1,5-Bis(3-thien­yloxy)-3-oxapenta­ne: a thio­phene-based precursor for thio­phene-based aza­cryptand Mannich bases

Labat, G.; Halfpenny, J.

doi:10.1107/S1600536805024517

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 61| Part 9| September 2005| Pages o2813-o2814

https://doi.org/10.1107/S1600536805024517

1,5-Bis(3-thienyloxy)-3-oxapentane: a thiophene-based precursor for thiophene-based azacryptand Mannich bases

Gaël Labat ^a and Joan Halfpenny ^b ^*

^aInstitut de Chimie, Université de Neuchâtel, Avenue de Bellevaux 51, CH-2007 Neuchâtel, Switzerland, and ^bDepartment of Chemistry and Physics, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, England
^*Correspondence e-mail: gael.labat@unine.ch

(Received 26 July 2005; accepted 1 August 2005; online 6 August 2005)

The title compound, C₁₂H₁₄O₃S₂, is composed of two thiophene rings bridged by an –O(CH₂)₂O(CH₂)₂O– chain. The molecule is U-shaped, with the two thiophene rings inclined to one another by 83.21 (10)°. In the crystal structure, the molecules are bridged by C—H⋯S and C—H⋯·O hydrogen bonds, forming a double-stranded polymer chain.

Comment

The preparation of a range of open-chain cryptand-like structures, incorporating thiophene rings, as precursors for azacryptand Mannich bases, was undertaken by Barker et al. (1993 ) and Chaffin et al. (2001 , 2002 ). The title compound, (I), was synthesized by the reaction of methyl 3-hydroxythiophene-2-carboxylate with 1,5-bis(p-tolylsulfonyloxy)-3-oxapentane and anhydrous potassium carbonate in anhydrous N,N-dimethylformamide, followed by saponification and decarboxylation.

The molecular structure of (I) is illustrated in Fig. 1 and selected bond distances and angles are given in Table 1. The molecule is U-shaped and has pseudo-C₂ symmetry, with the central –O(CH₂)₂O(CH₂)₂O– bridge having a cis–cis conformation. The two thiophene rings are inclined to one another by 83.21 (10)°. The thiophene bond lengths and bond angles are similar to those in an unsubstituted thiophene reported by Bonham & Momany (1963 ). The thienyloxy and other bond lengths and angles in (I) are in agreement with standard values (International Tables for Crystallography, Vol. C, 1995). In the crystal structure, symmetry-related molecules are bridged by C—H⋯S and C—H⋯O hydrogen bonds (Table 2), forming a double-stranded polymer chain (Fig. 2).

Figure 1
View of the molecular structure of compound (I)

, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Figure 2
The crystal packing of compound (I)

, viewed down the a axis. C—H⋯S and C—H⋯O hydrogen bonds are shown as dashed lines.

Experimental

Compound (I) was synthesized using the procedure described by Chaffin et al. (2001). Crystals suitable for X-ray analysis were obtained by slow evaporation of a 1:1 ethanol–dichloromethane solution.

Crystal data

C₁₂H₁₄O₃S₂
M_r = 270.35
Monoclinic, P 2₁ /n
a = 5.2998 (4) Å
b = 19.4005 (18) Å
c = 12.7277 (9) Å
β = 100.960 (8)°
V = 1284.78 (18) Å³
Z = 4
D_x = 1.398 Mg m⁻³
Mo Kα radiation
Cell parameters from 8000 reflections
θ = 1.7–26.1°
μ = 0.41 mm⁻¹
T = 153 (2) K
Plate, colourless
0.50 × 0.25 × 0.10 mm

Data collection

Stoe IPDS diffractometer
ω scans
Absorption correction: none
10146 measured reflections
2509 independent reflections
1609 reflections with I > 2σ(I)
R_int = 0.066
θ_max = 26.0°
h = −6 → 6
k = −23 → 23
l = −15 → 15

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.033
wR(F²) = 0.072
S = 0.85
2509 reflections
154 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0331P)²] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

S1—C4	1.705 (2)
S1—C1	1.717 (2)
S2—C12	1.701 (2)
S2—C9	1.716 (3)
O1—C2	1.368 (2)
O1—C5	1.425 (2)
O2—C6	1.414 (3)
O2—C7	1.421 (2)
O3—C10	1.362 (3)
O3—C8	1.428 (2)
C1—C2	1.356 (3)
C3—C4	1.353 (3)
C5—C6	1.503 (3)
C7—C8	1.490 (3)
C9—C10	1.362 (3)
C10—C11	1.414 (3)
C11—C12	1.346 (3)

C4—S1—C1	91.89 (10)
C12—S2—C9	91.92 (11)
C2—O1—C5	116.42 (15)
C6—O2—C7	111.88 (16)
C10—O3—C8	115.46 (16)
C2—C1—S1	110.59 (15)
C1—C2—O1	128.80 (18)
C1—C2—C3	113.61 (18)
O1—C2—C3	117.59 (17)
C4—C3—C2	111.76 (19)
C3—C4—S1	112.15 (16)
O1—C5—C6	107.58 (16)
O2—C6—C5	108.33 (17)
O2—C7—C8	109.35 (18)
C10—C9—S2	110.66 (17)
C9—C10—O3	128.5 (2)
C9—C10—C11	112.9 (2)
O3—C10—C11	118.64 (18)
C12—C11—C10	112.3 (2)
C11—C12—S2	112.15 (18)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C9—H9A⋯O1ⁱ	0.95	2.52	3.358 (2)	148
C12—H12A⋯S1ⁱⁱ	0.95	2.86	3.787 (2)	164
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (ii) x+1, y, z+1.

H atoms were included in calculated positions and treated as riding atoms, with C—H = 0.95–0.99 Å and U_iso(H) = 1.2 or 1.5 times U_eq(parent atom).

Data collection: EXPOSE (Stoe & Cie, 2002 ); cell refinement: CELL (Stoe & Cie, 2002); data reduction: INTEGRATE (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536805024517/is6111sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536805024517/is6111Isup2.hkl

Computing details top

Data collection: EXPOSE (Stoe & Cie, 2002); cell refinement: CELL (Stoe & Cie, 2002); data reduction: INTEGRATE (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97.

1,5-Bis(2-thienyloxy)-3-oxapentane top

Crystal data top

C₁₂H₁₄O₃S₂	F(000) = 568
M_r = 270.35	D_x = 1.398 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 8000 reflections
a = 5.2998 (4) Å	θ = 1.7–26.1°
b = 19.4005 (18) Å	µ = 0.41 mm⁻¹
c = 12.7277 (9) Å	T = 153 K
β = 100.960 (8)°	Plate, colourless
V = 1284.78 (18) Å³	0.50 × 0.25 × 0.10 mm
Z = 4

Data collection top

Stoe IPDS diffractometer	1609 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.066
Graphite monochromator	θ_max = 26.0°, θ_min = 1.9°
Detector resolution: 0.81Å pixels mm^-1	h = −6→6
ω scans	k = −23→23
10146 measured reflections	l = −15→15
2509 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.072	H-atom parameters constrained
S = 0.85	w = 1/[σ²(F_o²) + (0.0331P)²] where P = (F_o² + 2F_c²)/3
2509 reflections	(Δ/σ)_max = 0.001
154 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.29 e Å⁻³

Special details top

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
S1	0.16435 (11)	0.52004 (3)	0.70026 (4)	0.03420 (16)
S2	0.63304 (12)	0.70048 (3)	1.53098 (5)	0.03781 (17)
O1	−0.2011 (3)	0.62079 (7)	0.88858 (11)	0.0283 (3)
O2	−0.2260 (3)	0.63598 (7)	1.10645 (10)	0.0294 (4)
O3	0.0678 (3)	0.63305 (7)	1.31584 (11)	0.0278 (3)
C1	−0.0383 (4)	0.52702 (11)	0.79012 (15)	0.0257 (5)
H1A	−0.1231	0.4894	0.8162	0.031*
C2	−0.0605 (4)	0.59373 (10)	0.81876 (15)	0.0240 (4)
C3	0.0848 (4)	0.63996 (11)	0.76818 (16)	0.0298 (5)
H3A	0.0888	0.6884	0.7790	0.036*
C4	0.2175 (4)	0.60675 (12)	0.70255 (17)	0.0353 (6)
H4A	0.3274	0.6291	0.6624	0.042*
C5	−0.3283 (4)	0.57264 (10)	0.94515 (16)	0.0267 (5)
H5B	−0.2057	0.5371	0.9793	0.032*
H5A	−0.4691	0.5495	0.8954	0.032*
C6	−0.4344 (4)	0.61194 (11)	1.02881 (16)	0.0303 (5)
H6A	−0.5387	0.6513	0.9955	0.036*
H6B	−0.5459	0.5816	1.0628	0.036*
C7	−0.3098 (5)	0.66629 (12)	1.19548 (16)	0.0370 (6)
H7A	−0.4051	0.6318	1.2301	0.044*
H7B	−0.4268	0.7053	1.1711	0.044*
C8	−0.0825 (5)	0.69130 (11)	1.27361 (16)	0.0335 (5)
H8A	0.0214	0.7227	1.2377	0.040*
H8B	−0.1395	0.7169	1.3322	0.040*
C9	0.3544 (4)	0.70933 (11)	1.43801 (16)	0.0309 (5)
H9A	0.2668	0.7517	1.4202	0.037*
C10	0.2762 (4)	0.64727 (10)	1.39336 (15)	0.0242 (5)
C11	0.4412 (4)	0.59251 (11)	1.43531 (16)	0.0295 (5)
H11A	0.4134	0.5458	1.4138	0.035*
C12	0.6421 (5)	0.61409 (12)	1.50917 (17)	0.0351 (5)
H12A	0.7737	0.5845	1.5450	0.042*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0308 (3)	0.0404 (3)	0.0319 (3)	0.0047 (3)	0.0074 (3)	−0.0062 (2)
S2	0.0401 (4)	0.0398 (3)	0.0344 (3)	−0.0119 (3)	0.0093 (3)	−0.0054 (3)
O1	0.0409 (9)	0.0179 (7)	0.0296 (8)	−0.0022 (6)	0.0157 (7)	−0.0021 (6)
O2	0.0338 (9)	0.0334 (8)	0.0222 (7)	0.0027 (7)	0.0084 (7)	−0.0061 (6)
O3	0.0325 (9)	0.0216 (7)	0.0272 (7)	0.0070 (6)	0.0004 (7)	0.0002 (6)
C1	0.0273 (12)	0.0237 (11)	0.0247 (10)	0.0001 (9)	0.0014 (9)	−0.0004 (8)
C2	0.0242 (11)	0.0259 (11)	0.0212 (9)	0.0000 (9)	0.0022 (9)	−0.0004 (9)
C3	0.0340 (13)	0.0265 (12)	0.0282 (11)	−0.0085 (10)	0.0038 (10)	−0.0010 (9)
C4	0.0312 (14)	0.0454 (14)	0.0299 (11)	−0.0095 (11)	0.0072 (11)	0.0023 (10)
C5	0.0320 (13)	0.0221 (11)	0.0265 (11)	−0.0052 (9)	0.0070 (10)	0.0016 (9)
C6	0.0326 (13)	0.0317 (12)	0.0276 (11)	0.0002 (10)	0.0084 (11)	0.0014 (9)
C7	0.0430 (15)	0.0444 (14)	0.0236 (11)	0.0221 (12)	0.0066 (11)	−0.0005 (10)
C8	0.0488 (16)	0.0271 (12)	0.0237 (10)	0.0174 (11)	0.0042 (11)	0.0006 (9)
C9	0.0392 (13)	0.0251 (11)	0.0317 (11)	0.0009 (10)	0.0150 (11)	0.0027 (9)
C10	0.0287 (12)	0.0249 (11)	0.0205 (10)	0.0002 (9)	0.0087 (10)	−0.0005 (8)
C11	0.0341 (14)	0.0276 (11)	0.0271 (10)	0.0033 (10)	0.0062 (10)	−0.0028 (9)
C12	0.0321 (13)	0.0413 (13)	0.0313 (12)	0.0063 (11)	0.0047 (11)	0.0001 (10)

Geometric parameters (Å, º) top

S1—C4	1.705 (2)	C5—C6	1.503 (3)
S1—C1	1.717 (2)	C5—H5B	0.9900
S2—C12	1.701 (2)	C5—H5A	0.9900
S2—C9	1.716 (3)	C6—H6A	0.9900
O1—C2	1.368 (2)	C6—H6B	0.9900
O1—C5	1.425 (2)	C7—C8	1.490 (3)
O2—C6	1.414 (3)	C7—H7A	0.9900
O2—C7	1.421 (2)	C7—H7B	0.9900
O3—C10	1.362 (3)	C8—H8A	0.9900
O3—C8	1.428 (2)	C8—H8B	0.9900
C1—C2	1.356 (3)	C9—C10	1.362 (3)
C1—H1A	0.9500	C9—H9A	0.9500
C2—C3	1.414 (3)	C10—C11	1.414 (3)
C3—C4	1.353 (3)	C11—C12	1.346 (3)
C3—H3A	0.9500	C11—H11A	0.9500
C4—H4A	0.9500	C12—H12A	0.9500

C4—S1—C1	91.89 (10)	C5—C6—H6B	110.0
C12—S2—C9	91.92 (11)	H6A—C6—H6B	108.4
C2—O1—C5	116.42 (15)	O2—C7—C8	109.35 (18)
C6—O2—C7	111.88 (16)	O2—C7—H7A	109.8
C10—O3—C8	115.46 (16)	C8—C7—H7A	109.8
C2—C1—S1	110.59 (15)	O2—C7—H7B	109.8
C2—C1—H1A	124.7	C8—C7—H7B	109.8
S1—C1—H1A	124.7	H7A—C7—H7B	108.3
C1—C2—O1	128.80 (18)	O3—C8—C7	108.41 (18)
C1—C2—C3	113.61 (18)	O3—C8—H8A	110.0
O1—C2—C3	117.59 (17)	C7—C8—H8A	110.0
C4—C3—C2	111.76 (19)	O3—C8—H8B	110.0
C4—C3—H3A	124.1	C7—C8—H8B	110.0
C2—C3—H3A	124.1	H8A—C8—H8B	108.4
C3—C4—S1	112.15 (16)	C10—C9—S2	110.66 (17)
C3—C4—H4A	123.9	C10—C9—H9A	124.7
S1—C4—H4A	123.9	S2—C9—H9A	124.7
O1—C5—C6	107.58 (16)	C9—C10—O3	128.5 (2)
O1—C5—H5B	110.2	C9—C10—C11	112.9 (2)
C6—C5—H5B	110.2	O3—C10—C11	118.64 (18)
O1—C5—H5A	110.2	C12—C11—C10	112.3 (2)
C6—C5—H5A	110.2	C12—C11—H11A	123.8
H5B—C5—H5A	108.5	C10—C11—H11A	123.8
O2—C6—C5	108.33 (17)	C11—C12—S2	112.15 (18)
O2—C6—H6A	110.0	C11—C12—H12A	123.9
C5—C6—H6A	110.0	S2—C12—H12A	123.9
O2—C6—H6B	110.0

C4—S1—C1—C2	0.16 (17)	C6—O2—C7—C8	−179.31 (17)
S1—C1—C2—O1	−179.53 (17)	C10—O3—C8—C7	−176.48 (16)
S1—C1—C2—C3	0.3 (2)	O2—C7—C8—O3	−65.7 (2)
C5—O1—C2—C1	4.9 (3)	C12—S2—C9—C10	0.02 (15)
C5—O1—C2—C3	−174.89 (18)	S2—C9—C10—O3	−178.87 (15)
C1—C2—C3—C4	−0.7 (3)	S2—C9—C10—C11	0.5 (2)
O1—C2—C3—C4	179.13 (19)	C8—O3—C10—C9	2.4 (3)
C2—C3—C4—S1	0.8 (2)	C8—O3—C10—C11	−176.98 (16)
C1—S1—C4—C3	−0.55 (18)	C9—C10—C11—C12	−1.0 (2)
C2—O1—C5—C6	171.17 (17)	O3—C10—C11—C12	178.47 (17)
C7—O2—C6—C5	−172.63 (17)	C10—C11—C12—S2	1.0 (2)
O1—C5—C6—O2	−67.9 (2)	C9—S2—C12—C11	−0.60 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9A···O1ⁱ	0.95	2.52	3.358 (2)	148
C12—H12A···S1ⁱⁱ	0.95	2.86	3.787 (2)	164

Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) x+1, y, z+1.

Acknowledgements

The authors thank Professor Helen Stoeckli-Evans (Université de Neuchâtel) for making available the Stoe IPDS diffractometer for data collection.

References

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