organic compounds
rac-11-Selena-12,13-diazabicyclo[10.3.0]pentadeca-10a(13a),12-dien-1-ol
aJohannes Gutenberg University Mainz, Department of Chemistry, Duesbergweg 10-14, 55099 Mainz, Germany
*Correspondence e-mail: detert@uni-mainz.de
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 ), resulting in four molecules filling the 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.
(Fig. 1Synthesis 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 .
details are summarized in Table 2Structural data
CCDC reference: 2057509
https://doi.org/10.1107/S2414314621000699/bt4106sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314621000699/bt4106Isup2.hkl
Data collection: X-AREA WinXpose (Stoe & Cie, 2019); cell
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).C12H20N2OSe | F(000) = 592 |
Mr = 287.26 | Dx = 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 |
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 | Rint = 0.017 |
rotation method, ω scans | θmax = 27.9°, θmin = 2.6° |
Absorption correction: integration [X-Red32 (Stoe & Cie, 2019), absorption correction by Gaussian integration, analogous to Coppens (1970)] | h = −11→10 |
Tmin = 0.294, Tmax = 0.601 | k = −24→26 |
6412 measured reflections | l = −9→9 |
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(Fo2) + (0.0304P)2 + 0.7552P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max = 0.001 |
3020 reflections | Δρmax = 0.41 e Å−3 |
216 parameters | Δρmin = −0.67 e Å−3 |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
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)* |
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) |
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) |
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. |
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