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Crystal structure of a new polymorph of di(thio­phen-3-yl) ketone

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aTU Bergakademie Freiberg, Leipziger Strasse 29, D-09596 Freiberg/Sachsen, Germany
*Correspondence e-mail: edwin.weber@chemie.tu-freiberg.de

Edited by P. McArdle, National University of Ireland, Ireland (Received 16 September 2017; accepted 19 September 2017; online 29 September 2017)

The crystal structure of the title compound, C9H6OS2, represents a new polymorph. The crystal structure was solved in the ortho­rhom­bic space group Pbcn with one half of the mol­ecule in the asymmetric unit. The thio­phene rings are perfectly planar and twisted with respect to each other, showing the mol­ecule to be in an S,O-trans/S,O-trans conformation. In the crystal, C—H⋯O hydrogen bonds connect the mol­ecules into layers extending parallel to the ab plane. The crystal structure also features ππ inter­actions.

1. Chemical context

With reference to the principle of bioisosterism (Lima & Barreiro, 2005[Lima, L. M. & Barreiro, E. J. (2005). Curr. Med. Chem. 12, 23-49.]), thio­phene is an important structural moiety replacing benzene rings in drugs and biomolecules. Moreover, thio­phene is a highly polarizable group due to the presence of the π-electrons and the sulfur atom available in the ring, making it a structural unit worthy of investigation related to crystal engineering (Desiraju et al., 2012[Desiraju, G. R., Vittal, G. G. & Ramonau, A. (2012). In Crystal Engineering. London: Imperial College Press.]). This involves potential π-stacking (Tiekink & Zukerman-Schpector, 2012[Tiekink, E. R. T. & Zukerman-Schpector, J. (2012). In The Importance of Pi-Interactions in Crystal Engineering. Frontiers in Crystal Engineering. Chichester: Wiley.]) and C—H⋯π (Nishio et al., 2009[Nishio, M., Umezawa, Y., Honda, K., Tsuboyama, S. & Suezawa, H. (2009). CrystEngComm, 11, 1757-1788.]) inter­actions, as well as other contacts including a chalcogen atom such as sulfur (Gleiter et al., 2003[Gleiter, S., Werz, D. B. & Rausch, B. J. (2003). Chem. Eur. J. 9, 2676-2683.]). From this point of view, the title compound is likely to be an inter­esting study object. However, searching in the literature shows its crystal structure being already described twice (Sheldrick et al., 1978[Sheldrick, W. S., Becker, W. & Engel, J. (1978). Acta Cryst. B34, 3120-3122.]; Benassi et al., 1989[Benassi, R., Folli, U., Iarossi, D., Schenetti, L., Taddei, F., Musatti, A. & Nardelli, M. (1989). J. Chem. Soc. Perkin Trans. 2, pp. 1741-1751.]). On the other hand, a polymorph resulted from our work, the structure of which is reported here and comparatively discussed in connection with the previous findings, bearing in mind the attention currently attracted by the field of polymorphism in mol­ecular crystals (Bernstein, 2002[Bernstein, J. (2002). Polymorphism in Molecular Crystals. Oxford: Oxford University Press.]; Cabri et al., 2007[Cabri, W., Ghetti, P., Pozzi, G. & Alpegiani, M. (2007). Org. Process Res. Dev. 11, 64-72.]; Braga et al., 2009[Braga, D., Grepioni, F., Maini, L. & Polito, M. (2009). Struct. Bond. 132, 25-50.]).

[Scheme 1]

2. Structural commentary

The title compound crystallizes in the space group Pbcn with one half of the mol­ecule in the asymmetric unit, i.e. the mol­ecule is located on the twofold symmetry axis. A perspective view of the mol­ecular structure of the title compound is presented in Fig. 1[link]. The bond distances within the mol­ecule agree with those found in the reported crystal structures of the polymorphs of this compound (Sheldrick et al., 1978[Sheldrick, W. S., Becker, W. & Engel, J. (1978). Acta Cryst. B34, 3120-3122.]; Benassi et al., 1989[Benassi, R., Folli, U., Iarossi, D., Schenetti, L., Taddei, F., Musatti, A. & Nardelli, M. (1989). J. Chem. Soc. Perkin Trans. 2, pp. 1741-1751.]). Taking into account experimental error, the thio­phene rings are perfectly planar. The heteroatom of the ring is always on the opposite side with respect to C=O, showing the mol­ecule to be in an S,O-trans/S,O-trans conformation, as was predicted to be the more stable conformation for the compound (Benassi et al., 1989[Benassi, R., Folli, U., Iarossi, D., Schenetti, L., Taddei, F., Musatti, A. & Nardelli, M. (1989). J. Chem. Soc. Perkin Trans. 2, pp. 1741-1751.]). The torsion angle along the atomic sequence O1—C5—C3—C4 is −155.2 (3)° and corresponds to an inter­planar angle of 42.3 (1)° between the thio­phene rings, being ascribed to steric hindrance between the H atoms on C4 and C4′.

[Figure 1]
Figure 1
Perspective view of the mol­ecular structure of the title compound. Anisotropic displacement ellipsoids are drawn at the 30% probability level.

3. Supra­molecular features

The crystal structure is composed of mol­ecular layers extending parallel to the ab plane (Table 1[link], Fig. 2[link]). Within a given layer the mol­ecules are connected via C—H⋯O hydrogen bonds (Desiraju & Steiner, 1999[Desiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond. Oxford University Press.]) in which the oxygen atom acts as a bifurcated acceptor. Moreover, the layer structure features ππ stacking (Tiekink & Zukerman-Schpector, 2012[Tiekink, E. R. T. & Zukerman-Schpector, J. (2012). In The Importance of Pi-Interactions in Crystal Engineering. Frontiers in Crystal Engineering. Chichester: Wiley.]) with a centroid⋯centroid distance of 3.946 (2) Å and a slippage of 1.473 Å between the inter­acting thio­phene rings. No directed non-covalent bonding is observed between the mol­ecules of consecutive layers, so that the crystal structure appears to be stabilized only by van der Waals forces in the stacking direction of the mol­ecular layers.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C4—H4⋯O1i 0.93 2.42 3.261 (4) 151
Symmetry code: (i) [x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
Packing diagram of the title compound viewed down the a axis. Dashed lines represent hydrogen-bonding inter­actions.

4. Database survey

A search in the Cambridge Structural Database (CSD, Version 5.38, update February 2017; Groom et al. 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) revealed two crystal structures of the title compound [Refcodes DTHKET (Sheldrick et al., 1978[Sheldrick, W. S., Becker, W. & Engel, J. (1978). Acta Cryst. B34, 3120-3122.]) and DTHKET01 (Benassi et al., 1989[Benassi, R., Folli, U., Iarossi, D., Schenetti, L., Taddei, F., Musatti, A. & Nardelli, M. (1989). J. Chem. Soc. Perkin Trans. 2, pp. 1741-1751.])]. In these polymorphs (space group: P21/c, P21/n, Z = 4) the mol­ecules show slight conformational differences and one of their thio­phene rings is disordered over two positions. It is obvious that crystallization from different solvents may have a fundamental influence on the mol­ecular assembly in the solid-state structure, thus giving rise to polymorphism (Bernstein, 2002[Bernstein, J. (2002). Polymorphism in Molecular Crystals. Oxford: Oxford University Press.]; Cabri et al., 2007[Cabri, W., Ghetti, P., Pozzi, G. & Alpegiani, M. (2007). Org. Process Res. Dev. 11, 64-72.]; Braga et al., 2009[Braga, D., Grepioni, F., Maini, L. & Polito, M. (2009). Struct. Bond. 132, 25-50.]). Unfortunately, the previous reports do not include information about the solvent used for crystallization of the compound and thus it is not possible to engage in a more qualified discussion of the facts. In the structures of the reported polymorphs, C—H⋯O hydrogen bonds connect the mol­ecules into undulating sheets, in which the oxygen atom acts as a bifurcated acceptor (Fig. 3[link]). Inter­sheet association is accomplished by C—H⋯π contacts, resulting in a three-dimensional supra­molecular architecture. In summary, the structures of the two polymorphs differ basically in the mol­ecular assembly.

[Figure 3]
Figure 3
Packing excerpt of the previously reported polymorph (Benassi et al., 1989[Benassi, R., Folli, U., Iarossi, D., Schenetti, L., Taddei, F., Musatti, A. & Nardelli, M. (1989). J. Chem. Soc. Perkin Trans. 2, pp. 1741-1751.]). Hydrogen-bonding inter­actions are shown as dashed lines.

5. Synthesis and crystallization

The synthesis of the title compound has been reported by different groups and following different procedures (Gronowitz & Erickson, 1963[Gronowitz, R. & Erickson, B. (1963). Ark. Kemi, 21, 335-341.]; Pittman & Hanes, 1977[Pittman, C. U. & Hanes, R. M. (1977). J. Org. Chem. 42, 1194-1197.]; Lucas et al., 2000[Lucas, P., El Mehdi, N., Ho, H. A., Bélanger, D. & Breau, L. (2000). Synthesis, pp. 1253-1258.]). We used the method of Lucas et al.[Lucas, P., El Mehdi, N., Ho, H. A., Bélanger, D. & Breau, L. (2000). Synthesis, pp. 1253-1258.], reacting thio­phen-3-yl lithium (prepared from 3-bromo­thio­phene and n-BuLi in dry diethyl ether/n-hexane at 195 K under argon) with N,N-di­methyl­carbamoyl chloride. Column chromatography on SiO2 with n-hexa­ne/ethyl acetate (10:1) followed by recrystallization from methanol yielded the title compound as colourless crystals, m.p. 353 K. Previous values for the m.p. are 345–346 K (Gronowitz & Erickson, 1963[Gronowitz, R. & Erickson, B. (1963). Ark. Kemi, 21, 335-341.]) and 346 K (Lucas et al., 2000[Lucas, P., El Mehdi, N., Ho, H. A., Bélanger, D. & Breau, L. (2000). Synthesis, pp. 1253-1258.]) pointing to polymorphic structures of the previously and presently isolated crystals.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The hydrogen atoms were positioned geometrically and refined isotropically using the riding model with C—H = 0.93 Å and Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C9H6OS2
Mr 194.26
Crystal system, space group Orthorhombic, Pbcn
Temperature (K) 296
a, b, c (Å) 3.9464 (2), 11.5015 (5), 19.2970 (9)
V3) 875.88 (7)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.55
Crystal size (mm) 0.53 × 0.15 × 0.12
 
Data collection
Diffractometer Bruker APEXII CCD area detector
Absorption correction Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin.])
Tmin, Tmax 0.759, 0.937
No. of measured, independent and observed [I > 2σ(I)] reflections 6469, 972, 667
Rint 0.033
(sin θ/λ)max−1) 0.643
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.161, 1.13
No. of reflections 972
No. of parameters 56
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.35, −0.22
Computer programs: APEX2 (and SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin.]), SHELXS97 and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Bis(thiophen-3-yl)methanone top
Crystal data top
C9H6OS2Dx = 1.473 Mg m3
Mr = 194.26Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcnCell parameters from 1847 reflections
a = 3.9464 (2) Åθ = 3.2–24.5°
b = 11.5015 (5) ŵ = 0.55 mm1
c = 19.2970 (9) ÅT = 296 K
V = 875.88 (7) Å3Plate, colourless
Z = 40.53 × 0.15 × 0.12 mm
F(000) = 400
Data collection top
Bruker APEXII CCD area detector
diffractometer
667 reflections with I > 2σ(I)
φ and ω scansRint = 0.033
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
θmax = 27.2°, θmin = 3.5°
Tmin = 0.759, Tmax = 0.937h = 45
6469 measured reflectionsk = 1414
972 independent reflectionsl = 2424
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.161 w = 1/[σ2(Fo2) + (0.0648P)2 + 0.649P]
where P = (Fo2 + 2Fc2)/3
S = 1.13(Δ/σ)max < 0.001
972 reflectionsΔρmax = 0.35 e Å3
56 parametersΔρmin = 0.22 e Å3
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
S10.1430 (3)0.46670 (8)0.08955 (5)0.0781 (4)
O10.00000.1486 (3)0.25000.1066 (15)
C10.0185 (11)0.3364 (3)0.0641 (2)0.0791 (11)
H10.06500.31630.01840.095*
C20.0701 (9)0.2660 (3)0.1189 (2)0.0755 (10)
H20.15620.19100.11480.091*
C30.0202 (8)0.3174 (2)0.18397 (18)0.0608 (8)
C40.1397 (8)0.4274 (2)0.17415 (17)0.0604 (8)
H40.21160.47550.21000.073*
C50.00000.2550 (3)0.25000.0672 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0824 (8)0.0643 (6)0.0875 (7)0.0016 (4)0.0059 (5)0.0061 (4)
O10.136 (4)0.0338 (15)0.150 (4)0.0000.023 (3)0.000
C10.077 (2)0.072 (2)0.088 (2)0.005 (2)0.004 (2)0.029 (2)
C20.064 (2)0.0496 (16)0.113 (3)0.0041 (15)0.002 (2)0.0277 (18)
C30.0486 (17)0.0383 (13)0.096 (2)0.0003 (12)0.0013 (16)0.0127 (13)
C40.0570 (19)0.0442 (14)0.080 (2)0.0043 (13)0.0023 (15)0.0085 (14)
C50.054 (2)0.0367 (19)0.111 (4)0.0000.005 (3)0.000
Geometric parameters (Å, º) top
S1—C41.694 (3)C2—H20.9300
S1—C11.701 (4)C3—C41.363 (4)
O1—C51.225 (5)C3—C51.464 (4)
C1—C21.347 (6)C4—H40.9300
C1—H10.9300C5—C3i1.464 (4)
C2—C31.434 (5)
C4—S1—C192.30 (18)C4—C3—C5126.5 (3)
C2—C1—S1111.1 (3)C2—C3—C5123.1 (3)
C2—C1—H1124.5C3—C4—S1112.6 (2)
S1—C1—H1124.5C3—C4—H4123.7
C1—C2—C3113.7 (3)S1—C4—H4123.7
C1—C2—H2123.2O1—C5—C3i119.34 (17)
C3—C2—H2123.2O1—C5—C3119.34 (17)
C4—C3—C2110.3 (3)C3i—C5—C3121.3 (3)
C4—S1—C1—C20.3 (3)C1—S1—C4—C30.2 (3)
S1—C1—C2—C30.3 (4)C4—C3—C5—O1155.2 (3)
C1—C2—C3—C40.2 (4)C2—C3—C5—O121.2 (3)
C1—C2—C3—C5177.1 (3)C4—C3—C5—C3i24.8 (3)
C2—C3—C4—S10.1 (4)C2—C3—C5—C3i158.8 (3)
C5—C3—C4—S1176.8 (2)
Symmetry code: (i) x, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4···O1ii0.932.423.261 (4)151
Symmetry code: (ii) x+1/2, y+1/2, z+1/2.
 

Funding information

We acknowledge the financial support within the Cluster of Excellence `Structure Design of Novel High-Performance Materials via Atomic Design and Defect Engineering (ADDE)' provided to us by the European Union (European Regional Development Fund) and by the Ministry of Science and Art of Saxony (SMWK) as well as the Deutsche Forschungsgemeinschaft (DFG Priority Program 1362 `Porous Metal–Organic Frameworks').

References

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