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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1848.
Published online 2009 July 11. doi:  10.1107/S1600536809026725
PMCID: PMC2977453

3-Ethynyl-2,2,5,5-tetra­methyl-1-oxyl-3-pyrroline

Abstract

The five-membered ring of the title compound, C10H14NO, is almost planar [mean deviation from best plane = 0.006 (1) Å]. The N—O bond is in the plane of the five-membered ring. The mol­ecule is positioned about a pseudo-mirror plane at y = 0.375. In the crystal, mol­ecules are connected by inter­molecular C—H(...)O contacts into layers parallel to (010).

Related literature

For the preparation of the title compound, see: Schiemann et al. (2007 [triangle]). For its application as a spin label, see: Schiemann et al. (2007 [triangle]); Piton et al. (2007 [triangle]). For the crystal structure of a related compound, see: Fritscher et al. (2002 [triangle]).

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Object name is e-65-o1848-scheme1.jpg

Experimental

Crystal data

  • C10H14NO
  • M r = 164.22
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1848-efi1.jpg
  • a = 7.9326 (15) Å
  • b = 19.058 (4) Å
  • c = 6.5989 (11) Å
  • β = 104.333 (14)°
  • V = 966.6 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.07 mm−1
  • T = 167 K
  • 0.60 × 0.55 × 0.07 mm

Data collection

  • Siemens SMART 1K CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2000 [triangle]) T min = 0.870, T max = 0.995
  • 16848 measured reflections
  • 3301 independent reflections
  • 2214 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.062
  • wR(F 2) = 0.157
  • S = 1.19
  • 3301 reflections
  • 121 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: SMART (Siemens, 1995 [triangle]); cell refinement: SMART; data reduction: SAINT (Siemens, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809026725/nc2152sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809026725/nc2152Isup2.hkl

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

supplementary crystallographic information

Comment

For EPR measurements of RNA, DNA or proteins, the occurrence of paramagnetic species is required. The title compound is a nitroxide spin label compound. Its synthesis has been reported by Schiemann et al. (2007). The application for DNA and RNA labeling has been described by Schiemann et al. (2007) and Piton et al. (2007). Here we report the crystal structure of the compound.

The molecular structure of the title compound is shown in Fig. 1. The five-membered ring is almost planar: the mean deviation from the best plane is 0.006 (1) Å. The molecule approximately has mirror symmetry and is positioned about a pseudo-mirror plane at y = 0.375. The N atom is planar and deviates by only 0.006 (2)Å from the plane through C1, C4 and O1. A related molecule with a very similar conformation of the 3-ethynyl-2,2,5,5-tetramethyl-1-oxyl-3-pyrroline group has been reported by Fritscher et al. (2002).

The molecules are connected by intermolecular C—H···O contacts to layers parallel to [0 1 0] (Fig. 2 and Table 1).

Experimental

The preparation of the title compound has been reported by Schiemann et al. (2007). Crystals were obtained by recrystallization from ethanol.

Refinement

The H atoms at C2 and C6 were taken from a difference Fourier synthesis and were refined with isotropic thermal parameters. The remaining H atoms were geometrically positioned using: Cmethyl—H=0.98Å and Uiso(H)=1.5Ueq(Cmethyl). The torsion angles about the C—Cmethyl bonds were refined for the methyl groups

Figures

Fig. 1.
The structure of the title compound shown with 50% probability displacement ellipsoids. The H atoms are drawn as small spheres of arbitrary radius.
Fig. 2.
A hydrogen bonded layer of molecules, viewed down the b axis. Intermolecular C—H···O contacts are shown as dashed lines.

Crystal data

C10H14NOF(000) = 356
Mr = 164.22Dx = 1.129 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 130 reflections
a = 7.9326 (15) Åθ = 3–23°
b = 19.058 (4) ŵ = 0.07 mm1
c = 6.5989 (11) ÅT = 167 K
β = 104.333 (14)°Plate, yellow
V = 966.6 (3) Å30.6 × 0.55 × 0.07 mm
Z = 4

Data collection

Siemens SMART 1K CCD diffractometer3301 independent reflections
Radiation source: normal-focus sealed tube2214 reflections with I > 2σ(I)
graphiteRint = 0.035
ω scansθmax = 32.4°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)h = −11→11
Tmin = 0.870, Tmax = 0.995k = −27→28
16848 measured reflectionsl = −9→9

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.062Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.157H atoms treated by a mixture of independent and constrained refinement
S = 1.19w = 1/[σ2(Fo2) + (0.05P)2 + 0.35P] where P = (Fo2 + 2Fc2)/3
3301 reflections(Δ/σ)max = 0.005
121 parametersΔρmax = 0.44 e Å3
0 restraintsΔρmin = −0.23 e Å3

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.

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

xyzUiso*/Ueq
O10.62303 (13)0.37389 (6)0.53230 (15)0.0287 (3)
N10.54492 (14)0.37427 (7)0.33858 (17)0.0219 (2)
C10.63968 (16)0.37208 (8)0.1714 (2)0.0208 (3)
C20.48802 (18)0.37338 (8)−0.0187 (2)0.0230 (3)
C30.33449 (17)0.37599 (8)0.0304 (2)0.0213 (3)
C40.35322 (16)0.37802 (8)0.2659 (2)0.0203 (3)
C50.16502 (18)0.37655 (8)−0.1101 (2)0.0257 (3)
C60.0205 (2)0.37657 (10)−0.2191 (2)0.0326 (3)
C70.7461 (2)0.30471 (8)0.1866 (3)0.0286 (3)
H7A0.66830.26410.17190.043*
H7B0.83070.30280.32280.043*
H7C0.80770.30400.07500.043*
C80.7560 (2)0.43669 (9)0.1864 (3)0.0298 (3)
H8A0.68490.47920.17630.045*
H8B0.81460.43600.07190.045*
H8C0.84330.43630.32060.045*
C90.2700 (2)0.31455 (9)0.3439 (2)0.0302 (4)
H9A0.31920.27140.30170.045*
H9B0.14410.31530.28330.045*
H9C0.29330.31620.49670.045*
C100.2884 (2)0.44689 (9)0.3368 (3)0.0315 (4)
H10A0.34870.48620.28980.047*
H10B0.31190.44750.48970.047*
H10C0.16290.45120.27640.047*
H2A0.503 (2)0.3735 (9)−0.161 (3)0.029 (4)*
H6A−0.098 (3)0.3781 (10)−0.308 (3)0.045 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0254 (5)0.0447 (6)0.0133 (4)0.0007 (5)−0.0005 (3)−0.0003 (5)
N10.0177 (5)0.0338 (6)0.0135 (5)0.0002 (5)0.0025 (4)0.0002 (5)
C10.0185 (5)0.0273 (7)0.0171 (5)−0.0002 (5)0.0050 (4)0.0001 (6)
C20.0253 (6)0.0288 (7)0.0142 (5)−0.0006 (6)0.0039 (4)−0.0005 (5)
C30.0216 (6)0.0239 (6)0.0159 (5)−0.0007 (5)−0.0001 (4)0.0000 (5)
C40.0162 (5)0.0274 (7)0.0165 (5)0.0000 (5)0.0027 (4)−0.0013 (5)
C50.0252 (6)0.0334 (8)0.0176 (6)−0.0015 (6)0.0034 (5)−0.0006 (6)
C60.0262 (7)0.0466 (10)0.0229 (7)−0.0002 (7)0.0019 (5)−0.0017 (7)
C70.0248 (7)0.0312 (8)0.0298 (8)0.0050 (6)0.0065 (6)−0.0030 (6)
C80.0288 (7)0.0351 (9)0.0260 (8)−0.0081 (6)0.0081 (6)0.0007 (6)
C90.0278 (7)0.0388 (9)0.0241 (8)−0.0073 (6)0.0065 (6)0.0054 (6)
C100.0292 (8)0.0379 (9)0.0266 (8)0.0085 (7)0.0053 (6)−0.0071 (7)

Geometric parameters (Å, °)

O1—N11.2752 (14)C6—H6A0.97 (2)
N1—C41.4787 (16)C7—H7A0.9800
N1—C11.4815 (17)C7—H7B0.9800
C1—C21.5079 (18)C7—H7C0.9800
C1—C71.526 (2)C8—H8A0.9800
C1—C81.527 (2)C8—H8B0.9800
C2—C31.336 (2)C8—H8C0.9800
C2—H2A0.975 (19)C9—H9A0.9800
C3—C51.4317 (18)C9—H9B0.9800
C3—C41.5248 (18)C9—H9C0.9800
C4—C101.525 (2)C10—H10A0.9800
C4—C91.527 (2)C10—H10B0.9800
C5—C61.193 (2)C10—H10C0.9800
O1—N1—C4122.07 (11)C1—C7—H7B109.5
O1—N1—C1122.43 (11)H7A—C7—H7B109.5
C4—N1—C1115.50 (10)C1—C7—H7C109.5
N1—C1—C299.88 (10)H7A—C7—H7C109.5
N1—C1—C7110.43 (12)H7B—C7—H7C109.5
C2—C1—C7112.54 (12)C1—C8—H8A109.5
N1—C1—C8109.81 (12)C1—C8—H8B109.5
C2—C1—C8112.67 (12)H8A—C8—H8B109.5
C7—C1—C8111.00 (12)C1—C8—H8C109.5
C3—C2—C1112.74 (12)H8A—C8—H8C109.5
C3—C2—H2A124.7 (11)H8B—C8—H8C109.5
C1—C2—H2A122.5 (11)C4—C9—H9A109.5
C2—C3—C5127.55 (13)C4—C9—H9B109.5
C2—C3—C4112.53 (11)H9A—C9—H9B109.5
C5—C3—C4119.92 (12)C4—C9—H9C109.5
N1—C4—C399.34 (10)H9A—C9—H9C109.5
N1—C4—C10109.88 (12)H9B—C9—H9C109.5
C3—C4—C10112.29 (12)C4—C10—H10A109.5
N1—C4—C9110.37 (12)C4—C10—H10B109.5
C3—C4—C9112.47 (12)H10A—C10—H10B109.5
C10—C4—C9111.82 (13)C4—C10—H10C109.5
C6—C5—C3176.86 (16)H10A—C10—H10C109.5
C5—C6—H6A178.2 (12)H10B—C10—H10C109.5
C1—C7—H7A109.5
O1—N1—C1—C2179.84 (13)C1—N1—C4—C31.46 (17)
C4—N1—C1—C2−1.06 (17)O1—N1—C4—C1062.65 (18)
O1—N1—C1—C761.15 (17)C1—N1—C4—C10−116.46 (14)
C4—N1—C1—C7−119.74 (13)O1—N1—C4—C9−61.12 (18)
O1—N1—C1—C8−61.57 (17)C1—N1—C4—C9119.77 (13)
C4—N1—C1—C8117.54 (13)C2—C3—C4—N1−1.34 (17)
N1—C1—C2—C30.11 (17)C5—C3—C4—N1178.28 (14)
C7—C1—C2—C3117.23 (15)C2—C3—C4—C10114.75 (15)
C8—C1—C2—C3−116.35 (15)C5—C3—C4—C10−65.63 (18)
C1—C2—C3—C5−178.76 (15)C2—C3—C4—C9−118.07 (15)
C1—C2—C3—C40.82 (19)C5—C3—C4—C961.54 (18)
O1—N1—C4—C3−179.43 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C2—H2A···O1i0.975 (19)2.441 (18)3.3907 (18)164.6 (14)
C6—H6A···O1ii0.98 (2)2.20 (2)3.174 (2)171.2 (17)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NC2152).

References

  • Fritscher, J., Beyer, M. & Schiemann, O. (2002). Chem. Phys. Lett.364, 393–401.
  • Piton, N., Mu, Y., Stock, G., Prisner, T. F., Schiemann, O. & Engels, J. W. (2007). Nucleic Acids Res 35, 3128–3143. [PMC free article] [PubMed]
  • Schiemann, O., Piton, N., Plackmeyer, J., Bode, B. E., Prisner, T. F. & Engels, J. W. (2007). Nat. Protoc.2, 904–923. [PubMed]
  • Sheldrick, G. M. (2000). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Siemens (1995). SMART and SAINT Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

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