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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o428.
Published online 2010 January 23. doi:  10.1107/S1600536810002175
PMCID: PMC2979679

2-(1H-Indol-3-yl)-4,4,5,5-tetra­methyl­imidazolidine-1-oxyl 3-oxide

Abstract

In the title compound, C15H18N3O2, the plane of the indole ring system is twisted with respect to the plane of the nitronyl nitroxide moiety, exhibiting a dihedral angle of 21.61 (6)°. The crystal packing is stabilized by N—H(...)O hydrogen bonds and weak C—H(...)O inter­actions.

Related literature

For the preparation of nitronyl nitroxides, see: Ullman et al. (1974 [triangle]). For their biological activity, see: Soule et al. (2007 [triangle]) and their coordination properties, see: Masuda et al. (2009 [triangle]). For related structures, see: Iqbal et al. (2009 [triangle]); Qin et al. (2009 [triangle]); Tanaka et al. (2007 [triangle]).

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Object name is e-66-0o428-scheme1.jpg

Experimental

Crystal data

  • C15H18N3O2
  • M r = 272.32
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o428-efi1.jpg
  • a = 15.0810 (15) Å
  • b = 8.7700 (8) Å
  • c = 10.6108 (10) Å
  • V = 1403.4 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 296 K
  • 0.37 × 0.29 × 0.18 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2007 [triangle]) T min = 0.968, T max = 0.984
  • 6651 measured reflections
  • 1323 independent reflections
  • 1208 reflections with I > 2σ(I)
  • R int = 0.023

Refinement

  • R[F 2 > 2σ(F 2)] = 0.025
  • wR(F 2) = 0.067
  • S = 1.06
  • 1323 reflections
  • 186 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.13 e Å−3
  • Δρmin = −0.09 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 1998 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810002175/fl2283sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810002175/fl2283Isup2.hkl

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

Acknowledgments

We thank the Natural Science Foundation of China (grant Nos. 20972189, 20802092, 20802091) for financial support.

supplementary crystallographic information

Comment

Nitronyl nitroxides, stable organic radicals, that were originally synthesized more than 30 years ago (Ullman et al.1974), have recently received considerable attention (Iqbal et al. 2009; Qin et al. 2009; Tanaka et al. 2007) because of their biological properities as anticancer, antiradiation and antioxidation(Soule et al., 2007). The title compound itself can be used to form coordination compounds with many metal cations, such as Mn2+, Cu2+ and Ni2+ leading to some interesting magentic materials (Masuda, et al., 2009). The molecular structure of the title compound is shown in Fig1. The indole moiety and the nitronyl nitroxide ring are twisted with respect to each other making a dihedral angle of 21.6 (6)°. One of the oxygen atoms (O2) of the nitronyl nitroxide moietie acts as an acceptor in a hydrogen bond from the N—H group of an adjacent molecule and both oxygens (O1 and O2) are acceptors in weak C-H···O intermolecular interactions that help stabilize the crystal packing (Table 1).

Experimental

2,3-Dimethyl-2,3-bis(hydroxylamino) butane (1.48 g, 10.0 mmol) and 1H-indoline-3-carbaldehyde (1.47 g, 10.0 mmol) were dissolved in methanol. The reaction was stirred for 15 h at reflux temperature, then cooled to room temperature and filtered. The resulting white powder was washed by methanol and suspended in a mixed solution of dichloromethane (30.0 ml) and water (30.0 ml). Then the reaction mixture was added to an aqueous solution of NaIO4 and stirred for 15 min in an ice bath to give a blue solution. The aqueous phase was extracted with CH2Cl2 and the organic layer was combined and dried over MgSO4. Then the solvent was removed to give a dark blue residue which was purified by flash column chromatography with the elution of n-hexane/ ethyl acetate (1:3) to yield the title compound (I) as a dark blue powder. Single crystals of (I) were obtained from a mixed solution of n-heptane and dichloromethane (the ratio of volume is 1 to 1).

Refinement

In the structure, all the H atoms were discernible in the difference Fourier maps. However, they were constrained by riding model approximation. C—Hmethyl=0.96 Å; C—Haryl=0.93 Å; UisoHmethyl and UisoHaryl are 1.5 U eq(C) and 1.2 U eq (C), respectively. Since it was not possible to obtain information on the handedness of the molecule from the experimental data the Friedel euivalents were merged before the final cycles of refinement.

Figures

Fig. 1.
Molecular structure of the title compound (I), showing the atom labeling scheme. Displacement ellipsoids are drawn at the 30% probability level.

Crystal data

C15H18N3O2F(000) = 580
Mr = 272.32Dx = 1.289 Mg m3
Orthorhombic, Pca21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2acCell parameters from 2598 reflections
a = 15.0810 (15) Åθ = 2.7–24.4°
b = 8.7700 (8) ŵ = 0.09 mm1
c = 10.6108 (10) ÅT = 296 K
V = 1403.4 (2) Å3Block, blue
Z = 40.37 × 0.29 × 0.18 mm

Data collection

Bruker APEXII CCD area-detector diffractometer1323 independent reflections
Radiation source: fine-focus sealed tube1208 reflections with I > 2σ(I)
graphiteRint = 0.023
phi and ω scansθmax = 25.1°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2007)h = −14→17
Tmin = 0.968, Tmax = 0.984k = −8→10
6651 measured reflectionsl = −12→12

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.067w = 1/[σ2(Fo2) + (0.0394P)2 + 0.1053P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
1323 reflectionsΔρmax = 0.13 e Å3
186 parametersΔρmin = −0.09 e Å3
1 restraintExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0146 (19)

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 > 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.we could not determine the absolute configuration,because there is no atom heavier than Si in the molecular

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
N1−0.01319 (14)1.0261 (2)0.9413 (2)0.0605 (5)
H1−0.00871.09281.00040.073*
N20.11909 (10)0.60749 (18)0.83997 (15)0.0393 (4)
N30.05128 (10)0.62465 (17)0.65920 (15)0.0381 (4)
O10.14925 (11)0.64081 (18)0.94892 (14)0.0579 (4)
O20.01465 (11)0.68277 (17)0.56075 (14)0.0545 (4)
C1−0.08282 (15)1.0156 (2)0.8579 (2)0.0534 (6)
C2−0.16017 (18)1.1028 (3)0.8506 (3)0.0731 (8)
H2−0.17071.18250.90640.088*
C3−0.21965 (16)1.0666 (3)0.7587 (4)0.0795 (9)
H3−0.27151.12340.75160.095*
C4−0.20480 (15)0.9465 (3)0.6750 (3)0.0692 (7)
H4−0.24630.92550.61260.083*
C5−0.12892 (14)0.8583 (2)0.6839 (2)0.0529 (6)
H5−0.12010.77690.62920.063*
C6−0.06560 (13)0.8930 (2)0.7760 (2)0.0442 (5)
C70.01895 (13)0.8304 (2)0.81520 (18)0.0407 (5)
C80.04679 (15)0.9165 (2)0.9167 (2)0.0515 (5)
H80.09910.90100.96140.062*
C90.06218 (12)0.6932 (2)0.77161 (18)0.0363 (4)
C100.15347 (12)0.4734 (2)0.76668 (19)0.0385 (4)
C110.24518 (16)0.5183 (2)0.7176 (2)0.0523 (5)
H11A0.23950.60180.65970.079*
H11B0.27150.43280.67520.079*
H11C0.28210.54830.78700.079*
C120.15962 (15)0.3356 (2)0.8531 (2)0.0516 (5)
H12A0.20430.35320.91580.077*
H12B0.17490.24710.80450.077*
H12C0.10350.31950.89360.077*
C130.08199 (13)0.4624 (2)0.66190 (19)0.0381 (4)
C140.00154 (14)0.3668 (2)0.6989 (2)0.0516 (5)
H14A−0.01830.39650.78130.077*
H14B0.01760.26090.69970.077*
H14C−0.04530.38290.63910.077*
C150.11578 (16)0.4160 (3)0.5331 (2)0.0556 (6)
H15A0.06740.41500.47430.083*
H15B0.14150.31610.53790.083*
H15C0.15980.48760.50540.083*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0810 (13)0.0386 (10)0.0620 (12)0.0000 (9)0.0137 (11)−0.0174 (10)
N20.0440 (9)0.0423 (8)0.0315 (8)−0.0009 (7)0.0003 (7)−0.0031 (7)
N30.0481 (9)0.0330 (8)0.0333 (8)0.0030 (7)−0.0032 (7)0.0023 (7)
O10.0670 (9)0.0679 (10)0.0389 (8)0.0047 (7)−0.0128 (7)−0.0112 (8)
O20.0774 (10)0.0452 (8)0.0407 (8)0.0126 (7)−0.0113 (8)0.0051 (6)
C10.0613 (13)0.0344 (11)0.0644 (15)−0.0023 (9)0.0182 (12)−0.0009 (10)
C20.0771 (18)0.0385 (12)0.104 (2)0.0098 (11)0.0325 (17)0.0013 (14)
C30.0534 (14)0.0547 (14)0.130 (3)0.0105 (11)0.0192 (18)0.0178 (18)
C40.0492 (13)0.0600 (14)0.098 (2)−0.0007 (11)0.0023 (14)0.0130 (15)
C50.0485 (11)0.0439 (11)0.0663 (15)−0.0032 (9)0.0053 (11)0.0049 (11)
C60.0487 (10)0.0304 (10)0.0535 (12)−0.0032 (8)0.0117 (10)0.0034 (9)
C70.0485 (11)0.0329 (10)0.0406 (11)−0.0040 (8)0.0070 (8)−0.0021 (8)
C80.0614 (13)0.0411 (11)0.0520 (13)−0.0036 (10)0.0062 (11)−0.0070 (10)
C90.0405 (9)0.0333 (9)0.0351 (10)−0.0032 (8)0.0014 (8)0.0005 (9)
C100.0418 (10)0.0375 (10)0.0363 (9)0.0025 (7)0.0029 (8)0.0009 (9)
C110.0440 (10)0.0571 (12)0.0560 (12)−0.0003 (10)0.0081 (10)−0.0009 (12)
C120.0584 (13)0.0488 (12)0.0474 (12)0.0065 (9)−0.0017 (10)0.0091 (11)
C130.0464 (10)0.0323 (9)0.0357 (9)0.0031 (8)0.0015 (8)−0.0008 (8)
C140.0540 (11)0.0415 (11)0.0592 (13)−0.0070 (9)−0.0065 (11)−0.0003 (10)
C150.0734 (15)0.0521 (12)0.0412 (12)0.0127 (11)0.0007 (11)−0.0085 (10)

Geometric parameters (Å, °)

N1—C81.346 (3)C7—C81.381 (3)
N1—C11.377 (3)C7—C91.444 (3)
N1—H10.8600C8—H80.9300
N2—O11.276 (2)C10—C121.519 (3)
N2—C91.352 (2)C10—C111.529 (3)
N2—C101.502 (2)C10—C131.552 (3)
N3—O21.287 (2)C11—H11A0.9600
N3—C91.346 (2)C11—H11B0.9600
N3—C131.496 (2)C11—H11C0.9600
C1—C21.397 (3)C12—H12A0.9600
C1—C61.407 (3)C12—H12B0.9600
C2—C31.362 (5)C12—H12C0.9600
C2—H20.9300C13—C151.515 (3)
C3—C41.396 (4)C13—C141.526 (3)
C3—H30.9300C14—H14A0.9600
C4—C51.384 (3)C14—H14B0.9600
C4—H40.9300C14—H14C0.9600
C5—C61.400 (3)C15—H15A0.9600
C5—H50.9300C15—H15B0.9600
C6—C71.449 (3)C15—H15C0.9600
C8—N1—C1109.91 (19)N2—C10—C12109.33 (16)
C8—N1—H1125.0N2—C10—C11106.68 (15)
C1—N1—H1125.0C12—C10—C11110.80 (17)
O1—N2—C9125.79 (16)N2—C10—C13100.34 (14)
O1—N2—C10121.68 (16)C12—C10—C13115.19 (16)
C9—N2—C10112.14 (16)C11—C10—C13113.58 (17)
O2—N3—C9126.49 (15)C10—C11—H11A109.5
O2—N3—C13121.66 (15)C10—C11—H11B109.5
C9—N3—C13111.73 (15)H11A—C11—H11B109.5
N1—C1—C2129.5 (2)C10—C11—H11C109.5
N1—C1—C6107.89 (19)H11A—C11—H11C109.5
C2—C1—C6122.6 (3)H11B—C11—H11C109.5
C3—C2—C1117.5 (3)C10—C12—H12A109.5
C3—C2—H2121.2C10—C12—H12B109.5
C1—C2—H2121.2H12A—C12—H12B109.5
C2—C3—C4121.7 (2)C10—C12—H12C109.5
C2—C3—H3119.2H12A—C12—H12C109.5
C4—C3—H3119.2H12B—C12—H12C109.5
C5—C4—C3120.7 (3)N3—C13—C15110.02 (16)
C5—C4—H4119.6N3—C13—C14106.34 (15)
C3—C4—H4119.6C15—C13—C14110.62 (19)
C4—C5—C6119.3 (2)N3—C13—C1099.78 (14)
C4—C5—H5120.3C15—C13—C10115.44 (17)
C6—C5—H5120.3C14—C13—C10113.69 (17)
C5—C6—C1118.12 (19)C13—C14—H14A109.5
C5—C6—C7135.90 (19)C13—C14—H14B109.5
C1—C6—C7105.97 (19)H14A—C14—H14B109.5
C8—C7—C9124.61 (19)C13—C14—H14C109.5
C8—C7—C6106.51 (17)H14A—C14—H14C109.5
C9—C7—C6128.38 (18)H14B—C14—H14C109.5
N1—C8—C7109.7 (2)C13—C15—H15A109.5
N1—C8—H8125.1C13—C15—H15B109.5
C7—C8—H8125.1H15A—C15—H15B109.5
N3—C9—N2107.72 (15)C13—C15—H15C109.5
N3—C9—C7126.94 (17)H15A—C15—H15C109.5
N2—C9—C7125.30 (17)H15B—C15—H15C109.5
C8—N1—C1—C2178.2 (2)C10—N2—C9—C7−179.20 (17)
C8—N1—C1—C6−0.2 (2)C8—C7—C9—N3−163.74 (19)
N1—C1—C2—C3−179.1 (2)C6—C7—C9—N325.5 (3)
C6—C1—C2—C3−0.9 (4)C8—C7—C9—N218.9 (3)
C1—C2—C3—C40.4 (4)C6—C7—C9—N2−151.90 (19)
C2—C3—C4—C50.8 (4)O1—N2—C10—C1245.8 (2)
C3—C4—C5—C6−1.6 (4)C9—N2—C10—C12−141.06 (17)
C4—C5—C6—C11.1 (3)O1—N2—C10—C11−74.1 (2)
C4—C5—C6—C7179.4 (2)C9—N2—C10—C1199.07 (18)
N1—C1—C6—C5178.64 (19)O1—N2—C10—C13167.26 (16)
C2—C1—C6—C50.1 (3)C9—N2—C10—C13−19.56 (19)
N1—C1—C6—C7−0.1 (2)O2—N3—C13—C1534.2 (3)
C2—C1—C6—C7−178.6 (2)C9—N3—C13—C15−149.50 (18)
C5—C6—C7—C8−178.0 (2)O2—N3—C13—C14−85.6 (2)
C1—C6—C7—C80.4 (2)C9—N3—C13—C1490.7 (2)
C5—C6—C7—C9−6.0 (4)O2—N3—C13—C10155.98 (16)
C1—C6—C7—C9172.47 (19)C9—N3—C13—C10−27.72 (19)
C1—N1—C8—C70.5 (2)N2—C10—C13—N325.95 (17)
C9—C7—C8—N1−172.98 (19)C12—C10—C13—N3143.19 (16)
C6—C7—C8—N1−0.5 (2)C11—C10—C13—N3−87.50 (18)
O2—N3—C9—N2−167.34 (17)N2—C10—C13—C15143.77 (17)
C13—N3—C9—N216.6 (2)C12—C10—C13—C15−99.0 (2)
O2—N3—C9—C714.9 (3)C11—C10—C13—C1530.3 (2)
C13—N3—C9—C7−161.20 (17)N2—C10—C13—C14−86.84 (18)
O1—N2—C9—N3175.82 (17)C12—C10—C13—C1430.4 (2)
C10—N2—C9—N33.0 (2)C11—C10—C13—C14159.70 (17)
O1—N2—C9—C7−6.4 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.862.072.8506 (18)150
C12—H12C···O2ii0.962.513.434 (2)161
C14—H14C···O1iii0.962.563.495 (2)164

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FL2283).

References

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