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

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

doi:10.1107/S1600536809004681

organic compounds

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Volume 65| Part 3| March 2009| Page o529

doi:10.1107/S1600536809004681

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

Jan W. Bats,^a ^* Olga Frolow ^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 2 February 2009; accepted 9 February 2009; online 13 February 2009)

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 C_ethynyl—H⋯O contacts to form chains extending in the [10 $[\overline{1}]$ ] direction.

Related literature

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

Crystal data

C₁₁H₁₆NO
M_r = 178.25
Monoclinic, P 2₁ /c
a = 6.0996 (9) Å
b = 20.800 (3) Å
c = 8.3662 (13) Å
β = 97.434 (10)°
V = 1052.5 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.07 mm⁻¹
T = 167 K
0.60 × 0.50 × 0.50 mm

Data collection

Siemens SMART 1K CCD diffractometer
Absorption correction: none
18416 measured reflections
3580 independent reflections
3143 reflections with I > 2σ(I)
R_int = 0.039

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.112
S = 1.09
3580 reflections
131 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C7—H7A⋯O1ⁱ	0.944 (14)	2.354 (15)	3.2318 (13)	154.6 (13)
Symmetry code: (i) 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/S1600536809004681/su2096sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809004681/su2096Isup2.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 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 C_ethynyl—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.

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

	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.
	Fig. 2. The crystal packing of the title compound, viewed down the a axis. Intermolecular C_ethynyl—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

C₁₁H₁₆NO	F(000) = 388
M_r = 178.25	D_x = 1.125 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 212 reflections
a = 6.0996 (9) Å	θ = 3–23°
b = 20.800 (3) Å	µ = 0.07 mm⁻¹
c = 8.3662 (13) Å	T = 167 K
β = 97.434 (10)°	Block, yellow
V = 1052.5 (3) Å³	0.6 × 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 tube	R_int = 0.039
Graphite monochromator	θ_max = 32.2°, θ_min = 2.0°
ω scans	h = −8→8
18416 measured reflections	k = −31→27
3580 independent reflections	l = −12→12

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.112	w = 1/[σ²(F_o²) + (0.05P)² + 0.2P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max = 0.002
3580 reflections	Δρ_max = 0.34 e Å⁻³
131 parameters	Δρ_min = −0.17 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.074 (6)

Crystal data top

C₁₁H₁₆NO	V = 1052.5 (3) Å³
M_r = 178.25	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.0996 (9) Å	µ = 0.07 mm⁻¹
b = 20.800 (3) Å	T = 167 K
c = 8.3662 (13) Å	0.6 × 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 reflections	R_int = 0.039
3580 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	0 restraints
wR(F²) = 0.112	H atoms treated by a mixture of independent and constrained refinement
S = 1.09	Δρ_max = 0.34 e Å⁻³
3580 reflections	Δρ_min = −0.17 e Å⁻³
131 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	−0.00063 (12)	0.39282 (4)	0.01634 (8)	0.03761 (18)
N1	0.15408 (11)	0.38503 (3)	0.13455 (8)	0.02345 (15)
C1	0.31309 (14)	0.33197 (4)	0.11809 (9)	0.02439 (16)
C2	0.48668 (14)	0.32849 (4)	0.26317 (9)	0.02460 (16)
C3	0.48149 (12)	0.36207 (4)	0.39876 (9)	0.02137 (15)
C4	0.29668 (13)	0.40897 (4)	0.41379 (9)	0.02327 (16)
H4A	0.3526	0.4438	0.4887	0.028*
H4B	0.1769	0.3865	0.4607	0.028*
C5	0.20201 (12)	0.43844 (4)	0.25172 (8)	0.02002 (15)
C6	0.64656 (13)	0.35531 (4)	0.53690 (10)	0.02476 (16)
C7	0.77337 (15)	0.35377 (5)	0.65871 (11)	0.03106 (19)
C8	0.42478 (17)	0.34218 (5)	−0.03471 (10)	0.0348 (2)
H8A	0.5173	0.3808	−0.0220	0.052*
H8B	0.3112	0.3474	−0.1280	0.052*
H8C	0.5169	0.3048	−0.0515	0.052*
C9	0.17967 (17)	0.26909 (4)	0.10502 (11)	0.0344 (2)
H9A	0.1071	0.2635	0.2020	0.052*
H9B	0.2793	0.2328	0.0947	0.052*
H9C	0.0675	0.2709	0.0100	0.052*
C10	−0.01285 (14)	0.47358 (5)	0.27003 (10)	0.02967 (18)
H10A	−0.1216	0.4428	0.3008	0.045*
H10B	−0.0704	0.4939	0.1674	0.045*
H10C	0.0155	0.5066	0.3536	0.045*
C11	0.36583 (13)	0.48486 (4)	0.18847 (10)	0.02556 (16)
H11A	0.3027	0.5012	0.0826	0.038*
H11B	0.5043	0.4622	0.1786	0.038*
H11C	0.3953	0.5209	0.2637	0.038*
H2A	0.607 (2)	0.2984 (7)	0.2539 (16)	0.042 (3)*
H7A	0.870 (2)	0.3546 (8)	0.7563 (18)	0.057 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0374 (4)	0.0424 (4)	0.0274 (3)	0.0000 (3)	−0.0174 (3)	−0.0025 (3)
N1	0.0240 (3)	0.0261 (3)	0.0183 (3)	−0.0032 (2)	−0.0049 (2)	−0.0005 (2)
C1	0.0298 (4)	0.0241 (4)	0.0186 (3)	−0.0030 (3)	0.0005 (3)	−0.0028 (3)
C2	0.0266 (4)	0.0241 (4)	0.0223 (3)	0.0018 (3)	0.0000 (3)	−0.0008 (3)
C3	0.0221 (3)	0.0224 (3)	0.0187 (3)	0.0004 (2)	−0.0010 (2)	0.0020 (2)
C4	0.0242 (3)	0.0289 (4)	0.0158 (3)	0.0044 (3)	−0.0007 (3)	0.0006 (3)
C5	0.0189 (3)	0.0234 (3)	0.0167 (3)	−0.0001 (2)	−0.0017 (2)	0.0005 (2)
C6	0.0259 (4)	0.0242 (4)	0.0231 (3)	0.0030 (3)	−0.0008 (3)	0.0009 (3)
C7	0.0307 (4)	0.0341 (4)	0.0262 (4)	0.0056 (3)	−0.0049 (3)	0.0002 (3)
C8	0.0428 (5)	0.0408 (5)	0.0219 (4)	−0.0050 (4)	0.0080 (3)	−0.0045 (3)
C9	0.0450 (5)	0.0264 (4)	0.0303 (4)	−0.0095 (3)	−0.0009 (4)	−0.0039 (3)
C10	0.0227 (4)	0.0383 (5)	0.0273 (4)	0.0073 (3)	0.0006 (3)	0.0031 (3)
C11	0.0242 (3)	0.0241 (4)	0.0274 (4)	−0.0034 (3)	−0.0006 (3)	0.0026 (3)

Geometric parameters (Å, º) top

O1—N1	1.2858 (9)	C6—C7	1.1975 (12)
N1—C5	1.4854 (10)	C7—H7A	0.944 (15)
N1—C1	1.4874 (11)	C8—H8A	0.9800
C1—C2	1.5057 (11)	C8—H8B	0.9800
C1—C9	1.5368 (12)	C8—H8C	0.9800
C1—C8	1.5391 (12)	C9—H9A	0.9800
C2—C3	1.3360 (11)	C9—H9B	0.9800
C2—H2A	0.973 (13)	C9—H9C	0.9800
C3—C6	1.4381 (10)	C10—H10A	0.9800
C3—C4	1.5082 (11)	C10—H10B	0.9800
C4—C5	1.5314 (10)	C10—H10C	0.9800
C4—H4A	0.9900	C11—H11A	0.9800
C4—H4B	0.9900	C11—H11B	0.9800
C5—C10	1.5255 (11)	C11—H11C	0.9800
C5—C11	1.5322 (11)

O1—N1—C5	118.39 (7)	C7—C6—C3	174.02 (9)
O1—N1—C1	116.41 (6)	C6—C7—H7A	177.0 (10)
C5—N1—C1	122.76 (6)	C1—C8—H8A	109.5
N1—C1—C2	111.10 (6)	C1—C8—H8B	109.5
N1—C1—C9	107.01 (7)	H8A—C8—H8B	109.5
C2—C1—C9	109.09 (7)	C1—C8—H8C	109.5
N1—C1—C8	109.79 (7)	H8A—C8—H8C	109.5
C2—C1—C8	109.60 (7)	H8B—C8—H8C	109.5
C9—C1—C8	110.22 (7)	C1—C9—H9A	109.5
C3—C2—C1	124.60 (7)	C1—C9—H9B	109.5
C3—C2—H2A	120.3 (8)	H9A—C9—H9B	109.5
C1—C2—H2A	115.1 (8)	C1—C9—H9C	109.5
C2—C3—C6	122.69 (7)	H9A—C9—H9C	109.5
C2—C3—C4	120.60 (7)	H9B—C9—H9C	109.5
C6—C3—C4	116.70 (7)	C5—C10—H10A	109.5
C3—C4—C5	112.67 (6)	C5—C10—H10B	109.5
C3—C4—H4A	109.1	H10A—C10—H10B	109.5
C5—C4—H4A	109.1	C5—C10—H10C	109.5
C3—C4—H4B	109.1	H10A—C10—H10C	109.5
C5—C4—H4B	109.1	H10B—C10—H10C	109.5
H4A—C4—H4B	107.8	C5—C11—H11A	109.5
N1—C5—C10	109.04 (6)	C5—C11—H11B	109.5
N1—C5—C4	107.72 (6)	H11A—C11—H11B	109.5
C10—C5—C4	109.47 (6)	C5—C11—H11C	109.5
N1—C5—C11	108.95 (6)	H11A—C11—H11C	109.5
C10—C5—C11	109.87 (7)	H11B—C11—H11C	109.5
C4—C5—C11	111.72 (6)

O1—N1—C1—C2	179.37 (7)	C2—C3—C4—C5	−29.55 (11)
C5—N1—C1—C2	17.41 (10)	C6—C3—C4—C5	151.16 (7)
O1—N1—C1—C9	−61.65 (9)	O1—N1—C5—C10	33.57 (9)
C5—N1—C1—C9	136.40 (7)	C1—N1—C5—C10	−164.82 (7)
O1—N1—C1—C8	57.96 (9)	O1—N1—C5—C4	152.29 (7)
C5—N1—C1—C8	−103.99 (8)	C1—N1—C5—C4	−46.10 (9)
N1—C1—C2—C3	9.05 (11)	O1—N1—C5—C11	−86.35 (8)
C9—C1—C2—C3	−108.68 (9)	C1—N1—C5—C11	75.26 (8)
C8—C1—C2—C3	130.56 (9)	C3—C4—C5—N1	49.52 (8)
C1—C2—C3—C6	177.45 (7)	C3—C4—C5—C10	167.96 (7)
C1—C2—C3—C4	−1.79 (12)	C3—C4—C5—C11	−70.11 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7A···O1ⁱ	0.944 (14)	2.354 (15)	3.2318 (13)	154.6 (13)

Symmetry code: (i) x+1, y, z+1.

Experimental details

Crystal data
Chemical formula	C₁₁H₁₆NO
M_r	178.25
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	167
a, b, c (Å)	6.0996 (9), 20.800 (3), 8.3662 (13)
β (°)	97.434 (10)
V (Å³)	1052.5 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.07
Crystal size (mm)	0.6 × 0.5 × 0.5

Data collection
Diffractometer	Siemens SMART 1K CCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	18416, 3580, 3143
R_int	0.039
(sin θ/λ)_max (Å⁻¹)	0.750

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.112, 1.09
No. of reflections	3580
No. of parameters	131
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.17

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
C7—H7A···O1ⁱ	0.944 (14)	2.354 (15)	3.2318 (13)	154.6 (13)

Symmetry code: (i) x+1, y, z+1.

References

Frolow, O., Bode, B. E. & Engels, J. W. (2007). Nucleosides Nucleotides Nucleic Acids, 26, 655–659. Web of Science CrossRef PubMed CAS Google Scholar
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Igonin, V. A., Shklover, V. E., Struchkov, Yu. T., Lazareva, O. L. & Vinogradov, G. A. (1990). Acta Cryst. C46, 776–778. CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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. CrossRef CAS 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 3| March 2009| Page o529

doi:10.1107/S1600536809004681

Open

access