research communications
Comparison of the C—H⋯O bonding in two crystalline phases of 1,4-dithiane 1,1,4,4-tetraoxide
a838 Grooms Rd, Rexford, NY 12148, USA, bDept. of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA, cDuPont Experimental Station E500.com, 200 Powder Mill Road, PO Box 8352, Wilmington, DE 19803, USA, and d2 Baydons Lane, Chippenham SN15 3JX, UK
*Correspondence e-mail: r.harlow.whereareyou@gmail.com
The crystal structures of two crystalline phases of 1,4-dithiane 1,1,4,4-tetraoxide, C4H8O4S2, have been determined in order to examine the nature of possible intermolecular hydrogen bonds. Phase 1 is monoclinic, C2/m, with unit-cell dimensions of a = 9.073 (8), b = 7.077 (6), c = 5.597 (5) Å and β = 105.89 (1)°. The molecule adopts 2/m symmetry and all of the molecules are related by translation and thus have the same orientation. Phase 2 is also monoclinic but in P21/n with unit-cell dimensions of a = 7.1305 (5), b = 5.7245 (4), c = 8.3760 (6) Å and β = 91.138 (2)°. In this phase, the molecule sits on an inversion center and the molecules within the adopt quite different orientations. In both phases, examination of the potential C—H⋯O hydrogen bonds around each of the independent oxygen atoms (one axial and the other equatorial) shows the general O⋯H patterns to be quite similar with each oxygen atom in contact with four neighboring H atoms, and each H atom contacting two neighboring O atoms. While none of the H⋯O contacts is particularly short (all are greater than 2.5 Å), each molecule has 32 such contacts that form an extensive intermolecular network. A 1H NMR spectrum of the compound dissolved in DMSO shows a singlet of 8H at δ 3.677 which indicates that the C—H bonds are only moderately polarized by the single adjacent –SO2– moiety: strongly polarized C—H bonds have δ values in the 5–6 range [Li & Sammes (1983). J. Chem. Soc. Perkin Trans. 1, pp. 1303–1309]. The phase 1 crystal studied was non-merohedrally twinned.
1. Chemical context
Some years ago, multiple studies of C—H⋯X (X = N, O) intramolecular hydrogen bonds were carried out on a series of 1,3-dithiane 1,1,3,3-tetraoxides which had various substituents at the 2 position located between the two SO2 groups. The remaining C—H bond in the 2 position is strongly polarized given the electron-withdrawing properties of the two adjacent sulfone groups. The substituents bonded at the 2 position contained nitrogen or oxygen electron-pair donors which, with proper chain lengths, were able to form an intramolecular hydrogen bond to the polar hydrogen atom.
The chemistry and NMR/IR spectroscopic information of a wide variety of compounds were reported in a number of papers (see Li & Sammes, 1983, and references therein). Focusing on those compounds with significant shifts of the polar methine hydrogen in the 1H-NMR spectra, their determinations clearly demonstrated the formation of intramolecular hydrogen bonds (Harlow et al., 1984). Never explored, however, was the nature of the C—H⋯O interactions likely to be found in the unsubstituted compound itself. As a matter of curiosity, we consequently decided to undertake the determinations of the two possible (1,3- and 1,4-) dithiane tetraoxides and the unique 1,3,5-trithiane hexaoxide. All three of the compounds have unusually high melting/decomposition temperatures and we wanted to explore and compare the nature of the intermolecular C—H⋯O interactions in this group of uncomplicated compounds. As a start on this project, we report herein the completion of the structures of two crystalline phases of 1,4-dithiane 1,1,4,4-tetraoxide, a compound which has no has the same 1:2 O:H ratio as water, and decomposes above 627 K.
2. Structural commentary
1,4-Dithiane 1,1,4,4-tetraoxide contains two crystalline phases as determined from an X-ray diffraction pattern of the as-synthesized powder. When sublimed, crystals of both phases were also produced and it was only by chance that the two laboratories involved picked different phases. Fig. 1 compares the molecular ORTEP drawings of the molecules in the two phases. The molecule in phase 1 adopts 2/m symmetry while in phase 2 the molecule sits on a center of symmetry. The intramolecular bond distances and angles for the two phases are comparable.
3. Supramolecular features
Packing diagrams (Fig. 2) reveal that the packing for the two forms is quite different. In phase 1, all of the molecules are related by simple translational symmetries and thus all the molecules have the same orientation. In phase 2, the molecules have two different orientations in a somewhat herringbone fashion. Thus, one might expect any C—H⋯O contacts to be quite different for the two phases but, in fact, they are very similar. Figs. 3 and 4 compare the environments of O1 (equatorial oxygen atom) and O2 (axial oxygen atom). In all cases, each oxygen atom is in contact with four hydrogen atoms arranged in a distorted square. Probably for steric reasons, the distortion is less for the equatorial oxygen atom than for the axial oxygen atom.
Each oxygen atom in both phases `sees' four hydrogen atoms while each hydrogen atom `sees' two oxygen atoms. This bifurcation of the hydrogen contacts means that none of the H⋯O distances is particularly short. It should also be pointed out that each methylene group has only one neighboring sulfone group, which would limit the polarization of the C—H bonds compared to our previous studies where the C—H bond of interest sat between two sulfone groups. Thus, very short C—H⋯O bonds were not expected. The exact details of the C—H⋯O contacts are given in Table 1. Thus, while there are no really short C—H⋯O contacts (none less than 2.50 Å), every donor and every acceptor plays a role in forming a extensive network of contacts in which each molecule has a total of 32 interactions with its neighbors.
The shortest C—H⋯O contacts tend to be between the equatorial oxygen atoms, O1, and the equatorial hydrogen atoms labeled with the suffix B. These also come with C—H⋯O angles that are closest to being linear, 148 to 160°. Presumably the difference between axial and equatorial H⋯O contacts is mostly due to steric effects, the equatorial atoms being more accessible. The shorter contacts can undoubtedly be classified as true C—H⋯O hydrogen bonds using, as a guide, the seminal study of weak hydrogen bonds by Desiraju & Steiner (1999). The remaining bonds are probably better described as mostly electrostatic in nature. However, as Desiraju & Steiner point out, there are no hard limits for determining what may, and may not, be a true hydrogen bond.
4. Database survey
A Cambridge Crystallographic Database survey of 1,4-dithiane reveals over 200 structures with that base motif (CSD v. 5.40 + 1 update; Groom et al., 2016). A more modest survey, with one oxygen bonded to each sulfur yields 33 results, of which 1,4-dithiane 1,4-dioxide has two polymorphs [DTHDOX and DTHDOX01 (Shearer, 1959; Takemura et al., 2014) and DTHDSX (Montgomery, 1960)]. There is only one reported structure that incorporates 1,4-dithiane 1,1,4,4-tetraoxide into its structure, viz. 5,6,7-triphenyl-2,3-dihydro-6H-phospholo[3,4-b][1,4]dithiine 1,1,4,4,6-pentaoxide (GACCUK; Fadhel et al., 2010). One of the five oxygen atoms is located on the phosphorus, while the remaining four are on the sulfur atoms of the sulfone moiety.
5. Synthesis and crystallization
Following literature procedures (Schultz et al., 1963), a 100 mL round-bottom flask was charged with 1,4-thiane (Sigma–Aldrich; 1.005 g, 8.4 mmol) in 25 mL glacial acetic acid. To this were added 10 mL 30% hydrogen peroxide solution (excess) in 25 mL of glacial acetic acid. The solution was heated to 323 K for 12 h under stirring over an oil bath. The white solid that formed was filtered and washed with water (3 × 25 mL) and diethyl ether (3 × 25 mL) (yield: 1.325 g, 86%). Crystals suitable for structural analysis were grown by of the solid. NMR data were recorded on a Bruker Avance 400 MHz with d6-DMSO as solvent, referenced to residue proteo-DMSO. TGA/DSC data showed decomposition occurring from 627 to 739 K.
6. Refinement
Crystal data, data collection and structure . The of phase 1 used two sets of reflections as the crystal was non-merohedrally twinned. Non-hydrogen atoms were refined with anisotropic atomic displacement parameters. All hydrogen atoms were refined freely.
details are summarized in Table 2
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Supporting information
https://doi.org/10.1107/S2056989019004407/jj2210sup1.cif
contains datablocks 14-disulphone-phase1, 14-disulphone-phase2, global. DOI:Structure factors: contains datablock 14-disulphone-phase1. DOI: https://doi.org/10.1107/S2056989019004407/jj221014-disulphone-phase1sup2.hkl
Structure factors: contains datablock 14-disulphone-phase2. DOI: https://doi.org/10.1107/S2056989019004407/jj221014-disulphone-phase2sup3.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989019004407/jj221014-disulphone-phase1sup4.cml
Supporting information file. DOI: https://doi.org/10.1107/S2056989019004407/jj221014-disulphone-phase2sup5.cml
For both structures, data collection: APEX3 (Bruker, 2016); cell
SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: OLEX2 (Dolomanov et al., 2009); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009), CrystalMaker (Palmer, 2014). Software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009) and publCIF (Westrip, 2010) for 14-disulphone-phase1; OLEX2 (Dolomanov et al., 2009) for 14-disulphone-phase2.C4H8O4S2 | F(000) = 192 |
Mr = 184.22 | Dx = 1.770 Mg m−3 |
Monoclinic, C2/m | Mo Kα radiation, λ = 0.71073 Å |
a = 9.073 (8) Å | Cell parameters from 999 reflections |
b = 7.077 (6) Å | θ = 3.7–27.7° |
c = 5.597 (5) Å | µ = 0.72 mm−1 |
β = 105.894 (10)° | T = 233 K |
V = 345.6 (5) Å3 | Irregular block, colorless |
Z = 2 | 0.43 × 0.35 × 0.35 mm |
APEXII CCD diffractometer | 428 reflections with I > 2σ(I) |
θ/2θ scans | θmax = 27.6°, θmin = 3.7° |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | h = −11→11 |
Tmin = 0.747, Tmax = 0.787 | k = 0→9 |
433 measured reflections | l = 0→7 |
433 independent reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.023 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.067 | All H-atom parameters refined |
S = 1.19 | w = 1/[σ2(Fo2) + (0.0297P)2 + 0.2882P] where P = (Fo2 + 2Fc2)/3 |
433 reflections | (Δ/σ)max = 0.001 |
37 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
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. Refined as a 2-component twin. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.65320 (6) | 0.500000 | 0.24835 (9) | 0.01721 (19) | |
O1 | 0.6955 (2) | 0.500000 | 0.5165 (3) | 0.0273 (4) | |
O2 | 0.77466 (18) | 0.500000 | 0.1266 (3) | 0.0258 (4) | |
C1 | 0.53198 (17) | 0.3028 (2) | 0.1408 (3) | 0.0198 (3) | |
H1A | 0.454 (2) | 0.305 (3) | 0.225 (4) | 0.024 (5)* | |
H1B | 0.590 (2) | 0.200 (3) | 0.192 (4) | 0.028 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0144 (3) | 0.0179 (3) | 0.0173 (3) | 0.000 | 0.0010 (2) | 0.000 |
O1 | 0.0270 (8) | 0.0319 (10) | 0.0183 (8) | 0.000 | −0.0017 (7) | 0.000 |
O2 | 0.0166 (8) | 0.0289 (9) | 0.0326 (9) | 0.000 | 0.0080 (7) | 0.000 |
C1 | 0.0193 (7) | 0.0158 (7) | 0.0217 (8) | −0.0011 (5) | 0.0015 (6) | 0.0026 (6) |
S1—O1 | 1.444 (2) | C1—C1ii | 1.523 (3) |
S1—O2 | 1.4456 (19) | C1—H1A | 0.949 (19) |
S1—C1 | 1.7768 (19) | C1—H1B | 0.90 (2) |
S1—C1i | 1.7768 (19) | ||
O1—S1—O2 | 118.03 (11) | S1—C1—H1A | 106.9 (12) |
O1—S1—C1i | 108.42 (7) | S1—C1—H1B | 105.9 (13) |
O1—S1—C1 | 108.42 (7) | C1ii—C1—S1 | 112.07 (9) |
O2—S1—C1i | 108.74 (8) | C1ii—C1—H1A | 113.1 (11) |
O2—S1—C1 | 108.74 (8) | C1ii—C1—H1B | 110.6 (13) |
C1—S1—C1i | 103.52 (12) | H1A—C1—H1B | 108.0 (17) |
O1—S1—C1—C1ii | 174.03 (12) | C1i—S1—C1—C1ii | 59.03 (17) |
O2—S1—C1—C1ii | −56.47 (15) |
Symmetry codes: (i) x, −y+1, z; (ii) −x+1, y, −z. |
C4H8O4S2 | F(000) = 192 |
Mr = 184.22 | Dx = 1.790 Mg m−3 |
Monoclinic, P21/n | Synchrotron radiation, λ = 0.7288 Å |
a = 7.1308 (5) Å | Cell parameters from 4318 reflections |
b = 5.7245 (4) Å | θ = 29.1–3.8° |
c = 8.3760 (6) Å | µ = 0.78 mm−1 |
β = 91.138 (2)° | T = 150 K |
V = 341.84 (4) Å3 | Tablet, colorless |
Z = 2 | 0.04 × 0.03 × 0.02 mm |
Bruker D8 Photon-2 diffractometer | 1041 independent reflections |
Radiation source: synchrotron | 957 reflections with I > 2σ(I) |
Detector resolution: 10.34 pixels mm-1 | Rint = 0.036 |
φ and ω scans | θmax = 31.4°, θmin = 3.8° |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | h = −10→10 |
Tmin = 0.811, Tmax = 0.862 | k = −8→8 |
14904 measured reflections | l = −11→11 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.028 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.065 | All H-atom parameters refined |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0197P)2 + 0.3362P] where P = (Fo2 + 2Fc2)/3 |
1041 reflections | (Δ/σ)max = 0.001 |
62 parameters | Δρmax = 0.39 e Å−3 |
0 restraints | Δρmin = −0.44 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.19891 (5) | 0.14315 (6) | 0.54564 (4) | 0.01294 (10) | |
O1 | 0.35411 (15) | 0.14742 (19) | 0.65934 (13) | 0.0194 (2) | |
O2 | 0.19584 (15) | 0.31562 (19) | 0.41982 (12) | 0.0186 (2) | |
C1 | 0.1857 (2) | −0.1390 (2) | 0.45787 (17) | 0.0149 (3) | |
C2 | −0.0137 (2) | 0.1639 (3) | 0.65211 (17) | 0.0147 (3) | |
H1A | 0.186 (3) | −0.247 (4) | 0.541 (2) | 0.024 (5)* | |
H1B | 0.299 (3) | −0.156 (3) | 0.401 (2) | 0.020 (5)* | |
H2A | −0.006 (3) | 0.049 (3) | 0.734 (2) | 0.016 (4)* | |
H2B | −0.008 (3) | 0.314 (4) | 0.696 (2) | 0.024 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.01212 (16) | 0.01260 (16) | 0.01412 (17) | −0.00078 (11) | 0.00029 (11) | −0.00062 (12) |
O1 | 0.0153 (5) | 0.0218 (5) | 0.0208 (5) | −0.0010 (4) | −0.0042 (4) | −0.0031 (4) |
O2 | 0.0209 (5) | 0.0156 (5) | 0.0194 (5) | −0.0018 (4) | 0.0024 (4) | 0.0038 (4) |
C1 | 0.0135 (6) | 0.0134 (6) | 0.0177 (6) | 0.0010 (5) | 0.0011 (5) | −0.0018 (5) |
C2 | 0.0146 (6) | 0.0157 (6) | 0.0137 (6) | −0.0002 (5) | 0.0013 (5) | −0.0022 (5) |
S1—O1 | 1.4459 (11) | C1—H1A | 0.93 (2) |
S1—O2 | 1.4439 (11) | C1—H1B | 0.95 (2) |
S1—C1 | 1.7762 (14) | C2—H2A | 0.952 (19) |
S1—C2 | 1.7778 (14) | C2—H2B | 0.94 (2) |
C1—C2i | 1.5265 (19) | ||
O1—S1—C1 | 108.75 (7) | C2i—C1—H1A | 112.1 (12) |
O1—S1—C2 | 108.51 (7) | C2i—C1—H1B | 111.5 (11) |
O2—S1—O1 | 118.00 (7) | H1A—C1—H1B | 108.6 (16) |
O2—S1—C1 | 108.65 (7) | S1—C2—H2A | 106.2 (11) |
O2—S1—C2 | 108.65 (7) | S1—C2—H2B | 103.3 (12) |
C1—S1—C2 | 103.29 (7) | C1i—C2—S1 | 111.98 (10) |
S1—C1—H1A | 107.1 (13) | C1i—C2—H2A | 113.8 (11) |
S1—C1—H1B | 105.4 (12) | C1i—C2—H2B | 110.6 (12) |
C2i—C1—S1 | 111.72 (10) | H2A—C2—H2B | 110.4 (16) |
Symmetry code: (i) −x, −y, −z+1. |
Atoms | bond | angle | angle |
H···O | C—H···O | S—O···H | |
Phase 1 | |||
C1—H1A···O1i | 2.63 (2) | 148 (2) | 123 (2) |
C1—H1B···O1ii | 2.59 (2) | 157 (2) | 127 (2) |
C1—H1A···O2iii | 2.67 (2) | 112 (2) | 114 (2) |
C1—H1B···O2iv | 2.81 (2) | 122 (2) | 145 (2) |
Phase 2 | |||
C1—H1A···O1i | 2.60 (2) | 151 (1) | 123 (1) |
C1—H1B···O1ii | 2.54 (2) | 160 (1) | 127 (1) |
C2—H2A···O1i | 2.69 (2) | 149 (1) | 122 (1) |
C2—H2B···O1iii | 2.50 (2) | 155 (1) | 129 (1) |
C1—H1A···O2iv | 2.70 (2) | 110 (1) | 111 (1) |
C1—H1B···O2v | 2.69 (2) | 122 (1) | 140 (1) |
C2—H2A···O2vi | 2.77 (2) | 100 (1) | 127 (1) |
C2—H2B···O2vii | 2.68 (2) | 125 (1) | 144 (1) |
Symmetry codes for phase 1: (i) 1 - x, y, 1 - z; (ii) 3/2 - x, -1/2 + y, 1 - z; (iii) -1/2 + x, -1/2 + y, z; (iv) 3/2 - x, -1/2 + y, -z. Symmetry codes for phase 2: (i) 1/2 - x, -1/2 + y, 3/2 - z; (ii) 1 - x, -y, 1 - z; (iii) 1/2 - x, 1/2 + y, 3/2 - z; (iv) x, -1 + y, z; (v) 1/2 - x, -1/2 + y, 1/2 - z; (vi) -1/2 + x, 1/2 - y, 1/2 + z; (vii) -x, 1 - y, 1 - z. |
Acknowledgements
A sample of phase 2 was submitted through the SCrALS (Service Crystallography at the Advance Light Source) program. Crystallographic data were collected at Beamline 11.3.1 at the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory. The ALs is supported by the US Department of Energy Sciences, under Contract DE-AC02–05CH11231. The R. Harlow Foundation for Disabused Crystallographers partially funded this research through a grant to the University of Notre Dame.
Funding information
Funding for this research was provided by: R. Harlow Foundation for Disabused Crystallographers (grant to University of Notre Dame, SCRALS).
References
Bruker (2016). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press. Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Fadhel, O., Benkö, Z., Gras, M., Deborde, V., Joly, D., Lescop, C., Nyulászi, L., Hissler, M. & Réau, R. (2010). Chem. Eur. J. 16, 11340–11356. Web of Science CSD CrossRef CAS PubMed Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CrossRef IUCr Journals Google Scholar
Harlow, R. L., Li, C. & Sammes, M. P. (1984). J. Chem. Soc., Perkin Trans. I, 547–551. Google Scholar
Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Li, C. & Sammes, M. P. (1983). J. Chem. Soc. Perkin Trans. 1, pp. 1303–1309. CrossRef Web of Science Google Scholar
Montgomery, H. (1960). Acta Cryst. 13, 381–384. CSD CrossRef IUCr Journals Web of Science Google Scholar
Palmer, D. C. (2014). CrystalMaker. CrystalMaker Software Ltd, Begbroke, England. Google Scholar
Schultz, H. S., Freyermuth, H. B. & Buc, S. R. (1963). J. Org. Chem. 28, 1140–1142. CrossRef CAS Web of Science Google Scholar
Shearer, H. M. M. (1959). J. Chem. Soc. pp. 1394–1397. CSD CrossRef Web of Science Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Takemura, A., McAllister, L. J., Karadakov, P. B., Pridmore, N. E., Whitwood, A. C. & Bruce, D. W. (2014). CrystEngComm, 16, 4254–4264. Web of Science CSD CrossRef CAS Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
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