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Acta Crystallogr Sect E Struct Rep Online. 2009 January 1; 65(Pt 1): o62–o63.
Published online 2008 December 10. doi:  10.1107/S1600536808041020
PMCID: PMC2967975

(Z)-Methyl 4-({3-[(2,5-dioxoimidazolidin-4-yl­idene)meth­yl]-1H-indol-1-yl}meth­yl)benzoate

Abstract

In the title compound, C21H17N3O4, pairs of mol­ecules form a planar[maximum deviation 0.0566 (9) Å] centrosymmetric imidazole dimer via two N—H(...)O hydrogen bonds. These dimeric units are linked by further N—H(...)O hydrogen bonds between the ester carbonyl group and the imidazolidine ring, formiing chains parallel to the c-axis direction. In addition, there are π–π stacking inter­actions between the planar imidazole pairs, with an inter­planar spacing of 3.301 (2) Å. There is a double bond with Z geometry connecting the imidazolidine and indole units.

Related literature

For general background to the radiosensitization activity of (Z)-2-(N-benzyl­indol-3-ylmethyl­ene)quinuclidin-3-one and (Z)-(±)-2-(N-benzyl­indol-3-ylmethyl­ene)quinuclidin-3-ol derivatives, see: Sekhar et al. (2003 [triangle]); Sonar et al., (2007 [triangle]). For related structures, see: Mason et al. (2003 [triangle]); Zarza et al. (1988 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-00o62-scheme1.jpg

Experimental

Crystal data

  • C21H17N3O4
  • M r = 375.38
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-00o62-efi1.jpg
  • a = 7.6390 (1) Å
  • b = 8.0013 (1) Å
  • c = 15.0405 (3) Å
  • α = 91.9853 (9)°
  • β = 96.2291 (9)°
  • γ = 104.4242 (9)°
  • V = 883.25 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 90.0 (2) K
  • 0.25 × 0.22 × 0.15 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997 [triangle]) T min = 0.976, T max = 0.985
  • 19513 measured reflections
  • 3997 independent reflections
  • 3595 reflections with I > 2σ(I)
  • R int = 0.015

Refinement

  • R[F 2 > 2σ(F 2)] = 0.043
  • wR(F 2) = 0.127
  • S = 1.07
  • 3997 reflections
  • 255 parameters
  • H-atom parameters constrained
  • Δρmax = 0.48 e Å−3
  • Δρmin = −0.34 e Å−3

Data collection: COLLECT (Nonius, 1998 [triangle]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO-SMN (Otwinowski & Minor, 1997 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP in SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97 and local procedures.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808041020/fj2166sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808041020/fj2166Isup2.hkl

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

Acknowledgments

This investigation was supported by NIH/National Cancer Institute grant PO1 CA104457 (to PAC) and by NSF MRI grant CHE 0319176 (to SP).

supplementary crystallographic information

Comment

In continuation of our work on the radiosensitization activity of (Z)-2-(N-benzylindol-3-ylmethylene)quinuclidin-3-one and (Z)-(±)-2-(N-benzylindol-3-ylmethylene) quinuclidin-3-ol derivatives (Sekhar et al., 2003; Sonar et al., 2007), we have undertaken the design, synthesis and structural analysis of a series of (N-benzylindol-3-ylmethylene)imidazolidine-2,4-dione analogs with different substituents on both indole moiety and on the benzene ring of the N-benzyl group. The primary goal for X-ray analysis of the title compound is to confirm the double-bond geometry and to obtain detailed information on the structural conformation of the molecule. This information will be useful in structure-activity relationship (SAR) analysis. The title compound was prepared by the reaction of methyl 4-((3-formyl-1H-indol-1-yl)methyl)benzoate with imidazolidine-2,4-dione in the presence of ammonium acetate in acetic acid at 391 K. The compound was crystallized from a mixture of methanol and ethylacetate. The molecular structure and the atom-numbering scheme are shown in Fig.1. The indole ring is planar with bond distances and angles comparable with those previously reported for other indole derivatives (Mason et al., 2003; Zarza, et al., 1988). The X-ray studies revealed that the title compound is the Z isomer. The C8—C9 bond is in a transoid geometry with respect to the C10—C14 bond. The olefinic bond (C9=C10) has a planar atomic arrangement, since the r.m.s. deviation from the mean plane passing through atoms C1, C8, C9, N11 is 0.0349 (6) Å. Deviations from ideal geometry are observed in the bond angles around atoms C9, C10 and N11 (130.48 (12)°) due to repulsion between the indole ring C1 hydrogen and imidazolidine ring N11 hydrogen. The imidazolidine ring, which makes a dihedral angle of 10.03 (7)° with the adjacent aromatic ring, presents very small distortions around atoms N11, C12, N13 and C14.

Significant intermolecular hydrogen-bonding interactions are found between N(11)—H(11)···O(12) and N(13)—H(13)···O(22), and molecules are linked into chains by N—H···O hydrogen bonding.

Experimental

A mixture of methyl 4-((3-formyl-1H-indol-1-yl)methyl)benzoate (0.5 g, 1.70 mmol), imidazolidine-2,4-dione (0.18 g, 1.80 mmol) and ammonium acetate (0.132 g, 1.71 mmol) was stirred in acetic acid (5 ml) at 391 K for 8 hrs. The reaction mixture was cooled to room temperature and the yellow solid that separated was collected by filtration, washed with cold water and dried to afford the crude product. Crystallization from methanol and ethyl acetate (1:1) afforded a yellow crystalline product of (Z)Methyl-4-((3-((2,5- dioxoimidazolidin-4-ylidene)methyl)-1H-indol-1-yl)methyl)benzoate that was suitable for X-ray analysis. 1H NMR (DMSO d6): δ 3.81 (s, 3H), 5.54 (s, 2H), 6.74 (s, 1H), 7.15–7.23 (m, 2H), 7.40–7.42 (d, 2H), 7.50–7.52 (d, 1H), 7.79–7.81 (d, 1H), 7.91–7.93 (d, 2H), 8.32 (s, 1H), 10.15 (bs, 1H), 11.06 (bs, 1H); 13C NMR (DMSO d6): δ 49.52, 52.2, 101.44, 109.26, 111.26, 119.22, 121.35, 123.44, 124.01, 127.29, 128.95, 129.35, 131.23, 136.28, 142.64, 155.93, 165.85, 167.12.

Refinement

H atoms were found in difference Fourier maps and subsequently placed in idealized positions with constrained distances of 0.98 Å (RCH3), 0.99 Å (R2CH2), 0.95 Å (CArH), 0.88 Å (N—H), and with Uiso(H) values set to either 1.2Ueq or 1.5Ueq (RCH3) of the attached atom.

Figures

Fig. 1.
A view of the molecule with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C21H17N3O4Z = 2
Mr = 375.38F(000) = 392
Triclinic, P1Dx = 1.411 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.6390 (1) ÅCell parameters from 3966 reflections
b = 8.0013 (1) Åθ = 1.0–27.5°
c = 15.0405 (3) ŵ = 0.10 mm1
α = 91.9853 (9)°T = 90 K
β = 96.2291 (9)°Block, colourless
γ = 104.4242 (9)°0.25 × 0.22 × 0.15 mm
V = 883.25 (2) Å3

Data collection

Nonius KappaCCD diffractometer3997 independent reflections
Radiation source: fine-focus sealed tube3595 reflections with I > 2σ(I)
graphiteRint = 0.015
Detector resolution: 18 pixels mm-1θmax = 27.4°, θmin = 1.4°
ω scans at fixed χ = 55°h = −9→9
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997)k = −10→10
Tmin = 0.976, Tmax = 0.985l = −19→19
19513 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.043H-atom parameters constrained
wR(F2) = 0.127w = 1/[σ2(Fo2) + (0.0697P)2 + 0.3949P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
3997 reflectionsΔρmax = 0.48 e Å3
255 parametersΔρmin = −0.34 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.090 (15)

Special details

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 > 2σ(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
N10.62738 (14)0.06683 (14)0.69424 (7)0.0179 (2)
C10.64933 (17)0.16626 (17)0.62219 (8)0.0189 (3)
H10.76320.22980.60660.023*
C20.44342 (17)−0.00489 (16)0.69679 (8)0.0173 (3)
C30.35580 (18)−0.11990 (17)0.75529 (9)0.0196 (3)
H30.4221−0.15620.80480.024*
C40.16793 (19)−0.17896 (17)0.73816 (9)0.0221 (3)
H40.1044−0.25930.77600.027*
C50.06985 (18)−0.12239 (18)0.66605 (9)0.0226 (3)
H5−0.0589−0.16430.65620.027*
C60.15795 (18)−0.00650 (18)0.60918 (9)0.0209 (3)
H60.09040.03310.56130.025*
C70.34801 (17)0.05157 (16)0.62314 (8)0.0177 (3)
C80.48188 (17)0.16104 (17)0.57534 (8)0.0181 (3)
C90.44195 (17)0.23455 (16)0.49230 (8)0.0187 (3)
H90.31770.20330.46730.022*
C100.55628 (18)0.34163 (16)0.44489 (8)0.0186 (3)
N110.74423 (15)0.41748 (15)0.46348 (7)0.0197 (3)
H110.81140.40570.51310.024*
O120.96568 (13)0.59079 (14)0.38998 (7)0.0276 (3)
C120.80892 (18)0.51160 (16)0.39495 (9)0.0198 (3)
N130.66123 (15)0.50316 (14)0.33104 (7)0.0205 (3)
H130.66770.55740.28110.025*
O140.35435 (13)0.36140 (13)0.31095 (7)0.0247 (2)
C140.50269 (18)0.39906 (16)0.35539 (8)0.0191 (3)
C150.77114 (17)0.06679 (17)0.76616 (8)0.0197 (3)
H15A0.89080.10130.74320.024*
H15B0.7557−0.05160.78680.024*
C160.76755 (17)0.19009 (17)0.84440 (8)0.0186 (3)
C170.77627 (19)0.36332 (18)0.83052 (9)0.0230 (3)
H170.78910.40450.77250.028*
C180.76628 (19)0.47605 (17)0.90102 (9)0.0226 (3)
H180.77180.59370.89100.027*
C190.74814 (17)0.41658 (17)0.98642 (8)0.0190 (3)
C200.7411 (2)0.24417 (18)1.00064 (9)0.0244 (3)
H200.72980.20331.05880.029*
C210.7508 (2)0.13161 (18)0.92977 (9)0.0242 (3)
H210.74590.01400.93980.029*
O220.70603 (16)0.48178 (14)1.13762 (7)0.0298 (3)
C220.73352 (17)0.53113 (17)1.06416 (9)0.0196 (3)
O230.75282 (15)0.69475 (13)1.04391 (6)0.0274 (3)
C230.7376 (2)0.8120 (2)1.11646 (10)0.0316 (4)
H23A0.61190.78391.13090.047*
H23B0.77090.93111.09820.047*
H23C0.81970.80051.16940.047*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0158 (5)0.0211 (5)0.0150 (5)0.0023 (4)0.0008 (4)−0.0007 (4)
C10.0186 (6)0.0219 (6)0.0150 (6)0.0023 (5)0.0034 (4)−0.0005 (5)
C20.0163 (6)0.0184 (6)0.0162 (6)0.0033 (5)0.0020 (4)−0.0038 (5)
C30.0216 (6)0.0186 (6)0.0180 (6)0.0039 (5)0.0034 (5)−0.0005 (5)
C40.0230 (7)0.0205 (6)0.0219 (6)0.0018 (5)0.0077 (5)−0.0007 (5)
C50.0168 (6)0.0256 (7)0.0236 (7)0.0016 (5)0.0044 (5)−0.0046 (5)
C60.0196 (6)0.0248 (7)0.0173 (6)0.0052 (5)0.0003 (5)−0.0022 (5)
C70.0189 (6)0.0196 (6)0.0141 (6)0.0040 (5)0.0029 (4)−0.0025 (4)
C80.0185 (6)0.0198 (6)0.0152 (6)0.0031 (5)0.0034 (4)−0.0011 (4)
C90.0194 (6)0.0184 (6)0.0176 (6)0.0040 (5)0.0025 (5)−0.0010 (5)
C100.0202 (6)0.0176 (6)0.0176 (6)0.0047 (5)0.0018 (5)−0.0010 (5)
N110.0199 (5)0.0237 (6)0.0156 (5)0.0054 (4)0.0020 (4)0.0028 (4)
O120.0211 (5)0.0310 (6)0.0260 (5)−0.0024 (4)0.0022 (4)0.0074 (4)
C120.0234 (6)0.0173 (6)0.0177 (6)0.0032 (5)0.0021 (5)0.0006 (5)
N130.0232 (6)0.0196 (5)0.0172 (5)0.0025 (4)0.0013 (4)0.0039 (4)
O140.0234 (5)0.0281 (5)0.0219 (5)0.0058 (4)−0.0005 (4)0.0062 (4)
C140.0222 (6)0.0180 (6)0.0181 (6)0.0066 (5)0.0036 (5)0.0011 (5)
C150.0170 (6)0.0242 (6)0.0174 (6)0.0056 (5)−0.0011 (5)−0.0013 (5)
C160.0151 (6)0.0222 (6)0.0174 (6)0.0041 (5)−0.0008 (4)−0.0009 (5)
C170.0283 (7)0.0230 (7)0.0158 (6)0.0032 (5)0.0021 (5)0.0024 (5)
C180.0300 (7)0.0185 (6)0.0180 (6)0.0037 (5)0.0018 (5)0.0021 (5)
C190.0187 (6)0.0206 (6)0.0166 (6)0.0038 (5)0.0000 (5)−0.0001 (5)
C200.0336 (8)0.0239 (7)0.0167 (6)0.0089 (6)0.0033 (5)0.0037 (5)
C210.0330 (7)0.0202 (6)0.0205 (6)0.0091 (5)0.0023 (5)0.0024 (5)
O220.0460 (7)0.0272 (5)0.0174 (5)0.0101 (5)0.0075 (4)0.0024 (4)
C220.0182 (6)0.0214 (6)0.0180 (6)0.0039 (5)−0.0010 (5)0.0012 (5)
O230.0444 (6)0.0197 (5)0.0185 (5)0.0090 (4)0.0046 (4)−0.0005 (4)
C230.0490 (10)0.0245 (7)0.0224 (7)0.0130 (7)0.0023 (6)−0.0047 (6)

Geometric parameters (Å, °)

N1—C11.3668 (17)C12—N131.3869 (17)
N1—C21.3846 (16)N13—C141.3819 (17)
N1—C151.4554 (16)N13—H130.8800
C1—C81.3821 (18)O14—C141.2137 (16)
C1—H10.9500C15—C161.5162 (17)
C2—C31.3951 (18)C15—H15A0.9900
C2—C71.4093 (18)C15—H15B0.9900
C3—C41.3866 (19)C16—C211.3898 (18)
C3—H30.9500C16—C171.3951 (19)
C4—C51.403 (2)C17—C181.3890 (19)
C4—H40.9500C17—H170.9500
C5—C61.3833 (19)C18—C191.3940 (18)
C5—H50.9500C18—H180.9500
C6—C71.3996 (18)C19—C201.3921 (19)
C6—H60.9500C19—C221.4916 (18)
C7—C81.4445 (17)C20—C211.3915 (19)
C8—C91.4340 (18)C20—H200.9500
C9—C101.3454 (18)C21—H210.9500
C9—H90.9500O22—C221.2083 (16)
C10—N111.4053 (17)C22—O231.3303 (16)
C10—C141.4858 (18)O23—C231.4475 (16)
N11—C121.3612 (17)C23—H23A0.9800
N11—H110.8800C23—H23B0.9800
O12—C121.2189 (17)C23—H23C0.9800
C1—N1—C2109.12 (11)C14—N13—H13124.2
C1—N1—C15124.49 (11)C12—N13—H13124.2
C2—N1—C15125.24 (11)O14—C14—N13126.35 (12)
N1—C1—C8110.17 (11)O14—C14—C10128.62 (12)
N1—C1—H1124.9N13—C14—C10105.00 (11)
C8—C1—H1124.9N1—C15—C16111.22 (10)
N1—C2—C3129.95 (12)N1—C15—H15A109.4
N1—C2—C7107.54 (11)C16—C15—H15A109.4
C3—C2—C7122.43 (12)N1—C15—H15B109.4
C4—C3—C2117.24 (12)C16—C15—H15B109.4
C4—C3—H3121.4H15A—C15—H15B108.0
C2—C3—H3121.4C21—C16—C17119.35 (12)
C3—C4—C5121.30 (12)C21—C16—C15120.72 (12)
C3—C4—H4119.3C17—C16—C15119.91 (11)
C5—C4—H4119.3C18—C17—C16120.43 (12)
C6—C5—C4120.95 (12)C18—C17—H17119.8
C6—C5—H5119.5C16—C17—H17119.8
C4—C5—H5119.5C17—C18—C19120.04 (12)
C5—C6—C7119.10 (12)C17—C18—H18120.0
C5—C6—H6120.5C19—C18—H18120.0
C7—C6—H6120.5C20—C19—C18119.66 (12)
C6—C7—C2118.93 (12)C20—C19—C22118.03 (12)
C6—C7—C8133.86 (12)C18—C19—C22122.31 (12)
C2—C7—C8107.19 (11)C21—C20—C19120.11 (12)
C1—C8—C9128.94 (12)C21—C20—H20119.9
C1—C8—C7105.98 (11)C19—C20—H20119.9
C9—C8—C7124.90 (12)C16—C21—C20120.42 (13)
C10—C9—C8128.91 (12)C16—C21—H21119.8
C10—C9—H9115.5C20—C21—H21119.8
C8—C9—H9115.5O22—C22—O23123.20 (12)
C9—C10—N11130.48 (12)O22—C22—C19124.14 (12)
C9—C10—C14124.45 (12)O23—C22—C19112.66 (11)
N11—C10—C14105.04 (11)C22—O23—C23115.26 (11)
C12—N11—C10111.28 (11)O23—C23—H23A109.5
C12—N11—H11124.4O23—C23—H23B109.5
C10—N11—H11124.4H23A—C23—H23B109.5
O12—C12—N11127.32 (12)O23—C23—H23C109.5
O12—C12—N13125.72 (12)H23A—C23—H23C109.5
N11—C12—N13106.95 (11)H23B—C23—H23C109.5
C14—N13—C12111.67 (11)
C2—N1—C1—C8−0.64 (14)C10—N11—C12—N131.94 (14)
C15—N1—C1—C8−168.87 (11)O12—C12—N13—C14178.35 (13)
C1—N1—C2—C3177.11 (13)N11—C12—N13—C14−2.48 (15)
C15—N1—C2—C3−14.8 (2)C12—N13—C14—O14−176.40 (13)
C1—N1—C2—C70.36 (14)C12—N13—C14—C101.99 (14)
C15—N1—C2—C7168.48 (11)C9—C10—C14—O14−0.3 (2)
N1—C2—C3—C4−176.00 (12)N11—C10—C14—O14177.59 (13)
C7—C2—C3—C40.32 (18)C9—C10—C14—N13−178.67 (12)
C2—C3—C4—C5−1.33 (19)N11—C10—C14—N13−0.75 (13)
C3—C4—C5—C60.5 (2)C1—N1—C15—C1694.54 (14)
C4—C5—C6—C71.38 (19)C2—N1—C15—C16−71.81 (15)
C5—C6—C7—C2−2.33 (18)N1—C15—C16—C21122.96 (13)
C5—C6—C7—C8175.72 (13)N1—C15—C16—C17−55.33 (16)
N1—C2—C7—C6178.56 (11)C21—C16—C17—C18−0.7 (2)
C3—C2—C7—C61.52 (18)C15—C16—C17—C18177.60 (12)
N1—C2—C7—C80.03 (14)C16—C17—C18—C190.3 (2)
C3—C2—C7—C8−177.01 (11)C17—C18—C19—C200.4 (2)
N1—C1—C8—C9−174.63 (12)C17—C18—C19—C22−178.91 (12)
N1—C1—C8—C70.63 (14)C18—C19—C20—C21−0.5 (2)
C6—C7—C8—C1−178.62 (14)C22—C19—C20—C21178.79 (12)
C2—C7—C8—C1−0.40 (14)C17—C16—C21—C200.6 (2)
C6—C7—C8—C9−3.1 (2)C15—C16—C21—C20−177.73 (12)
C2—C7—C8—C9175.11 (12)C19—C20—C21—C160.0 (2)
C1—C8—C9—C10−7.9 (2)C20—C19—C22—O22−4.2 (2)
C7—C8—C9—C10177.63 (13)C18—C19—C22—O22175.06 (13)
C8—C9—C10—N11−2.6 (2)C20—C19—C22—O23176.23 (12)
C8—C9—C10—C14174.74 (12)C18—C19—C22—O23−4.50 (18)
C9—C10—N11—C12177.01 (13)O22—C22—O23—C23−0.3 (2)
C14—C10—N11—C12−0.74 (14)C19—C22—O23—C23179.24 (11)
C10—N11—C12—O12−178.91 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N11—H11···O12i0.882.112.9658 (15)163
N13—H13···O22ii0.882.292.9699 (15)134

Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) x, y, z−1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2166).

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