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

Harlow, R.L.; Oliver, A.G.; Sammes, M.P.

doi:10.1107/S2056989021000876

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Volume 77| Part 2| February 2021| Pages 204-207

https://doi.org/10.1107/S2056989021000876

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

Richard L. Harlow,^a ^* Allen G. Oliver ^b ^* and Michael P. Sammes ^c

^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.

Keywords: crystal structure; 1,3-dithiane 1,1,3,3,-tetraoxide; C—H⋯O contacts.

CCDC reference: 2058562

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 ) 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 ) as illustrated.

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 ) for further details of ¹H NMR spectra and hydrogen-atom polarity in disulfones.

2. Structural commentary

Fig. 1 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
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. 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) 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 for the details). In Table 1, these axial C—H⋯O contacts are designated with symmetry `i′.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O3a^iv	0.94 (4)	2.70 (4)	3.462 (4)	138 (3)
C4—H4e⋯O3e^v	0.94 (4)	2.63 (4)	3.454 (5)	146 (3)
C5—H5e⋯O1a^vi	1.00 (5)	2.91 (5)	3.598 (5)	127 (3)
C5—H5e⋯O1e^vii	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⋯O1e^vi	0.95 (4)	2.65 (4)	3.269 (5)	124 (3)
C6—H6e⋯O1a^vi	0.95 (4)	2.81 (4)	3.344 (5)	116 (3)
C6—H6e⋯O1e^viii	0.95 (4)	2.44 (4)	3.186 (5)	135 (3)
Symmetry codes: (i) ; (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
Packing diagram showing the stacking of the molecules parallel to the a axis.

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
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 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). 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 ). 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 ) 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, ³J_H,H = 5 Hz, H4a/e, H6a/e), 2.260 (pentet, 2H, ³J_H,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. 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
M_r	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)
V (Å³)	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 )
T_min, T_max	0.579, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	6109, 1513, 1473
R_int	0.039
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.40
Absolute structure	Flack x determined using 682 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 ).
Absolute structure parameter	0.07 (4)
Computer programs: APEX3 and SAINT (Bruker, 2015 ), olex2.solve (Dolomanov et al., 2009 ), SHELXL2018/3 (Sheldrick, 2015 ), CrystalMaker (Palmer, 2014 ), and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 2058562

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989021000876/ey2004sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021000876/ey2004Isup2.hkl

checkCIF report

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

C₄H₈O₄S₂	F(000) = 192
M_r = 184.22	D_x = 1.760 Mg m⁻³
Monoclinic, Pn	Mo Kα radiation, λ = 0.71073 Å
a = 4.9472 (5) Å	Cell parameters from 5408 reflections
b = 9.9021 (10) Å	θ = 3.5–27.1°
c = 7.1002 (7) Å	µ = 0.72 mm⁻¹
β = 91.464 (3)°	T = 120 K
V = 347.71 (6) Å³	Rod, colorless
Z = 2	0.54 × 0.11 × 0.05 mm

Data collection top

Bruker PHOTON-II diffractometer	1513 independent reflections
Radiation source: fine-focus sealed tube	1473 reflections with I > 2σ(I)
Bruker TRIUMPH curved-graphite monochromator	R_int = 0.039
Detector resolution: 7.41 pixels mm^-1	θ_max = 27.1°, θ_min = 2.1°
combination of ω and φ–scans	h = −6→6
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −12→12
T_min = 0.579, T_max = 0.746	l = −9→9
6109 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.027	All H-atom parameters refined
wR(F²) = 0.055	w = 1/[σ²(F_o²) + (0.0163P)² + 0.148P] where P = (F_o² + 2F_c²)/3
S = 1.15	(Δ/σ)_max < 0.001
1513 reflections	Δρ_max = 0.28 e Å⁻³
123 parameters	Δρ_min = −0.40 e Å⁻³
2 restraints	Absolute structure: Flack x determined using 682 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013).
Primary atom site location: iterative	Absolute 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

	x	y	z	U_iso*/U_eq
S1	0.56801 (14)	0.16084 (8)	0.31351 (11)	0.01036 (19)
S3	0.54595 (15)	0.42138 (8)	0.52142 (12)	0.01083 (19)
O1a	0.8592 (5)	0.1643 (3)	0.3226 (4)	0.0167 (5)
O1e	0.4403 (5)	0.0944 (3)	0.1549 (4)	0.0173 (6)
O3a	0.8376 (5)	0.4249 (3)	0.5291 (4)	0.0162 (5)
O3e	0.4048 (5)	0.5484 (2)	0.5189 (4)	0.0170 (6)
C2	0.4419 (7)	0.3292 (4)	0.3144 (5)	0.0125 (7)
C4	0.4299 (7)	0.3185 (4)	0.7058 (5)	0.0155 (7)
C5	0.5438 (8)	0.1749 (4)	0.6975 (5)	0.0166 (8)
C6	0.4464 (8)	0.0935 (4)	0.5261 (5)	0.0155 (8)
H2a	0.244 (8)	0.323 (3)	0.309 (6)	0.006 (9)*
H2e	0.515 (8)	0.376 (4)	0.206 (6)	0.004 (9)*
H4a	0.231 (8)	0.326 (4)	0.697 (5)	0.007 (9)*
H4e	0.489 (7)	0.362 (4)	0.817 (6)	0.011 (10)*
H5a	0.724 (9)	0.179 (4)	0.706 (6)	0.011 (10)*
H5e	0.475 (9)	0.123 (5)	0.807 (7)	0.025 (12)*
H6a	0.255 (7)	0.094 (4)	0.513 (6)	0.002 (8)*
H6e	0.523 (8)	0.005 (4)	0.529 (6)	0.007 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0083 (4)	0.0114 (4)	0.0114 (4)	0.0005 (4)	0.0006 (3)	−0.0008 (3)
S3	0.0098 (4)	0.0107 (4)	0.0120 (4)	−0.0004 (3)	−0.0004 (3)	−0.0015 (3)
O1a	0.0091 (12)	0.0200 (13)	0.0209 (14)	0.0015 (10)	0.0017 (10)	−0.0001 (11)
O1e	0.0161 (13)	0.0203 (13)	0.0153 (13)	−0.0022 (11)	−0.0004 (10)	−0.0076 (10)
O3a	0.0085 (12)	0.0191 (13)	0.0210 (13)	−0.0026 (10)	−0.0019 (10)	−0.0017 (11)
O3e	0.0167 (14)	0.0120 (13)	0.0224 (14)	0.0027 (10)	0.0024 (11)	−0.0019 (10)
C2	0.0120 (18)	0.0124 (17)	0.0130 (17)	−0.0006 (13)	−0.0015 (14)	0.0003 (13)
C4	0.0146 (18)	0.0211 (19)	0.0108 (16)	0.0000 (15)	0.0023 (14)	−0.0010 (14)
C5	0.0138 (19)	0.022 (2)	0.0136 (19)	0.0005 (15)	0.0007 (15)	0.0071 (14)
C6	0.0119 (16)	0.0177 (19)	0.0170 (18)	0.0002 (14)	−0.0002 (14)	0.0021 (14)

Geometric parameters (Å, º) top

S1—O1e	1.437 (3)	C2—H2e	0.97 (4)
S1—O1a	1.441 (3)	C4—C5	1.531 (5)
S1—C6	1.769 (4)	C4—H4a	0.99 (4)
S1—C2	1.780 (4)	C4—H4e	0.94 (4)
S3—O3e	1.439 (3)	C5—C6	1.528 (5)
S3—O3a	1.443 (3)	C5—H5a	0.89 (4)
S3—C4	1.767 (4)	C5—H5e	1.00 (5)
S3—C2	1.795 (4)	C6—H6a	0.95 (4)
C2—H2a	0.98 (4)	C6—H6e	0.95 (4)

O1e—S1—O1a	117.72 (16)	C5—C4—S3	112.3 (3)
O1e—S1—C6	110.10 (17)	C5—C4—H4a	116 (2)
O1a—S1—C6	109.38 (17)	S3—C4—H4a	105 (2)
O1e—S1—C2	106.54 (16)	C5—C4—H4e	111 (2)
O1a—S1—C2	109.14 (16)	S3—C4—H4e	105 (3)
C6—S1—C2	102.89 (17)	H4a—C4—H4e	108 (3)
O3e—S3—O3a	117.64 (15)	C6—C5—C4	114.3 (3)
O3e—S3—C4	110.27 (17)	C6—C5—H5a	112 (3)
O3a—S3—C4	109.24 (17)	C4—C5—H5a	109 (3)
O3e—S3—C2	107.81 (16)	C6—C5—H5e	104 (3)
O3a—S3—C2	107.99 (16)	C4—C5—H5e	108 (3)
C4—S3—C2	102.81 (18)	H5a—C5—H5e	109 (4)
S1—C2—S3	112.73 (19)	C5—C6—S1	111.9 (3)
S1—C2—H2a	107 (2)	C5—C6—H6a	112 (2)
S3—C2—H2a	109 (2)	S1—C6—H6a	106 (2)
S1—C2—H2e	108 (2)	C5—C6—H6e	111 (3)
S3—C2—H2e	107 (2)	S1—C6—H6e	103 (2)
H2a—C2—H2e	113 (3)	H6a—C6—H6e	114 (3)

O1e—S1—C2—S3	172.32 (18)	O3a—S3—C4—C5	−57.4 (3)
O1a—S1—C2—S3	−59.6 (2)	C2—S3—C4—C5	57.1 (3)
C6—S1—C2—S3	56.5 (2)	S3—C4—C5—C6	−66.1 (4)
O3e—S3—C2—S1	−172.54 (18)	C4—C5—C6—S1	66.5 (4)
O3a—S3—C2—S1	59.4 (2)	O1e—S1—C6—C5	−171.4 (3)
C4—S3—C2—S1	−56.0 (2)	O1a—S1—C6—C5	57.8 (3)
O3e—S3—C4—C5	171.8 (3)	C2—S1—C6—C5	−58.2 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···O3a^iv	0.94 (4)	2.70 (4)	3.462 (4)	138 (3)
C4—H4e···O3e^v	0.94 (4)	2.63 (4)	3.454 (5)	146 (3)
C5—H5e···O1a^vi	1.00 (5)	2.91 (5)	3.598 (5)	127 (3)
C5—H5e···O1e^vii	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···O1e^vi	0.95 (4)	2.65 (4)	3.269 (5)	124 (3)
C6—H6e···O1a^vi	0.95 (4)	2.81 (4)	3.344 (5)	116 (3)
C6—H6e···O1e^viii	0.95 (4)	2.44 (4)	3.186 (5)	135 (3)

Symmetry codes: (i) x−1, y, z; (ii) x−1/2, −y+1, z−1/2; (iii) x+1/2, −y+1, z−1/2; (iv) x−1/2, −y+1, z+1/2; (v) x+1/2, −y+1, z+1/2; (vi) x−1/2, −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].

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