1,5-[5,5'-(3-Oxa-1,5-pentyl­enedi­thio)­bis(2,3-di­hydro-2-oxo-1,3,4-thia­diazol-3-yl)]-3-oxa­pentane

The title compound, 4,14-dioxa-9,11,17,19-tetra­thia-1,7,21,22-tetr­aaza­tri­cyclo­[16.2.1.1^7,10]­docosa-18(21),10(22)-diene-8,20-dione, C₁₂H₁₆N₄O₄S₄, has crystallographic twofold symmetry, with a half mol­ecule in the asymmetric unit and a dihedral angle of 52.59 (6)° between the two planar five-membered rings of the macrocycle, giving the mol­ecule a twisted conformation.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.035
• wR factor = 0.089
• Data-to-parameter ratio = 12.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_301  Alert C Main Residue Disorder ........................       9.00 Perc.

PLAT_302  Alert C Anion/Solvent Disorder .......................      39.00 Perc.

PLAT_320  Alert C Check Hybridisation of  S1     in main residue          ?


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 3 Alert Level C = Please check

---

S1. Comment

As a continuation of our studies of macrocyclic compounds containing 1,3,4-thiadiazole subunits (Cho, Park & Hwang, 1999; Cho, Park, Kim et al., 1999; Cho, Park, Hwang et al., 1999; Cho et al., 2000), we have turned our attention to macrocycles composed of two 5-mercapto-2,3-dihydro-1,3,4-thiadizole-2-one units. For the formation of macrocycle (I), these two heterocyclic rings are linked by ether chains. These compounds have been shown to be artificial receptors of transition metals (Cho, Park, Kim et al., 1999) and futhermore are potential hosts of small organic molecules. The determination of the structure of title compound, (I), is part a study of these macrocycles.

The title compound, (I), with the atom-labelling scheme is shown in Fig. 1. A half molecule belongs to an asymmetric unit and the other half molecule is generated by applying a twofold rotation [symmetry code: (i) -x, y, -z + 3/2] passing through O1 and O3. The S—C distances range from 1.674 (5) to 1.970 (9) Å, with a mean value of 1.782 (2) Å, and the N2—C4 and O2—C3 distances of 1.279 (3) and 1.215 (3) clearly show double-bond character. The remainder of the bonds are single bonds; in the five-membered ring, C3—S1—C4 = 88.89 (11)°. These values are comparable with those found in 4,17,25,26-tetraaza-6,9,12,15-tetraoxa-2,19,21,24-tetrathiatricyclo- [18.4.1^1,4.1^17,20]hexacosa-1(25),20 (26)-diene-3,5,16,18-tetraone (Cho et al., 2000) and 1,5-[5,5'-(1,3-phenylenedimethylenedithio)bis(2,3-dihydro-2-oxo- 1,3,4-thiadiazol-3-yl)]-3-oxapentane (Cho et al., 2001)

The five-membered ring, 5-mercapto-2,3-dihydro-1,3,4-thiadizole-2-one, is planar within 0.016 (1) Å and the ethyl ether linkage (atoms C2, C1, O1, C1ⁱ and C2ⁱ) is planar within 0.085 (2) Å. The dihedral angle between the five-membered ring and its own self-related by twofold symmetry is 52.59 (6)°, and the dihedral angle between the five-membered ring and the ethyl ether linkage is 79.02 (6)°. Therefore, the molecule has a twisted conformation with a C2—C1—O1—C1ⁱ torsion angle of 171.4 (2)°. The interatomic distances N1···N1ⁱ = 5.609 (4) Å, N2···N2ⁱ = 4.842 (4) Å, N2···O3 = 4.223 (3) Å, N2···S2ⁱ = 6.158 (2) Å, O1···O3 = 5.431 (3) Å and S2···S2ⁱ = 7.322 (2) Å appear to be sufficient to introduce a guest ion inside the molecule. The closest intermolecular distance is O2···H5A = 2.572 (5) Å.

S2. Experimental

The preparation of (I) followed the general procedure previously reported by Cho, Park, Kim et al. (1999). Details will be reported elsewhere.

S3. Refinement

Atoms C5 and C6 were disordered over two positions and their coordinates together with site-occupation factors were refined anisotropically using the PART command of SHELXL97 (Sheldrick, 1997). All H atoms were located geometrically with U_iso constrained to be 1.2 times the equivalent isotropic displacement of the parent atoms. The highest peak and deepest holes in the final difference density map are at 0.85 Å from H6A and 0.91 Å from S1, respectively.

Computing details

Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

Fig. 1. ORTEP-3 (Farrugia, 1997) diagram of (I) showing 25% probability displacement ellipsoids. C atoms are shown with ellipsoids with only enveloping ellipses and the remaining atoms are shown with ellipsoids with octant shading. Only the asymmetric unit is labelled and H atoms have been omitted for clarity [symmetry code: (i) -x, y, -z + 3/2].

(I)

Crystal data

C12H16N4O4S4	F(000) = 848
Mr = 408.53	Dx = 1.517 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71069 Å
a = 8.7369 (8) Å	Cell parameters from 25 reflections
b = 15.741 (3) Å	θ = 11.4–13.7°
c = 13.3967 (12) Å	µ = 0.56 mm^−1
β = 103.833 (8)°	T = 293 K
V = 1788.9 (4) Å^3	Block, colorless
Z = 4	0.53 × 0.43 × 0.26 mm

Data collection

Enraf Nonius CAD4 diffractometer	1201 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.026
Graphite monochromator	θmax = 25.0°, θmin = 2.6°
non–profiled ω/2θ scans	h = −10→10
Absorption correction: ψ scan (North et al., 1968)	k = −18→18
Tmin = 0.745, Tmax = 0.861	l = −15→0
3139 measured reflections	3 standard reflections every 300 min
1573 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.035	H-atom parameters constrained
wR(F^2) = 0.089	w = 1/[σ^2(Fo^2) + (0.0409P)^2 + 0.708P] where P = (Fo^2 + 2Fc^2)/3
S = 1.02	(Δ/σ)max < 0.001
1573 reflections	Δρmax = 0.16 e Å^−3
130 parameters	Δρmin = −0.20 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0028 (6)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
S1	0.02169 (9)	0.17999 (5)	0.40152 (5)	0.0665 (3)
S2	−0.10009 (10)	0.34446 (5)	0.46857 (6)	0.0777 (3)
N1	0.1523 (2)	0.15102 (12)	0.58796 (13)	0.0493 (5)
N2	0.0813 (2)	0.22914 (11)	0.58945 (14)	0.0509 (5)
O1	0.0000	0.10389 (13)	0.7500	0.0572 (6)
O2	0.1839 (2)	0.04098 (12)	0.48204 (14)	0.0735 (5)
O3	0.0000	0.44894 (14)	0.7500	0.0717 (7)
C1	0.1209 (3)	0.05431 (15)	0.72579 (19)	0.0631 (7)
H1A	0.0758	0.0123	0.6741	0.076*
H1B	0.1791	0.0248	0.7866	0.076*
C2	0.2287 (3)	0.11229 (16)	0.68591 (18)	0.0585 (7)
H2A	0.2657	0.1567	0.7360	0.070*
H2B	0.3198	0.0803	0.6777	0.070*
C3	0.1338 (3)	0.11066 (16)	0.49686 (18)	0.0529 (6)
C4	0.0094 (3)	0.25109 (15)	0.49841 (18)	0.0514 (6)
C5'	−0.0748 (6)	0.3878 (3)	0.6839 (4)	0.0534 (17)	0.491 (6)
H5'A	−0.0539	0.3294	0.7062	0.064*	0.491 (6)
H5'B	−0.1847	0.3983	0.6511	0.064*	0.491 (6)
C5	−0.1169 (7)	0.3735 (3)	0.5857 (4)	0.0545 (17)	0.509 (6)
H5A	−0.2103	0.4068	0.5854	0.065*	0.509 (6)
H5B	−0.1059	0.3269	0.6343	0.065*	0.509 (6)
C6	0.0284 (11)	0.4232 (6)	0.6411 (6)	0.0555 (18)	0.491 (6)
H6A	−0.0094	0.4613	0.5836	0.067*	0.491 (6)
H6B	0.1231	0.3916	0.6394	0.067*	0.491 (6)
C6'	−0.0104 (13)	0.4112 (6)	0.5932 (7)	0.063 (2)	0.509 (6)
H6'A	0.0858	0.3907	0.6391	0.076*	0.509 (6)
H6'B	−0.0211	0.4725	0.5891	0.076*	0.509 (6)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0779 (5)	0.0815 (5)	0.0381 (4)	−0.0132 (4)	0.0099 (3)	−0.0048 (3)
S2	0.0926 (6)	0.0697 (5)	0.0616 (5)	0.0137 (4)	0.0002 (4)	0.0224 (4)
N1	0.0549 (12)	0.0526 (11)	0.0406 (10)	0.0094 (9)	0.0120 (9)	−0.0051 (8)
N2	0.0632 (12)	0.0485 (11)	0.0411 (11)	0.0082 (10)	0.0126 (9)	0.0008 (9)
O1	0.0811 (17)	0.0388 (12)	0.0541 (14)	0.000	0.0206 (12)	0.000
O2	0.0798 (13)	0.0742 (12)	0.0709 (12)	0.0070 (10)	0.0270 (10)	−0.0252 (10)
O3	0.0890 (19)	0.0428 (13)	0.0758 (18)	0.000	0.0051 (14)	0.000
C1	0.0887 (19)	0.0455 (13)	0.0500 (14)	0.0132 (13)	0.0064 (13)	0.0015 (11)
C2	0.0636 (16)	0.0573 (15)	0.0491 (14)	0.0180 (12)	0.0028 (12)	−0.0026 (11)
C3	0.0502 (14)	0.0637 (16)	0.0482 (13)	−0.0054 (12)	0.0188 (11)	−0.0098 (12)
C4	0.0529 (13)	0.0573 (14)	0.0430 (13)	−0.0060 (11)	0.0094 (10)	0.0054 (11)
C5'	0.058 (3)	0.049 (3)	0.056 (4)	−0.002 (2)	0.020 (2)	0.001 (2)
C5	0.052 (3)	0.043 (3)	0.065 (4)	0.005 (2)	0.008 (3)	0.004 (2)
C6	0.065 (5)	0.041 (3)	0.063 (5)	0.000 (3)	0.019 (4)	0.001 (4)
C6'	0.087 (7)	0.036 (4)	0.070 (6)	0.004 (4)	0.025 (5)	0.009 (4)

Geometric parameters (Å, º)

S1—C4	1.737 (2)	O1—C1	1.412 (3)
S1—C3	1.784 (3)	O2—C3	1.215 (3)
S2—C5	1.674 (5)	O3—C5'	1.365 (5)
S2—C4	1.747 (3)	O3—C5'^i	1.365 (5)
S2—C6'	1.970 (9)	O3—C6	1.590 (8)
N1—C3	1.351 (3)	O3—C6^i	1.590 (8)
N1—N2	1.380 (2)	C1—C2	1.499 (3)
N1—C2	1.456 (3)	C5'—C6	1.304 (11)
N2—C4	1.279 (3)	C5'—C5'^i	1.934 (11)
O1—C1^i	1.412 (3)	C5—C6'	1.088 (11)
C4—S1—C3	88.89 (11)	O1—C1—C2	108.28 (18)
C5—S2—C4	100.42 (18)	N1—C2—C1	112.6 (2)
C5—S2—C6'	33.5 (3)	O2—C3—N1	127.0 (2)
C4—S2—C6'	99.8 (3)	O2—C3—S1	126.36 (19)
C3—N1—N2	118.37 (18)	N1—C3—S1	106.60 (17)
C3—N1—C2	123.19 (19)	N2—C4—S1	115.76 (18)
N2—N1—C2	118.09 (17)	N2—C4—S2	124.25 (18)
C4—N2—N1	110.31 (18)	S1—C4—S2	119.97 (14)
C1^i—O1—C1	112.9 (3)	C6—C5'—O3	73.1 (4)
C5'—O3—C5'^i	90.2 (4)	C6—C5'—C5'^i	90.9 (5)
C5'—O3—C6	51.7 (4)	O3—C5'—C5'^i	44.9 (2)
C5'^i—O3—C6	105.1 (4)	C6'—C5—S2	88.3 (6)
C5'—O3—C6^i	105.1 (4)	C5'—C6—O3	55.2 (4)
C5'^i—O3—C6^i	51.7 (4)	C5—C6'—S2	58.2 (5)
C6—O3—C6^i	150.5 (7)
C3—N1—N2—C4	−1.4 (3)	C3—S1—C4—S2	−176.91 (15)
C2—N1—N2—C4	−174.9 (2)	C5—S2—C4—N2	−14.0 (3)
C1^i—O1—C1—C2	171.4 (2)	C6'—S2—C4—N2	20.1 (4)
C3—N1—C2—C1	−80.7 (3)	C5—S2—C4—S1	164.5 (2)
N2—N1—C2—C1	92.4 (2)	C6'—S2—C4—S1	−161.4 (3)
O1—C1—C2—N1	−66.3 (2)	C5'^i—O3—C5'—C6	−109.2 (5)
N2—N1—C3—O2	−177.7 (2)	C6^i—O3—C5'—C6	−159.3 (5)
C2—N1—C3—O2	−4.7 (4)	C6—O3—C5'—C5'^i	109.2 (5)
N2—N1—C3—S1	2.6 (2)	C6^i—O3—C5'—C5'^i	−50.1 (4)
C2—N1—C3—S1	175.63 (18)	C4—S2—C5—C6'	92.0 (5)
C4—S1—C3—O2	178.1 (2)	C5'^i—C5'—C6—O3	−41.8 (2)
C4—S1—C3—N1	−2.22 (17)	C5'^i—O3—C6—C5'	78.0 (6)
N1—N2—C4—S1	−0.6 (3)	C6^i—O3—C6—C5'	43.8 (3)
N1—N2—C4—S2	177.96 (16)	C4—S2—C6'—C5	−94.2 (5)
C3—S1—C4—N2	1.7 (2)

Symmetry code: (i) −x, y, −z+3/2.