organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

2-[5-Bromo-1-(3-chloro­benz­yl)-2-methyl-1H-indol-3-yl]acetic acid

aEberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany, and bUniversity Mainz, Institut of Organic Chemistry, Duesbergweg 10-14, 55099 Mainz, Germany
*Correspondence e-mail: stefan.laufer@uni-tuebingen.de

(Received 12 November 2012; accepted 13 November 2012; online 24 November 2012)

In the title compound, C18H15BrClNO2, the indole ring system forms a dihedral angle of 86.9 (2)° with the 3-chloro­benzyl ring. In the crystal, mol­ecules form inversion dimers connected via pairs of O—H⋯O hydrogen bonds.

Related literature

For biological activity of inhibitors for the microsomal prostaglandin E2 synthase-1 (mPGES-1) and 5-lipoxygenase (5-LO), see: Elkady et al. (2012[Elkady, M., Niess, R., Schaible, A. M., Bauer, J., Luderer, S., Ambrosi, G., Werz, O. & Laufer, S. A. (2012). J. Med. Chem. 55, 8958-8962.]). For details of the synthesis, see: Maguire et al. (2001[Maguire, A. R., Plunkett, S. J., Papot, S., Clynes, M., O'Connor, R. & Touhey, S. (2001). Bioorg. Med. Chem. 9, 745-762.]).

[Scheme 1]

Experimental

Crystal data
  • C18H15BrClNO2

  • Mr = 392.67

  • Triclinic, [P \overline 1]

  • a = 8.5386 (11) Å

  • b = 10.0157 (10) Å

  • c = 11.0821 (12) Å

  • α = 109.221 (8)°

  • β = 106.229 (9)°

  • γ = 101.886 (9)°

  • V = 811.52 (16) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 2.71 mm−1

  • T = 298 K

  • 0.44 × 0.15 × 0.12 mm

Data collection
  • Stoe IPDS 2T diffractometer

  • Absorption correction: integration (X-RED; Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA and X-RED. Stoe & Cie GmbH, Darmstadt, Germany.]) Tmin = 0.388, Tmax = 0.785

  • 9139 measured reflections

  • 4400 independent reflections

  • 2791 reflections with I > 2σ(I)

  • Rint = 0.040

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.150

  • S = 1.02

  • 4400 reflections

  • 209 parameters

  • H-atom parameters constrained

  • Δρmax = 0.72 e Å−3

  • Δρmin = −0.69 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O18—H18⋯O17i 0.82 1.87 2.679 (3) 170
Symmetry code: (i) -x+2, -y+1, -z+2.

Data collection: X-AREA (Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA and X-RED. Stoe & Cie GmbH, Darmstadt, Germany.]); cell refinement: X-AREA; data reduction: X-RED (Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA and X-RED. Stoe & Cie GmbH, Darmstadt, Germany.]); 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

We synthesized and evaluated inhibitors for the microsomal prostaglandin E2 synthase-1 (mPGES-1) and 5-lipoxygenase (5-LO) (Elkady et al., 2012). The title compound was synthesized to obtain a template which leads to series of different derivates of the indole scaffold.

The indole ring is oriented with dihedral angle of 86.9 (2)° with the 3-chlorobenzyl ring in the crystal structure. Each two molecules form centrosymmetrical dimers connected via O18–H18···O17 hydrogen bridges (O18···O17 2.679 (3) Å) (Tab.1).

Related literature top

For biological activity of inhibitors for the microsomal prostaglandin E2 synthase-1 (mPGES-1) and 5-lipoxygenase (5-LO), see: Elkady et al. (2012). For details of the synthesis, see: Maguire et al. (2001).

Experimental top

0.2 g (0.74 mmol) of 2-(5-bromo-2-methyl-1H-indol-3-yl) acetic acid were dissolved in 5 ml dry dimethylformamide. Then 60 mg of Sodium hydride were slowly added and the mixture was stirred under argon at 273 K for 30 min (Maguire et al., 2001). Then, 0.18 ml (1.48 mmol) of 3-chlorobenzyl chloride were dissolved in 3 ml of dry dimethylformamide and this was then slowly added to the mixture and stirred for 1 h at 273 K. The reaction was stopped by quenching with ice cooled water; the pH was adjusted to 1 by 5 N aqueous hydrochloric acid. The product was extracted with ethyl acetate three times, dried over anhydrous sodium sulfate and finally concentrated under vacuum. The product was purified by washing with methanol. Crystals of the title compound were obtained by slow evaporation of methanol at room temperature.

Refinement top

Hydrogen atoms were placed at calculated positions with O—H = 0.82 Å, C—H = 0.95 Å (aromatic) or 0.99–1.00 Å (sp3 C-atom). All H atoms were refined with isotropic displacement parameters set to 1.2–1.5 times of the Ueq of the parent atom.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2010); cell refinement: X-AREA (Stoe & Cie, 2010); data reduction: X-RED (Stoe & Cie, 2010); 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.
2-[5-Bromo-1-(3-chlorobenzyl)-2-methyl-1H-indol-3-yl]acetic acid top
Crystal data top
C18H15BrClNO2Z = 2
Mr = 392.67F(000) = 396
Triclinic, P1Dx = 1.607 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5386 (11) ÅCell parameters from 6836 reflections
b = 10.0157 (10) Åθ = 2.4–29.3°
c = 11.0821 (12) ŵ = 2.71 mm1
α = 109.221 (8)°T = 298 K
β = 106.229 (9)°Block, colourless
γ = 101.886 (9)°0.44 × 0.15 × 0.12 mm
V = 811.52 (16) Å3
Data collection top
Stoe IPDS 2T
diffractometer
4400 independent reflections
Radiation source: sealed Tube2791 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.040
Detector resolution: 6.67 pixels mm-1θmax = 29.3°, θmin = 2.4°
rotation method scansh = 1111
Absorption correction: integration
(X-RED; Stoe & Cie, 2010)
k = 1312
Tmin = 0.388, Tmax = 0.785l = 1515
9139 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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.150H-atom parameters constrained
S = 1.02 w = 1/[σ2(Fo2) + (0.069P)2 + 0.4677P]
where P = (Fo2 + 2Fc2)/3
4400 reflections(Δ/σ)max < 0.001
209 parametersΔρmax = 0.72 e Å3
0 restraintsΔρmin = 0.69 e Å3
Crystal data top
C18H15BrClNO2γ = 101.886 (9)°
Mr = 392.67V = 811.52 (16) Å3
Triclinic, P1Z = 2
a = 8.5386 (11) ÅMo Kα radiation
b = 10.0157 (10) ŵ = 2.71 mm1
c = 11.0821 (12) ÅT = 298 K
α = 109.221 (8)°0.44 × 0.15 × 0.12 mm
β = 106.229 (9)°
Data collection top
Stoe IPDS 2T
diffractometer
4400 independent reflections
Absorption correction: integration
(X-RED; Stoe & Cie, 2010)
2791 reflections with I > 2σ(I)
Tmin = 0.388, Tmax = 0.785Rint = 0.040
9139 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.150H-atom parameters constrained
S = 1.02Δρmax = 0.72 e Å3
4400 reflectionsΔρmin = 0.69 e Å3
209 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
Br10.98960 (7)0.99173 (4)0.68263 (5)0.0811 (2)
Cl10.82521 (16)0.14242 (15)0.02826 (13)0.0943 (4)
N10.5804 (3)0.3419 (3)0.3758 (2)0.0436 (5)
C1A0.6557 (4)0.4936 (3)0.4301 (3)0.0398 (6)
C20.6079 (4)0.5993 (4)0.3871 (3)0.0478 (7)
H20.50970.57140.30940.057*
C30.7091 (5)0.7457 (4)0.4622 (3)0.0520 (8)
H30.68010.81880.43510.062*
C40.8553 (5)0.7865 (4)0.5788 (3)0.0516 (7)
C50.9056 (4)0.6835 (4)0.6232 (3)0.0465 (7)
H51.00370.71300.70150.056*
C5A0.8048 (4)0.5337 (3)0.5472 (3)0.0396 (6)
C60.8162 (4)0.3989 (3)0.5604 (3)0.0426 (6)
C70.6776 (4)0.2843 (3)0.4540 (3)0.0458 (7)
C80.4319 (4)0.2570 (4)0.2463 (3)0.0527 (7)
H8A0.34320.30380.24710.063*
H8B0.38480.15640.23870.063*
C90.4776 (4)0.2482 (4)0.1228 (3)0.0476 (7)
C100.6134 (4)0.2012 (4)0.1056 (3)0.0521 (7)
H100.67780.17240.16920.063*
C110.6520 (5)0.1976 (4)0.0080 (3)0.0602 (9)
C120.5554 (6)0.2388 (5)0.1038 (3)0.0733 (12)
H120.58330.23660.17970.088*
C130.4217 (6)0.2818 (5)0.0869 (4)0.0765 (12)
H130.35600.30830.15190.092*
C140.3804 (5)0.2871 (5)0.0259 (3)0.0644 (9)
H140.28710.31690.03670.077*
C150.9604 (5)0.3856 (4)0.6627 (3)0.0514 (7)
H15A1.06810.44300.66460.062*
H15B0.95480.28160.63020.062*
C160.9669 (4)0.4356 (3)0.8074 (3)0.0436 (6)
O170.8593 (3)0.4791 (3)0.8448 (2)0.0632 (7)
O181.1017 (3)0.4268 (4)0.8893 (2)0.0717 (8)
H181.10120.45490.96750.108*
C190.6253 (6)0.1216 (4)0.4211 (4)0.0663 (10)
H19A0.70000.10430.49280.099*
H19B0.63390.06820.33490.099*
H19C0.50830.08710.41410.099*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.1083 (4)0.0471 (2)0.0743 (3)0.0105 (2)0.0368 (3)0.01569 (18)
Cl10.0830 (8)0.0973 (8)0.0888 (8)0.0194 (6)0.0543 (7)0.0096 (6)
N10.0509 (14)0.0486 (13)0.0299 (10)0.0130 (11)0.0149 (10)0.0167 (10)
C1A0.0468 (15)0.0489 (15)0.0299 (11)0.0190 (12)0.0183 (11)0.0185 (11)
C20.0545 (18)0.0626 (18)0.0394 (14)0.0274 (15)0.0207 (13)0.0289 (14)
C30.071 (2)0.0532 (17)0.0516 (17)0.0312 (16)0.0327 (17)0.0310 (15)
C40.067 (2)0.0444 (15)0.0469 (16)0.0165 (14)0.0307 (15)0.0172 (13)
C50.0494 (17)0.0543 (17)0.0339 (13)0.0152 (14)0.0171 (12)0.0160 (12)
C5A0.0476 (16)0.0494 (15)0.0287 (11)0.0198 (12)0.0188 (11)0.0184 (11)
C60.0575 (18)0.0530 (16)0.0280 (12)0.0266 (14)0.0198 (12)0.0213 (11)
C70.0638 (19)0.0467 (15)0.0363 (13)0.0209 (14)0.0264 (13)0.0201 (12)
C80.0466 (17)0.0630 (19)0.0382 (14)0.0075 (15)0.0134 (13)0.0171 (14)
C90.0476 (17)0.0497 (16)0.0304 (12)0.0046 (13)0.0091 (12)0.0103 (11)
C100.0514 (18)0.0563 (18)0.0382 (14)0.0070 (14)0.0151 (13)0.0149 (13)
C110.061 (2)0.0509 (17)0.0470 (17)0.0009 (15)0.0243 (16)0.0027 (14)
C120.092 (3)0.074 (2)0.0359 (16)0.000 (2)0.0260 (19)0.0160 (16)
C130.091 (3)0.094 (3)0.0468 (19)0.026 (3)0.023 (2)0.037 (2)
C140.072 (2)0.076 (2)0.0431 (17)0.0236 (19)0.0166 (16)0.0258 (16)
C150.064 (2)0.068 (2)0.0361 (14)0.0342 (17)0.0225 (14)0.0267 (14)
C160.0503 (17)0.0512 (16)0.0351 (13)0.0191 (13)0.0156 (12)0.0235 (12)
O170.0651 (15)0.104 (2)0.0362 (11)0.0458 (15)0.0230 (11)0.0328 (12)
O180.0711 (17)0.121 (2)0.0421 (12)0.0550 (17)0.0221 (12)0.0410 (14)
C190.096 (3)0.0489 (18)0.059 (2)0.0244 (19)0.032 (2)0.0248 (16)
Geometric parameters (Å, º) top
Br1—C41.897 (3)C8—H8B0.9700
Cl1—C111.727 (4)C9—C101.376 (5)
N1—C1A1.365 (4)C9—C141.380 (5)
N1—C71.378 (4)C10—C111.379 (5)
N1—C81.458 (4)C10—H100.9300
C1A—C21.384 (4)C11—C121.384 (6)
C1A—C5A1.411 (4)C12—C131.340 (7)
C2—C31.364 (5)C12—H120.9300
C2—H20.9300C13—C141.379 (5)
C3—C41.391 (5)C13—H130.9300
C3—H30.9300C14—H140.9300
C4—C51.375 (5)C15—C161.495 (4)
C5—C5A1.390 (4)C15—H15A0.9700
C5—H50.9300C15—H15B0.9700
C5A—C61.425 (4)C16—O171.210 (4)
C6—C71.370 (4)C16—O181.291 (4)
C6—C151.485 (4)O18—H180.8200
C7—C191.485 (4)C19—H19A0.9600
C8—C91.506 (4)C19—H19B0.9600
C8—H8A0.9700C19—H19C0.9600
C1A—N1—C7109.2 (2)C10—C9—C8120.8 (3)
C1A—N1—C8123.7 (3)C14—C9—C8119.1 (3)
C7—N1—C8126.7 (3)C9—C10—C11118.6 (3)
N1—C1A—C2130.6 (3)C9—C10—H10120.7
N1—C1A—C5A107.6 (2)C11—C10—H10120.7
C2—C1A—C5A121.8 (3)C10—C11—C12121.0 (4)
C3—C2—C1A118.1 (3)C10—C11—Cl1118.8 (3)
C3—C2—H2121.0C12—C11—Cl1120.2 (3)
C1A—C2—H2121.0C13—C12—C11119.7 (3)
C2—C3—C4120.6 (3)C13—C12—H12120.1
C2—C3—H3119.7C11—C12—H12120.1
C4—C3—H3119.7C12—C13—C14120.6 (4)
C5—C4—C3122.4 (3)C12—C13—H13119.7
C5—C4—Br1118.3 (3)C14—C13—H13119.7
C3—C4—Br1119.3 (2)C13—C14—C9119.9 (4)
C4—C5—C5A117.8 (3)C13—C14—H14120.0
C4—C5—H5121.1C9—C14—H14120.0
C5A—C5—H5121.1C6—C15—C16117.1 (3)
C5—C5A—C1A119.4 (3)C6—C15—H15A108.0
C5—C5A—C6133.6 (3)C16—C15—H15A108.0
C1A—C5A—C6107.0 (3)C6—C15—H15B108.0
C7—C6—C5A106.9 (2)C16—C15—H15B108.0
C7—C6—C15127.0 (3)H15A—C15—H15B107.3
C5A—C6—C15125.8 (3)O17—C16—O18123.3 (3)
C6—C7—N1109.2 (3)O17—C16—C15124.6 (3)
C6—C7—C19129.3 (3)O18—C16—C15112.0 (3)
N1—C7—C19121.4 (3)C16—O18—H18109.5
N1—C8—C9112.4 (3)C7—C19—H19A109.5
N1—C8—H8A109.1C7—C19—H19B109.5
C9—C8—H8A109.1H19A—C19—H19B109.5
N1—C8—H8B109.1C7—C19—H19C109.5
C9—C8—H8B109.1H19A—C19—H19C109.5
H8A—C8—H8B107.9H19B—C19—H19C109.5
C10—C9—C14120.1 (3)
C7—N1—C1A—C2179.0 (3)C15—C6—C7—C196.7 (5)
C8—N1—C1A—C25.5 (5)C1A—N1—C7—C60.5 (3)
C7—N1—C1A—C5A0.5 (3)C8—N1—C7—C6173.8 (3)
C8—N1—C1A—C5A174.1 (3)C1A—N1—C7—C19178.9 (3)
N1—C1A—C2—C3179.9 (3)C8—N1—C7—C197.8 (5)
C5A—C1A—C2—C30.4 (4)C1A—N1—C8—C971.6 (4)
C1A—C2—C3—C40.3 (5)C7—N1—C8—C9100.8 (4)
C2—C3—C4—C50.5 (5)N1—C8—C9—C1051.7 (4)
C2—C3—C4—Br1178.6 (2)N1—C8—C9—C14128.7 (3)
C3—C4—C5—C5A0.1 (5)C14—C9—C10—C111.6 (5)
Br1—C4—C5—C5A179.2 (2)C8—C9—C10—C11178.8 (3)
C4—C5—C5A—C1A0.8 (4)C9—C10—C11—C120.7 (5)
C4—C5—C5A—C6179.5 (3)C9—C10—C11—Cl1178.7 (3)
N1—C1A—C5A—C5179.4 (2)C10—C11—C12—C130.5 (6)
C2—C1A—C5A—C51.0 (4)Cl1—C11—C12—C13179.8 (3)
N1—C1A—C5A—C60.3 (3)C11—C12—C13—C140.7 (7)
C2—C1A—C5A—C6179.2 (3)C12—C13—C14—C90.1 (7)
C5—C5A—C6—C7179.6 (3)C10—C9—C14—C131.3 (6)
C1A—C5A—C6—C70.1 (3)C8—C9—C14—C13179.1 (4)
C5—C5A—C6—C155.5 (5)C7—C6—C15—C16109.5 (4)
C1A—C5A—C6—C15174.9 (3)C5A—C6—C15—C1676.6 (4)
C5A—C6—C7—N10.2 (3)C6—C15—C16—O173.5 (5)
C15—C6—C7—N1175.1 (3)C6—C15—C16—O18176.6 (3)
C5A—C6—C7—C19178.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O18—H18···O17i0.821.872.679 (3)170
Symmetry code: (i) x+2, y+1, z+2.

Experimental details

Crystal data
Chemical formulaC18H15BrClNO2
Mr392.67
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)8.5386 (11), 10.0157 (10), 11.0821 (12)
α, β, γ (°)109.221 (8), 106.229 (9), 101.886 (9)
V3)811.52 (16)
Z2
Radiation typeMo Kα
µ (mm1)2.71
Crystal size (mm)0.44 × 0.15 × 0.12
Data collection
DiffractometerStoe IPDS 2T
diffractometer
Absorption correctionIntegration
(X-RED; Stoe & Cie, 2010)
Tmin, Tmax0.388, 0.785
No. of measured, independent and
observed [I > 2σ(I)] reflections
9139, 4400, 2791
Rint0.040
(sin θ/λ)max1)0.689
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.150, 1.02
No. of reflections4400
No. of parameters209
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.72, 0.69

Computer programs: X-AREA (Stoe & Cie, 2010), X-RED (Stoe & Cie, 2010), 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
O18—H18···O17i0.821.872.679 (3)170
Symmetry code: (i) x+2, y+1, z+2.
 

Acknowledgements

This research was supported financially by the Lan­desgraduiertenförderung program of the Ministry of Science, Research and Arts of the state of Baden-Württemberg, Germany.

References

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