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

Frolow, O.; Bats, J.W.; Engels, J.W.

doi:10.1107/S1600536809026725

organic compounds

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Volume 65| Part 8| August 2009| Page o1848

doi:10.1107/S1600536809026725

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

Olga Frolow,^a Jan W. Bats ^a ^* and Joachim W. Engels ^a

^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 ). 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

Crystal data

C₁₀H₁₄NO
M_r = 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 ) 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[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
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SMART; 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.

Supporting information

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

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

checkCIF report

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.

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

	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.

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

Crystal data top

C₁₀H₁₄NO	F(000) = 356
M_r = 164.22	D_x = 1.129 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 130 reflections
a = 7.9326 (15) Å	θ = 3–23°
b = 19.058 (4) Å	µ = 0.07 mm⁻¹
c = 6.5989 (11) Å	T = 167 K
β = 104.333 (14)°	Plate, yellow
V = 966.6 (3) Å³	0.6 × 0.55 × 0.07 mm
Z = 4

Data collection top

Siemens SMART 1K CCD diffractometer	3301 independent reflections
Radiation source: normal-focus sealed tube	2214 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.035
ω scans	θ_max = 32.4°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)	h = −11→11
T_min = 0.870, T_max = 0.995	k = −27→28
16848 measured reflections	l = −9→9

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.062	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.157	H atoms treated by a mixture of independent and constrained refinement
S = 1.19	w = 1/[σ²(F_o²) + (0.05P)² + 0.35P] where P = (F_o² + 2F_c²)/3
3301 reflections	(Δ/σ)_max = 0.005
121 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₁₀H₁₄NO	V = 966.6 (3) Å³
M_r = 164.22	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 7.9326 (15) Å	µ = 0.07 mm⁻¹
b = 19.058 (4) Å	T = 167 K
c = 6.5989 (11) Å	0.6 × 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)
T_min = 0.870, T_max = 0.995	R_int = 0.035
16848 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.062	0 restraints
wR(F²) = 0.157	H atoms treated by a mixture of independent and constrained refinement
S = 1.19	Δρ_max = 0.44 e Å⁻³
3301 reflections	Δρ_min = −0.23 e Å⁻³
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

	x	y	z	U_iso*/U_eq
O1	0.62303 (13)	0.37389 (6)	0.53230 (15)	0.0287 (3)
N1	0.54492 (14)	0.37427 (7)	0.33858 (17)	0.0219 (2)
C1	0.63968 (16)	0.37208 (8)	0.1714 (2)	0.0208 (3)
C2	0.48802 (18)	0.37338 (8)	−0.0187 (2)	0.0230 (3)
C3	0.33449 (17)	0.37599 (8)	0.0304 (2)	0.0213 (3)
C4	0.35322 (16)	0.37802 (8)	0.2659 (2)	0.0203 (3)
C5	0.16502 (18)	0.37655 (8)	−0.1101 (2)	0.0257 (3)
C6	0.0205 (2)	0.37657 (10)	−0.2191 (2)	0.0326 (3)
C7	0.7461 (2)	0.30471 (8)	0.1866 (3)	0.0286 (3)
H7A	0.6683	0.2641	0.1719	0.043*
H7B	0.8307	0.3028	0.3228	0.043*
H7C	0.8077	0.3040	0.0750	0.043*
C8	0.7560 (2)	0.43669 (9)	0.1864 (3)	0.0298 (3)
H8A	0.6849	0.4792	0.1763	0.045*
H8B	0.8146	0.4360	0.0719	0.045*
H8C	0.8433	0.4363	0.3206	0.045*
C9	0.2700 (2)	0.31455 (9)	0.3439 (2)	0.0302 (4)
H9A	0.3192	0.2714	0.3017	0.045*
H9B	0.1441	0.3153	0.2833	0.045*
H9C	0.2933	0.3162	0.4967	0.045*
C10	0.2884 (2)	0.44689 (9)	0.3368 (3)	0.0315 (4)
H10A	0.3487	0.4862	0.2898	0.047*
H10B	0.3119	0.4475	0.4897	0.047*
H10C	0.1629	0.4512	0.2764	0.047*
H2A	0.503 (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) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0254 (5)	0.0447 (6)	0.0133 (4)	0.0007 (5)	−0.0005 (3)	−0.0003 (5)
N1	0.0177 (5)	0.0338 (6)	0.0135 (5)	0.0002 (5)	0.0025 (4)	0.0002 (5)
C1	0.0185 (5)	0.0273 (7)	0.0171 (5)	−0.0002 (5)	0.0050 (4)	0.0001 (6)
C2	0.0253 (6)	0.0288 (7)	0.0142 (5)	−0.0006 (6)	0.0039 (4)	−0.0005 (5)
C3	0.0216 (6)	0.0239 (6)	0.0159 (5)	−0.0007 (5)	−0.0001 (4)	0.0000 (5)
C4	0.0162 (5)	0.0274 (7)	0.0165 (5)	0.0000 (5)	0.0027 (4)	−0.0013 (5)
C5	0.0252 (6)	0.0334 (8)	0.0176 (6)	−0.0015 (6)	0.0034 (5)	−0.0006 (6)
C6	0.0262 (7)	0.0466 (10)	0.0229 (7)	−0.0002 (7)	0.0019 (5)	−0.0017 (7)
C7	0.0248 (7)	0.0312 (8)	0.0298 (8)	0.0050 (6)	0.0065 (6)	−0.0030 (6)
C8	0.0288 (7)	0.0351 (9)	0.0260 (8)	−0.0081 (6)	0.0081 (6)	0.0007 (6)
C9	0.0278 (7)	0.0388 (9)	0.0241 (8)	−0.0073 (6)	0.0065 (6)	0.0054 (6)
C10	0.0292 (8)	0.0379 (9)	0.0266 (8)	0.0085 (7)	0.0053 (6)	−0.0071 (7)

Geometric parameters (Å, º) top

O1—N1	1.2752 (14)	C6—H6A	0.97 (2)
N1—C4	1.4787 (16)	C7—H7A	0.9800
N1—C1	1.4815 (17)	C7—H7B	0.9800
C1—C2	1.5079 (18)	C7—H7C	0.9800
C1—C7	1.526 (2)	C8—H8A	0.9800
C1—C8	1.527 (2)	C8—H8B	0.9800
C2—C3	1.336 (2)	C8—H8C	0.9800
C2—H2A	0.975 (19)	C9—H9A	0.9800
C3—C5	1.4317 (18)	C9—H9B	0.9800
C3—C4	1.5248 (18)	C9—H9C	0.9800
C4—C10	1.525 (2)	C10—H10A	0.9800
C4—C9	1.527 (2)	C10—H10B	0.9800
C5—C6	1.193 (2)	C10—H10C	0.9800

O1—N1—C4	122.07 (11)	C1—C7—H7B	109.5
O1—N1—C1	122.43 (11)	H7A—C7—H7B	109.5
C4—N1—C1	115.50 (10)	C1—C7—H7C	109.5
N1—C1—C2	99.88 (10)	H7A—C7—H7C	109.5
N1—C1—C7	110.43 (12)	H7B—C7—H7C	109.5
C2—C1—C7	112.54 (12)	C1—C8—H8A	109.5
N1—C1—C8	109.81 (12)	C1—C8—H8B	109.5
C2—C1—C8	112.67 (12)	H8A—C8—H8B	109.5
C7—C1—C8	111.00 (12)	C1—C8—H8C	109.5
C3—C2—C1	112.74 (12)	H8A—C8—H8C	109.5
C3—C2—H2A	124.7 (11)	H8B—C8—H8C	109.5
C1—C2—H2A	122.5 (11)	C4—C9—H9A	109.5
C2—C3—C5	127.55 (13)	C4—C9—H9B	109.5
C2—C3—C4	112.53 (11)	H9A—C9—H9B	109.5
C5—C3—C4	119.92 (12)	C4—C9—H9C	109.5
N1—C4—C3	99.34 (10)	H9A—C9—H9C	109.5
N1—C4—C10	109.88 (12)	H9B—C9—H9C	109.5
C3—C4—C10	112.29 (12)	C4—C10—H10A	109.5
N1—C4—C9	110.37 (12)	C4—C10—H10B	109.5
C3—C4—C9	112.47 (12)	H10A—C10—H10B	109.5
C10—C4—C9	111.82 (13)	C4—C10—H10C	109.5
C6—C5—C3	176.86 (16)	H10A—C10—H10C	109.5
C5—C6—H6A	178.2 (12)	H10B—C10—H10C	109.5
C1—C7—H7A	109.5

O1—N1—C1—C2	179.84 (13)	C1—N1—C4—C3	1.46 (17)
C4—N1—C1—C2	−1.06 (17)	O1—N1—C4—C10	62.65 (18)
O1—N1—C1—C7	61.15 (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—C9	119.77 (13)
C4—N1—C1—C8	117.54 (13)	C2—C3—C4—N1	−1.34 (17)
N1—C1—C2—C3	0.11 (17)	C5—C3—C4—N1	178.28 (14)
C7—C1—C2—C3	117.23 (15)	C2—C3—C4—C10	114.75 (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—C4	0.82 (19)	C5—C3—C4—C9	61.54 (18)
O1—N1—C4—C3	−179.43 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₄NO
M_r	164.22
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	167
a, b, c (Å)	7.9326 (15), 19.058 (4), 6.5989 (11)
β (°)	104.333 (14)
V (Å³)	966.6 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.07
Crystal size (mm)	0.6 × 0.55 × 0.07

Data collection
Diffractometer	Siemens SMART 1K CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2000)
T_min, T_max	0.870, 0.995
No. of measured, independent and observed [I > 2σ(I)] reflections	16848, 3301, 2214
R_int	0.035
(sin θ/λ)_max (Å⁻¹)	0.753

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.062, 0.157, 1.19
No. of reflections	3301
No. of parameters	121
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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.

References

Fritscher, J., Beyer, M. & Schiemann, O. (2002). Chem. Phys. Lett. 364, 393–401. Web of Science CSD CrossRef CAS Google Scholar
Piton, 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
Schiemann, 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
Sheldrick, G. M. (2000). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Siemens (1995). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1848

doi:10.1107/S1600536809026725

Open

access