organic compounds
Indomethacin methyl ester
aDepartment of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England, and Pfizer Institute for Pharmaceutical Materials Science, bInstitute of Chemical and Engineering Sciences, Ayer Rajah Crescent, Block 28, Unit 02-08, Singapore 139959, and Pfizer Institute for Pharmaceutical Materials Science, and cCambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
*Correspondence e-mail: avt21@cam.ac.uk
The cystal structure of the title compound [systematic name: methyl 1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indole-3-acetate], C20H18ClNO4, exhibits a short axis similar to another indomethacin analogue. Also observed in the structure is a packing of molecules influenced by weak C—H⋯O hydrogen bonds.
Comment
As part of an investigation into the crystallization of pharmaceutical compounds, the crystal structures of indomethacin derivatives are of interest. Numerous studies have been reported on various crystal structures of the drug indomethacin (γ-form: Kistenmacher & Marsh, 1972; α-form: Chen et al., 2002; t-butanol and methanol solvates: Joshi et al., 1998). In contrast, the structure of its methyl ester, (I), has not been reported to date. We report here its and describe the intermolecular interactions involved.
The ) comprises one molecule (Fig. 1). Although the of the indomethacin methyl ester differs significantly from that of the parent carboxylic acid, it bears some similarity to the structure of another indomethacin derivative, iodoindomethacin (Loll et al., 1996). Both crystal structures exhibit a relatively short axis [4.8326 (1) Å for the methyl ester derivative versus 4.7250 (10) Å for the iodo derivative]. In addition, both crystal structures show a halogen contact to a carbonyl O atom [Cl1⋯O4 = 3.575 (2) Å versus I1⋯O4 = 3.162 (5) Å].
of (IIn the absence of the carboxylic acid group of indomethacin, no strong O—H⋯O hydrogen bonding can be expected in the . Hydrogen-bond distances and angles are provided in Table 1.
of the methyl ester. Instead, C—H⋯O hydrogen bonds form a three-dimensional supramolecular network, as shown in Fig. 2Experimental
Indomethacin and anhydrous benzenesulfonic acid were obtained from Sigma–Aldrich and were used as received. Indomethacin (130 mg, 0.364 mmol) and benzensulfonic acid (115 mg, 0.727 mmol) were dissolved in methanol with heating. Crystals precipitated as the solution cooled to room temperature and were immediately isolated and dried.
Crystal data
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Refinement
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All H atoms were placed geometrically and treated using a riding model. The Uiso values for methyl H atoms were fixed at 1.5Ueq of the For all other H atoms, Uiso(H) = 1.2Ueq(carrier atom). The C—H distances of methyl groups were fixed at 0.98 Å; all other C—H distances were fixed at 0.95 Å.
Data collection: COLLECT (Nonius, 1998); cell HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP (Sheldrick, 1993) and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S1600536804004453/om6215sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804004453/om6215Isup2.hkl
Data collection: Collect (Nonius, 1998); cell
HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997b); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: XP (Sheldrick, 1993) and Diamond (Brandenburg, 1999); software used to prepare material for publication: SHELXL97.C20H18ClNO4 | Dx = 1.404 Mg m−3 |
Mr = 371.82 | Melting point: not measured K |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 19.0206 (5) Å | Cell parameters from 6724 reflections |
b = 4.8326 (1) Å | θ = 1.0–25.0° |
c = 19.3092 (8) Å | µ = 0.24 mm−1 |
β = 97.739 (1)° | T = 180 K |
V = 1758.72 (9) Å3 | Needle, yellow |
Z = 4 | 0.46 × 0.07 × 0.05 mm |
F(000) = 776 |
Nonius KappaCCD diffractometer | 3086 independent reflections |
Radiation source: fine-focus sealed tube | 2410 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.035 |
ω and φ scans | θmax = 25.0°, θmin = 3.6° |
Absorption correction: multi-scan Sortav (Blessing, 1995) | h = −22→22 |
Tmin = 0.946, Tmax = 0.985 | k = −5→5 |
10009 measured reflections | l = −22→23 |
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)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.117 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0481P)2 + 1.0445P] where P = (Fo2 + 2Fc2)/3 |
3086 reflections | (Δ/σ)max = 0.002 |
238 parameters | Δρmax = 0.31 e Å−3 |
0 restraints | Δρmin = −0.39 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.65787 (4) | −0.17803 (18) | 0.86754 (4) | 0.0706 (3) | |
O1 | 0.98228 (10) | 0.2360 (4) | 0.95373 (9) | 0.0550 (5) | |
O2 | 1.24396 (8) | 0.8532 (3) | 0.84051 (8) | 0.0436 (4) | |
O3 | 1.09430 (9) | 0.0986 (3) | 0.56653 (8) | 0.0458 (4) | |
O4 | 1.02616 (11) | 0.3946 (4) | 0.61588 (9) | 0.0613 (5) | |
N1 | 1.00383 (9) | 0.2127 (3) | 0.84188 (9) | 0.0299 (4) | |
C1 | 0.96165 (12) | 0.1665 (5) | 0.89405 (11) | 0.0355 (5) | |
C2 | 0.88813 (12) | 0.0526 (5) | 0.87820 (11) | 0.0354 (5) | |
C3 | 0.86722 (13) | −0.1409 (5) | 0.92464 (12) | 0.0431 (6) | |
H3 | 0.9013 | −0.2196 | 0.9596 | 0.052* | |
C4 | 0.79675 (14) | −0.2190 (5) | 0.92002 (13) | 0.0498 (7) | |
H4 | 0.7824 | −0.3554 | 0.9507 | 0.060* | |
C5 | 0.74766 (13) | −0.0969 (5) | 0.87051 (13) | 0.0451 (6) | |
C6 | 0.76742 (13) | 0.0955 (5) | 0.82406 (13) | 0.0451 (6) | |
H6 | 0.7329 | 0.1779 | 0.7901 | 0.054* | |
C7 | 0.83837 (12) | 0.1670 (5) | 0.82758 (12) | 0.0404 (6) | |
H7 | 0.8529 | 0.2953 | 0.7950 | 0.049* | |
C8 | 0.95660 (12) | −0.1570 (5) | 0.75198 (12) | 0.0377 (5) | |
H8A | 0.9761 | −0.2628 | 0.7156 | 0.057* | |
H8B | 0.9113 | −0.0739 | 0.7323 | 0.057* | |
H8C | 0.9491 | −0.2806 | 0.7905 | 0.057* | |
C9 | 1.09125 (12) | 0.0424 (4) | 0.68596 (10) | 0.0335 (5) | |
H9A | 1.0756 | −0.1523 | 0.6792 | 0.040* | |
H9B | 1.1438 | 0.0434 | 0.6931 | 0.040* | |
C10 | 1.06587 (12) | 0.2015 (4) | 0.62062 (11) | 0.0339 (5) | |
C11 | 1.00736 (11) | 0.0656 (4) | 0.77853 (10) | 0.0307 (5) | |
C12 | 1.26800 (13) | 1.0394 (5) | 0.89591 (13) | 0.0465 (6) | |
H12A | 1.3122 | 1.1275 | 0.8866 | 0.070* | |
H12B | 1.2765 | 0.9371 | 0.9401 | 0.070* | |
H12C | 1.2318 | 1.1815 | 0.8991 | 0.070* | |
C13 | 1.06544 (11) | 0.1519 (4) | 0.75071 (10) | 0.0302 (5) | |
C14 | 1.10167 (11) | 0.3605 (4) | 0.79639 (10) | 0.0286 (5) | |
C15 | 1.16259 (11) | 0.5171 (4) | 0.79317 (11) | 0.0321 (5) | |
H15 | 1.1895 | 0.4955 | 0.7555 | 0.039* | |
C16 | 1.18318 (11) | 0.7055 (4) | 0.84620 (11) | 0.0325 (5) | |
C17 | 1.14376 (11) | 0.7377 (4) | 0.90166 (11) | 0.0332 (5) | |
H17 | 1.1586 | 0.8689 | 0.9373 | 0.040* | |
C18 | 1.08335 (11) | 0.5814 (4) | 0.90559 (11) | 0.0332 (5) | |
H18 | 1.0564 | 0.6038 | 0.9432 | 0.040* | |
C19 | 1.06351 (11) | 0.3918 (4) | 0.85293 (10) | 0.0289 (5) | |
C20 | 1.07509 (17) | 0.2359 (7) | 0.50019 (13) | 0.0614 (8) | |
H20A | 1.0996 | 0.1470 | 0.4646 | 0.092* | |
H20B | 1.0890 | 0.4311 | 0.5045 | 0.092* | |
H20C | 1.0237 | 0.2227 | 0.4865 | 0.092* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0484 (4) | 0.0997 (6) | 0.0658 (5) | −0.0277 (4) | 0.0158 (3) | −0.0150 (4) |
O1 | 0.0611 (11) | 0.0762 (13) | 0.0302 (10) | −0.0255 (10) | 0.0156 (8) | −0.0075 (9) |
O2 | 0.0426 (10) | 0.0463 (10) | 0.0448 (10) | −0.0091 (7) | 0.0166 (8) | −0.0041 (7) |
O3 | 0.0578 (11) | 0.0550 (10) | 0.0263 (8) | 0.0105 (8) | 0.0117 (7) | −0.0011 (7) |
O4 | 0.0880 (14) | 0.0593 (12) | 0.0367 (10) | 0.0352 (11) | 0.0081 (9) | 0.0053 (8) |
N1 | 0.0325 (10) | 0.0326 (10) | 0.0253 (9) | 0.0025 (7) | 0.0065 (7) | 0.0004 (7) |
C1 | 0.0416 (13) | 0.0373 (12) | 0.0291 (12) | −0.0008 (10) | 0.0097 (10) | 0.0004 (9) |
C2 | 0.0394 (13) | 0.0363 (12) | 0.0324 (12) | −0.0015 (10) | 0.0124 (10) | −0.0048 (10) |
C3 | 0.0472 (14) | 0.0451 (14) | 0.0381 (13) | −0.0045 (11) | 0.0096 (11) | 0.0023 (11) |
C4 | 0.0604 (17) | 0.0491 (15) | 0.0429 (15) | −0.0159 (12) | 0.0181 (13) | −0.0009 (12) |
C5 | 0.0420 (14) | 0.0543 (15) | 0.0408 (14) | −0.0127 (11) | 0.0123 (11) | −0.0147 (12) |
C6 | 0.0422 (14) | 0.0513 (15) | 0.0414 (14) | 0.0002 (11) | 0.0043 (11) | −0.0049 (11) |
C7 | 0.0424 (14) | 0.0411 (13) | 0.0392 (14) | −0.0013 (10) | 0.0109 (11) | 0.0019 (10) |
C8 | 0.0403 (13) | 0.0369 (12) | 0.0358 (13) | 0.0031 (10) | 0.0046 (10) | −0.0046 (10) |
C9 | 0.0419 (13) | 0.0329 (12) | 0.0265 (11) | 0.0082 (9) | 0.0075 (9) | −0.0016 (9) |
C10 | 0.0385 (12) | 0.0353 (13) | 0.0286 (12) | 0.0004 (10) | 0.0067 (10) | −0.0044 (9) |
C11 | 0.0369 (12) | 0.0286 (11) | 0.0261 (11) | 0.0074 (9) | 0.0028 (9) | 0.0009 (8) |
C12 | 0.0437 (14) | 0.0465 (14) | 0.0492 (15) | −0.0077 (11) | 0.0063 (12) | −0.0006 (12) |
C13 | 0.0385 (12) | 0.0286 (11) | 0.0234 (11) | 0.0089 (9) | 0.0035 (9) | 0.0019 (8) |
C14 | 0.0335 (12) | 0.0297 (11) | 0.0231 (11) | 0.0083 (9) | 0.0054 (9) | 0.0042 (8) |
C15 | 0.0363 (12) | 0.0338 (12) | 0.0284 (12) | 0.0093 (9) | 0.0124 (9) | 0.0041 (9) |
C16 | 0.0340 (12) | 0.0313 (12) | 0.0332 (12) | 0.0033 (9) | 0.0078 (9) | 0.0065 (9) |
C17 | 0.0394 (12) | 0.0317 (11) | 0.0291 (12) | 0.0008 (9) | 0.0063 (10) | −0.0016 (9) |
C18 | 0.0380 (12) | 0.0361 (12) | 0.0272 (11) | 0.0026 (9) | 0.0104 (9) | −0.0012 (9) |
C19 | 0.0318 (11) | 0.0293 (11) | 0.0260 (11) | 0.0039 (8) | 0.0054 (9) | 0.0028 (9) |
C20 | 0.078 (2) | 0.081 (2) | 0.0256 (13) | 0.0024 (16) | 0.0099 (13) | 0.0064 (13) |
Cl1—C5 | 1.746 (2) | C8—H8B | 0.9800 |
O1—C1 | 1.214 (3) | C8—H8C | 0.9800 |
O2—C16 | 1.376 (3) | C9—C13 | 1.500 (3) |
O2—C12 | 1.425 (3) | C9—C10 | 1.501 (3) |
O3—C10 | 1.335 (3) | C9—H9A | 0.9900 |
O3—C20 | 1.445 (3) | C9—H9B | 0.9900 |
O4—C10 | 1.196 (3) | C11—C13 | 1.357 (3) |
N1—C1 | 1.388 (3) | C12—H12A | 0.9800 |
N1—C19 | 1.420 (3) | C12—H12B | 0.9800 |
N1—C11 | 1.424 (3) | C12—H12C | 0.9800 |
C1—C2 | 1.496 (3) | C13—C14 | 1.451 (3) |
C2—C7 | 1.381 (3) | C14—C15 | 1.393 (3) |
C2—C3 | 1.390 (3) | C14—C19 | 1.398 (3) |
C3—C4 | 1.384 (3) | C15—C16 | 1.386 (3) |
C3—H3 | 0.9500 | C15—H15 | 0.9500 |
C4—C5 | 1.376 (4) | C16—C17 | 1.396 (3) |
C4—H4 | 0.9500 | C17—C18 | 1.386 (3) |
C5—C6 | 1.379 (4) | C17—H17 | 0.9500 |
C6—C7 | 1.386 (3) | C18—C19 | 1.383 (3) |
C6—H6 | 0.9500 | C18—H18 | 0.9500 |
C7—H7 | 0.9500 | C20—H20A | 0.9800 |
C8—C11 | 1.490 (3) | C20—H20B | 0.9800 |
C8—H8A | 0.9800 | C20—H20C | 0.9800 |
C16—O2—C12 | 117.11 (17) | O4—C10—C9 | 126.3 (2) |
C10—O3—C20 | 116.21 (19) | O3—C10—C9 | 110.39 (18) |
C1—N1—C19 | 121.17 (17) | C13—C11—N1 | 108.76 (18) |
C1—N1—C11 | 129.92 (18) | C13—C11—C8 | 127.59 (19) |
C19—N1—C11 | 107.69 (16) | N1—C11—C8 | 123.55 (18) |
O1—C1—N1 | 120.0 (2) | O2—C12—H12A | 109.5 |
O1—C1—C2 | 118.03 (19) | O2—C12—H12B | 109.5 |
N1—C1—C2 | 121.79 (19) | H12A—C12—H12B | 109.5 |
C7—C2—C3 | 119.8 (2) | O2—C12—H12C | 109.5 |
C7—C2—C1 | 122.0 (2) | H12A—C12—H12C | 109.5 |
C3—C2—C1 | 117.2 (2) | H12B—C12—H12C | 109.5 |
C4—C3—C2 | 120.0 (2) | C11—C13—C14 | 108.55 (18) |
C4—C3—H3 | 120.0 | C11—C13—C9 | 126.6 (2) |
C2—C3—H3 | 120.0 | C14—C13—C9 | 124.73 (19) |
C5—C4—C3 | 119.2 (2) | C15—C14—C19 | 119.89 (19) |
C5—C4—H4 | 120.4 | C15—C14—C13 | 132.90 (19) |
C3—C4—H4 | 120.4 | C19—C14—C13 | 107.21 (18) |
C4—C5—C6 | 121.5 (2) | C16—C15—C14 | 118.56 (18) |
C4—C5—Cl1 | 119.7 (2) | C16—C15—H15 | 120.7 |
C6—C5—Cl1 | 118.8 (2) | C14—C15—H15 | 120.7 |
C5—C6—C7 | 119.0 (2) | O2—C16—C15 | 116.01 (18) |
C5—C6—H6 | 120.5 | O2—C16—C17 | 123.2 (2) |
C7—C6—H6 | 120.5 | C15—C16—C17 | 120.8 (2) |
C2—C7—C6 | 120.3 (2) | C18—C17—C16 | 121.1 (2) |
C2—C7—H7 | 119.8 | C18—C17—H17 | 119.5 |
C6—C7—H7 | 119.8 | C16—C17—H17 | 119.5 |
C11—C8—H8A | 109.5 | C19—C18—C17 | 117.84 (19) |
C11—C8—H8B | 109.5 | C19—C18—H18 | 121.1 |
H8A—C8—H8B | 109.5 | C17—C18—H18 | 121.1 |
C11—C8—H8C | 109.5 | C18—C19—C14 | 121.80 (19) |
H8A—C8—H8C | 109.5 | C18—C19—N1 | 130.35 (19) |
H8B—C8—H8C | 109.5 | C14—C19—N1 | 107.77 (17) |
C13—C9—C10 | 114.56 (17) | O3—C20—H20A | 109.5 |
C13—C9—H9A | 108.6 | O3—C20—H20B | 109.5 |
C10—C9—H9A | 108.6 | H20A—C20—H20B | 109.5 |
C13—C9—H9B | 108.6 | O3—C20—H20C | 109.5 |
C10—C9—H9B | 108.6 | H20A—C20—H20C | 109.5 |
H9A—C9—H9B | 107.6 | H20B—C20—H20C | 109.5 |
O4—C10—O3 | 123.3 (2) | ||
C19—N1—C1—O1 | −13.8 (3) | N1—C11—C13—C9 | 176.99 (18) |
C11—N1—C1—O1 | 152.0 (2) | C8—C11—C13—C9 | 0.6 (3) |
C19—N1—C1—C2 | 161.21 (19) | C10—C9—C13—C11 | 94.3 (3) |
C11—N1—C1—C2 | −33.0 (3) | C10—C9—C13—C14 | −89.3 (2) |
O1—C1—C2—C7 | 123.7 (2) | C11—C13—C14—C15 | −179.5 (2) |
N1—C1—C2—C7 | −51.4 (3) | C9—C13—C14—C15 | 3.5 (3) |
O1—C1—C2—C3 | −44.9 (3) | C11—C13—C14—C19 | 0.9 (2) |
N1—C1—C2—C3 | 140.0 (2) | C9—C13—C14—C19 | −176.05 (18) |
C7—C2—C3—C4 | 0.1 (3) | C19—C14—C15—C16 | −1.1 (3) |
C1—C2—C3—C4 | 169.0 (2) | C13—C14—C15—C16 | 179.3 (2) |
C2—C3—C4—C5 | −2.0 (4) | C12—O2—C16—C15 | −177.32 (19) |
C3—C4—C5—C6 | 1.9 (4) | C12—O2—C16—C17 | 2.3 (3) |
C3—C4—C5—Cl1 | −176.15 (19) | C14—C15—C16—O2 | 179.62 (18) |
C4—C5—C6—C7 | 0.0 (4) | C14—C15—C16—C17 | 0.0 (3) |
Cl1—C5—C6—C7 | 178.05 (18) | O2—C16—C17—C18 | −179.13 (19) |
C3—C2—C7—C6 | 1.8 (3) | C15—C16—C17—C18 | 0.5 (3) |
C1—C2—C7—C6 | −166.5 (2) | C16—C17—C18—C19 | 0.2 (3) |
C5—C6—C7—C2 | −1.8 (4) | C17—C18—C19—C14 | −1.4 (3) |
C20—O3—C10—O4 | 0.6 (3) | C17—C18—C19—N1 | −177.6 (2) |
C20—O3—C10—C9 | −179.1 (2) | C15—C14—C19—C18 | 1.9 (3) |
C13—C9—C10—O4 | −2.9 (3) | C13—C14—C19—C18 | −178.48 (19) |
C13—C9—C10—O3 | 176.79 (19) | C15—C14—C19—N1 | 178.81 (17) |
C1—N1—C11—C13 | −168.3 (2) | C13—C14—C19—N1 | −1.5 (2) |
C19—N1—C11—C13 | −1.1 (2) | C1—N1—C19—C18 | −13.2 (3) |
C1—N1—C11—C8 | 8.3 (3) | C11—N1—C19—C18 | 178.2 (2) |
C19—N1—C11—C8 | 175.50 (19) | C1—N1—C19—C14 | 170.21 (18) |
N1—C11—C13—C14 | 0.1 (2) | C11—N1—C19—C14 | 1.6 (2) |
C8—C11—C13—C14 | −176.28 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
C18—H18···O1i | 0.95 | 2.34 | 3.260 (3) | 162 |
C3—H3···O1ii | 0.95 | 2.59 | 3.480 (3) | 156 |
C9—H9A···O4iii | 0.99 | 2.62 | 3.565 (3) | 160 |
C15—H15···O2iv | 0.95 | 2.48 | 3.419 (2) | 170 |
Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+2, −y, −z+2; (iii) x, y−1, z; (iv) −x+5/2, y−1/2, −z+3/2. |
Acknowledgements
The authors are grateful for funding from the Pfizer Institute for Pharmaceutical Materials Science at the University of Cambridge. We thank Dr J. E. Davies for the data collection.
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