rac-4H,5H,6H,7H,8H,9H,10H,11H-Cyclo­deca­[d][1,2,3]selena­diazole-8-carb­oxy­lic acid

Schollmeyer, D.; Detert, H.

doi:10.1107/S2414314625002421

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 10| Part 3| March 2025| x250242

https://doi.org/10.1107/S2414314625002421

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rac-4H,5H,6H,7H,8H,9H,10H,11H-Cyclodeca[d][1,2,3]selenadiazole-8-carboxylic acid

Dieter Schollmeyer ^a and Heiner Detert ^a ^*

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

Edited by L. Van Meervelt, Katholieke Universiteit Leuven, Belgium (Received 6 March 2025; accepted 17 March 2025; online 25 March 2025)

The chair-shaped molecules in the title crystal, C₁₁H₁₆N₂O₂Se, consist of two pairs of enantiomers with two conformations (ratio 1:3), differing only in the position of two ring carbon atoms. Two molecules are connected via carboxylic acid hydrogen bridges.

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

CCDC reference: 2431691

Structure description

The title compound, C₁₁H₁₆N₂O₂Se, was prepared in a project focusing on transannular cyclizations in medium-sized cycloalkynes (Detert et al., 1992 ; Detert & Schollmeyer, 2021 ; Krämer et al., 2009 ). The unit cell contains four chair-shaped molecules, two pairs of enantiomers with different conformations of the octamethylene chain in an approximate ratio of 1:3 (Fig. 1). The selenadiazole ring is planar to within 0.005 (2) Å; the adjacent carbon atoms are slightly below this plane [C5: −0.029 (2) Å, C12: −0.087 (2) Å]. Torsion angles in the octamethylene tether of the main conformer are C4—C5—C6—C7: −49.4 (3)°, C5—C6—C7—C8: −76.3 (3)°, C6—C7—C8—C9: 70.8 (4)°, C7—C8—C9—C10: 65.5 (5)°, C8—C9—C10—C11: −150.4 (3)°, C9—C10—C11—C12: 62.8 (3)°, and C10—C11—C12—C13: 49.3 (3)°. Interestingly, the positions of most atoms of both conformers are essentially identical, differing only in C8A and C9A and their attached H atoms. This change provokes a torsion angle C8A—C9A—C10—C11: −71.5 (9)°. Whereas the C9—H9 bond in the main conformer points in the direction of the selenadiazole plane, this is inverted in the minor conformer. In the extended structure, two molecules are connected via H-bridging carboxylic acids, the distances are O16—H16 = 0.94 (3) Å and O15—H15 = 1.69 (3) Å (Table 1, Fig. 2). With an angle of 174 (3)°, the hydrogen bond is slightly bent. The planes of selenadiazole and carboxylic acid dimer are close to parallel, the dihedral angle being only 7.1 (1)°. The disorder is the consequence of the flexibility of the large ring.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O16—H16⋯O15ⁱ	0.94 (3)	1.69 (3)	2.630 (2)	174 (3)
Symmetry code: (i) .

Figure 1
View of the title compound with displacement ellipsoids drawn at the 50% probability level and the minor component shown with red lines (Macrae et al., 2020

Figure 2
Part of the packing diagram viewed along the a-axis direction. Hydrogen bonds are indicated by dashed lines. Only the major disorder component is shown for clarity (Spek, 2009

Synthesis and crystallization

The sample was prepared by G. Krämer (1996 ) from 6-hydroxymethyldecan-1-ol (Becker & Chappuis, 1979 ) via Jones oxidation, formation of the semicarbazone and reaction with selenous acid in 44% overall yield, m.p. 418 K. Crystallization by slow evaporation of a solution in methanol/dichlormethane. ¹H-NMR (400 MHz, CDCl₃): 11.0 (vbs, 1 H), 3.2 (m, 3H), 3.05 (m, 1H), 2.62 (m, 1 H), 2.22 (m, 1 H), 1.90 (m, 3 H), 1.80-1.50 (m, 3H), 1.30 (m, 2 H), 1.03 (m, 1 H). ¹³C-NMR (100 MHz, CDCl₃): 181.6, 159.7, 159.6, 41.5, 29.4, 28.5, 27.4, 25.5, 22.5, 20.0.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. Atoms C8 and C9 and their attached H atoms are disordered over two positions [0.759 (8):0.241 (8)].

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₆N₂O₂Se
M_r	287.22
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	120
a, b, c (Å)	7.4231 (4), 13.2052 (5), 12.2802 (7)
β (°)	99.725 (4)
V (Å³)	1186.45 (10)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	3.15
Crystal size (mm)	0.50 × 0.42 × 0.32

Data collection
Diffractometer	Stoe Stadivari
Absorption correction	Integration (X-RED32; Stoe & Cie, 2020 )
T_min, T_max	0.277, 0.408
No. of measured, independent and observed [I > 2σ(I)] reflections	7535, 2993, 2458
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.671

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.085, 1.04
No. of reflections	2993
No. of parameters	168
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.61, −0.62
Computer programs: X-AREA WinXpose, Recipe and Integrate (Stoe & Cie, 2020), SHELXT2014 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ), PLATON (Spek, 2009 ) and Mercury (Macrae et al., 2020 ).

Structural data

CCDC reference: 2431691

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314625002421/vm4065sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314625002421/vm4065Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314625002421/vm4065Isup3.cml

checkCIF report

Computing details top

rac-4H,5H,6H,7H,8H,9H,10H,11H-Cyclodeca[d][1,2,3]selenadiazole-8-carboxylic acid top

Crystal data top

C₁₁H₁₆N₂O₂Se	F(000) = 584
M_r = 287.22	D_x = 1.608 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 7.4231 (4) Å	Cell parameters from 13455 reflections
b = 13.2052 (5) Å	θ = 2.3–33.3°
c = 12.2802 (7) Å	µ = 3.15 mm⁻¹
β = 99.725 (4)°	T = 120 K
V = 1186.45 (10) Å³	Block, brown
Z = 4	0.50 × 0.42 × 0.32 mm

Data collection top

Stoe Stadivari diffractometer	2993 independent reflections
Radiation source: Axo Mo	2458 reflections with I > 2σ(I)
Detector resolution: 13.33 pixels mm^-1	R_int = 0.019
rotation method, ω scans	θ_max = 28.5°, θ_min = 2.3°
Absorption correction: integration (X-Red32; Stoe & Cie, 2020)	h = −9→8
T_min = 0.277, T_max = 0.408	k = −17→11
7535 measured reflections	l = −13→16

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.032	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.085	w = 1/[σ²(F_o²) + (0.0477P)² + 0.4785P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
2993 reflections	Δρ_max = 0.61 e Å⁻³
168 parameters	Δρ_min = −0.62 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 carbons were placed at calculated positions and were refined in the riding-model approximation with C–H = 0.99 Å, and with U_i_so(H) = 1.2 U_eq(C). Hydrogen atom H16 attached to O16 was refined with an isotropic displacement parameter.

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
Se1	0.42558 (3)	0.52341 (2)	0.82295 (2)	0.03699 (10)
N2	0.5805 (3)	0.61713 (15)	0.77083 (18)	0.0457 (5)
N3	0.7176 (3)	0.57253 (16)	0.74387 (17)	0.0414 (5)
C4	0.7278 (3)	0.46859 (17)	0.75666 (18)	0.0318 (5)
C5	0.8880 (3)	0.4149 (2)	0.7219 (2)	0.0459 (6)
H5A	0.877920	0.341396	0.735378	0.055*
H5B	1.002410	0.439400	0.767597	0.055*
C6	0.8980 (3)	0.4323 (2)	0.5990 (2)	0.0451 (6)
H6A	0.938296	0.502895	0.590196	0.054*
H6B	0.993277	0.387084	0.578566	0.054*
C7	0.7242 (3)	0.41505 (16)	0.51877 (19)	0.0330 (5)
H7A	0.738068	0.451200	0.450044	0.040*	0.759 (8)
H7B	0.626215	0.450426	0.549313	0.040*	0.759 (8)
H7C	0.737146	0.428425	0.441144	0.040*	0.241 (8)
H7D	0.618827	0.452876	0.538069	0.040*	0.241 (8)
C8	0.6499 (5)	0.3088 (2)	0.4837 (3)	0.0323 (9)	0.759 (8)
H8A	0.551274	0.315954	0.419001	0.039*	0.759 (8)
H8B	0.749317	0.268862	0.459877	0.039*	0.759 (8)
C9	0.5750 (5)	0.2491 (2)	0.5736 (4)	0.0253 (8)	0.759 (8)
H9	0.672683	0.245793	0.640491	0.030*	0.759 (8)
C8A	0.7192 (13)	0.2967 (6)	0.5470 (10)	0.024 (3)	0.241 (8)
H8C	0.795335	0.258614	0.502232	0.028*	0.241 (8)
H8D	0.769474	0.285547	0.626060	0.028*	0.241 (8)
C9A	0.5227 (15)	0.2591 (6)	0.5220 (11)	0.020 (2)	0.241 (8)
H9A	0.465069	0.279025	0.445437	0.024*	0.241 (8)
C10	0.4030 (3)	0.29664 (15)	0.60785 (18)	0.0300 (4)
H10A	0.405841	0.371012	0.598136	0.036*	0.759 (8)
H10B	0.292402	0.270147	0.559887	0.036*	0.759 (8)
H10C	0.419373	0.371049	0.608245	0.036*	0.241 (8)
H10D	0.276217	0.284916	0.569739	0.036*	0.241 (8)
C11	0.3948 (3)	0.27181 (16)	0.72804 (19)	0.0356 (5)
H11A	0.392631	0.197255	0.736219	0.043*
H11B	0.278436	0.298372	0.745791	0.043*
C12	0.5532 (4)	0.31423 (17)	0.8131 (2)	0.0377 (5)
H12A	0.525003	0.304052	0.888300	0.045*
H12B	0.665876	0.275742	0.807827	0.045*
C13	0.5875 (3)	0.42449 (15)	0.79660 (17)	0.0278 (4)
C14	0.5316 (3)	0.14114 (16)	0.5328 (2)	0.0326 (5)
O15	0.3937 (2)	0.09629 (11)	0.54373 (14)	0.0366 (4)
O16	0.6672 (2)	0.09795 (12)	0.49285 (14)	0.0359 (4)
H16	0.637 (4)	0.029 (2)	0.481 (3)	0.051 (9)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Se1	0.03657 (15)	0.03565 (14)	0.04147 (16)	0.00471 (10)	0.01446 (10)	−0.00838 (10)
N2	0.0629 (15)	0.0245 (9)	0.0463 (12)	−0.0081 (10)	0.0000 (10)	−0.0051 (9)
N3	0.0413 (11)	0.0357 (11)	0.0465 (12)	−0.0110 (9)	0.0056 (9)	0.0039 (9)
C4	0.0290 (11)	0.0375 (12)	0.0290 (11)	−0.0022 (9)	0.0057 (8)	−0.0019 (9)
C5	0.0291 (12)	0.0719 (18)	0.0383 (13)	0.0079 (12)	0.0103 (10)	0.0043 (12)
C6	0.0314 (12)	0.0673 (17)	0.0408 (13)	0.0034 (12)	0.0181 (10)	0.0060 (13)
C7	0.0404 (12)	0.0226 (9)	0.0396 (12)	0.0003 (9)	0.0170 (10)	0.0017 (9)
C8	0.0418 (19)	0.0257 (14)	0.031 (2)	0.0011 (13)	0.0113 (16)	0.0014 (13)
C9	0.0288 (17)	0.0209 (13)	0.026 (2)	0.0001 (12)	0.0051 (14)	0.0003 (13)
C8A	0.026 (5)	0.017 (4)	0.028 (6)	0.005 (3)	0.006 (4)	0.010 (3)
C9A	0.026 (5)	0.014 (4)	0.018 (5)	0.005 (3)	−0.001 (4)	0.002 (4)
C10	0.0288 (10)	0.0206 (9)	0.0424 (12)	0.0009 (8)	0.0115 (9)	−0.0055 (8)
C11	0.0414 (13)	0.0234 (9)	0.0428 (13)	−0.0089 (9)	0.0093 (10)	−0.0023 (9)
C12	0.0459 (14)	0.0249 (10)	0.0408 (13)	−0.0033 (10)	0.0031 (10)	0.0002 (9)
C13	0.0297 (10)	0.0250 (9)	0.0293 (10)	−0.0014 (8)	0.0062 (8)	−0.0069 (8)
C14	0.0360 (12)	0.0235 (9)	0.0415 (12)	0.0014 (9)	0.0157 (9)	−0.0040 (9)
O15	0.0368 (9)	0.0240 (7)	0.0526 (10)	−0.0040 (7)	0.0184 (7)	−0.0080 (7)
O16	0.0399 (9)	0.0220 (7)	0.0501 (10)	−0.0016 (6)	0.0203 (7)	−0.0092 (7)

Geometric parameters (Å, º) top

Se1—C13	1.840 (2)	C9—C10	1.544 (4)
Se1—N2	1.874 (2)	C9—H9	1.0000
N2—N3	1.267 (3)	C8A—C9A	1.522 (15)
N3—C4	1.382 (3)	C8A—H8C	0.9900
C4—C13	1.355 (3)	C8A—H8D	0.9900
C4—C5	1.507 (3)	C9A—C14	1.564 (9)
C5—C6	1.540 (3)	C9A—C10	1.570 (9)
C5—H5A	0.9900	C9A—H9A	1.0000
C5—H5B	0.9900	C10—C11	1.523 (3)
C6—C7	1.503 (3)	C10—H10A	0.9900
C6—H6A	0.9900	C10—H10B	0.9900
C6—H6B	0.9900	C10—H10C	0.9900
C7—C8	1.543 (4)	C10—H10D	0.9900
C7—C8A	1.603 (8)	C11—C12	1.540 (3)
C7—H7A	0.9900	C11—H11A	0.9900
C7—H7B	0.9900	C11—H11B	0.9900
C7—H7C	0.9900	C12—C13	1.498 (3)
C7—H7D	0.9900	C12—H12A	0.9900
C8—C9	1.536 (5)	C12—H12B	0.9900
C8—H8A	0.9900	C14—O15	1.210 (3)
C8—H8B	0.9900	C14—O16	1.321 (3)
C9—C14	1.527 (4)	O16—H16	0.94 (3)

C13—Se1—N2	87.26 (10)	C7—C8A—H8C	109.8
N3—N2—Se1	110.39 (15)	C9A—C8A—H8D	109.8
N2—N3—C4	117.57 (19)	C7—C8A—H8D	109.8
C13—C4—N3	115.9 (2)	H8C—C8A—H8D	108.3
C13—C4—C5	126.3 (2)	C8A—C9A—C14	106.4 (8)
N3—C4—C5	117.7 (2)	C8A—C9A—C10	113.1 (9)
C4—C5—C6	112.2 (2)	C14—C9A—C10	106.1 (6)
C4—C5—H5A	109.2	C8A—C9A—H9A	110.3
C6—C5—H5A	109.2	C14—C9A—H9A	110.3
C4—C5—H5B	109.2	C10—C9A—H9A	110.3
C6—C5—H5B	109.2	C11—C10—C9	110.3 (2)
H5A—C5—H5B	107.9	C11—C10—C9A	134.7 (5)
C7—C6—C5	116.2 (2)	C11—C10—H10A	109.6
C7—C6—H6A	108.2	C9—C10—H10A	109.6
C5—C6—H6A	108.2	C11—C10—H10B	109.6
C7—C6—H6B	108.2	C9—C10—H10B	109.6
C5—C6—H6B	108.2	H10A—C10—H10B	108.1
H6A—C6—H6B	107.4	C11—C10—H10C	103.5
C6—C7—C8	123.2 (3)	C9A—C10—H10C	103.5
C6—C7—C8A	93.1 (5)	C11—C10—H10D	103.5
C6—C7—H7A	106.5	C9A—C10—H10D	103.5
C8—C7—H7A	106.5	H10C—C10—H10D	105.3
C6—C7—H7B	106.5	C10—C11—C12	115.33 (19)
C8—C7—H7B	106.5	C10—C11—H11A	108.4
H7A—C7—H7B	106.5	C12—C11—H11A	108.4
C6—C7—H7C	113.1	C10—C11—H11B	108.4
C8A—C7—H7C	113.1	C12—C11—H11B	108.4
C6—C7—H7D	113.1	H11A—C11—H11B	107.5
C8A—C7—H7D	113.1	C13—C12—C11	112.92 (19)
H7C—C7—H7D	110.5	C13—C12—H12A	109.0
C9—C8—C7	115.0 (3)	C11—C12—H12A	109.0
C9—C8—H8A	108.5	C13—C12—H12B	109.0
C7—C8—H8A	108.5	C11—C12—H12B	109.0
C9—C8—H8B	108.5	H12A—C12—H12B	107.8
C7—C8—H8B	108.5	C4—C13—C12	128.7 (2)
H8A—C8—H8B	107.5	C4—C13—Se1	108.86 (16)
C14—C9—C8	109.0 (3)	C12—C13—Se1	122.37 (17)
C14—C9—C10	109.3 (2)	O15—C14—O16	122.81 (19)
C8—C9—C10	113.8 (3)	O15—C14—C9	123.8 (2)
C14—C9—H9	108.2	O16—C14—C9	113.1 (2)
C8—C9—H9	108.2	O15—C14—C9A	118.2 (4)
C10—C9—H9	108.2	O16—C14—C9A	115.0 (4)
C9A—C8A—C7	109.3 (8)	C14—O16—H16	107 (2)
C9A—C8A—H8C	109.8

C13—Se1—N2—N3	−0.48 (17)	C9—C10—C11—C12	62.8 (3)
Se1—N2—N3—C4	0.2 (3)	C9A—C10—C11—C12	73.3 (6)
N2—N3—C4—C13	0.4 (3)	C10—C11—C12—C13	49.3 (3)
N2—N3—C4—C5	178.4 (2)	N3—C4—C13—C12	175.9 (2)
C13—C4—C5—C6	119.0 (3)	C5—C4—C13—C12	−1.8 (4)
N3—C4—C5—C6	−58.7 (3)	N3—C4—C13—Se1	−0.8 (2)
C4—C5—C6—C7	−49.4 (3)	C5—C4—C13—Se1	−178.56 (18)
C5—C6—C7—C8	−76.3 (3)	C11—C12—C13—C4	−107.2 (3)
C5—C6—C7—C8A	−64.3 (4)	C11—C12—C13—Se1	69.1 (2)
C6—C7—C8—C9	70.8 (4)	N2—Se1—C13—C4	0.68 (16)
C7—C8—C9—C14	−172.2 (3)	N2—Se1—C13—C12	−176.28 (19)
C7—C8—C9—C10	65.5 (5)	C8—C9—C14—O15	−136.1 (3)
C6—C7—C8A—C9A	154.6 (8)	C10—C9—C14—O15	−11.2 (5)
C7—C8A—C9A—C14	171.0 (5)	C8—C9—C14—O16	49.5 (4)
C7—C8A—C9A—C10	−72.8 (11)	C10—C9—C14—O16	174.5 (2)
C14—C9—C10—C11	87.5 (3)	C8A—C9A—C14—O15	162.0 (7)
C8—C9—C10—C11	−150.4 (3)	C10—C9A—C14—O15	41.2 (9)
C8A—C9A—C10—C11	−71.5 (9)	C8A—C9A—C14—O16	−39.9 (11)
C14—C9A—C10—C11	44.9 (10)	C10—C9A—C14—O16	−160.7 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O16—H16···O15ⁱ	0.94 (3)	1.69 (3)	2.630 (2)	174 (3)

Symmetry code: (i) −x+1, −y, −z+1.

References

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