organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

aInstitut für Organische Chemie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
*Correspondence e-mail: bats@chemie.uni-frankfurt.de

(Received 7 July 2009; accepted 8 July 2009; online 11 July 2009)

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[Schiemann, O., Piton, N., Plackmeyer, J., Bode, B. E., Prisner, T. F. & Engels, J. W. (2007). Nat. Protoc. 2, 904-923.]). For its application as a spin label, see: Schiemann et al. (2007[Schiemann, O., Piton, N., Plackmeyer, J., Bode, B. E., Prisner, T. F. & Engels, J. W. (2007). Nat. Protoc. 2, 904-923.]); Piton et al. (2007[Piton, N., Mu, Y., Stock, G., Prisner, T. F., Schiemann, O. & Engels, J. W. (2007). Nucleic Acids Res. 35, 3128-3143.]). For the crystal structure of a related compound, see: Fritscher et al. (2002[Fritscher, J., Beyer, M. & Schiemann, O. (2002). Chem. Phys. Lett. 364, 393-401.]).

[Scheme 1]

Experimental

Crystal data
  • C10H14NO

  • Mr = 164.22

  • Monoclinic, P 21 /c

  • 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[Sheldrick, G. M. (2000). SADABS. University of Göttingen, Germany.]) Tmin = 0.870, Tmax = 0.995

  • 16848 measured reflections

  • 3301 independent reflections

  • 2214 reflections with I > 2σ(I)

  • Rint = 0.035

Refinement
  • R[F2 > 2σ(F2)] = 0.062

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2A⋯O1i 0.975 (19) 2.441 (18) 3.3907 (18) 164.6 (14)
C6—H6A⋯O1ii 0.98 (2) 2.20 (2) 3.174 (2) 171.2 (17)
Symmetry codes: (i) x, y, z-1; (ii) x-1, y, z-1.

Data collection: SMART (Siemens, 1995[Siemens (1995). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]); cell refinement: SMART; data reduction: SAINT (Siemens, 1995[Siemens (1995). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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).

Related literature top

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

Experimental top

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

Refinement top

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

Computing details top

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

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. A hydrogen bonded layer of molecules, viewed down the b axis. Intermolecular C—H···O contacts are shown as dashed lines.
3-Ethynyl-2,2,5,5-tetramethyl-1-oxyl-3-pyrroline top
Crystal data top
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 top
Siemens SMART 1K CCD
diffractometer
3301 independent reflections
Radiation source: normal-focus sealed tube2214 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
ω scansθmax = 32.4°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2000)
h = 1111
Tmin = 0.870, Tmax = 0.995k = 2728
16848 measured reflectionsl = 99
Refinement top
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 = 1.19 w = 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
Crystal data top
C10H14NOV = 966.6 (3) Å3
Mr = 164.22Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.9326 (15) ŵ = 0.07 mm1
b = 19.058 (4) ÅT = 167 K
c = 6.5989 (11) Å0.6 × 0.55 × 0.07 mm
β = 104.333 (14)°
Data collection top
Siemens SMART 1K CCD
diffractometer
3301 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2000)
2214 reflections with I > 2σ(I)
Tmin = 0.870, Tmax = 0.995Rint = 0.035
16848 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0620 restraints
wR(F2) = 0.157H atoms treated by a mixture of independent and constrained refinement
S = 1.19Δρmax = 0.44 e Å3
3301 reflectionsΔρmin = 0.23 e Å3
121 parameters
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
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)*
H6A0.098 (3)0.3781 (10)0.308 (3)0.045 (6)*
Atomic displacement parameters (Å2) top
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, º) top
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—C21.06 (17)O1—N1—C4—C1062.65 (18)
O1—N1—C1—C761.15 (17)C1—N1—C4—C10116.46 (14)
C4—N1—C1—C7119.74 (13)O1—N1—C4—C961.12 (18)
O1—N1—C1—C861.57 (17)C1—N1—C4—C9119.77 (13)
C4—N1—C1—C8117.54 (13)C2—C3—C4—N11.34 (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—C3116.35 (15)C5—C3—C4—C1065.63 (18)
C1—C2—C3—C5178.76 (15)C2—C3—C4—C9118.07 (15)
C1—C2—C3—C40.82 (19)C5—C3—C4—C961.54 (18)
O1—N1—C4—C3179.43 (13)
Hydrogen-bond geometry (Å, º) top
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, z1; (ii) x1, y, z1.

Experimental details

Crystal data
Chemical formulaC10H14NO
Mr164.22
Crystal system, space groupMonoclinic, P21/c
Temperature (K)167
a, b, c (Å)7.9326 (15), 19.058 (4), 6.5989 (11)
β (°) 104.333 (14)
V3)966.6 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.07
Crystal size (mm)0.6 × 0.55 × 0.07
Data collection
DiffractometerSiemens SMART 1K CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2000)
Tmin, Tmax0.870, 0.995
No. of measured, independent and
observed [I > 2σ(I)] reflections
16848, 3301, 2214
Rint0.035
(sin θ/λ)max1)0.753
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.062, 0.157, 1.19
No. of reflections3301
No. of parameters121
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.44, 0.23

Computer programs: SMART (Siemens, 1995), SAINT (Siemens, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
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, z1; (ii) x1, y, z1.
 

References

First citationFritscher, J., Beyer, M. & Schiemann, O. (2002). Chem. Phys. Lett. 364, 393–401.  Web of Science CSD CrossRef CAS Google Scholar
First citationPiton, N., Mu, Y., Stock, G., Prisner, T. F., Schiemann, O. & Engels, J. W. (2007). Nucleic Acids Res. 35, 3128–3143.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSchiemann, O., Piton, N., Plackmeyer, J., Bode, B. E., Prisner, T. F. & Engels, J. W. (2007). Nat. Protoc. 2, 904–923.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2000). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSiemens (1995). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.  Google Scholar

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