rac-12-Selena-13,14-di­aza­tri­cyclo­[9.3.0.02,4]tetra­deca-11,13-diene

Detert, H.; Schollmeyer, D.

doi:10.1107/S2414314620010810

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 5| Part 8| August 2020| x201081

https://doi.org/10.1107/S2414314620010810

Open

access

rac-12-Selena-13,14-diazatricyclo[9.3.0.0^2,4]tetradeca-11,13-diene

Heiner Detert ^a ^* and Dieter Schollmeyer ^a

^aJohannes Gutenberg University Mainz, Department of Chemistry, Duesbergweg 10-14, 55099 Mainz, Germany
^*Correspondence e-mail: detert@uni-mainz.de

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 17 July 2020; accepted 4 August 2020; online 11 August 2020)

The centrosymmetric crystal structure of the title compound, C₁₁H₁₆N₂Se, is built up from alternating strands of (R,R)- and (S,S)-enantiomers. These strands, which propagate along the c-axis direction, are composed of homochiral molecules related to each other by twofold screw axes. The shape of the molecule is an almost planar unit around the selenadiazole ring with a hexamethylene chain as an arched handle.

Keywords: crystal structure; heterocycles; medium-sized ring; selenium.

CCDC reference: 2021398

Structure description

1,2,3-Selenadiazoles are synthesized from SeO₂-oxidation of semicarbazones (Yalpani et al., 1971 ; Al-Smadi & Ratrout, 2004 ) and are important intermediates for the synthesis of medium-sized (Meier, 1972 ), heterocyclic (Detert, 2011 ), and strained cycloalkynes (Bissinger et al. 1988 ).

The arbitrarily chosen asymmetric molecule of the title compound (Fig. 1) has S configurations for atoms C5 and C6 but crystal symmetry generates a racemic mixture. The selenadiazole ring with the directly bound carbon atoms and one bond of the cyclopropane ring is almost planar, with a maximum deviation from this plane of 0.037 (2) Å at C12 and the dihedral angle between the selenadiazole ring and the cyclopropane ring is 69.0 (2)°. Though the carbocyclic part is of medium ring size, the hexamethylene tether appears to be free of Pitzer and Prelog strain.

Figure 1
Perspective view of the title compound with displacement ellipsoids drawn at the 50% probability level.

No directional interactions beyond normal van der Waals contacts could be identified in the crystal. The packing consists of strands of homochiral molecules, related to each other by twofold screw axes, propagating along the c-axis direction. The (R,R)- and (S,S)-enantiomers alternate along the a-axis direction, being related by crystallographic c-glides (Fig. 2).

Figure 2
Packing diagram of the title compound viewed along the b-axis direction. Colour key: the asymmetric molecule and its translation clones along [010] grey; molecules generated by twofold screw axes green; molecules generated by inversion symmetry orange; molecules generated by c-glides purple.

Synthesis and crystallization

The title compound was prepared in ten steps from cyclooctene according to Moore & Ward (1963 ), Moore & Bertelson (1962 ), Gardner & Narayana (1961 ), Detert & Meier (1997 ) and Whitham & Zaidlewicz (1972 ). Recrystallization from petroleum ether gave slightly pinkish crystals with m.p. 369 K.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1.

Table 1
Experimental details

Crystal data
Chemical formula	C₁₁H₁₆N₂Se
M_r	255.22
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	120
a, b, c (Å)	12.0239 (6), 7.1317 (3), 12.6836 (7)
β (°)	101.104 (4)
V (Å³)	1067.27 (9)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	3.48
Crystal size (mm)	0.55 × 0.47 × 0.10

Data collection
Diffractometer	Stoe IPDS 2T
Absorption correction	Integration
T_min, T_max	0.228, 0.704
No. of measured, independent and observed [I > 2σ(I)] reflections	5541, 2570, 2364
R_int	0.021
(sin θ/λ)_max (Å⁻¹)	0.661

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.097, 1.10
No. of reflections	2570
No. of parameters	127
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.13, −0.90
Computer programs: X-AREA WinXpose, Recipe and Integrate (Stoe & Cie, 2019 ), SIR2004 (Burla et al., 2005 ), SHELXL2018/3 (Sheldrick, 2015 ) and PLATON (Spek, 2020 ).

Structural data

CCDC reference: 2021398

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314620010810/hb4354sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620010810/hb4354Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314620010810/hb4354Isup3.cml

checkCIF report

Computing details top

Data collection: X-AREA WinXpose (Stoe & Cie, 2019); cell refinement: X-AREA Recipe (Stoe & Cie, 2019); data reduction: X-AREA Integrate (Stoe & Cie, 2019); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2020).

rac-12-Selena-13,14-diazatricyclo[9.3.0.0^2,4]tetradeca-11,13-diene top

Crystal data top

C₁₁H₁₆N₂Se	F(000) = 520
M_r = 255.22	D_x = 1.588 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 12.0239 (6) Å	Cell parameters from 11220 reflections
b = 7.1317 (3) Å	θ = 2.9–28.5°
c = 12.6836 (7) Å	µ = 3.48 mm⁻¹
β = 101.104 (4)°	T = 120 K
V = 1067.27 (9) Å³	Plate, colourless
Z = 4	0.55 × 0.47 × 0.10 mm

Data collection top

Stoe IPDS 2T diffractometer	2570 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	2364 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm^-1	R_int = 0.021
rotation method, ω scans	θ_max = 28.0°, θ_min = 3.3°
Absorption correction: integration	h = −15→15
T_min = 0.228, T_max = 0.704	k = −9→9
5541 measured reflections	l = −15→16

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.035	H-atom parameters constrained
wR(F²) = 0.097	w = 1/[σ²(F_o²) + (0.0573P)² + 1.4452P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max < 0.001
2570 reflections	Δρ_max = 1.13 e Å⁻³
127 parameters	Δρ_min = −0.90 e Å⁻³
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Hydrogen atoms attached to carbon atoms were placed at calculated positions and were refined in the riding-model approximation with C—H = 0.95 Å and U_iso(H) = 1.2 U_eq(C).

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

	x	y	z	U_iso*/U_eq
Se1	0.01806 (2)	0.53889 (3)	0.19801 (2)	0.01717 (11)
N2	0.08518 (19)	0.7735 (3)	0.24245 (18)	0.0195 (4)
N3	0.16960 (17)	0.7494 (3)	0.31890 (17)	0.0167 (4)
C4	0.1961 (2)	0.5686 (3)	0.35355 (19)	0.0131 (4)
C5	0.2954 (2)	0.5360 (3)	0.4406 (2)	0.0144 (4)
H5	0.337544	0.417298	0.433140	0.017*
C6	0.2942 (2)	0.5921 (3)	0.55614 (18)	0.0149 (4)
H6	0.225279	0.662016	0.567102	0.018*
C7	0.3456 (2)	0.4626 (3)	0.6468 (2)	0.0177 (5)
H7A	0.375621	0.539411	0.711012	0.021*
H7B	0.410401	0.396039	0.626172	0.021*
C8	0.2633 (2)	0.3164 (4)	0.67731 (19)	0.0178 (5)
H8A	0.203057	0.382731	0.705866	0.021*
H8B	0.305015	0.236704	0.735703	0.021*
C9	0.2071 (2)	0.1890 (3)	0.58429 (19)	0.0173 (5)
H9A	0.260533	0.170100	0.534790	0.021*
H9B	0.192121	0.064881	0.613659	0.021*
C10	0.09558 (19)	0.2684 (3)	0.52058 (18)	0.0154 (4)
H10A	0.035621	0.252598	0.563508	0.018*
H10B	0.105037	0.404482	0.509630	0.018*
C11	0.0569 (2)	0.1748 (3)	0.41110 (19)	0.0170 (5)
H11A	−0.022326	0.212211	0.382070	0.020*
H11B	0.058059	0.037076	0.421121	0.020*
C12	0.1307 (2)	0.2250 (3)	0.32802 (19)	0.0147 (4)
H12A	0.210110	0.187617	0.356552	0.018*
H12B	0.103796	0.153162	0.261179	0.018*
C13	0.1270 (2)	0.4310 (3)	0.30231 (19)	0.0143 (4)
C14	0.3690 (2)	0.6950 (4)	0.4927 (2)	0.0195 (5)
H14A	0.451685	0.673076	0.511923	0.023*
H14B	0.346890	0.824166	0.468684	0.023*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Se1	0.01788 (15)	0.01843 (16)	0.01400 (15)	0.00192 (8)	0.00010 (10)	0.00198 (8)
N2	0.0245 (10)	0.0147 (9)	0.0200 (11)	0.0019 (8)	0.0059 (8)	0.0027 (8)
N3	0.0199 (10)	0.0135 (9)	0.0180 (10)	0.0013 (8)	0.0068 (8)	0.0017 (7)
C4	0.0150 (10)	0.0136 (9)	0.0112 (10)	0.0013 (8)	0.0038 (8)	0.0011 (8)
C5	0.0148 (10)	0.0156 (11)	0.0130 (11)	−0.0013 (8)	0.0034 (9)	−0.0015 (8)
C6	0.0164 (10)	0.0163 (10)	0.0117 (10)	−0.0020 (9)	0.0021 (8)	−0.0022 (8)
C7	0.0177 (11)	0.0213 (12)	0.0135 (11)	−0.0028 (9)	0.0017 (9)	−0.0002 (8)
C8	0.0199 (11)	0.0200 (11)	0.0130 (11)	−0.0020 (9)	0.0021 (9)	0.0013 (9)
C9	0.0218 (11)	0.0166 (10)	0.0128 (11)	−0.0008 (9)	0.0013 (9)	0.0013 (8)
C10	0.0170 (10)	0.0162 (10)	0.0136 (11)	−0.0025 (8)	0.0044 (9)	0.0010 (8)
C11	0.0184 (11)	0.0157 (10)	0.0166 (11)	−0.0058 (9)	0.0027 (9)	−0.0015 (9)
C12	0.0176 (10)	0.0127 (10)	0.0134 (10)	−0.0011 (8)	0.0022 (8)	−0.0013 (8)
C13	0.0154 (10)	0.0166 (10)	0.0109 (10)	0.0020 (9)	0.0027 (8)	0.0024 (8)
C14	0.0211 (11)	0.0197 (11)	0.0179 (12)	−0.0054 (10)	0.0040 (9)	−0.0016 (9)

Geometric parameters (Å, º) top

Se1—C13	1.841 (2)	C8—H8A	0.9900
Se1—N2	1.896 (2)	C8—H8B	0.9900
N2—N3	1.273 (3)	C9—C10	1.535 (3)
N3—C4	1.379 (3)	C9—H9A	0.9900
C4—C13	1.367 (3)	C9—H9B	0.9900
C4—C5	1.480 (3)	C10—C11	1.530 (3)
C5—C14	1.510 (3)	C10—H10A	0.9900
C5—C6	1.522 (3)	C10—H10B	0.9900
C5—H5	1.0000	C11—C12	1.544 (3)
C6—C14	1.507 (3)	C11—H11A	0.9900
C6—C7	1.511 (3)	C11—H11B	0.9900
C6—H6	1.0000	C12—C13	1.504 (3)
C7—C8	1.538 (3)	C12—H12A	0.9900
C7—H7A	0.9900	C12—H12B	0.9900
C7—H7B	0.9900	C14—H14A	0.9900
C8—C9	1.538 (3)	C14—H14B	0.9900

C13—Se1—N2	87.26 (10)	C8—C9—H9A	108.9
N3—N2—Se1	109.79 (16)	C10—C9—H9B	108.9
N2—N3—C4	118.1 (2)	C8—C9—H9B	108.9
C13—C4—N3	115.9 (2)	H9A—C9—H9B	107.7
C13—C4—C5	124.8 (2)	C11—C10—C9	113.5 (2)
N3—C4—C5	119.3 (2)	C11—C10—H10A	108.9
C4—C5—C14	121.9 (2)	C9—C10—H10A	108.9
C4—C5—C6	121.4 (2)	C11—C10—H10B	108.9
C14—C5—C6	59.64 (15)	C9—C10—H10B	108.9
C4—C5—H5	114.4	H10A—C10—H10B	107.7
C14—C5—H5	114.4	C10—C11—C12	113.84 (19)
C6—C5—H5	114.4	C10—C11—H11A	108.8
C14—C6—C7	120.4 (2)	C12—C11—H11A	108.8
C14—C6—C5	59.79 (15)	C10—C11—H11B	108.8
C7—C6—C5	119.6 (2)	C12—C11—H11B	108.8
C14—C6—H6	115.3	H11A—C11—H11B	107.7
C7—C6—H6	115.3	C13—C12—C11	112.17 (19)
C5—C6—H6	115.3	C13—C12—H12A	109.2
C6—C7—C8	114.7 (2)	C11—C12—H12A	109.2
C6—C7—H7A	108.6	C13—C12—H12B	109.2
C8—C7—H7A	108.6	C11—C12—H12B	109.2
C6—C7—H7B	108.6	H12A—C12—H12B	107.9
C8—C7—H7B	108.6	C4—C13—C12	127.5 (2)
H7A—C7—H7B	107.6	C4—C13—Se1	108.95 (17)
C7—C8—C9	114.6 (2)	C12—C13—Se1	123.47 (18)
C7—C8—H8A	108.6	C6—C14—C5	60.58 (15)
C9—C8—H8A	108.6	C6—C14—H14A	117.7
C7—C8—H8B	108.6	C5—C14—H14A	117.7
C9—C8—H8B	108.6	C6—C14—H14B	117.7
H8A—C8—H8B	107.6	C5—C14—H14B	117.7
C10—C9—C8	113.3 (2)	H14A—C14—H14B	114.8
C10—C9—H9A	108.9

C13—Se1—N2—N3	0.23 (17)	C7—C8—C9—C10	−89.4 (3)
Se1—N2—N3—C4	0.2 (3)	C8—C9—C10—C11	163.53 (19)
N2—N3—C4—C13	−0.8 (3)	C9—C10—C11—C12	−70.9 (3)
N2—N3—C4—C5	178.6 (2)	C10—C11—C12—C13	−62.5 (3)
C13—C4—C5—C14	179.2 (2)	N3—C4—C13—C12	−175.5 (2)
N3—C4—C5—C14	−0.1 (3)	C5—C4—C13—C12	5.1 (4)
C13—C4—C5—C6	−109.3 (3)	N3—C4—C13—Se1	0.9 (3)
N3—C4—C5—C6	71.3 (3)	C5—C4—C13—Se1	−178.47 (18)
C4—C5—C6—C14	−111.1 (2)	C11—C12—C13—C4	89.1 (3)
C4—C5—C6—C7	138.9 (2)	C11—C12—C13—Se1	−86.8 (2)
C14—C5—C6—C7	−110.0 (2)	N2—Se1—C13—C4	−0.62 (17)
C14—C6—C7—C8	−159.1 (2)	N2—Se1—C13—C12	175.9 (2)
C5—C6—C7—C8	−88.8 (3)	C7—C6—C14—C5	108.7 (2)
C6—C7—C8—C9	56.9 (3)	C4—C5—C14—C6	110.3 (2)

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