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

Hübscher, J.; Augustin, A.U.; Seichter, W.; Weber, E.

doi:10.1107/S2056989017013342

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Volume 73| Part 10| October 2017| Pages 1560-1562

https://doi.org/10.1107/S2056989017013342

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

Jörg Hübscher,^a André U. Augustin,^a Wilhelm Seichter ^a and Edwin Weber ^a ^*

^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 π–π interactions.

Keywords: crystal structure; di(thiophen-3-yl) ketone; polymorphism; C—H⋯O hydrogen bonding; C—H⋯π interaction.

CCDC reference: 1575296

1. Chemical context

With reference to the principle of bioisosterism (Lima & Barreiro, 2005 ), 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 ). This involves potential π-stacking (Tiekink & Zukerman-Schpector, 2012 ) and C—H⋯π (Nishio et al., 2009 ) interactions, as well as other contacts including a chalcogen atom such as sulfur (Gleiter et al., 2003 ). 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 ; Benassi et al., 1989 ). 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 ; Cabri et al., 2007 ; Braga et al., 2009 ).

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. 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; Benassi et al., 1989). 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). 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
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, Fig. 2). Within a given layer the molecules are connected via C—H⋯O hydrogen bonds (Desiraju & Steiner, 1999 ) in which the oxygen atom acts as a bifurcated acceptor. Moreover, the layer structure features π–π stacking (Tiekink & Zukerman-Schpector, 2012) 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	D⋯A	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
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 ) revealed two crystal structures of the title compound [Refcodes DTHKET (Sheldrick et al., 1978) and DTHKET01 (Benassi et al., 1989)]. 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; Cabri et al., 2007; Braga et al., 2009). 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). 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
Packing excerpt of the previously reported polymorph (Benassi et al., 1989

). 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 ; Pittman & Hanes, 1977 ; Lucas et al., 2000 ). We used the method of Lucas et al., 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) and 346 K (Lucas et al., 2000) 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. The hydrogen atoms were positioned geometrically and refined isotropically using the riding model with C—H = 0.93 Å and U_iso(H) = 1.2U_eq(C).

Table 2
Experimental details

Crystal data
Chemical formula	C₉H₆OS₂
M_r	194.26
Crystal system, space group	Orthorhombic, Pbcn
Temperature (K)	296
a, b, c (Å)	3.9464 (2), 11.5015 (5), 19.2970 (9)
V (Å³)	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 )
T_min, T_max	0.759, 0.937
No. of measured, independent and observed [I > 2σ(I)] reflections	6469, 972, 667
R_int	0.033
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.22
Computer programs: APEX2 (and SAINT (Bruker, 2008), SHELXS97 and SHELXTL (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ) and ORTEP-3 for Windows (Farrugia, 2012 ).

Supporting information

CCDC reference: 1575296

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017013342/qm2119sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017013342/qm2119Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017013342/qm2119Isup3.cml

checkCIF report

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

C₉H₆OS₂	D_x = 1.473 Mg m⁻³
M_r = 194.26	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbcn	Cell parameters from 1847 reflections
a = 3.9464 (2) Å	θ = 3.2–24.5°
b = 11.5015 (5) Å	µ = 0.55 mm⁻¹
c = 19.2970 (9) Å	T = 296 K
V = 875.88 (7) Å³	Plate, colourless
Z = 4	0.53 × 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 scans	R_int = 0.033
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 27.2°, θ_min = 3.5°
T_min = 0.759, T_max = 0.937	h = −4→5
6469 measured reflections	k = −14→14
972 independent reflections	l = −24→24

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.047	H-atom parameters constrained
wR(F²) = 0.161	w = 1/[σ²(F_o²) + (0.0648P)² + 0.649P] where P = (F_o² + 2F_c²)/3
S = 1.13	(Δ/σ)_max < 0.001
972 reflections	Δρ_max = 0.35 e Å⁻³
56 parameters	Δρ_min = −0.22 e Å⁻³

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	0.1430 (3)	0.46670 (8)	0.08955 (5)	0.0781 (4)
O1	0.0000	0.1486 (3)	0.2500	0.1066 (15)
C1	−0.0185 (11)	0.3364 (3)	0.0641 (2)	0.0791 (11)
H1	−0.0650	0.3163	0.0184	0.095*
C2	−0.0701 (9)	0.2660 (3)	0.1189 (2)	0.0755 (10)
H2	−0.1562	0.1910	0.1148	0.091*
C3	0.0202 (8)	0.3174 (2)	0.18397 (18)	0.0608 (8)
C4	0.1397 (8)	0.4274 (2)	0.17415 (17)	0.0604 (8)
H4	0.2116	0.4755	0.2100	0.073*
C5	0.0000	0.2550 (3)	0.2500	0.0672 (13)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0824 (8)	0.0643 (6)	0.0875 (7)	−0.0016 (4)	0.0059 (5)	−0.0061 (4)
O1	0.136 (4)	0.0338 (15)	0.150 (4)	0.000	0.023 (3)	0.000
C1	0.077 (2)	0.072 (2)	0.088 (2)	0.005 (2)	−0.004 (2)	−0.029 (2)
C2	0.064 (2)	0.0496 (16)	0.113 (3)	−0.0041 (15)	−0.002 (2)	−0.0277 (18)
C3	0.0486 (17)	0.0383 (13)	0.096 (2)	0.0003 (12)	−0.0013 (16)	−0.0127 (13)
C4	0.0570 (19)	0.0442 (14)	0.080 (2)	−0.0043 (13)	−0.0023 (15)	−0.0085 (14)
C5	0.054 (2)	0.0367 (19)	0.111 (4)	0.000	0.005 (3)	0.000

Geometric parameters (Å, º) top

S1—C4	1.694 (3)	C2—H2	0.9300
S1—C1	1.701 (4)	C3—C4	1.363 (4)
O1—C5	1.225 (5)	C3—C5	1.464 (4)
C1—C2	1.347 (6)	C4—H4	0.9300
C1—H1	0.9300	C5—C3ⁱ	1.464 (4)
C2—C3	1.434 (5)

C4—S1—C1	92.30 (18)	C4—C3—C5	126.5 (3)
C2—C1—S1	111.1 (3)	C2—C3—C5	123.1 (3)
C2—C1—H1	124.5	C3—C4—S1	112.6 (2)
S1—C1—H1	124.5	C3—C4—H4	123.7
C1—C2—C3	113.7 (3)	S1—C4—H4	123.7
C1—C2—H2	123.2	O1—C5—C3ⁱ	119.34 (17)
C3—C2—H2	123.2	O1—C5—C3	119.34 (17)
C4—C3—C2	110.3 (3)	C3ⁱ—C5—C3	121.3 (3)

C4—S1—C1—C2	−0.3 (3)	C1—S1—C4—C3	0.2 (3)
S1—C1—C2—C3	0.3 (4)	C4—C3—C5—O1	−155.2 (3)
C1—C2—C3—C4	−0.2 (4)	C2—C3—C5—O1	21.2 (3)
C1—C2—C3—C5	−177.1 (3)	C4—C3—C5—C3ⁱ	24.8 (3)
C2—C3—C4—S1	−0.1 (4)	C2—C3—C5—C3ⁱ	−158.8 (3)
C5—C3—C4—S1	176.8 (2)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···O1ⁱⁱ	0.93	2.42	3.261 (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').

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