dufour et al. (1990) and for the structure of 3-iodo-7-azaindole (C7H5IN2), see: Chou et al. (2000). For the utilization of the title compound as the N-donor carrier ligand of highly cytotoxic platinum(II) dichlorido complexes, see: Štarha et al. (2012).

Experimental top

The title compound was employed as a starting compound of the syntheses of cis-[PtCl2(5BrHaza)2] and [Pt(ox)(5BrHaza)2].0.75H2O (Štarha et al., 2012). These complexes were prepared by the reactions of the appropriate platinum(II) salt (K2[PtCl4] or K2[Pt(ox)2].2H2O; water solution, 0.5 mmol) with 1.0 mmol of 5BrHaza dissolved in ethanol at 50 °C. Microcrystals obtained as a main product during 2 days of stirring were filtered off and the filtrate was left to crystalize at laboratory temperature in the case of the oxalato-5BrHaza complex. The colourless crystals, which formed as a by-product during a slow evaporation in next 2 weeks, were collected and characterized by elemental analysis, NMR spectroscopy and single-crystal X-ray analysis. 1H NMR (DMF-d7, TMS, 298 K, p.p.m.): δ 11.91 (bs, 1H, HN1), 8.30 (d, J = 2.2 Hz, 1H, HC6), 8.20 (d, J = 2.0 Hz, 1H, HC4), 7.63 (t, J = 2.8 Hz, 1H, HC2), 6.50 (m, 1H, HC3). 13C NMR (DMF-d7, TMS, 298 K, p.p.m.): δ 147.5 (C8), 142.9 (C6), 130.3 (C4), 128.2 (C2), 122.1 (C7), 111.1 (C5), 100.0 (C3). 15N NMR (DMF-d7, relative to DMF, 298 K, p.p.m.): δ 140.9 [s, 11.93, HN1; s, 7.63, HC2; s, 6.50, HC3 (N1)], 277.5 [s, 8.30, HC6 (N7)]. Analysis calculated for C7H6BrN2: C 42.67, H 2.56, N 14.22%; found: C 42.58, H 2.62, N 14.09%. Elemental analysis (C, H, N) was performed on a Thermo Scientific Flash 2000 CHNO-S Analyzer. The 1H, 13C and 15N NMR spectra of the DMF-d7 solutions were collected at 300 K on a Varian 400 spectrometer at 400.00 MHz, 100.58 MHz and 40.53 MHz, respectively. 1H and 13C spectra were calibrated using tetramethylsilane (TMS) as a reference. The 15N NMR spectrum was measured relative to the DMF signals.

Refinement top

Hydrogen atoms were located in difference maps and refined using the riding model with C—H = 0.95 Å and N—H = 0.88 Å, and with Uiso(H) = 1.2Ueq(CH, NH). The maximum and minimum residual electron density peaks of 1.69 and -0.33 eÅ-3, respectively, were located 1.72 Å and 1.25 Å from the H6 and C6 atoms, respectively.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg et al., 2011); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the non-hydrogen atoms depicted as displacement ellipsoids at the 50% probability level and given with the atom numbering scheme.
[Figure 2] Fig. 2. A view of the title compound showing the mutual orientation of the six-membered pyridine (least-squares plane created through the C4, C5, C6, N7, C8 and C7 atoms; in blue) and five-membered pyrrole rings (least-squares plane created through the N1, C2, C3, C7 and C8 atoms; in green). The planes are nearly coplanar forming the dihedral angle of 2.09 (14)°.
[Figure 3] Fig. 3. Part of the crystal structure of the title compound (ball-and-stick model) showing the N—H···N hydrogen bonds (dashed green lines) and C—H···C non-covalent contacts (dashed orange lines). [Symmetry codes: (i) 1 - x, 1 - y, 1 - z; (ii) x, 0.5 - y, z - 0.5; (iii) x, 0.5 - y, z + 0.5; (iv) 1 - x, y + 0.5, 1.5 - z; (v) 1 - x, y + 0.5, 0.5 - z; (vi) 1 - x, y - 0.5, 0.5 - z; (vii) 1 - x, y - 0.5, 1.5 - z; (viii) x, 1.5 - y, z + 0.5; (ix) x, 1.5 - y, z - 0.5].
[Figure 4] Fig. 4. Part of the crystal structure of the title compound (ball-and-stick model) showing the formation of zigzag chains; dashed green lines indicate the N—H···N hydrogen bonds and dashed orange lines indicate C—H···C non-covalent contacts.
5-Bromo-1H-pyrrolo[2,3-b]pyridine top
Crystal data top
C7H5BrN2F(000) = 384
Mr = 197.04Dx = 1.938 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4062 reflections
a = 8.9082 (4) Åθ = 3.0–33.1°
b = 13.3632 (6) ŵ = 6.00 mm1
c = 5.8330 (3) ÅT = 100 K
β = 103.403 (5)°Prim, colourless
V = 675.47 (6) Å30.24 × 0.24 × 0.12 mm
Z = 4
Data collection top
Oxford Diffraction Xcalibur Sapphire2 CCD
diffractometer
1185 independent reflections
Radiation source: Enhance (Mo) X-ray Source1047 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
Detector resolution: 8.3611 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω scansh = 109
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2009)
k = 1515
Tmin = 0.327, Tmax = 0.533l = 66
3977 measured reflections
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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092H-atom parameters constrained
S = 1.13 w = 1/[σ2(Fo2) + (0.0578P)2 + 1.0071P]
where P = (Fo2 + 2Fc2)/3
1185 reflections(Δ/σ)max < 0.001
91 parametersΔρmax = 1.69 e Å3
0 restraintsΔρmin = 0.33 e Å3
Crystal data top
C7H5BrN2V = 675.47 (6) Å3
Mr = 197.04Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.9082 (4) ŵ = 6.00 mm1
b = 13.3632 (6) ÅT = 100 K
c = 5.8330 (3) Å0.24 × 0.24 × 0.12 mm
β = 103.403 (5)°
Data collection top
Oxford Diffraction Xcalibur Sapphire2 CCD
diffractometer
1185 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2009)
1047 reflections with I > 2σ(I)
Tmin = 0.327, Tmax = 0.533Rint = 0.022
3977 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.092H-atom parameters constrained
S = 1.13Δρmax = 1.69 e Å3
1185 reflectionsΔρmin = 0.33 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
Br10.02317 (5)0.34425 (3)0.26611 (7)0.0188 (2)
N10.6033 (4)0.4228 (3)0.3167 (6)0.0151 (7)
H10.63640.45190.45450.018*
C20.6944 (5)0.3858 (3)0.1738 (8)0.0168 (9)
H20.80390.38860.20960.020*
C30.6054 (5)0.3447 (3)0.0253 (8)0.0151 (9)
H30.64110.31350.14910.018*
C40.3052 (5)0.3375 (3)0.1574 (7)0.0143 (9)
H40.29420.30570.30600.017*
C50.1780 (5)0.3665 (3)0.0748 (7)0.0153 (9)
C60.1933 (5)0.4118 (3)0.1439 (7)0.0150 (9)
H60.10230.42810.19440.018*
N70.3299 (4)0.4335 (2)0.2865 (6)0.0153 (7)
C70.4494 (5)0.3572 (3)0.0129 (7)0.0148 (9)
C80.4527 (5)0.4061 (3)0.2052 (7)0.0150 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0135 (3)0.0203 (3)0.0197 (3)0.00003 (15)0.00191 (18)0.00174 (16)
N10.0141 (19)0.0143 (16)0.0167 (18)0.0019 (13)0.0034 (15)0.0021 (14)
C20.011 (2)0.015 (2)0.025 (2)0.0024 (16)0.0054 (18)0.0023 (18)
C30.015 (2)0.013 (2)0.018 (2)0.0006 (15)0.0045 (17)0.0006 (16)
C40.018 (2)0.010 (2)0.015 (2)0.0014 (15)0.0040 (18)0.0003 (15)
C50.017 (2)0.010 (2)0.018 (2)0.0010 (15)0.0015 (18)0.0021 (15)
C60.014 (2)0.010 (2)0.022 (2)0.0001 (15)0.0050 (17)0.0028 (16)
N70.0166 (18)0.0121 (16)0.0179 (18)0.0007 (13)0.0057 (15)0.0016 (14)
C70.021 (2)0.0087 (19)0.016 (2)0.0007 (15)0.0063 (18)0.0006 (15)
C80.014 (2)0.010 (2)0.021 (2)0.0002 (15)0.0032 (17)0.0033 (16)
Geometric parameters (Å, º) top
Br1—C51.902 (4)C4—C51.385 (6)
N1—C81.367 (6)C4—C71.389 (6)
N1—C21.383 (5)C4—H40.9500
N1—H10.8800C5—C61.390 (6)
C2—C31.361 (6)C6—N71.337 (5)
C2—H20.9500C6—H60.9500
C3—C71.418 (6)N7—C81.339 (5)
C3—H30.9500C7—C81.425 (6)
C8—N1—C2107.6 (4)C4—C5—Br1119.2 (3)
C8—N1—H1126.2C6—C5—Br1119.0 (3)
C2—N1—H1126.2N7—C6—C5123.1 (4)
C3—C2—N1110.6 (4)N7—C6—H6118.4
C3—C2—H2124.7C5—C6—H6118.4
N1—C2—H2124.7C6—N7—C8114.9 (3)
C2—C3—C7107.0 (4)C4—C7—C3136.6 (4)
C2—C3—H3126.5C4—C7—C8116.9 (4)
C7—C3—H3126.5C3—C7—C8106.4 (4)
C5—C4—C7116.9 (4)N7—C8—N1125.4 (4)
C5—C4—H4121.5N7—C8—C7126.3 (4)
C7—C4—H4121.5N1—C8—C7108.3 (4)
C4—C5—C6121.8 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N7i0.882.122.960 (5)159
C4—H4···C4ii0.952.823.738 (6)162
C4—H4···C5ii0.952.843.656 (6)144
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC7H5BrN2
Mr197.04
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)8.9082 (4), 13.3632 (6), 5.8330 (3)
β (°) 103.403 (5)
V3)675.47 (6)
Z4
Radiation typeMo Kα
µ (mm1)6.00
Crystal size (mm)0.24 × 0.24 × 0.12
Data collection
DiffractometerOxford Diffraction Xcalibur Sapphire2 CCD
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2009)
Tmin, Tmax0.327, 0.533
No. of measured, independent and
observed [I > 2σ(I)] reflections
3977, 1185, 1047
Rint0.022
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.092, 1.13
No. of reflections1185
No. of parameters91
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)1.69, 0.33

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg et al., 2011), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N7i0.882.122.960 (5)159
C4—H4···C4ii0.952.823.738 (6)162
C4—H4···C5ii0.952.843.656 (6)144
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1/2, z1/2.
 

Acknowledgements

This work was supported by Palacký University (grant No. PrF_2012_009). The authors wish to thank Dr Igor Popa for carrying out the NMR spectroscopy measurements and Mr Tomáš Šilha for performing the CHN elemental analysis.

References

First citationBrandenburg, K. (2011). DIAMOND. Crystal Impact GbR, Bonn, Germany.
First citationChou, P. T., Liao, J. H., Wei, C. Y., Yang, C. Y., Yu, W. S. & Chou, Y. H. (2000). J. Am. Chem. Soc. 122, 986–987.  Web of Science CSD CrossRef CAS
First citationDufour, P., Dartiguenave, Y., Dartiguenave, M., Dufour, N., Lebuis, A. M., Belanger-Gariepy, F. & Beauchamp, A. L. (1990). Can. J. Chem. 68, 193–202.  CrossRef CAS Web of Science
First citationOxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationŠtarha, P., Trávníček, Z., Popa, A., Popa, I., Muchová, T. & Brabec, V. (2012). J. Inorg. Biochem. 115, 57–63.  Web of Science PubMed
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals

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