supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

Acta Cryst. (2010). E66, o428    [ doi:10.1107/S1600536810002175 ]

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

H.-B. Wang, L.-L. Jing, R. Jiang, P. Liu and X.-L. Sun

Abstract top

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.

Comment top

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).

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound (I), showing the atom labeling scheme. Displacement ellipsoids are drawn at the 30% probability level.
2-(1H-Indol-3-yl)-4,4,5,5-tetramethylimidazolidine-1-oxyl 3-oxide top
Crystal data top
C15H18N3O2F(000) = 580
Mr = 272.32Dx = 1.289 Mg m−3
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 mm−1
c = 10.6108 (10) ÅT = 296 K
V = 1403.4 (2) Å3Block, blue
Z = 40.37 × 0.29 × 0.18 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer		1323 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 top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.067 w = 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 Å−3
186 parametersΔρmin = −0.09 e Å−3
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)
Crystal data top
C15H18N3O2V = 1403.4 (2) Å3
Mr = 272.32Z = 4
Orthorhombic, Pca21Mo Kα radiation
a = 15.0810 (15) ŵ = 0.09 mm−1
b = 8.7700 (8) ÅT = 296 K
c = 10.6108 (10) Å0.37 × 0.29 × 0.18 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer		1323 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2007)		1208 reflections with I > 2σ(I)
Tmin = 0.968, Tmax = 0.984Rint = 0.023
6651 measured reflectionsθmax = 25.1°
Refinement top
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.067Δρmax = 0.13 e Å−3
S = 1.06Δρmin = −0.09 e Å−3
1323 reflectionsAbsolute structure: ?
186 parametersFlack parameter: ?
1 restraintRogers parameter: ?
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.

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) top
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
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.
Acknowledgements top

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

references
References top

Brandenburg, K. (1998). DIAMOND. Crystal Impact GbR, Bonn, Germany.

Bruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

Iqbal, A. L., Anirban, P. & Sambhu, N. D. (2009). J. Phys.Chem. A, 113, 1595–4673.

Masuda, Y., Kurats, M., Suzuki, S., Kozaki, M., Shiomi, D., Sato, K., Takui, T., Hosokoshi, Y., Miyazaki, Y., Inada, A. & Okada, K. (2009). J. Am. Chem. Soc. 131, 4670-4673.

Qin, X.-Y., Wang, P.-A. & Sun, X.-L. (2009). Acta Cryst. E65, o1031.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Soule, B. P., Hyodo, F., Matsumoto, K., Simone, N. L., Cook, J. A., Krishna, M. C. & Mitchell, J. B. (2007). Free Radic. Biol. Med. 42, 1632–1650.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Tanaka, K., Furuichi, K., Kozaki, M., Suzuki, S., Shiomi, D., Sato, K., Takui, T. & Okada, K. (2007). Polyhedron, 26, 2021–2026.

Ullman, E. F., Osiecki, J. H., Boocock, D. G. B. & Darcy, R. (1974). J. Am. Chem. Soc. 96, 7049–7053.