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ISSN: 2056-9890

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

aEberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany, bUniversity Mainz, Duesbergweg 10-14, 55099 Mainz, Germany, and cc-a-i-r biosciences GmbH, Paul-Ehrlich-Strasse 15, 72076 Tübingen, Germany
*Correspondence e-mail: stefan.laufer@uni-tuebingen.de

(Received 8 March 2010; accepted 8 March 2010; online 13 March 2010)

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 ππ 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[Layek, M., Gajare, V., Kalita, D., Islam, A., Mukkanti, K. & Pal, M. (2009). Tetrahedron, 65, 4814-4819]).

[Scheme 1]

Experimental

Crystal data
  • C15H13ClN2O

  • Mr = 272.72

  • Orthorhombic, P 21 21 21

  • 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)

  • Rint = 0.028

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1299 Friedel pairs

  • Flack parameter: 0.02 (6)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C5—H5⋯O15i 0.95 2.32 3.237 (2) 162
Symmetry code: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: APEX2 (Bruker, 2006[Bruker (2006). APEX2 and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2006[Bruker (2006). APEX2 and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999[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.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: PLATON.

Supporting information


Comment top

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, -0.5z).

Related literature top

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

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. View of compound I. Displacement ellipsoids are drawn at the 50% probability level.
4-Chloro-7-methoxymethyl-2-phenyl-7H-pyrrolo[2,3-b]pyridine top
Crystal data top
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 top
Bruker SMART APEXII
diffractometer
2667 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.028
Graphite monochromatorθmax = 27.9°, θmin = 2.5°
CCD scanh = 119
5977 measured reflectionsk = 1112
3084 independent reflectionsl = 1820
Refinement top
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) = 0.079 w = 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 methodsAbsolute structure parameter: 0.02 (6)
Crystal data top
C15H13ClN2OV = 1298.3 (2) Å3
Mr = 272.72Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.4785 (8) ŵ = 0.29 mm1
b = 9.6576 (10) ÅT = 173 K
c = 15.8560 (16) Å0.32 × 0.21 × 0.08 mm
Data collection top
Bruker SMART APEXII
diffractometer
2667 reflections with I > 2σ(I)
5977 measured reflectionsRint = 0.028
3084 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.079Δρmax = 0.21 e Å3
S = 1.03Δρmin = 0.22 e Å3
3084 reflectionsAbsolute structure: Flack (1983), 1294 Friedel pairs
173 parametersAbsolute structure parameter: 0.02 (6)
0 restraints
Special details top

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) top
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) top
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, º) top
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—C30.8 (2)C14—N7—C7A—C3A177.31 (16)
C7A—N1—C2—C8176.10 (15)C4—C3A—C7A—N1178.06 (17)
N1—C2—C3—C3A1.3 (2)C3—C3A—C7A—N10.7 (2)
C8—C2—C3—C3A175.36 (16)C4—C3A—C7A—N72.8 (3)
C2—C3—C3A—C4177.3 (2)C3—C3A—C7A—N7178.39 (16)
C2—C3—C3A—C7A1.13 (19)C3—C2—C8—C13178.33 (18)
C3—C3A—C4—C5180.0 (2)N1—C2—C8—C135.2 (3)
C7A—C3A—C4—C51.8 (3)C3—C2—C8—C94.5 (3)
C3—C3A—C4—Cl11.1 (3)N1—C2—C8—C9171.98 (17)
C7A—C3A—C4—Cl1179.34 (13)C13—C8—C9—C100.7 (3)
C3A—C4—C5—C60.3 (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—C7A0.4 (3)C10—C11—C12—C131.8 (3)
C5—C6—N7—C14179.51 (17)C9—C8—C13—C120.2 (3)
C2—N1—C7A—N7179.07 (17)C2—C8—C13—C12177.44 (17)
C2—N1—C7A—C3A0.0 (2)C11—C12—C13—C81.4 (3)
C6—N7—C7A—N1179.26 (18)C6—N7—C14—O1568.9 (2)
C14—N7—C7A—N11.7 (3)C7A—N7—C14—O15111.99 (17)
C6—N7—C7A—C3A1.8 (3)N7—C14—O15—C1673.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···O15i0.952.323.237 (2)162
Symmetry code: (i) x+1, y1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC15H13ClN2O
Mr272.72
Crystal system, space groupOrthorhombic, P212121
Temperature (K)173
a, b, c (Å)8.4785 (8), 9.6576 (10), 15.8560 (16)
V3)1298.3 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.29
Crystal size (mm)0.32 × 0.21 × 0.08
Data collection
DiffractometerBruker SMART APEXII
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5977, 3084, 2667
Rint0.028
(sin θ/λ)max1)0.659
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.079, 1.03
No. of reflections3084
No. of parameters173
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.21, 0.22
Absolute structureFlack (1983), 1294 Friedel pairs
Absolute structure parameter0.02 (6)

Computer programs: APEX2 (Bruker, 2006), SAINT (Bruker, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···O15i0.952.323.237 (2)162
Symmetry code: (i) x+1, y1/2, z+3/2.
 

Acknowledgements

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.

References

First citationAltomare, 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.  Web of Science CrossRef CAS IUCr Journals
First citationBruker (2006). APEX2 and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals
First citationLayek, M., Gajare, V., Kalita, D., Islam, A., Mukkanti, K. & Pal, M. (2009). Tetrahedron, 65, 4814–4819  Web of Science CrossRef CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals

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