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C—H⋯O contacts in the crystal structure of 1,3-di­thiane 1,1,3,3-tetra­oxide

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a624 Erlen Rd., Plymouth Meeting, PA 19462 , USA, bDept. of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA, and c2 Baydons Lane, Chippenham SN15 3JX, UK
*Correspondence e-mail: r.harlow.whereareyou@gmail.com, aoliver2@nd.edu

Edited by D. Gray, University of Illinois Urbana-Champaign, USA (Received 15 December 2020; accepted 25 January 2021; online 29 January 2021)

The crystal structure of 1,3-di­thiane 1,1,3,3-tetra­oxide, C4H8O4S2, has been determined to examine the inter­molecular C—H⋯O hydrogen bonds in a small mol­ecule with highly polarized hydrogen atoms. The crystals are monoclinic, space group Pn, with a = 4.9472 (5), b = 9.9021 (10), c = 7.1002 (7) Å and β = 91.464 (3)° with Z = 2. The mol­ecules form two stacks parallel to the a axis with the molecules being one a translation distance from each other. This stacking involves axial hydrogen atoms on one mol­ecule and the axial oxygen atoms on the adjacent mol­ecule in the stack. None of these C—H⋯O contacts is particularly short (all are > 2.4 Å). The many C—H⋯O contacts between the two stacks involve at least one equatorial hydrogen or oxygen atom. Again, no unusually short contacts are found. The whole crystal structure basically consists of a complex network of C—H⋯O contacts with no single, linear C—H⋯O contacts, only contacts that involve two (bifurcated), and mostly three or four neighbors.

1. Chemical context

This is the second in a series looking at the C—H⋯O contacts in cyclic organic structures containing multiple sulfone groups [see Harlow et al. (2019[Harlow, R. L., Oliver, A. G., Baker, J. M., Marshall, W. J. & Sammes, M. P. (2019). Acta Cryst. E75, 576-579.]) for the first structure in the series: 1,4-di­thiane 1,1,4,4-tetra­oxide]. Any methyl­ene group adjacent to a sulfone has polarized hydrogen atoms. Methyl­ene groups bonded to two sulfones are polarized to such an extent that they may form a C—H⋯X (X = N, O) hydrogen bond (Harlow et al., 1984[Harlow, R. L., Li, C. & Sammes, M. P. (1984). J. Chem. Soc. Perkin Trans. 1, pp. 547-551.]) as illustrated.

[Scheme 2]

The structure of the unsubstituted 1,3-di­sulfone, however, has not been previously reported and was of inter­est particularly because of its high melting point (583 K) and decomposition temperatures (ca 623 K), which are suggestive of potentially strong C—H⋯O contacts. The 1H NMR spectrum of the compound dissolved in DMSO shows a singlet, 2H, at δ = 5.238 ppm (highly polarized hydrogen atoms on C2 between the two SO2 groups); a triplet, 4H, at 3.370 ppm (moderately polarized hydrogen atoms on C4 and C6 with one adjacent SO2 group); and a pentet, 2H, at 2.260 ppm (relatively unpolarized hydrogen atoms on C5). See Li & Sammes (1983[Li, C. & Sammes, M. P. (1983). J. Chem. Soc. Perkin Trans. 1, pp. 1303-1309.]) for further details of 1H NMR spectra and hydrogen-atom polarity in di­sulfones.

[Scheme 1]

2. Structural commentary

Fig. 1[link] is an ORTEP drawing of the 1,3-di­thiane 1,1,3,3-tetra­oxide mol­ecule with atom labels using the suffix `a′ for axial and `e′ for equatorial atoms. The bond distances and angles are very similar to those reported for the 1,4-di­sulfone taking into consideration the small amount of distortion related to the different positions of the two sulfonyl groups, i.e. 1,3- vs 1,4-sites in the ring.

[Figure 1]
Figure 1
Labeled ORTEP drawing (50% probability) of the 1,3-di­thiane 1,1,3,3-tetra­oxide mol­ecule. The lower case suffixes `a′ and `e′ are used to distinguish whether the atoms are in the axial or equatorial position on the ring.

The hydrogen atoms were fully refined with isotropic displacement parameters as there seemed to be a correlation between the `strength' of the C—H polarization and the displacement parameters of the hydrogen atoms: more polarization seems to yield a smaller radius. Any further comments on this correlation from a structural standpoint would require a diffraction study using neutrons instead of X-rays to better define both the positions and the displacement parameters of the hydrogen atoms.

3. Supra­molecular features

Obviously, it is the packing of the mol­ecules that is especially fascinating given that the mol­ecules stack parallel to the a axis at a distance of one translation on a, i.e. the length of the a axis, ca 4.9472 (5) Å at 120 K. A general packing diagram is shown in Fig. 2[link]. The n-glide, the only symmetry operator in space group Pn, curiously preserves the polarity of the stacks and creates a polar crystal with, for example, all of the axial oxygen atoms in the stacks pointing in the same a-axis direction (up in Fig. 3[link]) and most of the axial hydrogen atoms pointing down. The stacking is directly stabilized by C—H⋯O contacts between neighboring mol­ecules in the stack and only involves the axial oxygen and hydrogen atoms (see Fig. 4[link] for the details). In Table 1[link], these axial C—H⋯O contacts are designated with symmetry `i′.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2a⋯O1ai 0.98 (4) 2.47 (4) 3.315 (4) 143 (3)
C2—H2a⋯O3ai 0.98 (4) 2.76 (4) 3.520 (5) 134 (3)
C2—H2a⋯O3eii 0.98 (4) 2.91 (4) 3.556 (4) 124 (3)
C2—H2e⋯O3aii 0.97 (4) 2.49 (4) 3.201 (4) 130 (3)
C2—H2e⋯O3eiii 0.97 (4) 2.49 (4) 3.370 (4) 151 (3)
C4—H4a⋯O3ai 0.99 (4) 2.46 (4) 3.329 (4) 147 (3)
C4—H4e⋯O3aiv 0.94 (4) 2.70 (4) 3.462 (4) 138 (3)
C4—H4e⋯O3ev 0.94 (4) 2.63 (4) 3.454 (5) 146 (3)
C5—H5e⋯O1avi 1.00 (5) 2.91 (5) 3.598 (5) 127 (3)
C5—H5e⋯O1evii 1.00 (5) 2.50 (5) 3.395 (4) 150 (4)
C6—H6a⋯O1ai 0.95 (4) 2.45 (4) 3.287 (4) 147 (3)
C6—H6a⋯O1evi 0.95 (4) 2.65 (4) 3.269 (5) 124 (3)
C6—H6e⋯O1avi 0.95 (4) 2.81 (4) 3.344 (5) 116 (3)
C6—H6e⋯O1eviii 0.95 (4) 2.44 (4) 3.186 (5) 135 (3)
Symmetry codes: (i) [x-1, y, z]; (ii) [x-{\script{1\over 2}}, -y+1, z-{\script{1\over 2}}]; (iii) [x+{\script{1\over 2}}, -y+1, z-{\script{1\over 2}}]; (iv) [x-{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (v) [x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (vi) [x-{\script{1\over 2}}, -y, z+{\script{1\over 2}}]; (vii) x, y, z+1; (viii) [x+{\script{1\over 2}}, -y, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
Packing diagram showing the stacking of the mol­ecules parallel to the a axis.
[Figure 3]
Figure 3
Packing diagram rotated to a view approximately parallel to the b axis to show that the stacks created by the n-glide are displaced by x + [{1\over 2}]. The figure also shows that both stacks are crystallographically polar with, for example, all the axial oxygen atoms pointing upward and most of the axial hydrogen atoms pointing downward except those on C5.
[Figure 4]
Figure 4
Two adjacent mol­ecules of a stack with the O⋯H contacts detailed. The discrepancy in the H2a⋯O bonds is caused by the mol­ecules in the stacks being slightly tilted as evidenced by S1 and S3 not having the same x coordinate: 0.568 vs 0.546 (even though the mol­ecules are related by a translation along a). This leads to a difference in the S1⋯S3i and S3⋯S1i distances, for example, of 5.646 vs 5.898 Å. The longer S⋯S distance is associated with the longer H2a⋯O distance.

In addition, there are multiple O⋯H contacts between the stacks, all of which involve at least one equatorial atom. Some of these also serve to bridge adjacent mol­ecules within a stack further cementing the mol­ecules in the stack. Examination of the O⋯H contacts in Table 1[link] quickly shows that there are no short H⋯O contacts (disappointing) but simply a plethora of contacts that hold the mol­ecules in this crystal structure together. When the environment of each oxygen atom is surveyed in detail, it is found that they all inter­act with four hydrogen atoms, which generally form a distorted quadrilateral with O⋯H contact distances that vary from 2.44 to 3.09 Å. This is very similar to what was found for the 1,4-di­sulfone structure where example figures can be found (Harlow et al., 2019[Harlow, R. L., Oliver, A. G., Baker, J. M., Marshall, W. J. & Sammes, M. P. (2019). Acta Cryst. E75, 576-579.]). The main difference is that the O⋯H distances in the 1,4-di­sulfone structure were relatively uniform and, in this structure, they are not.

One mystery that remains is why a small mol­ecule with mirror symmetry crystallizes in a non-centrosymmetric, polar space group?

4. Database survey

A Cambridge Crystallographic Database survey of the 1,3-di­sulfone moiety reveals 22 structures with that motif (CSD version 5.41 + three updates; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]). Four of the structures were authored by Harlow and Sammes and served as an impetus for the present study. A paper entitled in part `Study of the Inter­action of Silver(I) with β-Di­sulfone in Aqueous Alkaline Media' was of particular inter­est because it suggested that metal salts could be made with our title compound, i.e. one of the hydrogen atoms on C2 was acidic enough to be easily removed (DeMember et al., 1983[DeMember, J. R., Evans, H. F., Wallace, F. A. & Tariverdian, P. A. (1983). J. Am. Chem. Soc. 105, 5647-5652.]) in a solution of KOH.

5. Synthesis and crystallization

To a stirred solution of 1,3-di­thiane (1.05 g, 5.70 mmol, Alfa-Aeser) in glacial acetic acid (25 mL) was added a solution of 30% H2O2 (10 mL) in glacial acetic acid (25 mL) and the mixture was heated to 323 K overnight. The white precipitate was separated on a Buchner funnel and washed with water (3 × 25 mL) and dried in air. Colorless, rod-like crystals of the compound were harvested from an evaporated KOH (0.5 M) solution of the the 1,3-di­sulfone. 1H NMR (400 MHz, DMSO-d6), δ: 5.238 (singlet, 2H, H2a/e), 3.370 (triplet, 4H, 3JH,H = 5 Hz, H4a/e, H6a/e), 2.260 (pentet, 2H, 3JH,H = 6 Hz, H5a/e); 13C NMR (100.13 MHz, DMSO-d6), δ: 70.12 (C2), 50.09 (C4/C6), 17.60 (C4). HRMS (negative ion mode, [C4H7O4S2]) m/z found: 182.9803; calculated: 182.9786.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. Non-hydrogen atoms were refined with anisotropic displacement parameters and all hydrogen atoms were located from a difference-Fourier map and refined freely.

Table 2
Experimental details

Crystal data
Chemical formula C4H8O4S2
Mr 184.22
Crystal system, space group Monoclinic, Pn
Temperature (K) 120
a, b, c (Å) 4.9472 (5), 9.9021 (10), 7.1002 (7)
β (°) 91.464 (3)
V3) 347.71 (6)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.72
Crystal size (mm) 0.54 × 0.11 × 0.05
 
Data collection
Diffractometer Bruker PHOTON-II
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.579, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 6109, 1513, 1473
Rint 0.039
(sin θ/λ)max−1) 0.640
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.055, 1.15
No. of reflections 1513
No. of parameters 123
No. of restraints 2
H-atom treatment All H-atom parameters refined
Δρmax, Δρmin (e Å−3) 0.28, −0.40
Absolute structure Flack x determined using 682 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]).
Absolute structure parameter 0.07 (4)
Computer programs: APEX3 and SAINT (Bruker, 2015[Bruker (2015). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), olex2.solve (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]), SHELXL2018/3 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), CrystalMaker (Palmer, 2014[Palmer, D. C. (2014). CrystalMaker. CrystalMaker Software Ltd., Pegbroke, England.]), and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Computing details top

Data collection: APEX3 (Bruker, 2015); cell refinement: SAINT (Bruker, 2015); data reduction: SAINT (Bruker, 2015); program(s) used to solve structure: olex2.solve (Dolomanov et al., 2009); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: CrystalMaker (Palmer, 2014); software used to prepare material for publication: publCIF (Westrip, 2010).

1,3-Dithiane 1,1,3,3-tetraoxide top
Crystal data top
C4H8O4S2F(000) = 192
Mr = 184.22Dx = 1.760 Mg m3
Monoclinic, PnMo Kα radiation, λ = 0.71073 Å
a = 4.9472 (5) ÅCell parameters from 5408 reflections
b = 9.9021 (10) Åθ = 3.5–27.1°
c = 7.1002 (7) ŵ = 0.72 mm1
β = 91.464 (3)°T = 120 K
V = 347.71 (6) Å3Rod, colorless
Z = 20.54 × 0.11 × 0.05 mm
Data collection top
Bruker PHOTON-II
diffractometer
1513 independent reflections
Radiation source: fine-focus sealed tube1473 reflections with I > 2σ(I)
Bruker TRIUMPH curved-graphite monochromatorRint = 0.039
Detector resolution: 7.41 pixels mm-1θmax = 27.1°, θmin = 2.1°
combination of ω and φ–scansh = 66
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)
k = 1212
Tmin = 0.579, Tmax = 0.746l = 99
6109 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.027All H-atom parameters refined
wR(F2) = 0.055 w = 1/[σ2(Fo2) + (0.0163P)2 + 0.148P]
where P = (Fo2 + 2Fc2)/3
S = 1.15(Δ/σ)max < 0.001
1513 reflectionsΔρmax = 0.28 e Å3
123 parametersΔρmin = 0.40 e Å3
2 restraintsAbsolute structure: Flack x determined using 682 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
Primary atom site location: iterativeAbsolute structure parameter: 0.07 (4)
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.56801 (14)0.16084 (8)0.31351 (11)0.01036 (19)
S30.54595 (15)0.42138 (8)0.52142 (12)0.01083 (19)
O1a0.8592 (5)0.1643 (3)0.3226 (4)0.0167 (5)
O1e0.4403 (5)0.0944 (3)0.1549 (4)0.0173 (6)
O3a0.8376 (5)0.4249 (3)0.5291 (4)0.0162 (5)
O3e0.4048 (5)0.5484 (2)0.5189 (4)0.0170 (6)
C20.4419 (7)0.3292 (4)0.3144 (5)0.0125 (7)
C40.4299 (7)0.3185 (4)0.7058 (5)0.0155 (7)
C50.5438 (8)0.1749 (4)0.6975 (5)0.0166 (8)
C60.4464 (8)0.0935 (4)0.5261 (5)0.0155 (8)
H2a0.244 (8)0.323 (3)0.309 (6)0.006 (9)*
H2e0.515 (8)0.376 (4)0.206 (6)0.004 (9)*
H4a0.231 (8)0.326 (4)0.697 (5)0.007 (9)*
H4e0.489 (7)0.362 (4)0.817 (6)0.011 (10)*
H5a0.724 (9)0.179 (4)0.706 (6)0.011 (10)*
H5e0.475 (9)0.123 (5)0.807 (7)0.025 (12)*
H6a0.255 (7)0.094 (4)0.513 (6)0.002 (8)*
H6e0.523 (8)0.005 (4)0.529 (6)0.007 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0083 (4)0.0114 (4)0.0114 (4)0.0005 (4)0.0006 (3)0.0008 (3)
S30.0098 (4)0.0107 (4)0.0120 (4)0.0004 (3)0.0004 (3)0.0015 (3)
O1a0.0091 (12)0.0200 (13)0.0209 (14)0.0015 (10)0.0017 (10)0.0001 (11)
O1e0.0161 (13)0.0203 (13)0.0153 (13)0.0022 (11)0.0004 (10)0.0076 (10)
O3a0.0085 (12)0.0191 (13)0.0210 (13)0.0026 (10)0.0019 (10)0.0017 (11)
O3e0.0167 (14)0.0120 (13)0.0224 (14)0.0027 (10)0.0024 (11)0.0019 (10)
C20.0120 (18)0.0124 (17)0.0130 (17)0.0006 (13)0.0015 (14)0.0003 (13)
C40.0146 (18)0.0211 (19)0.0108 (16)0.0000 (15)0.0023 (14)0.0010 (14)
C50.0138 (19)0.022 (2)0.0136 (19)0.0005 (15)0.0007 (15)0.0071 (14)
C60.0119 (16)0.0177 (19)0.0170 (18)0.0002 (14)0.0002 (14)0.0021 (14)
Geometric parameters (Å, º) top
S1—O1e1.437 (3)C2—H2e0.97 (4)
S1—O1a1.441 (3)C4—C51.531 (5)
S1—C61.769 (4)C4—H4a0.99 (4)
S1—C21.780 (4)C4—H4e0.94 (4)
S3—O3e1.439 (3)C5—C61.528 (5)
S3—O3a1.443 (3)C5—H5a0.89 (4)
S3—C41.767 (4)C5—H5e1.00 (5)
S3—C21.795 (4)C6—H6a0.95 (4)
C2—H2a0.98 (4)C6—H6e0.95 (4)
O1e—S1—O1a117.72 (16)C5—C4—S3112.3 (3)
O1e—S1—C6110.10 (17)C5—C4—H4a116 (2)
O1a—S1—C6109.38 (17)S3—C4—H4a105 (2)
O1e—S1—C2106.54 (16)C5—C4—H4e111 (2)
O1a—S1—C2109.14 (16)S3—C4—H4e105 (3)
C6—S1—C2102.89 (17)H4a—C4—H4e108 (3)
O3e—S3—O3a117.64 (15)C6—C5—C4114.3 (3)
O3e—S3—C4110.27 (17)C6—C5—H5a112 (3)
O3a—S3—C4109.24 (17)C4—C5—H5a109 (3)
O3e—S3—C2107.81 (16)C6—C5—H5e104 (3)
O3a—S3—C2107.99 (16)C4—C5—H5e108 (3)
C4—S3—C2102.81 (18)H5a—C5—H5e109 (4)
S1—C2—S3112.73 (19)C5—C6—S1111.9 (3)
S1—C2—H2a107 (2)C5—C6—H6a112 (2)
S3—C2—H2a109 (2)S1—C6—H6a106 (2)
S1—C2—H2e108 (2)C5—C6—H6e111 (3)
S3—C2—H2e107 (2)S1—C6—H6e103 (2)
H2a—C2—H2e113 (3)H6a—C6—H6e114 (3)
O1e—S1—C2—S3172.32 (18)O3a—S3—C4—C557.4 (3)
O1a—S1—C2—S359.6 (2)C2—S3—C4—C557.1 (3)
C6—S1—C2—S356.5 (2)S3—C4—C5—C666.1 (4)
O3e—S3—C2—S1172.54 (18)C4—C5—C6—S166.5 (4)
O3a—S3—C2—S159.4 (2)O1e—S1—C6—C5171.4 (3)
C4—S3—C2—S156.0 (2)O1a—S1—C6—C557.8 (3)
O3e—S3—C4—C5171.8 (3)C2—S1—C6—C558.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2a···O1ai0.98 (4)2.47 (4)3.315 (4)143 (3)
C2—H2a···O3ai0.98 (4)2.76 (4)3.520 (5)134 (3)
C2—H2a···O3eii0.98 (4)2.91 (4)3.556 (4)124 (3)
C2—H2e···O3aii0.97 (4)2.49 (4)3.201 (4)130 (3)
C2—H2e···O3eiii0.97 (4)2.49 (4)3.370 (4)151 (3)
C4—H4a···O3ai0.99 (4)2.46 (4)3.329 (4)147 (3)
C4—H4e···O3aiv0.94 (4)2.70 (4)3.462 (4)138 (3)
C4—H4e···O3ev0.94 (4)2.63 (4)3.454 (5)146 (3)
C5—H5e···O1avi1.00 (5)2.91 (5)3.598 (5)127 (3)
C5—H5e···O1evii1.00 (5)2.50 (5)3.395 (4)150 (4)
C6—H6a···O1ai0.95 (4)2.45 (4)3.287 (4)147 (3)
C6—H6a···O1evi0.95 (4)2.65 (4)3.269 (5)124 (3)
C6—H6e···O1avi0.95 (4)2.81 (4)3.344 (5)116 (3)
C6—H6e···O1eviii0.95 (4)2.44 (4)3.186 (5)135 (3)
Symmetry codes: (i) x1, y, z; (ii) x1/2, y+1, z1/2; (iii) x+1/2, y+1, z1/2; (iv) x1/2, y+1, z+1/2; (v) x+1/2, y+1, z+1/2; (vi) x1/2, y, z+1/2; (vii) x, y, z+1; (viii) x+1/2, y, z+1/2.
 

Funding information

Funding for this research was provided by: The R. Harlow Foundation for Disabused Crystallographers [gift No. 174(3) to Allen G. Oliver].

References

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