organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

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

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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

1,2,3-Selena­diazo­les are inter­mediates in the synthesis of other heterocycles (Detert, 2011[Detert, H. (2011). Targets in Heterocyclic Systems, 15, 1-49.]), strained (Bissinger et al., 1988[Bissinger, H.-J., Detert, H. & Meier, H. (1988). Liebigs Ann. Chem. pp. 221-224.]) and functionalized cyclo­alkynes. In addition, they are important for strain-accelerated 3 + 2-cyclo­additions (Ziegler & Wilms, 1950[Ziegler, K. & Wilms, H. (1950). Justus Liebigs Ann. Chem. 567, 1-43.]; Agard et al., 2004[Agard, N. J., Prescher, J. A. & Bertozzi, C. R. (2004). J. Am. Chem. Soc. 126, 15046-15047.]).

There is one mol­ecule of the title compound in the asymmetric unit (Fig. 1[link]), 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[link]). Within the strands, the enanti­omeric mol­ecules are connected via c-glide symmetry. Additionally, the hydrogen bond O16—H16⋯N14 (Table 1[link]) consolidates the structure. The geometry of the heterocycle matches nearly perfectly that of a recently reported congener (Detert & Schollmeyer, 2020[Detert, H. & Schollmeyer, D. (2020). IUCrData, 5, x201081.]). 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 DA 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]
Figure 1
Perspective view of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
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[Stoll, M. & Rouvé, A. (1947). Helv. Chim. Acta, 30, 1822-1836.]; Rühlmann, 1971[Rühlmann, K. (1971). Synthesis, pp. 236-253.]), acetyl­ation with acetic anhydride in pyridine, reaction with semicarbazide and oxidation with SeO2 (Lalezari et al., 1972[Lalezari, I., Shafiee, A. & Yalpani, M. (1972). J. Heterocycl. Chem. 9, 1411-1412.]) 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[link].

Table 2
Experimental details

Crystal data
Chemical formula C12H20N2OSe
Mr 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)
V3) 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[Stoe & Cie (2019). X-RED and X-AREA. Stoe & Cie, Darmstadt, Germany.]), absorption correction by Gaussian integration, analogous to Coppens (1970[Coppens, P. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 255-270. Copenhagen: Munksgaard.])]
Tmin, Tmax 0.294, 0.601
No. of measured, independent and observed [I > 2σ(I)] reflections 6412, 3020, 2721
Rint 0.017
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.41, −0.68
Computer programs: X-AREA WinXpose, Recipe and Integrate (Stoe & Cie, 2019[Stoe & Cie (2019). X-RED and X-AREA. Stoe & Cie, Darmstadt, Germany.]), SIR2004 (Burla et al., 2005[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.]), SHELXL2018/3 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and PLATON (Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.]).

Structural data


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
C12H20N2OSeF(000) = 592
Mr = 287.26Dx = 1.493 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 8.9261 (5) ÅCell parameters from 9207 reflections
b = 19.9277 (9) Åθ = 2.6–28.4°
c = 7.3829 (4) ŵ = 2.92 mm1
β = 103.321 (4)°T = 193 K
V = 1277.91 (12) Å3Block, colourless
Z = 40.71 × 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 focus2721 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm-1Rint = 0.017
rotation method, ω scansθmax = 27.9°, θmin = 2.6°
Absorption correction: integration
[X-Red32 (Stoe & Cie, 2019), absorption correction by Gaussian integration, analogous to Coppens (1970)]
h = 1110
Tmin = 0.294, Tmax = 0.601k = 2426
6412 measured reflectionsl = 99
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.029All 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 reflectionsΔρmax = 0.41 e Å3
216 parametersΔρmin = 0.67 e Å3
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
xyzUiso*/Ueq
Se10.82417 (2)0.15493 (2)0.75710 (3)0.03612 (8)
C20.6550 (2)0.16090 (9)0.5593 (2)0.0263 (3)
C30.6625 (2)0.15035 (10)0.3601 (3)0.0296 (4)
H3A0.755 (3)0.1703 (11)0.344 (3)0.034 (4)*
H3B0.579 (3)0.1750 (12)0.279 (3)0.034 (4)*
C40.6544 (3)0.07597 (12)0.3019 (3)0.0389 (5)
H4A0.687 (3)0.0747 (13)0.183 (4)0.044 (5)*
H4B0.730 (3)0.0518 (13)0.394 (4)0.044 (5)*
C50.4957 (3)0.04424 (11)0.2800 (3)0.0378 (5)
H5A0.462 (3)0.0536 (13)0.390 (4)0.046 (5)*
H5B0.499 (3)0.0049 (14)0.271 (4)0.046 (5)*
C60.3781 (3)0.06857 (11)0.1084 (3)0.0348 (4)
H6A0.372 (3)0.1168 (12)0.112 (3)0.034 (4)*
H6B0.420 (3)0.0588 (11)0.000 (3)0.034 (4)*
C70.2171 (3)0.03777 (13)0.0816 (3)0.0470 (6)
H7A0.221 (3)0.0077 (15)0.071 (4)0.058 (6)*
H7B0.149 (3)0.0529 (14)0.043 (4)0.058 (6)*
C80.1357 (3)0.05394 (12)0.2377 (3)0.0459 (5)
H8A0.200 (3)0.0389 (14)0.359 (4)0.056 (6)*
H8B0.040 (3)0.0265 (14)0.224 (4)0.056 (6)*
C90.0886 (2)0.12727 (13)0.2466 (3)0.0388 (5)
H9A0.151 (3)0.1562 (12)0.186 (4)0.041 (5)*
H9B0.010 (3)0.1333 (13)0.172 (4)0.041 (5)*
C100.0892 (2)0.15211 (12)0.4425 (3)0.0356 (4)
H10A0.049 (3)0.1978 (14)0.435 (3)0.042 (5)*
H10B0.016 (3)0.1240 (13)0.494 (3)0.042 (5)*
C110.2460 (2)0.15032 (10)0.5800 (3)0.0286 (4)
H11A0.282 (3)0.1034 (13)0.606 (3)0.036 (4)*
H11B0.238 (3)0.1680 (12)0.694 (4)0.036 (4)*
C120.36991 (19)0.19034 (9)0.5151 (2)0.0235 (3)
H120.372 (2)0.1780 (10)0.388 (3)0.019 (5)*
C130.52951 (19)0.17624 (9)0.6290 (2)0.0229 (3)
N140.55574 (18)0.18287 (8)0.8195 (2)0.0273 (3)
N150.6932 (2)0.17459 (9)0.9149 (2)0.0337 (4)
O160.33526 (16)0.26009 (7)0.52548 (19)0.0298 (3)
H160.385 (3)0.2790 (13)0.471 (4)0.042 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Se10.02420 (11)0.05973 (15)0.02309 (11)0.00772 (8)0.00266 (7)0.00148 (8)
C20.0242 (8)0.0346 (9)0.0195 (8)0.0024 (7)0.0041 (6)0.0016 (6)
C30.0259 (9)0.0447 (11)0.0199 (8)0.0060 (8)0.0087 (7)0.0013 (7)
C40.0465 (12)0.0474 (12)0.0247 (9)0.0209 (10)0.0122 (8)0.0004 (8)
C50.0617 (14)0.0285 (10)0.0255 (9)0.0074 (9)0.0147 (9)0.0011 (7)
C60.0507 (12)0.0313 (10)0.0237 (9)0.0019 (8)0.0116 (8)0.0038 (7)
C70.0634 (15)0.0433 (13)0.0350 (11)0.0173 (11)0.0127 (10)0.0138 (10)
C80.0552 (13)0.0454 (13)0.0395 (12)0.0232 (11)0.0162 (10)0.0096 (9)
C90.0289 (10)0.0558 (13)0.0286 (9)0.0081 (9)0.0002 (8)0.0025 (9)
C100.0237 (9)0.0506 (12)0.0325 (10)0.0025 (8)0.0063 (7)0.0029 (8)
C110.0244 (8)0.0383 (10)0.0235 (8)0.0032 (7)0.0061 (7)0.0013 (7)
C120.0227 (8)0.0293 (9)0.0191 (7)0.0020 (6)0.0060 (6)0.0017 (6)
C130.0239 (8)0.0269 (8)0.0183 (7)0.0003 (6)0.0058 (6)0.0006 (6)
N140.0288 (7)0.0346 (8)0.0187 (7)0.0013 (6)0.0059 (6)0.0008 (6)
N150.0319 (8)0.0479 (10)0.0204 (7)0.0047 (7)0.0042 (6)0.0000 (6)
O160.0314 (7)0.0297 (7)0.0303 (7)0.0044 (5)0.0113 (5)0.0029 (5)
Geometric parameters (Å, º) top
Se1—C21.8467 (18)C8—C91.526 (4)
Se1—N151.8723 (17)C8—H8A0.99 (3)
C2—C131.371 (2)C8—H8B1.00 (3)
C2—C31.502 (2)C9—C101.528 (3)
C3—C41.540 (3)C9—H9A0.98 (3)
C3—H3A0.95 (2)C9—H9B0.93 (3)
C3—H3B0.97 (2)C10—C111.529 (3)
C4—C51.525 (3)C10—H10A0.98 (3)
C4—H4A0.99 (3)C10—H10B1.00 (3)
C4—H4B0.97 (3)C11—C121.527 (2)
C5—C61.526 (3)C11—H11A0.99 (2)
C5—H5A0.94 (3)C11—H11B0.93 (3)
C5—H5B0.98 (3)C12—O161.430 (2)
C6—C71.533 (3)C12—C131.505 (2)
C6—H6A0.96 (2)C12—H120.97 (2)
C6—H6B0.97 (2)C13—N141.378 (2)
C7—C81.532 (3)N14—N151.276 (2)
C7—H7A0.91 (3)O16—H160.77 (3)
C7—H7B1.03 (3)
C2—Se1—N1587.97 (7)C9—C8—H8A111.0 (17)
C13—C2—C3128.55 (16)C7—C8—H8A109.7 (17)
C13—C2—Se1107.90 (12)C9—C8—H8B106.9 (17)
C3—C2—Se1123.55 (13)C7—C8—H8B110.7 (17)
C2—C3—C4113.45 (16)H8A—C8—H8B103 (2)
C2—C3—H3A107.5 (14)C8—C9—C10114.19 (19)
C4—C3—H3A110.8 (14)C8—C9—H9A110.9 (14)
C2—C3—H3B109.0 (14)C10—C9—H9A111.2 (16)
C4—C3—H3B109.5 (14)C8—C9—H9B109.3 (16)
H3A—C3—H3B106 (2)C10—C9—H9B108.2 (16)
C5—C4—C3114.30 (16)H9A—C9—H9B102 (2)
C5—C4—H4A110.8 (15)C9—C10—C11115.09 (17)
C3—C4—H4A105.5 (15)C9—C10—H10A109.0 (15)
C5—C4—H4B110.2 (15)C11—C10—H10A109.2 (15)
C3—C4—H4B107.5 (15)C9—C10—H10B108.6 (15)
H4A—C4—H4B108 (2)C11—C10—H10B108.1 (14)
C4—C5—C6113.62 (17)H10A—C10—H10B107 (2)
C4—C5—H5A107.3 (16)C12—C11—C10113.45 (16)
C6—C5—H5A110.8 (16)C12—C11—H11A109.0 (14)
C4—C5—H5B112.2 (16)C10—C11—H11A111.0 (14)
C6—C5—H5B106.6 (15)C12—C11—H11B107.5 (15)
H5A—C5—H5B106 (2)C10—C11—H11B109.8 (15)
C5—C6—C7115.13 (19)H11A—C11—H11B106 (2)
C5—C6—H6A108.9 (14)O16—C12—C13109.89 (14)
C7—C6—H6A110.5 (14)O16—C12—C11108.02 (14)
C5—C6—H6B107.3 (14)C13—C12—C11112.81 (14)
C7—C6—H6B109.7 (14)O16—C12—H12110.3 (12)
H6A—C6—H6B104.7 (19)C13—C12—H12105.6 (12)
C8—C7—C6114.35 (18)C11—C12—H12110.2 (12)
C8—C7—H7A107.9 (19)C2—C13—N14116.31 (15)
C6—C7—H7A110.7 (19)C2—C13—C12125.62 (15)
C8—C7—H7B109.3 (17)N14—C13—C12117.96 (14)
C6—C7—H7B109.9 (16)N15—N14—C13117.79 (15)
H7A—C7—H7B104 (2)N14—N15—Se1110.03 (12)
C9—C8—C7114.6 (2)C12—O16—H16107 (2)
N15—Se1—C2—C130.38 (14)C10—C11—C12—C13167.50 (16)
N15—Se1—C2—C3179.79 (17)C3—C2—C13—N14179.73 (18)
C13—C2—C3—C496.5 (2)Se1—C2—C13—N140.5 (2)
Se1—C2—C3—C483.7 (2)C3—C2—C13—C124.2 (3)
C2—C3—C4—C572.5 (2)Se1—C2—C13—C12175.63 (14)
C3—C4—C5—C671.9 (2)O16—C12—C13—C2108.7 (2)
C4—C5—C6—C7179.99 (18)C11—C12—C13—C2130.74 (19)
C5—C6—C7—C862.7 (3)O16—C12—C13—N1467.4 (2)
C6—C7—C8—C968.6 (3)C11—C12—C13—N1453.2 (2)
C7—C8—C9—C10149.0 (2)C2—C13—N14—N150.3 (3)
C8—C9—C10—C1162.1 (3)C12—C13—N14—N15176.12 (17)
C9—C10—C11—C1257.0 (2)C13—N14—N15—Se10.1 (2)
C10—C11—C12—O1670.83 (19)C2—Se1—N15—N140.26 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O16—H16···N14i0.77 (3)2.22 (3)2.976 (2)170 (3)
Symmetry code: (i) x, y+1/2, z1/2.
 

References

First citationAgard, N. J., Prescher, J. A. & Bertozzi, C. R. (2004). J. Am. Chem. Soc. 126, 15046–15047.  CrossRef PubMed CAS Google Scholar
First citationBissinger, H.-J., Detert, H. & Meier, H. (1988). Liebigs Ann. Chem. pp. 221–224.  CrossRef Google Scholar
First citationBurla, 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
First citationCoppens, P. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 255–270. Copenhagen: Munksgaard.  Google Scholar
First citationDetert, H. (2011). Targets in Heterocyclic Systems, 15, 1–49.  CAS Google Scholar
First citationDetert, H. & Schollmeyer, D. (2020). IUCrData, 5, x201081.  Google Scholar
First citationLalezari, I., Shafiee, A. & Yalpani, M. (1972). J. Heterocycl. Chem. 9, 1411–1412.  CrossRef CAS Google Scholar
First citationRühlmann, K. (1971). Synthesis, pp. 236–253.  Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSpek, A. L. (2020). Acta Cryst. E76, 1–11.  Web of Science CrossRef IUCr Journals Google Scholar
First citationStoe & Cie (2019). X-RED and X-AREA. Stoe & Cie, Darmstadt, Germany.  Google Scholar
First citationStoll, M. & Rouvé, A. (1947). Helv. Chim. Acta, 30, 1822–1836.  CrossRef CAS PubMed Google Scholar
First citationZiegler, K. & Wilms, H. (1950). Justus Liebigs Ann. Chem. 567, 1–43.  CrossRef CAS Google Scholar

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