supplementary materials


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

Acta Cryst. (2009). E65, o529    [ doi:10.1107/S1600536809004681 ]

4-Ethynyl-2,2,6,6-tetramethyl-1,2,5,6-tetrahydropyridine N-oxide

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

Abstract top

The six-membered ring of the title compound, C11H16NO, has a distorted envelope conformation. The piperidine N atom deviates by 0.128 (1) Å from the plane through its three neighbouring atoms. In the crystal structure, molecules are connected by intermolecular Cethynyl-H...O contacts to form chains extending in the [10\overline{1}] direction.

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 and application for DNA labeling have been reported by Gannett et al. (2001). Frolow et al. (2007) reported an improved synthesis of the compound and its coupling to uridine. Here we report on the crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The geometrical parameters in the title compound are very similar to those in the 2,2,6,6-tetramethyl-1-oxyl-3,4-dehydropiperidine fragment of closely related molecules (Igonin et al., 1990; Wiley et al., 1991; Shklover et al., 1990). The six-membered ring has a distorted envelope conformation with atoms N1 and C5 deviating by 0.186 (1) and 0.725 (2) Å, respectively, in the same direction from the mean plane through atoms C1-C4 [planar to within 0.005 (1) Å]. Atom N1 shows a small degree of pyramidalization. The sum of the three valence angles about N1 is 357.6 (1)° and it deviates by 0.128 (1) Å from the plane through the three neighbouring atoms, O1, C1 and C5.

In the crystal structure molecules are connected by intermolecular Cethynyl—H···O contacts to form chains extending in the [1 0 -1] direction (Fig. 2 and Table 1).

Related literature top

For the preparation of the title compound, see: Gannett et al. (2001); Frolow et al. (2007). For the crystal structures of related compounds see: Igonin et al. (1990); Wiley et al. (1991); Shklover et al. (1990).

Experimental top

The synthesis of the title compound has been reported by Frolow et al. (2007). Crystals were obtained by sublimation at atmospheric pressure.

Refinement top

The H atoms at C2 and C7 were located in difference Fourier maps and freely refined: C-H = 0.973 (13) and 0.944 (15) Å, respectively. The remainder of the H atoms were positioned geometrically and treated as riding: C-H = 0.98 - 0.99 Å with UisoH = k × Ueq(C), where k = 1.2 for (CH and CH2) and 1.5 for (CH3).

Computing details top

Data collection: SMART (Siemens, 1995); cell refinement: SAINT (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 molecular structure of the title compound, shown with 50% probability displacement ellipsoids. H atoms are drawn as small spheres of arbitrary radiius.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed down the a axis. Intermolecular Cethynyl—H···O contacts are shown as dashed lines.
4-Ethynyl-2,2,6,6-tetramethyl-1,2,5,6-tetrahydropyridine N-oxide top
Crystal data top
C11H16NOF(000) = 388
Mr = 178.25Dx = 1.125 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 212 reflections
a = 6.0996 (9) Åθ = 3–23°
b = 20.800 (3) ŵ = 0.07 mm−1
c = 8.3662 (13) ÅT = 167 K
β = 97.434 (10)°Block, yellow
V = 1052.5 (3) Å30.6 × 0.5 × 0.5 mm
Z = 4
Data collection top
Siemens SMART 1K CCD
diffractometer		3143 reflections with I > 2σ(I)
Radiation source: normal-focus sealed tubeRint = 0.039
graphiteθmax = 32.2°, θmin = 2.0°
ω scansh = −8→8
18416 measured reflectionsk = −31→27
3580 independent 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)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.112 w = 1/[σ2(Fo2) + (0.05P)2 + 0.2P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.002
3580 reflectionsΔρmax = 0.34 e Å−3
131 parametersΔρmin = −0.17 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.074 (6)
Crystal data top
C11H16NOV = 1052.5 (3) Å3
Mr = 178.25Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.0996 (9) ŵ = 0.07 mm−1
b = 20.800 (3) ÅT = 167 K
c = 8.3662 (13) Å0.6 × 0.5 × 0.5 mm
β = 97.434 (10)°
Data collection top
Siemens SMART 1K CCD
diffractometer		3143 reflections with I > 2σ(I)
18416 measured reflectionsRint = 0.039
3580 independent reflectionsθmax = 32.2°
Refinement top
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.112Δρmax = 0.34 e Å−3
S = 1.09Δρmin = −0.17 e Å−3
3580 reflectionsAbsolute structure: ?
131 parametersFlack parameter: ?
0 restraintsRogers 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O1−0.00063 (12)0.39282 (4)0.01634 (8)0.03761 (18)
N10.15408 (11)0.38503 (3)0.13455 (8)0.02345 (15)
C10.31309 (14)0.33197 (4)0.11809 (9)0.02439 (16)
C20.48668 (14)0.32849 (4)0.26317 (9)0.02460 (16)
C30.48149 (12)0.36207 (4)0.39876 (9)0.02137 (15)
C40.29668 (13)0.40897 (4)0.41379 (9)0.02327 (16)
H4A0.35260.44380.48870.028*
H4B0.17690.38650.46070.028*
C50.20201 (12)0.43844 (4)0.25172 (8)0.02002 (15)
C60.64656 (13)0.35531 (4)0.53690 (10)0.02476 (16)
C70.77337 (15)0.35377 (5)0.65871 (11)0.03106 (19)
C80.42478 (17)0.34218 (5)−0.03471 (10)0.0348 (2)
H8A0.51730.3808−0.02200.052*
H8B0.31120.3474−0.12800.052*
H8C0.51690.3048−0.05150.052*
C90.17967 (17)0.26909 (4)0.10502 (11)0.0344 (2)
H9A0.10710.26350.20200.052*
H9B0.27930.23280.09470.052*
H9C0.06750.27090.01000.052*
C10−0.01285 (14)0.47358 (5)0.27003 (10)0.02967 (18)
H10A−0.12160.44280.30080.045*
H10B−0.07040.49390.16740.045*
H10C0.01550.50660.35360.045*
C110.36583 (13)0.48486 (4)0.18847 (10)0.02556 (16)
H11A0.30270.50120.08260.038*
H11B0.50430.46220.17860.038*
H11C0.39530.52090.26370.038*
H2A0.607 (2)0.2984 (7)0.2539 (16)0.042 (3)*
H7A0.870 (2)0.3546 (8)0.7563 (18)0.057 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0374 (4)0.0424 (4)0.0274 (3)0.0000 (3)−0.0174 (3)−0.0025 (3)
N10.0240 (3)0.0261 (3)0.0183 (3)−0.0032 (2)−0.0049 (2)−0.0005 (2)
C10.0298 (4)0.0241 (4)0.0186 (3)−0.0030 (3)0.0005 (3)−0.0028 (3)
C20.0266 (4)0.0241 (4)0.0223 (3)0.0018 (3)0.0000 (3)−0.0008 (3)
C30.0221 (3)0.0224 (3)0.0187 (3)0.0004 (2)−0.0010 (2)0.0020 (2)
C40.0242 (3)0.0289 (4)0.0158 (3)0.0044 (3)−0.0007 (3)0.0006 (3)
C50.0189 (3)0.0234 (3)0.0167 (3)−0.0001 (2)−0.0017 (2)0.0005 (2)
C60.0259 (4)0.0242 (4)0.0231 (3)0.0030 (3)−0.0008 (3)0.0009 (3)
C70.0307 (4)0.0341 (4)0.0262 (4)0.0056 (3)−0.0049 (3)0.0002 (3)
C80.0428 (5)0.0408 (5)0.0219 (4)−0.0050 (4)0.0080 (3)−0.0045 (3)
C90.0450 (5)0.0264 (4)0.0303 (4)−0.0095 (3)−0.0009 (4)−0.0039 (3)
C100.0227 (4)0.0383 (5)0.0273 (4)0.0073 (3)0.0006 (3)0.0031 (3)
C110.0242 (3)0.0241 (4)0.0274 (4)−0.0034 (3)−0.0006 (3)0.0026 (3)
Geometric parameters (Å, °) top
O1—N11.2858 (9)C6—C71.1975 (12)
N1—C51.4854 (10)C7—H7A0.944 (15)
N1—C11.4874 (11)C8—H8A0.9800
C1—C21.5057 (11)C8—H8B0.9800
C1—C91.5368 (12)C8—H8C0.9800
C1—C81.5391 (12)C9—H9A0.9800
C2—C31.3360 (11)C9—H9B0.9800
C2—H2A0.973 (13)C9—H9C0.9800
C3—C61.4381 (10)C10—H10A0.9800
C3—C41.5082 (11)C10—H10B0.9800
C4—C51.5314 (10)C10—H10C0.9800
C4—H4A0.9900C11—H11A0.9800
C4—H4B0.9900C11—H11B0.9800
C5—C101.5255 (11)C11—H11C0.9800
C5—C111.5322 (11)
O1—N1—C5118.39 (7)C7—C6—C3174.02 (9)
O1—N1—C1116.41 (6)C6—C7—H7A177.0 (10)
C5—N1—C1122.76 (6)C1—C8—H8A109.5
N1—C1—C2111.10 (6)C1—C8—H8B109.5
N1—C1—C9107.01 (7)H8A—C8—H8B109.5
C2—C1—C9109.09 (7)C1—C8—H8C109.5
N1—C1—C8109.79 (7)H8A—C8—H8C109.5
C2—C1—C8109.60 (7)H8B—C8—H8C109.5
C9—C1—C8110.22 (7)C1—C9—H9A109.5
C3—C2—C1124.60 (7)C1—C9—H9B109.5
C3—C2—H2A120.3 (8)H9A—C9—H9B109.5
C1—C2—H2A115.1 (8)C1—C9—H9C109.5
C2—C3—C6122.69 (7)H9A—C9—H9C109.5
C2—C3—C4120.60 (7)H9B—C9—H9C109.5
C6—C3—C4116.70 (7)C5—C10—H10A109.5
C3—C4—C5112.67 (6)C5—C10—H10B109.5
C3—C4—H4A109.1H10A—C10—H10B109.5
C5—C4—H4A109.1C5—C10—H10C109.5
C3—C4—H4B109.1H10A—C10—H10C109.5
C5—C4—H4B109.1H10B—C10—H10C109.5
H4A—C4—H4B107.8C5—C11—H11A109.5
N1—C5—C10109.04 (6)C5—C11—H11B109.5
N1—C5—C4107.72 (6)H11A—C11—H11B109.5
C10—C5—C4109.47 (6)C5—C11—H11C109.5
N1—C5—C11108.95 (6)H11A—C11—H11C109.5
C10—C5—C11109.87 (7)H11B—C11—H11C109.5
C4—C5—C11111.72 (6)
O1—N1—C1—C2179.37 (7)C2—C3—C4—C5−29.55 (11)
C5—N1—C1—C217.41 (10)C6—C3—C4—C5151.16 (7)
O1—N1—C1—C9−61.65 (9)O1—N1—C5—C1033.57 (9)
C5—N1—C1—C9136.40 (7)C1—N1—C5—C10−164.82 (7)
O1—N1—C1—C857.96 (9)O1—N1—C5—C4152.29 (7)
C5—N1—C1—C8−103.99 (8)C1—N1—C5—C4−46.10 (9)
N1—C1—C2—C39.05 (11)O1—N1—C5—C11−86.35 (8)
C9—C1—C2—C3−108.68 (9)C1—N1—C5—C1175.26 (8)
C8—C1—C2—C3130.56 (9)C3—C4—C5—N149.52 (8)
C1—C2—C3—C6177.45 (7)C3—C4—C5—C10167.96 (7)
C1—C2—C3—C4−1.79 (12)C3—C4—C5—C11−70.11 (9)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C7—H7A···O1i0.944 (14)2.354 (15)3.2318 (13)154.6 (13)
Symmetry codes: (i) x+1, y, z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C7—H7A···O1i0.944 (14)2.354 (15)3.2318 (13)154.6 (13)
Symmetry codes: (i) x+1, y, z+1.
Acknowledgements top

(type here to add acknowledgements)

references
References top

Frolow, O., Bode, B. E. & Engels, J. W. (2007). Nucleosides Nucleotides Nucleic Acids, 26, 655–659.

Gannett, P. M., Darian, E., Powell, J. H. & Johnson, E. M. (2001). Synth. Commun. 31, 2137–2141.

Igonin, V. A., Shklover, V. E., Struchkov, Yu. T., Lazareva, O. L. & Vinogradov, G. A. (1990). Acta Cryst. C46, 776–778.

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

Shklover, V. E., Zamaev, I. A., Struchkov, Y. T., Medvedeva, T. V., Korshak, Y. V., Ovchinnikov, A. A. & Spector, V. N. (1990). Z. Kristallogr. 191, 9–14.

Siemens (1995). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

Wiley, D. W., Calabrese, J. C., Harlow, R. L. & Miller, J. S. (1991). Angew. Chem. Int. Ed. 30, 450–452.