rac-11-Selena-12,13-di­aza­bicyclo­[10.3.0]penta­deca-10a(13a),12-dien-1-ol

Detert, H.; Schollmeyer, D.

doi:10.1107/S2414314621000699

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 6| Part 1| January 2021| x210069

https://doi.org/10.1107/S2414314621000699

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rac-11-Selena-12,13-diazabicyclo[10.3.0]pentadeca-10a(13a),12-dien-1-ol

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 M. Bolte, Goethe-Universität Frankfurt, Germany (Received 19 January 2021; accepted 20 January 2021; online 26 January 2021)

The title compound, C₁₂H₂₀N₂OSe, crystallizes in strands of enantiomeric molecules connected via O—H⋯N hydrogen bonds. There are only slight deviations from an ideal gauche conformation in the decamethylene chain, indicating just a little strain.

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

CCDC reference: 2057509

Structure description

1,2,3-Selenadiazoles are intermediates in the synthesis of other heterocycles (Detert, 2011 ), strained (Bissinger et al., 1988 ) and functionalized cycloalkynes. In addition, they are important for strain-accelerated 3 + 2-cycloadditions (Ziegler & Wilms, 1950 ; Agard et al., 2004 ).

There is one molecule of the title compound in the asymmetric unit (Fig. 1), resulting in four molecules filling the unit cell. The crystal is formed from two strands of molecules without directional bonding between the strands (Fig. 2). Within the strands, the enantiomeric molecules are connected via c-glide symmetry. Additionally, the hydrogen bond O16—H16⋯N14 (Table 1) consolidates the structure. The geometry of the heterocycle matches nearly perfectly that of a recently reported congener (Detert & Schollmeyer, 2020 ). Within the decamethylene tether, strain is only visible at C7—C8—C9—C10: the torsion angle of −149.0 (2)° differs by more than 30° from the ideal trans conformation. C—C—C bond angles in the tether are 112–115°, giving further proof of a nearly strain-free ring system.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O16—H16⋯N14ⁱ	0.77 (3)	2.22 (3)	2.976 (2)	170 (3)
Symmetry code: (i) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

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

Figure 2
Partial packing diagram of the title compound. View along the a-axis. The dotted line indicates the O—H⋯N hydrogen bond.

Synthesis and crystallization

Acyloin condensation of diethyl dodecanedioate (Stoll & Rouvé, 1947 ; Rühlmann, 1971 ), acetylation with acetic anhydride in pyridine, reaction with semicarbazide and oxidation with SeO₂ (Lalezari et al., 1972 ) to acetoxycyclododeceno-1,2,3-selenadiazole followed by aminolysis of the ester led to the title compound as a viscous oil. Crystallization via slow evaporation of a solution in CDCl₃ gave colorless crystals with m.p. = 380 K. Characterization: ¹H NMR (CDCl₃, 400 MHz): 4.98 (dd, 1 H), 3.14 (ddd, 1 H), 3.01 (ddd, 1 H), 2.30–2.00 (m, 3 H), 1.88 (m, 1 H), 1.62 (m, 1 H). 1.55–0.90 (m, 13 H). ¹³C-NMR (CDCl₃, 75 MHz): 163.3 (Se-satellites, J = 134 Hz), 162.1 (Se-satellites, J = 27 Hz), 37.1, 32.2, 25.0, 24.9, 24.9, 24.3, 24.3, 22.8, 22.8, 22.1. ⁷⁷Se NMR: (CDCl3, 76.4 MHz, Me₂Se = 0 p.p.m.) δ = 1528.23 p.p.m. MS (EI) m/z = 174 (9%, M—N₂—Se), 146 (14%, M—N₂—Se—C₂H₄, 94 (100%).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₂₀N₂OSe
M_r	287.26
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	193
a, b, c (Å)	8.9261 (5), 19.9277 (9), 7.3829 (4)
β (°)	103.321 (4)
V (Å³)	1277.91 (12)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	2.92
Crystal size (mm)	0.71 × 0.26 × 0.20

Data collection
Diffractometer	Stoe IPDS 2T
Absorption correction	Integration [X-RED32 (Stoe & Cie, 2019 ), absorption correction by Gaussian integration, analogous to Coppens (1970 )]
T_min, T_max	0.294, 0.601
No. of measured, independent and observed [I > 2σ(I)] reflections	6412, 3020, 2721
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.070, 1.14
No. of reflections	3020
No. of parameters	216
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.41, −0.68
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: 2057509

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314621000699/bt4106sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314621000699/bt4106Isup2.hkl

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-11-Selena-12,13-diazabicyclo[10.3.0]pentadeca-10a(13a),12-dien-1-ol top

Crystal data top

C₁₂H₂₀N₂OSe	F(000) = 592
M_r = 287.26	D_x = 1.493 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 8.9261 (5) Å	Cell parameters from 9207 reflections
b = 19.9277 (9) Å	θ = 2.6–28.4°
c = 7.3829 (4) Å	µ = 2.92 mm⁻¹
β = 103.321 (4)°	T = 193 K
V = 1277.91 (12) Å³	Block, colourless
Z = 4	0.71 × 0.26 × 0.20 mm

Data collection top

Stoe IPDS 2T diffractometer	3020 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	2721 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm^-1	R_int = 0.017
rotation method, ω scans	θ_max = 27.9°, θ_min = 2.6°
Absorption correction: integration [X-Red32 (Stoe & Cie, 2019), absorption correction by Gaussian integration, analogous to Coppens (1970)]	h = −11→10
T_min = 0.294, T_max = 0.601	k = −24→26
6412 measured reflections	l = −9→9

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.029	All H-atom parameters refined
wR(F²) = 0.070	w = 1/[σ²(F_o²) + (0.0304P)² + 0.7552P] where P = (F_o² + 2F_c²)/3
S = 1.14	(Δ/σ)_max = 0.001
3020 reflections	Δρ_max = 0.41 e Å⁻³
216 parameters	Δρ_min = −0.67 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 were refined with isotropic displacement parameters constraining the Us of two H atoms bonded to the same C atom to the same value.

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

	x	y	z	U_iso*/U_eq
Se1	0.82417 (2)	0.15493 (2)	0.75710 (3)	0.03612 (8)
C2	0.6550 (2)	0.16090 (9)	0.5593 (2)	0.0263 (3)
C3	0.6625 (2)	0.15035 (10)	0.3601 (3)	0.0296 (4)
H3A	0.755 (3)	0.1703 (11)	0.344 (3)	0.034 (4)*
H3B	0.579 (3)	0.1750 (12)	0.279 (3)	0.034 (4)*
C4	0.6544 (3)	0.07597 (12)	0.3019 (3)	0.0389 (5)
H4A	0.687 (3)	0.0747 (13)	0.183 (4)	0.044 (5)*
H4B	0.730 (3)	0.0518 (13)	0.394 (4)	0.044 (5)*
C5	0.4957 (3)	0.04424 (11)	0.2800 (3)	0.0378 (5)
H5A	0.462 (3)	0.0536 (13)	0.390 (4)	0.046 (5)*
H5B	0.499 (3)	−0.0049 (14)	0.271 (4)	0.046 (5)*
C6	0.3781 (3)	0.06857 (11)	0.1084 (3)	0.0348 (4)
H6A	0.372 (3)	0.1168 (12)	0.112 (3)	0.034 (4)*
H6B	0.420 (3)	0.0588 (11)	0.000 (3)	0.034 (4)*
C7	0.2171 (3)	0.03777 (13)	0.0816 (3)	0.0470 (6)
H7A	0.221 (3)	−0.0077 (15)	0.071 (4)	0.058 (6)*
H7B	0.149 (3)	0.0529 (14)	−0.043 (4)	0.058 (6)*
C8	0.1357 (3)	0.05394 (12)	0.2377 (3)	0.0459 (5)
H8A	0.200 (3)	0.0389 (14)	0.359 (4)	0.056 (6)*
H8B	0.040 (3)	0.0265 (14)	0.224 (4)	0.056 (6)*
C9	0.0886 (2)	0.12727 (13)	0.2466 (3)	0.0388 (5)
H9A	0.151 (3)	0.1562 (12)	0.186 (4)	0.041 (5)*
H9B	−0.010 (3)	0.1333 (13)	0.172 (4)	0.041 (5)*
C10	0.0892 (2)	0.15211 (12)	0.4425 (3)	0.0356 (4)
H10A	0.049 (3)	0.1978 (14)	0.435 (3)	0.042 (5)*
H10B	0.016 (3)	0.1240 (13)	0.494 (3)	0.042 (5)*
C11	0.2460 (2)	0.15032 (10)	0.5800 (3)	0.0286 (4)
H11A	0.282 (3)	0.1034 (13)	0.606 (3)	0.036 (4)*
H11B	0.238 (3)	0.1680 (12)	0.694 (4)	0.036 (4)*
C12	0.36991 (19)	0.19034 (9)	0.5151 (2)	0.0235 (3)
H12	0.372 (2)	0.1780 (10)	0.388 (3)	0.019 (5)*
C13	0.52951 (19)	0.17624 (9)	0.6290 (2)	0.0229 (3)
N14	0.55574 (18)	0.18287 (8)	0.8195 (2)	0.0273 (3)
N15	0.6932 (2)	0.17459 (9)	0.9149 (2)	0.0337 (4)
O16	0.33526 (16)	0.26009 (7)	0.52548 (19)	0.0298 (3)
H16	0.385 (3)	0.2790 (13)	0.471 (4)	0.042 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Se1	0.02420 (11)	0.05973 (15)	0.02309 (11)	0.00772 (8)	0.00266 (7)	0.00148 (8)
C2	0.0242 (8)	0.0346 (9)	0.0195 (8)	0.0024 (7)	0.0041 (6)	0.0016 (6)
C3	0.0259 (9)	0.0447 (11)	0.0199 (8)	0.0060 (8)	0.0087 (7)	0.0013 (7)
C4	0.0465 (12)	0.0474 (12)	0.0247 (9)	0.0209 (10)	0.0122 (8)	−0.0004 (8)
C5	0.0617 (14)	0.0285 (10)	0.0255 (9)	0.0074 (9)	0.0147 (9)	0.0011 (7)
C6	0.0507 (12)	0.0313 (10)	0.0237 (9)	−0.0019 (8)	0.0116 (8)	−0.0038 (7)
C7	0.0634 (15)	0.0433 (13)	0.0350 (11)	−0.0173 (11)	0.0127 (10)	−0.0138 (10)
C8	0.0552 (13)	0.0454 (13)	0.0395 (12)	−0.0232 (11)	0.0162 (10)	−0.0096 (9)
C9	0.0289 (10)	0.0558 (13)	0.0286 (9)	−0.0081 (9)	0.0002 (8)	−0.0025 (9)
C10	0.0237 (9)	0.0506 (12)	0.0325 (10)	−0.0025 (8)	0.0063 (7)	−0.0029 (8)
C11	0.0244 (8)	0.0383 (10)	0.0235 (8)	−0.0032 (7)	0.0061 (7)	−0.0013 (7)
C12	0.0227 (8)	0.0293 (9)	0.0191 (7)	0.0020 (6)	0.0060 (6)	−0.0017 (6)
C13	0.0239 (8)	0.0269 (8)	0.0183 (7)	−0.0003 (6)	0.0058 (6)	−0.0006 (6)
N14	0.0288 (7)	0.0346 (8)	0.0187 (7)	0.0013 (6)	0.0059 (6)	−0.0008 (6)
N15	0.0319 (8)	0.0479 (10)	0.0204 (7)	0.0047 (7)	0.0042 (6)	0.0000 (6)
O16	0.0314 (7)	0.0297 (7)	0.0303 (7)	0.0044 (5)	0.0113 (5)	0.0029 (5)

Geometric parameters (Å, º) top

Se1—C2	1.8467 (18)	C8—C9	1.526 (4)
Se1—N15	1.8723 (17)	C8—H8A	0.99 (3)
C2—C13	1.371 (2)	C8—H8B	1.00 (3)
C2—C3	1.502 (2)	C9—C10	1.528 (3)
C3—C4	1.540 (3)	C9—H9A	0.98 (3)
C3—H3A	0.95 (2)	C9—H9B	0.93 (3)
C3—H3B	0.97 (2)	C10—C11	1.529 (3)
C4—C5	1.525 (3)	C10—H10A	0.98 (3)
C4—H4A	0.99 (3)	C10—H10B	1.00 (3)
C4—H4B	0.97 (3)	C11—C12	1.527 (2)
C5—C6	1.526 (3)	C11—H11A	0.99 (2)
C5—H5A	0.94 (3)	C11—H11B	0.93 (3)
C5—H5B	0.98 (3)	C12—O16	1.430 (2)
C6—C7	1.533 (3)	C12—C13	1.505 (2)
C6—H6A	0.96 (2)	C12—H12	0.97 (2)
C6—H6B	0.97 (2)	C13—N14	1.378 (2)
C7—C8	1.532 (3)	N14—N15	1.276 (2)
C7—H7A	0.91 (3)	O16—H16	0.77 (3)
C7—H7B	1.03 (3)

C2—Se1—N15	87.97 (7)	C9—C8—H8A	111.0 (17)
C13—C2—C3	128.55 (16)	C7—C8—H8A	109.7 (17)
C13—C2—Se1	107.90 (12)	C9—C8—H8B	106.9 (17)
C3—C2—Se1	123.55 (13)	C7—C8—H8B	110.7 (17)
C2—C3—C4	113.45 (16)	H8A—C8—H8B	103 (2)
C2—C3—H3A	107.5 (14)	C8—C9—C10	114.19 (19)
C4—C3—H3A	110.8 (14)	C8—C9—H9A	110.9 (14)
C2—C3—H3B	109.0 (14)	C10—C9—H9A	111.2 (16)
C4—C3—H3B	109.5 (14)	C8—C9—H9B	109.3 (16)
H3A—C3—H3B	106 (2)	C10—C9—H9B	108.2 (16)
C5—C4—C3	114.30 (16)	H9A—C9—H9B	102 (2)
C5—C4—H4A	110.8 (15)	C9—C10—C11	115.09 (17)
C3—C4—H4A	105.5 (15)	C9—C10—H10A	109.0 (15)
C5—C4—H4B	110.2 (15)	C11—C10—H10A	109.2 (15)
C3—C4—H4B	107.5 (15)	C9—C10—H10B	108.6 (15)
H4A—C4—H4B	108 (2)	C11—C10—H10B	108.1 (14)
C4—C5—C6	113.62 (17)	H10A—C10—H10B	107 (2)
C4—C5—H5A	107.3 (16)	C12—C11—C10	113.45 (16)
C6—C5—H5A	110.8 (16)	C12—C11—H11A	109.0 (14)
C4—C5—H5B	112.2 (16)	C10—C11—H11A	111.0 (14)
C6—C5—H5B	106.6 (15)	C12—C11—H11B	107.5 (15)
H5A—C5—H5B	106 (2)	C10—C11—H11B	109.8 (15)
C5—C6—C7	115.13 (19)	H11A—C11—H11B	106 (2)
C5—C6—H6A	108.9 (14)	O16—C12—C13	109.89 (14)
C7—C6—H6A	110.5 (14)	O16—C12—C11	108.02 (14)
C5—C6—H6B	107.3 (14)	C13—C12—C11	112.81 (14)
C7—C6—H6B	109.7 (14)	O16—C12—H12	110.3 (12)
H6A—C6—H6B	104.7 (19)	C13—C12—H12	105.6 (12)
C8—C7—C6	114.35 (18)	C11—C12—H12	110.2 (12)
C8—C7—H7A	107.9 (19)	C2—C13—N14	116.31 (15)
C6—C7—H7A	110.7 (19)	C2—C13—C12	125.62 (15)
C8—C7—H7B	109.3 (17)	N14—C13—C12	117.96 (14)
C6—C7—H7B	109.9 (16)	N15—N14—C13	117.79 (15)
H7A—C7—H7B	104 (2)	N14—N15—Se1	110.03 (12)
C9—C8—C7	114.6 (2)	C12—O16—H16	107 (2)

N15—Se1—C2—C13	0.38 (14)	C10—C11—C12—C13	−167.50 (16)
N15—Se1—C2—C3	−179.79 (17)	C3—C2—C13—N14	179.73 (18)
C13—C2—C3—C4	−96.5 (2)	Se1—C2—C13—N14	−0.5 (2)
Se1—C2—C3—C4	83.7 (2)	C3—C2—C13—C12	−4.2 (3)
C2—C3—C4—C5	72.5 (2)	Se1—C2—C13—C12	175.63 (14)
C3—C4—C5—C6	71.9 (2)	O16—C12—C13—C2	−108.7 (2)
C4—C5—C6—C7	−179.99 (18)	C11—C12—C13—C2	130.74 (19)
C5—C6—C7—C8	62.7 (3)	O16—C12—C13—N14	67.4 (2)
C6—C7—C8—C9	68.6 (3)	C11—C12—C13—N14	−53.2 (2)
C7—C8—C9—C10	−149.0 (2)	C2—C13—N14—N15	0.3 (3)
C8—C9—C10—C11	62.1 (3)	C12—C13—N14—N15	−176.12 (17)
C9—C10—C11—C12	57.0 (2)	C13—N14—N15—Se1	0.1 (2)
C10—C11—C12—O16	70.83 (19)	C2—Se1—N15—N14	−0.26 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O16—H16···N14ⁱ	0.77 (3)	2.22 (3)	2.976 (2)	170 (3)

Symmetry code: (i) x, −y+1/2, z−1/2.

References

Agard, N. J., Prescher, J. A. & Bertozzi, C. R. (2004). J. Am. Chem. Soc. 126, 15046–15047. CrossRef PubMed CAS Google Scholar
Bissinger, H.-J., Detert, H. & Meier, H. (1988). Liebigs Ann. Chem. pp. 221–224. CrossRef Google Scholar
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Coppens, P. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 255–270. Copenhagen: Munksgaard. Google Scholar
Detert, H. (2011). Targets in Heterocyclic Systems, 15, 1–49. CAS Google Scholar
Detert, H. & Schollmeyer, D. (2020). IUCrData, 5, x201081. Google Scholar
Lalezari, I., Shafiee, A. & Yalpani, M. (1972). J. Heterocycl. Chem. 9, 1411–1412. CrossRef CAS Google Scholar
Rühlmann, K. (1971). Synthesis, pp. 236–253. Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Spek, A. L. (2020). Acta Cryst. E76, 1–11. Web of Science CrossRef IUCr Journals Google Scholar
Stoe & Cie (2019). X-RED and X-AREA. Stoe & Cie, Darmstadt, Germany. Google Scholar
Stoll, M. & Rouvé, A. (1947). Helv. Chim. Acta, 30, 1822–1836. CrossRef CAS PubMed Google Scholar
Ziegler, K. & Wilms, H. (1950). Justus Liebigs Ann. Chem. 567, 1–43. CrossRef CAS Google Scholar

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