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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o822.
Published online 2010 March 13. doi:  10.1107/S1600536810008822
PMCID: PMC2983947

4-Chloro-7-methoxy­methyl-2-phenyl-7H-pyrrolo[2,3-b]pyridine

Abstract

In the title compound, C15H13ClN2O, the phenyl group makes a dihedral angle of 7.91 (8)° with the pyrrole ring. The crystal structure forms a three-dimensional network stabilized by π–π inter­actions [centroid–centroid distances = 3.807 (1) Å] between the pyridine and phenyl rings and via inter­molecular C—H(...)O hydrogen bonds.

Related literature

Chlorination of 2-phenyl-1H-pyrrolo[2,3-b]pyridine was performed by an analogous procedure, see: Layek et al. (2009 [triangle]).

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Object name is e-66-0o822-scheme1.jpg

Experimental

Crystal data

  • C15H13ClN2O
  • M r = 272.72
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o822-efi1.jpg
  • a = 8.4785 (8) Å
  • b = 9.6576 (10) Å
  • c = 15.8560 (16) Å
  • V = 1298.3 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.29 mm−1
  • T = 173 K
  • 0.32 × 0.21 × 0.08 mm

Data collection

  • Bruker SMART APEXII diffractometer
  • 5977 measured reflections
  • 3084 independent reflections
  • 2667 reflections with I > 2σ(I)
  • R int = 0.028

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.079
  • S = 1.03
  • 3084 reflections
  • 173 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.22 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1299 Friedel pairs
  • Flack parameter: 0.02 (6)

Data collection: APEX2 (Bruker, 2006 [triangle]); cell refinement: SAINT (Bruker, 2006 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810008822/bt5211sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810008822/bt5211Isup2.hkl

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

Acknowledgments

The authors would like to thank the Federal Ministry of Education and Research, Germany, Merckle GmbH, Ulm, Germany, and the Fonds der Chemischen Industrie, Germany, for their generous support of this work.

supplementary crystallographic information

Comment

N-protection of 7-azaindoles is a often used and necessary procedure for further NH sensitive reactions. Many protecting procedures with 4-chloro-1H-pyrrolo[2,3-b]pyridine are kown in literature. By N-protection of 4-chloro-2-phenyl-1H-pyrrolo[2,3-b]pyridine with methoxymethylchloride, two regioisomeres are formed, the expected 4-chloro-1-(methoxymethyl)-2-phenyl-1H-pyrrolo[2,3-b]pyridine and the title compound in a ratio of 1:1.6. The title compound and its regioisomer demonstrate the delocalization of the deprotonated anionic 4-chloro-1-(methoxymethyl)-2-phenyl-1H-pyrrolo[2,3-b]pyridine species. The phenyl moiety encloses a dihedral angle of 7.91 (8)° toward the azaindole system. The crystal structure is characterized by intermolecular hydrogen bond C5—H5···O15 (2.32 Å) and intramolecular hydrogen interactions C13—H13···N1 (2.54 Å), C14—H14B···N1 (2.48°). Stabilization of the three dimensional network is performed by π -π interactions between the pyridine and the phenyl rings with centroid distances of 3.807 (1) Å (symmetry operator 1.5-x, 1-y, -0.5[minus-or-plus sign]z).

Experimental

2,5 g (11 mmol) 4-chloro-1-(methoxymethyl)-2-phenyl-1H-pyrrolo[2,3-b]pyridine was dissolved in dry THF (15 ml). After addition of 0.61 g (15 mmol) NaH (60% in mineral oil) the reaction mixture was stirred for 15 minutes at room temperature. 7.3 ml (15 mmol) methoxymethylchloride (2.1M in toluene) was added and the mixture was stirred for further 15 minutes. The reaction mixture was quenched with concentrated aqueous ammonium chloride solution. After extraction with ethyl acetate, the crude product was purified by flash chromatography. Crystals suitable for X-ray analysis were obtained by slow crystallisation from methanol.

Refinement

Hydrogen atoms attached to carbons were placed at calculated positions with C—H = 0.95 Å (aromatic) or 0.98–0.99 Å (sp3 C-atom). All H atoms were refined in the riding-model approximation with isotropic displacement parameters (set at 1.2–1.5 times of the Ueq of the parent atom).

Figures

Fig. 1.
View of compound I. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C15H13ClN2OF(000) = 568
Mr = 272.72Dx = 1.395 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1903 reflections
a = 8.4785 (8) Åθ = 2.5–26.5°
b = 9.6576 (10) ŵ = 0.29 mm1
c = 15.8560 (16) ÅT = 173 K
V = 1298.3 (2) Å3Block, yellow
Z = 40.32 × 0.21 × 0.08 mm

Data collection

Bruker SMART APEXII diffractometer2667 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.028
graphiteθmax = 27.9°, θmin = 2.5°
CCD scanh = −11→9
5977 measured reflectionsk = −11→12
3084 independent reflectionsl = −18→20

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.079w = 1/[σ2(Fo2) + (0.0335P)2 + 0.0915P] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
3084 reflectionsΔρmax = 0.21 e Å3
173 parametersΔρmin = −0.22 e Å3
0 restraintsAbsolute structure: Flack (1983), 1294 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.02 (6)

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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)

xyzUiso*/Ueq
Cl10.29645 (6)0.30454 (5)0.60634 (3)0.03778 (14)
N10.64025 (18)0.65066 (16)0.45780 (9)0.0247 (3)
C20.5784 (2)0.55036 (19)0.40408 (11)0.0237 (4)
C30.4866 (2)0.4524 (2)0.44513 (11)0.0258 (4)
H30.43520.37460.42080.031*
C3A0.4856 (2)0.4927 (2)0.53056 (11)0.0245 (4)
C40.4173 (2)0.44943 (18)0.60500 (12)0.0270 (4)
C50.4472 (2)0.5205 (2)0.68003 (11)0.0300 (4)
H50.39970.49090.73120.036*
C60.5454 (2)0.6330 (2)0.67921 (11)0.0299 (4)
H60.56690.67930.73080.036*
N70.61298 (17)0.68081 (16)0.60720 (9)0.0263 (3)
C7A0.5837 (2)0.61451 (19)0.53258 (11)0.0242 (4)
C80.6076 (2)0.56108 (19)0.31251 (10)0.0246 (4)
C90.5316 (2)0.4728 (2)0.25586 (13)0.0328 (5)
H90.46470.40170.27670.039*
C100.5525 (3)0.4874 (2)0.16978 (12)0.0367 (5)
H100.49950.42680.13210.044*
C110.6500 (3)0.5900 (2)0.13843 (12)0.0349 (5)
H110.66300.60080.07930.042*
C120.7285 (2)0.6765 (2)0.19367 (12)0.0329 (5)
H120.79800.74530.17250.040*
C130.7061 (2)0.6632 (2)0.28038 (11)0.0289 (4)
H130.75870.72450.31780.035*
C140.7186 (2)0.8020 (2)0.61091 (11)0.0305 (4)
H14A0.80050.78610.65440.037*
H14B0.77230.81310.55590.037*
O150.63663 (17)0.92266 (14)0.62990 (7)0.0332 (3)
C160.5440 (3)0.9729 (2)0.56147 (14)0.0435 (6)
H16A0.49211.05940.57810.065*
H16B0.46400.90390.54660.065*
H16C0.61230.99010.51270.065*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0405 (3)0.0307 (2)0.0422 (3)−0.0039 (2)0.0068 (2)0.0094 (2)
N10.0236 (8)0.0267 (8)0.0239 (8)−0.0023 (7)0.0015 (6)−0.0018 (6)
C20.0219 (9)0.0252 (9)0.0241 (8)0.0029 (8)−0.0003 (7)−0.0015 (7)
C30.0272 (10)0.0230 (9)0.0272 (9)0.0013 (8)−0.0015 (7)−0.0004 (7)
C3A0.0233 (9)0.0239 (9)0.0262 (9)0.0038 (8)−0.0022 (7)0.0026 (7)
C40.0257 (9)0.0239 (9)0.0313 (9)0.0040 (8)0.0024 (8)0.0059 (8)
C50.0341 (11)0.0309 (11)0.0251 (10)0.0071 (9)0.0047 (8)0.0063 (8)
C60.0337 (11)0.0344 (11)0.0215 (9)0.0066 (9)−0.0002 (8)−0.0019 (7)
N70.0258 (8)0.0294 (8)0.0237 (7)0.0014 (7)−0.0018 (6)−0.0014 (7)
C7A0.0222 (9)0.0261 (9)0.0242 (9)0.0026 (8)−0.0022 (7)0.0000 (7)
C80.0242 (10)0.0260 (10)0.0238 (8)0.0052 (8)0.0013 (7)−0.0008 (7)
C90.0377 (12)0.0317 (11)0.0290 (10)−0.0023 (9)0.0015 (8)0.0001 (8)
C100.0430 (13)0.0395 (12)0.0276 (10)0.0049 (11)−0.0036 (8)−0.0056 (8)
C110.0397 (12)0.0418 (12)0.0233 (9)0.0141 (10)0.0025 (8)0.0027 (8)
C120.0301 (11)0.0364 (11)0.0323 (10)0.0053 (10)0.0070 (8)0.0084 (8)
C130.0259 (10)0.0311 (10)0.0297 (9)0.0020 (9)0.0013 (8)−0.0005 (7)
C140.0276 (10)0.0328 (9)0.0311 (9)−0.0026 (10)−0.0024 (8)−0.0067 (9)
O150.0412 (8)0.0321 (7)0.0263 (7)0.0032 (7)0.0014 (5)−0.0073 (5)
C160.0458 (14)0.0366 (13)0.0480 (13)0.0034 (12)−0.0096 (10)0.0018 (10)

Geometric parameters (Å, °)

Cl1—C41.7345 (19)C8—C91.396 (3)
N1—C7A1.326 (2)C9—C101.383 (3)
N1—C21.393 (2)C9—H90.9500
C2—C31.387 (3)C10—C111.383 (3)
C2—C81.476 (2)C10—H100.9500
C3—C3A1.409 (2)C11—C121.381 (3)
C3—H30.9500C11—H110.9500
C3A—C41.379 (3)C12—C131.394 (3)
C3A—C7A1.441 (3)C12—H120.9500
C4—C51.396 (3)C13—H130.9500
C5—C61.369 (3)C14—O151.390 (2)
C5—H50.9500C14—H14A0.9900
C6—N71.358 (2)C14—H14B0.9900
C6—H60.9500O15—C161.425 (2)
N7—C7A1.368 (2)C16—H16A0.9800
N7—C141.475 (2)C16—H16B0.9800
C8—C131.389 (3)C16—H16C0.9800
C7A—N1—C2103.15 (15)C10—C9—C8120.91 (19)
C3—C2—N1113.49 (16)C10—C9—H9119.5
C3—C2—C8127.11 (16)C8—C9—H9119.5
N1—C2—C8119.31 (16)C11—C10—C9120.27 (19)
C2—C3—C3A105.44 (16)C11—C10—H10119.9
C2—C3—H3127.3C9—C10—H10119.9
C3A—C3—H3127.3C12—C11—C10119.57 (18)
C4—C3A—C3137.84 (18)C12—C11—H11120.2
C4—C3A—C7A118.06 (16)C10—C11—H11120.2
C3—C3A—C7A104.08 (15)C11—C12—C13120.28 (19)
C3A—C4—C5120.28 (17)C11—C12—H12119.9
C3A—C4—Cl1120.18 (14)C13—C12—H12119.9
C5—C4—Cl1119.54 (14)C8—C13—C12120.59 (17)
C6—C5—C4119.48 (17)C8—C13—H13119.7
C6—C5—H5120.3C12—C13—H13119.7
C4—C5—H5120.3O15—C14—N7111.71 (14)
N7—C6—C5122.29 (17)O15—C14—H14A109.3
N7—C6—H6118.9N7—C14—H14A109.3
C5—C6—H6118.9O15—C14—H14B109.3
C6—N7—C7A119.43 (16)N7—C14—H14B109.3
C6—N7—C14119.50 (15)H14A—C14—H14B107.9
C7A—N7—C14121.07 (15)C14—O15—C16113.35 (14)
N1—C7A—N7125.76 (17)O15—C16—H16A109.5
N1—C7A—C3A113.83 (15)O15—C16—H16B109.5
N7—C7A—C3A120.40 (15)H16A—C16—H16B109.5
C13—C8—C9118.36 (17)O15—C16—H16C109.5
C13—C8—C2120.75 (16)H16A—C16—H16C109.5
C9—C8—C2120.84 (17)H16B—C16—H16C109.5
C7A—N1—C2—C3−0.8 (2)C14—N7—C7A—C3A177.31 (16)
C7A—N1—C2—C8176.10 (15)C4—C3A—C7A—N1−178.06 (17)
N1—C2—C3—C3A1.3 (2)C3—C3A—C7A—N10.7 (2)
C8—C2—C3—C3A−175.36 (16)C4—C3A—C7A—N72.8 (3)
C2—C3—C3A—C4177.3 (2)C3—C3A—C7A—N7−178.39 (16)
C2—C3—C3A—C7A−1.13 (19)C3—C2—C8—C13−178.33 (18)
C3—C3A—C4—C5180.0 (2)N1—C2—C8—C135.2 (3)
C7A—C3A—C4—C5−1.8 (3)C3—C2—C8—C94.5 (3)
C3—C3A—C4—Cl11.1 (3)N1—C2—C8—C9−171.98 (17)
C7A—C3A—C4—Cl1179.34 (13)C13—C8—C9—C10−0.7 (3)
C3A—C4—C5—C6−0.3 (3)C2—C8—C9—C10176.57 (18)
Cl1—C4—C5—C6178.58 (14)C8—C9—C10—C110.3 (3)
C4—C5—C6—N71.5 (3)C9—C10—C11—C121.0 (3)
C5—C6—N7—C7A−0.4 (3)C10—C11—C12—C13−1.8 (3)
C5—C6—N7—C14−179.51 (17)C9—C8—C13—C12−0.2 (3)
C2—N1—C7A—N7179.07 (17)C2—C8—C13—C12−177.44 (17)
C2—N1—C7A—C3A0.0 (2)C11—C12—C13—C81.4 (3)
C6—N7—C7A—N1179.26 (18)C6—N7—C14—O15−68.9 (2)
C14—N7—C7A—N1−1.7 (3)C7A—N7—C14—O15111.99 (17)
C6—N7—C7A—C3A−1.8 (3)N7—C14—O15—C16−73.6 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C5—H5···O15i0.952.323.237 (2)162

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5211).

References

  • Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst.32, 115–119.
  • Bruker (2006). APEX2 and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Layek, M., Gajare, V., Kalita, D., Islam, A., Mukkanti, K. & Pal, M. (2009). Tetrahedron, 65, 4814–4819
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst D65, 148–155. [PMC free article] [PubMed]

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