The crystal structures, Hirshfeld surface analyses and energy frameworks of two hexa­thia­pyrazino­phane regioisomers; 2,5,8,11,14,17-hexa­thia-[9.9](2,6,3,5)-pyrazino­phane and 2,5,8,11,14,17-hexa­thia-[9.9](2,5,3,6)-pyrazino­phane

Assoumatine, T.; Stoeckli-Evans, H.

doi:10.1107/S2056989020007057

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ISSN: 2056-9890

Volume 76| Part 7| July 2020| Pages 977-983

https://doi.org/10.1107/S2056989020007057

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The crystal structures, Hirshfeld surface analyses and energy frameworks of two hexathiapyrazinophane regioisomers; 2,5,8,11,14,17-hexathia-[9.9](2,6,3,5)-pyrazinophane and 2,5,8,11,14,17-hexathia-[9.9](2,5,3,6)-pyrazinophane

Tokouré Assoumatine ^a and Helen Stoeckli-Evans ^b ^*

^aInstitute of Chemistry, University of Neuchâtel, Av. de Bellevax 51, CH-2000 Neuchâtel, Switzerland, and ^bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
^*Correspondence e-mail: helen.stoeckli-evans@unine.ch

Edited by S. Parkin, University of Kentucky, USA (Received 19 May 2020; accepted 25 May 2020; online 2 June 2020)

The title thiapyrazinophanes, 2,5,8,11,14,17-hexathia-[9.9](2,6,3,5)-pyrazinophane, C₁₆H₂₄N₂S₆, (I), and 2,5,8,11,14,17-hexathia-[9.9](2,5,3,6)-pyrazinophane, C₁₆H₂₄N₂S₆, (II), are regioisomers; m-bis L1 and p-bis L1, respectively. Both compounds have a central tetra-2,3,5,6-methylenepyrazine unit with two –S—CH₂—CH₂—S—CH₂—CH₂—S– chains, linking the methylene C atoms at positions 2 and 6 and 3 and 5 on the pyrazine ring of I, but linking the methylene C atoms at positions 2 and 5 and 3 and 6 on the pyrazine ring of II. Both compounds crystallize with half a molecule in the asymmetric unit. The whole molecule of I is generated by inversion symmetry, with the pyrazine ring being located about a center of symmetry. The whole molecule of II is generated by twofold rotation symmetry, with the pyrazine N atoms being located on the twofold rotation axis. In compound I, there are pairs of intramolecular C—H⋯S contacts present, but none in compound II. In the crystal of I, there are no significant intermolecular interactions present, while in the crystal of II, molecules are linked by pairs of C—H⋯S hydrogen bonds, forming corrugated layers lying parallel the ac plane. The Hirshfeld surfaces and the energy frameworks of the two regioisomers indicate little difference in the interatomic contacts, which are dominated by dispersion forces.

Keywords: crystal structure; regioisomers; m-bis; p-bis; thiapyrazinophanes; hexathiapyrazinophanes; Hirshfeld surface analysis; fingerprint plots; energy frameworks.

CCDC references: 2005740; 2005739

1. Chemical context

Ligands with mixed hard and soft binding characters, such as O, N and S donor atoms, are known to display diverse coordination modes by binding selectively to metal centres giving rise to unusual coordination geometries (Kim et al., 2018 ; Klinga et al., 1994 ; Lockhart et al., 1992 ). Three regioisomers, o, m and p, of a bis-dioxadithia-benzenophane (L, O₄S₄) have been reported on by the group of Shim Sung Lee (Kim et al., 2018). The structures of a number of metal complexes have also been described; for example, both o-bis L and m-bis L form one-dimensional coordination polymers with AgPF₆ (Siewe et al., 2014 ), while with lead(II) perchlorate a binuclear complex was obtained with o-bis L and a one-dimensional coordination polymer with m-bis L (Kim et al., 2018). In all four complexes the metal atoms coordinate to both the O and S atoms.

The title compounds, I and II, are new N_xS_y (x = 2, y = 2, 4 or 6) thiapyrazinophane ligands designed for the formation of coordination polymers (Assoumatine, 1999 ). We have recently reported on the crystal structures of two thiapyrazinophanes; the N₂S₄ ligand 3,4,8,10,11,13-hexahydro-1H,6H-bis([1,4]dithiocino)[6,7-b:6′,7′-e]pyrazine (L2) and the N₂S₂ ligand 5,7-dihydro-1H,3H-dithieno[3,4-b:3′,4′-e]pyrazine (L3) (Assoumatine & Stoeckli-Evans, 2020a ). On reaction of both L2 and L3 with AgNO₃, two-dimensional coordination polymers were formed, with the silver(I) atoms coordinating to the S atoms only (Assoumatine & Stoeckli-Evans, 2020a). On reaction of L2 with CuI, a two-dimensional coordination polymer was formed with the ligand coordinating via the S atoms only (Assoumatine & Stoeckli-Evans, 2020b ). On reaction of L3 with CuI, a three-dimensional coordination polymer was formed with the ligand coordinating via both the N and S atoms (Assoumatine & Stoeckli-Evans, 2020c ). Ligand L3 was also shown to form one-dimensional coordination polymers with CuCl₂ and CuBr₂ (Assoumatine & Stoeckli-Evans, 2020d ), with the ligand coordinating via the N atoms only.

The coordination chemistry of the title compound m-bis L1 (I), an N₂S₆ thiapyrazinophane, has also been studied and shown to form a binuclear complex with CuBr₂ and a two-dimensional coordination polymer with CuI (Assoumatine & Stoeckli-Evans, 2020e ). In both cases, the ligand coordinates to both the N and S atoms. Herein, we report on and compare the crystal structures, the Hirshfeld surfaces and the energy frameworks of the regioisomers m-bis L1 (I) and p-bis L1 (II).

2. Structural commentary

The title thiapyrazinophanes, 2,5,8,11,14,17-hexathia-[9.9](2,6,3,5)-pyrazinophane (I) and 2,5,8,11,14,17-hexathia-[9.9](2,5,3,6)-pyrazinophane (II), are regioisomers; m-bis L1 and p-bis L1, respectively. Both compounds crystallize with half a molecule in the asymmetric unit. The whole molecule of I is generated by inversion symmetry, with the pyrazine ring being located about a center of symmetry (Fig. 1). The whole molecule of II is generated by twofold rotation symmetry, with the pyrazine N atoms, N1 and N2, being located on the twofold rotation axis (Fig. 2). Both compounds have a central rigid tetra-2,3,5,6-methylene pyrazine unit with two –S—CH₂—CH₂—S—CH₂—CH₂—S– chains linking the methylene C atoms C3 and C8 [and C3ⁱ and C8ⁱ; symmetry code: (i) −x, −y, −z + 1] on the pyrazine ring of I (Fig. 1), and linking the methylene C atoms C3 and C8ⁱ [C3ⁱ and C8; here symmetry code: (i) −x + 2, y, −z + $[{3\over 2}]$ ] on the pyrazine ring of II (Fig. 2).

Figure 1
A view of the molecular structure of compound I, the regioisomer m-bis L1, with atom labelling for the asymmetric unit [symmetry code: (i) −x, −y, −z + 1]. Displacement ellipsoids are drawn at the 50% probability level. For clarity, the minor components of the disordered atoms in the chains have been omitted.

Figure 2
A view of the molecular structure of compound II, the regioisomer p-bis L1, with atom labelling for the asymmetric unit [symmetry code: (i) −x + 2, y, −z + $[{3\over 2}]$ ]. Displacement ellipsoids are drawn at the 50% probability level.

In I there are intramolecular C—H⋯S contacts present (Table 1) but none in the molecule of II. The pyrazine ring in I is planar (r.m.s. deviation = 0.003 Å), while in II it has a flat twist-boat conformation [puckering parameters: amplitude Q = 0.1158 (15) Å, θ = 90.0 (7)°, φ = 270.0 (6)°; r.m.s. deviation = 0.067 Å). In I atoms C4 and C5 of the –S—CH₂—CH₂—S—CH₂—CH₂—S– chain are disordered over two positions. They were refined with a fixed occupancy ratio (C4A:C4B and C5A:C5B) of 0.85:0.15.

Table 1
Hydrogen-bond geometry (Å, °) for I

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3B⋯S3ⁱ	0.98	2.77	3.524 (3)	134
Symmetry code: (i) -x, -y, -z+1.

3. Supramolecular features

In the crystal of I, molecules pack in layers that lie parallel to the (10 $[\overline{1}]$ ) plane, as shown in Fig. 3. In the crystal of II, molecules are linked by C—H⋯S hydrogen bonds, forming corrugated layers that lie parallel to the ac plane (Table 2 and Fig. 4). There are no significant inter-layer interactions present in the crystals of either compound.

Table 2
Hydrogen-bond geometry (Å, °) for II

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C4—H4A⋯S3ⁱ	0.98	2.83	3.581 (2)	134
Symmetry code: (i) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Figure 3
A view along the b axis of the crystal packing of I. For clarity, the minor components of the disordered atoms in the chains and the H atoms have been omitted.

Figure 4
A view along the b axis of the crystal packing of II, with the C—H⋯S hydrogen bonds (Table 2

) shown as dashed lines.

4. Hirshfeld surface analyses, two-dimensional fingerprint plots and energy frameworks for I (m-bis L1) and II (p-bis L1).

The Hirshfeld surface analysis (Spackman & Jayatilaka, 2009 ), the associated two-dimensional fingerprint plots and the calculation of the energy frameworks (McKinnon et al., 2007 ; Turner et al., 2015 ) were performed with CrystalExplorer17.5 (Turner et al., 2017 ), following the protocol of Tiekink and collaborators (Tan et al., 2019 ). The Hirshfeld surface is colour-mapped with the normalized contact distance, d_norm, from red (distances shorter than the sum of the van der Waals radii) through white to blue (distances longer than the sum of the van der Waals radii). The energy frameworks are represented by cylinders joining the centroids of molecular pairs using red, green and blue colour codes for the E_elect (electrostatic potential forces), E_disp (dispersion forces) and E_total (total energy) energy components, respectively. The radius of the cylinder is proportional to the magnitude of the interaction energy.

A summary of the short interatomic contacts in I (m-bis L1) and II (p-bis L1) is given in Table 3. The Hirshfeld surfaces of I and II mapped over d_norm, are given in Fig. 5a and b, respectively. The faint red spots indicate that short contacts are significant in the crystal packing of both compounds.

Table 3
Table 3. Short interatomic contacts^a (Å) for I (m-bis L1) and II (p-bis L1)

Atom1⋯Atom2	Length	Length − VdW	Symm. op. 1	Symm. op. 2
I
S1⋯S1	3.3938 (11)	−0.206	−x, −y, 1 − z	−1 + x, y, z
S3⋯S1	3.5135 (11)	−0.086	x, y, z	−1 + x, y, z
H3A⋯S2	2.969	−0.031	−x, −y, 1 − z	− $[{1\over 2}]$ + x, − $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z
H8A⋯S1	3.007	0.007	x, y, z	−1 + x, y, z
H6A⋯H7A	2.415	0.015	−x, −y, 1 − z	x, y, −1 + z
H4A2⋯H5A2	2.487	0.087	−x, −y, 1 − z	− $[{1\over 2}]$ + x, − $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z

II
H4A⋯S3	2.828	−0.172	−1 + x, y, z	− $[{3\over 2}]$ + x, $[{1\over 2}]$ − y, 1 − z
C3⋯H7A	2.842	−0.058	1 − x, y, $[{3\over 2}]$ − z	$[{1\over 2}]$ − x, − $[{1\over 2}]$ + y, z
H3A⋯H7A	2.345	−0.055	1 − x, y, $[{3\over 2}]$ − z	$[{1\over 2}]$ − x, − $[{1\over 2}]$ + y, z
N1⋯H7A	2.700	−0.050	−1 + x, y, z	$[{1\over 2}]$ − x, − $[{1\over 2}]$ + y, z
S1⋯S3	3.6360 (6)	0.036	−1 + x, y, z	− $[{3\over 2}]$ + x, $[{1\over 2}]$ − y, 1 − z
H8B⋯H8B	2.444	0.044	−1 + x, y, z	1 − x, 1 − y, 1 − z
S3⋯H5A	3.072	0.072	−1 + x, y, z	1 − x, 1 − y, 1 − z
C1⋯H7A	2.976	0.076	1 − x, y, $[{3\over 2}]$ − z	$[{1\over 2}]$ − x, − $[{1\over 2}]$ + y, z
C4⋯S3	3.5806 (16)	0.081	−1 + x, y, z	− $[{3\over 2}]$ + x, $[{1\over 2}]$ − y, 1 − z
Note: (a) Values were calculated using Mercury (Macrae et al., 2020 ).

Figure 5
(a) The Hirshfeld surface of I, mapped over d_norm in the colour range −0.1136 to 1.0310 a.u., (b) the Hirshfeld surface of II, mapped over d_norm in the colour range −0.0862 to 1.1988 a.u.

The Hirshfeld surfaces mapped over the calculated electrostatic potential for I and II, given in Fig. 6a and b, respectively, are very similar. The red and blue regions represent negative and positive electrostatic potentials, respectively. The red regions around the sulfur atoms indicate their participation in the C—H⋯S contacts (see Table 3).

Figure 6
(a) The Hirshfeld surface of I, mapped over the calculated electrostatic potential in the range −0.0488 to +0.0302 atomic units, (b) the Hirshfeld surface of II, mapped over the calculated electrostatic potential in the range −0.0393 to +0.0283 atomic units. (The red and blue regions represent negative and positive electrostatic potentials, respectively.)

The full two-dimensional fingerprint plots for I and II are given in Fig. 7. The principal interatomic interactions for I (Fig. 7a) are delineated into H⋯H at 56.9%, S⋯H/H⋯S at 33.1%, N⋯H/H⋯N at 4.0% and S⋯S at 4.0% contacts. These values are very similar to those for II where the principal interatomic interactions (Fig. 7b) are delineated into H⋯H at 58.4%, S⋯H/H⋯S at 34.6%, N⋯H/H⋯N at 3.3%, and S⋯S at 3.3% contacts.

Figure 7
(a) The full two-dimensional fingerprint plot for I, and the fingerprint plots delineated into H⋯H, S⋯H/H⋯S, N⋯H/H⋯N and S⋯S contacts, (b) the full two-dimensional fingerprint plot for II, and the fingerprint plots delineated into H⋯H, S⋯H/H⋯S, N⋯H/H⋯N and S⋯S contacts.

For both I and II the interatomic contacts are dominated by dispersion forces, as can be seen when comparing the electrostatic potential (E_elect) and dispersion (E_disp) energy frameworks in Fig. 8a and b, respectively. The energy frameworks (Fig. 8) were adjusted to the same scale factor of 80 with a cut-off value of 5 kJ mol⁻¹ within a radius of 6 Å about a central molecule, and were obtained using the wave function calculated at the HF/3-21G level theory.

Figure 8
(a) The energy frameworks for I viewed down the b-axis direction, (b) the energy frameworks for II viewed down the c-axis direction: comprising, E_elect (electrostatic potential forces), E_disp (dispersion forces) and E_total (total energy) for a cluster about a reference molecule.

5. Database survey

A search of the Cambridge Structural Database (Version 5.41, last update March 2020; Groom et al., 2016 ) for benzene analogues of L1 gave no hits for either m-bis or p-bis hexathiabenzenophanes. However, the structure of the o-bis hexathiabenzenophane has been reported; 2,5,8,17,20,23-hexathia(9)(1,2)(9)(4,5)cyclophane (CSD refcode YESNEP: Loeb & Shimizu, 1994 ). There are also reports of the structures of two polymorphs of the o-mono trithiabenzenophane, 2,5,8-trithia(9)-o-benzenophane (POCPAY: Klinga et al., 1994; VEYNIW01: Lockhart et al., 1992) and that of the m-mono trithiabenzenophane, 2,5,8-trithia(9)-m-benzenophane (VEYNES: De Groot & Loeb, 1990 ). The coordination chemistry of all three compounds has been studied, especially that of YESNEP (o-bis hexathiabenzenophane). Binuclear complexes were obtained with copper(II) salts and AgBF₄ (Loeb & Shimizu, 1991 ; 1993 ), with all six S atoms involved in coordination.

6. Synthesis and crystallization

Synthesis of 2,5,8,11,14,17-hexathia-[9.9](2,6,3,5)-pyrazinophane (I): A 500 ml three-necked flask was equipped with a reflux condenser, a 50 ml addition funnel, and a magnetic stirring bar. The entire system was purged and kept under an atmosphere of nitrogen using vacuum line techniques. KOH (0.62 g, 11 mmol) was dissolved in a solution of MeOH/CH₂Cl₂ (250 ml, 1/1 v/v) in the flask. To this well-stirred mixture was added slowly and dropwise through the addition funnel, a solution of 1 g (2.21 mmol) of 2,3,5,6-tetrakis(bromomethyl)pyrazine (Ferigo et al., 1994 ; Assoumatine & Stoeckli-Evans, 2014 ) and bis-(2-mercaptoethyl)sulfide (0.6 ml, 4.42 mmol, 95%) dissolved in CH₂Cl₂ (25 ml), at a rate of ca 10 ml h⁻¹. The mixture was stirred for a further 20 h. The reaction mixture was taken to dryness on a rotary evaporator. The residue was extracted into CH₂Cl₂ (300 ml), washed with water (3 × 30 ml), dried over anhydrous MgSO₄, filtered and then evaporated to dryness. The resultant yellowish solid was chromatographed over deactivated silica gel using CH₂Cl₂ as eluent. The main eluted fraction was evaporated to give a white solid, which was dried under vacuum to obtain 0.42 g (43% yield) of pure L1 (m.p. 581–584 K, with decomposition). Slow evaporation of a CHCl₃ solution of L1 gave colourless rod-like crystals of I, the m-bis L1 regioisomer, after ca one month. ¹H NMR (CDCl₃, 400 MHz): δ = 4.17 (s, 8H, Pz-CH₂-S), 2.73–2.49 (m, 16H, S–CH₂–CH₂–S) ppm. ¹³C NMR (CDCl₃, 100 MHz): δ = 149.55, 32.12, 32.08, 30.85 ppm. Analysis for C₁₆H₂₄N₂S₆ (M_r = 436.78 g mol⁻¹). Calculated (%): C 44.00, H 5.55, N 6.42, S 44.13. Found (%): C 43.48, H 5.25, N 6.40, S 44.34. MS (EI, 70 eV), m/z: 436 ([M⁺]. IR (KBr disc, cm⁻¹): ν = 2930 s, 1423 vs, 1397 vs, 1189 s, 795 ms, 760 ms, 689 ms, 482 ms.

Synthesis of 2,5,8,11,14,17-hexathia-[9.9](2,5,3,6)-pyrazinophane (II): Pale-yellow block-like crystals of compound II were obtained unexpectedly during a complexation reaction of L1 with ZnI₂ (Assoumatine, 1999). It is difficult to imagine that the complexation reaction resulted in the transformation of m-bis L1 (I) into p-bis L1 (II). We believe it is more likely that the latter was obtained in small quantities during the various syntheses of L1 and was present in the main eluted fraction used subsequently for the complexation reaction. There are no analytical or spectroscopic data available for this compound.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 4. The C-bound H atoms were included in calculated positions and treated as riding on their parent C atom: C—H = 0.98 Å with U_iso(H) = 1.2U_eq(C). In I atoms C4 and C5 of the –CH₂—S—CH₂—CH₂—S—CH₂—CH₂—S—CH₂– chain are disordered over two positions. They were refined with a fixed occupancy ratio (C4A:C4B and C5A:C5B) of 0.85:0.15.

Table 4
Experimental details

	I	II
Crystal data
Chemical formula	C₁₆H₂₄N₂S₆	C₁₆H₂₄N₂S₆
M_r	436.73	436.73
Crystal system, space group	Monoclinic, P2₁/n	Orthorhombic, Pbcn
Temperature (K)	223	223
a, b, c (Å)	9.4078 (7), 9.2511 (7), 11.6953 (8)	12.2613 (8), 9.9564 (6), 16.2828 (12)
α, β, γ (°)	90, 105.722 (8), 90	90, 90, 90
V (Å³)	979.79 (13)	1987.8 (2)
Z	2	4
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.70	0.69
Crystal size (mm)	0.40 × 0.15 × 0.15	0.25 × 0.20 × 0.10

Data collection
Diffractometer	Stoe IPDS 1	Stoe IPDS 1
Absorption correction	Multi-scan (MULABS; Spek, 2020 )	Multi-scan (MULABS; Spek, 2020)
T_min, T_max	0.964, 1.000	0.915, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7493, 1812, 1469	12271, 1927, 1521
R_int	0.030	0.033
(sin θ/λ)_max (Å⁻¹)	0.613	0.615

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.108, 1.03	0.025, 0.064, 0.97
No. of reflections	1812	1927
No. of parameters	127	110
H-atom treatment	H-atom parameters constrained	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.80, −0.35	0.27, −0.19
Computer programs: EXPOSE, CELL (Stoe & Cie, 1998 ) and INTEGRATE (Stoe & Cie, 1998), SHELXS97 (Sheldrick, 2008 ), SHELXL2018/3 (Sheldrick, 2015 ), Mercury (Macrae et al., 2020), PLATON (Spek, 2020) and publCIF (Westrip, 2010 ).

Intensity data were measured using a STOE IPDS-1 one-circle diffractometer. For the monoclinic system often only 93% of the Ewald sphere is accessible, which explains why the B alert diffrn_reflns_laue_measured_fraction_full value low at 0.957 for compound I is given. This involves 76 random reflections out of the expected 1765 for the IUCr cutoff limit of sin θ/λ = 0.60 for I.

Supporting information

CCDC references: 2005740; 2005739

Crystal structure: contains datablocks I, II, Global. DOI: https://doi.org/10.1107/S2056989020007057/pk2633sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020007057/pk2633Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989020007057/pk2633IIsup3.hkl

checkCIF report

Computing details top

For both structures, data collection: EXPOSE (Stoe & Cie, 1998); cell refinement: CELL (Stoe & Cie, 1998); data reduction: INTEGRATE (Stoe & Cie, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: SHELXL2018/3 (Sheldrick, 2015), PLATON (Spek, 2020) and publCIF (Westrip, 2010).

2,5,8,11,14,17-Hexathia-[9.9](2,6,3,5)-pyrazinophane (I) top

Crystal data top

C₁₆H₂₄N₂S₆	F(000) = 460
M_r = 436.73	D_x = 1.480 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 9.4078 (7) Å	Cell parameters from 5000 reflections
b = 9.2511 (7) Å	θ = 2.9–25.8°
c = 11.6953 (8) Å	µ = 0.70 mm⁻¹
β = 105.722 (8)°	T = 223 K
V = 979.79 (13) Å³	Rod, colourless
Z = 2	0.40 × 0.15 × 0.15 mm

Data collection top

STOE IPDS 1 diffractometer	1812 independent reflections
Radiation source: fine-focus sealed tube	1469 reflections with I > 2σ(I)
Plane graphite monochromator	R_int = 0.030
φ rotation scans	θ_max = 25.8°, θ_min = 2.9°
Absorption correction: multi-scan (MULABS; Spek, 2020)	h = −11→11
T_min = 0.964, T_max = 1.000	k = −11→11
7493 measured reflections	l = −14→14

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.108	H-atom parameters constrained
S = 1.03	w = 1/[σ²(F_o²) + (0.0489P)² + 1.0972P] where P = (F_o² + 2F_c²)/3
1812 reflections	(Δ/σ)_max < 0.001
127 parameters	Δρ_max = 0.80 e Å⁻³
0 restraints	Δρ_min = −0.35 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	Occ. (<1)
S1	0.43465 (7)	0.06030 (10)	0.61310 (7)	0.0448 (2)
S2	0.29210 (9)	0.05009 (10)	0.94357 (7)	0.0506 (3)
S3	−0.18897 (9)	0.04529 (10)	0.76708 (7)	0.0455 (2)
N1	0.0478 (2)	0.1229 (2)	0.56726 (18)	0.0282 (5)
C1	0.1307 (3)	0.0623 (3)	0.5033 (2)	0.0275 (5)
C2	−0.0828 (3)	0.0624 (3)	0.5644 (2)	0.0273 (5)
C3	0.2743 (3)	0.1366 (3)	0.5079 (3)	0.0364 (6)
H3A	0.265885	0.238486	0.528088	0.044*
H3B	0.290236	0.133282	0.428547	0.044*
C4A	0.3996 (4)	0.1160 (4)	0.7527 (3)	0.0361 (8)	0.85
H4A1	0.490907	0.153803	0.806259	0.043*	0.85
H4A2	0.325885	0.193463	0.737391	0.043*	0.85
C5A	0.3448 (4)	−0.0092 (4)	0.8112 (3)	0.0366 (8)	0.85
H5A1	0.422534	−0.082600	0.833774	0.044*	0.85
H5A2	0.259364	−0.053204	0.754762	0.044*	0.85
C4B	0.373 (2)	−0.010 (2)	0.7494 (17)	0.032 (4)	0.15
H4B1	0.272978	−0.051440	0.724257	0.039*	0.15
H4B2	0.440973	−0.083717	0.793123	0.039*	0.15
C5B	0.375 (2)	0.122 (2)	0.823 (2)	0.038 (4)	0.15
H5B1	0.315371	0.199332	0.777647	0.045*	0.15
H5B2	0.476508	0.156417	0.857125	0.045*	0.15
C6	0.1059 (3)	0.1134 (3)	0.8751 (3)	0.0405 (7)
H6A	0.072122	0.171931	0.932460	0.049*
H6B	0.106432	0.175041	0.807071	0.049*
C7	0.0005 (4)	−0.0096 (3)	0.8340 (2)	0.0413 (7)
H7A	0.002992	−0.072264	0.902097	0.050*
H7B	0.034589	−0.066909	0.776044	0.050*
C8	−0.1725 (3)	0.1385 (3)	0.6345 (2)	0.0349 (6)
H8A	−0.271975	0.154582	0.582373	0.042*
H8B	−0.128240	0.233573	0.657957	0.042*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0174 (3)	0.0797 (6)	0.0381 (4)	0.0007 (3)	0.0089 (3)	−0.0106 (4)
S2	0.0430 (5)	0.0790 (6)	0.0271 (4)	0.0006 (4)	0.0050 (3)	0.0023 (4)
S3	0.0354 (4)	0.0713 (6)	0.0365 (4)	−0.0095 (4)	0.0212 (3)	−0.0040 (4)
N1	0.0184 (10)	0.0387 (12)	0.0281 (10)	0.0012 (9)	0.0071 (9)	0.0016 (9)
C1	0.0159 (11)	0.0415 (14)	0.0254 (12)	0.0008 (10)	0.0059 (10)	0.0052 (10)
C2	0.0177 (11)	0.0415 (14)	0.0234 (12)	0.0025 (10)	0.0066 (9)	0.0041 (10)
C3	0.0209 (12)	0.0500 (17)	0.0405 (15)	−0.0066 (11)	0.0120 (12)	−0.0037 (13)
C4A	0.0294 (17)	0.043 (2)	0.0362 (19)	−0.0055 (14)	0.0089 (16)	−0.0103 (15)
C5A	0.036 (2)	0.037 (2)	0.035 (2)	0.0039 (14)	0.0060 (17)	0.0004 (16)
C4B	0.022 (10)	0.050 (13)	0.020 (9)	−0.005 (8)	−0.002 (8)	0.004 (8)
C5B	0.034 (11)	0.036 (11)	0.045 (12)	−0.002 (8)	0.014 (10)	−0.011 (9)
C6	0.0411 (16)	0.0496 (18)	0.0337 (14)	−0.0030 (13)	0.0153 (13)	−0.0045 (12)
C7	0.0492 (18)	0.0459 (16)	0.0306 (14)	−0.0032 (14)	0.0138 (13)	0.0029 (12)
C8	0.0222 (12)	0.0481 (16)	0.0369 (14)	0.0031 (11)	0.0126 (11)	−0.0026 (12)

Geometric parameters (Å, º) top

S1—C3	1.811 (3)	C4A—H4A1	0.9800
S1—C4A	1.825 (4)	C4A—H4A2	0.9800
S1—C4B	1.95 (2)	C5A—H5A1	0.9800
S2—C6	1.814 (3)	C5A—H5A2	0.9800
S2—C5A	1.833 (4)	C4B—C5B	1.49 (3)
S2—C5B	1.90 (2)	C4B—H4B1	0.9800
S3—C7	1.815 (3)	C4B—H4B2	0.9800
S3—C8	1.817 (3)	C5B—H5B1	0.9800
N1—C1	1.341 (3)	C5B—H5B2	0.9800
N1—C2	1.342 (3)	C6—C7	1.500 (4)
C1—C2ⁱ	1.402 (4)	C6—H6A	0.9800
C1—C3	1.504 (3)	C6—H6B	0.9800
C2—C8	1.501 (4)	C7—H7A	0.9800
C3—H3A	0.9800	C7—H7B	0.9800
C3—H3B	0.9800	C8—H8A	0.9800
C4A—C5A	1.505 (5)	C8—H8B	0.9800

C3—S1—C4A	100.29 (15)	C5B—C4B—S1	103.8 (15)
C3—S1—C4B	107.8 (6)	C5B—C4B—H4B1	111.0
C6—S2—C5A	100.00 (15)	S1—C4B—H4B1	111.0
C6—S2—C5B	95.9 (6)	C5B—C4B—H4B2	111.0
C7—S3—C8	101.53 (13)	S1—C4B—H4B2	111.0
C1—N1—C2	118.6 (2)	H4B1—C4B—H4B2	109.0
N1—C1—C2ⁱ	120.8 (2)	C4B—C5B—S2	101.5 (15)
N1—C1—C3	116.2 (2)	C4B—C5B—H5B1	111.5
C2ⁱ—C1—C3	123.0 (2)	S2—C5B—H5B1	111.5
N1—C2—C1ⁱ	120.6 (2)	C4B—C5B—H5B2	111.5
N1—C2—C8	115.9 (2)	S2—C5B—H5B2	111.5
C1ⁱ—C2—C8	123.5 (2)	H5B1—C5B—H5B2	109.3
C1—C3—S1	114.9 (2)	C7—C6—S2	111.8 (2)
C1—C3—H3A	108.5	C7—C6—H6A	109.3
S1—C3—H3A	108.5	S2—C6—H6A	109.3
C1—C3—H3B	108.5	C7—C6—H6B	109.3
S1—C3—H3B	108.5	S2—C6—H6B	109.3
H3A—C3—H3B	107.5	H6A—C6—H6B	107.9
C5A—C4A—S1	110.9 (3)	C6—C7—S3	114.4 (2)
C5A—C4A—H4A1	109.5	C6—C7—H7A	108.7
S1—C4A—H4A1	109.5	S3—C7—H7A	108.7
C5A—C4A—H4A2	109.5	C6—C7—H7B	108.7
S1—C4A—H4A2	109.5	S3—C7—H7B	108.7
H4A1—C4A—H4A2	108.0	H7A—C7—H7B	107.6
C4A—C5A—S2	111.0 (3)	C2—C8—S3	115.73 (19)
C4A—C5A—H5A1	109.4	C2—C8—H8A	108.3
S2—C5A—H5A1	109.4	S3—C8—H8A	108.3
C4A—C5A—H5A2	109.4	C2—C8—H8B	108.3
S2—C5A—H5A2	109.4	S3—C8—H8B	108.3
H5A1—C5A—H5A2	108.0	H8A—C8—H8B	107.4

C2—N1—C1—C2ⁱ	−0.6 (4)	C6—S2—C5A—C4A	83.6 (3)
C2—N1—C1—C3	178.7 (2)	S1—C4B—C5B—S2	173.4 (8)
C1—N1—C2—C1ⁱ	0.6 (4)	C5A—S2—C6—C7	73.8 (2)
C1—N1—C2—C8	−177.9 (2)	C5B—S2—C6—C7	112.7 (6)
N1—C1—C3—S1	97.1 (2)	S2—C6—C7—S3	178.84 (15)
C2ⁱ—C1—C3—S1	−83.5 (3)	C8—S3—C7—C6	65.5 (2)
C4A—S1—C3—C1	−70.9 (2)	N1—C2—C8—S3	−109.9 (2)
C4B—S1—C3—C1	−33.9 (7)	C1ⁱ—C2—C8—S3	71.6 (3)
C3—S1—C4A—C5A	103.8 (3)	C7—S3—C8—C2	45.9 (2)
S1—C4A—C5A—S2	−174.34 (17)

Symmetry code: (i) −x, −y, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3B···S3ⁱ	0.98	2.77	3.524 (3)	134

Symmetry code: (i) −x, −y, −z+1.

2,5,8,11,14,17-Hexathia-[9.9](2,5,3,6)-pyrazinophane (II) top

Crystal data top

C₁₆H₂₄N₂S₆	D_x = 1.459 Mg m⁻³
M_r = 436.73	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbcn	Cell parameters from 5000 reflections
a = 12.2613 (8) Å	θ = 2.5–25.9°
b = 9.9564 (6) Å	µ = 0.69 mm⁻¹
c = 16.2828 (12) Å	T = 223 K
V = 1987.8 (2) Å³	Block, pale yellow
Z = 4	0.25 × 0.20 × 0.10 mm
F(000) = 920

Data collection top

STOE IPDS 1 diffractometer	1927 independent reflections
Radiation source: fine-focus sealed tube	1521 reflections with I > 2σ(I)
Plane graphite monochromator	R_int = 0.033
φ rotation scans	θ_max = 25.9°, θ_min = 2.5°
Absorption correction: multi-scan (MULABS; Spek, 2020)	h = −15→14
T_min = 0.915, T_max = 1.000	k = −12→10
12271 measured reflections	l = −19→19

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.025	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.064	H-atom parameters constrained
S = 0.97	w = 1/[σ²(F_o²) + (0.0418P)²] where P = (F_o² + 2F_c²)/3
1927 reflections	(Δ/σ)_max = 0.001
110 parameters	Δρ_max = 0.27 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.92584 (3)	0.20291 (5)	0.52666 (2)	0.03769 (13)
S2	0.62939 (3)	0.32039 (5)	0.66508 (3)	0.04190 (13)
S3	1.22003 (4)	0.45569 (5)	0.60156 (2)	0.04264 (14)
N1	1.000000	0.18412 (17)	0.750000	0.0261 (4)
N2	1.000000	0.46125 (17)	0.750000	0.0281 (4)
C1	1.01977 (11)	0.25255 (15)	0.68044 (9)	0.0251 (3)
C2	1.02875 (11)	0.39270 (15)	0.68267 (9)	0.0265 (3)
C3	1.03062 (13)	0.16999 (18)	0.60363 (9)	0.0332 (4)
H3A	1.027915	0.074691	0.618548	0.040*
H3B	1.102268	0.187440	0.579190	0.040*
C4	0.80303 (13)	0.19184 (16)	0.58900 (9)	0.0314 (3)
H4A	0.750656	0.131963	0.562050	0.038*
H4B	0.821427	0.152829	0.642492	0.038*
C5	0.75070 (14)	0.32828 (17)	0.60188 (9)	0.0337 (4)
H5A	0.731576	0.366522	0.548318	0.040*
H5B	0.803729	0.388415	0.627872	0.040*
C6	0.69013 (14)	0.31977 (17)	0.76694 (10)	0.0375 (4)
H6A	0.636307	0.286838	0.806617	0.045*
H6B	0.752112	0.257625	0.767392	0.045*
C7	0.72885 (13)	0.45755 (16)	0.79340 (9)	0.0329 (4)
H7A	0.668292	0.521440	0.789306	0.039*
H7B	0.786870	0.487818	0.756366	0.039*
C8	1.07313 (13)	0.47543 (17)	0.61355 (9)	0.0353 (4)
H8A	1.056488	0.570261	0.623694	0.042*
H8B	1.036924	0.449113	0.562359	0.042*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0380 (2)	0.0540 (3)	0.02104 (19)	0.0029 (2)	−0.00241 (16)	−0.00421 (16)
S2	0.0272 (2)	0.0514 (3)	0.0471 (3)	0.0005 (2)	−0.00419 (18)	−0.0071 (2)
S3	0.0389 (2)	0.0636 (3)	0.0254 (2)	−0.0117 (2)	0.00714 (17)	0.00324 (19)
N1	0.0227 (8)	0.0281 (9)	0.0274 (9)	0.000	−0.0039 (7)	0.000
N2	0.0274 (9)	0.0291 (10)	0.0277 (9)	0.000	−0.0043 (7)	0.000
C1	0.0192 (7)	0.0322 (8)	0.0239 (7)	0.0024 (6)	−0.0018 (5)	−0.0003 (6)
C2	0.0235 (7)	0.0318 (8)	0.0244 (7)	0.0009 (6)	−0.0038 (6)	0.0030 (6)
C3	0.0311 (8)	0.0405 (9)	0.0280 (8)	0.0049 (7)	−0.0021 (6)	−0.0058 (7)
C4	0.0341 (8)	0.0313 (9)	0.0288 (8)	−0.0015 (7)	−0.0050 (6)	−0.0020 (6)
C5	0.0379 (8)	0.0338 (9)	0.0294 (8)	0.0011 (7)	−0.0045 (7)	0.0004 (7)
C6	0.0362 (9)	0.0393 (9)	0.0369 (8)	0.0005 (8)	0.0056 (7)	0.0040 (7)
C7	0.0322 (8)	0.0357 (9)	0.0307 (8)	0.0094 (7)	0.0019 (7)	0.0002 (7)
C8	0.0387 (9)	0.0398 (9)	0.0273 (8)	−0.0036 (7)	−0.0011 (7)	0.0076 (7)

Geometric parameters (Å, º) top

S1—C4	1.8193 (17)	C3—H3B	0.9800
S1—C3	1.8245 (16)	C4—C5	1.517 (2)
S2—C5	1.8104 (17)	C4—H4A	0.9800
S2—C6	1.8182 (17)	C4—H4B	0.9800
S3—C7ⁱ	1.8218 (16)	C5—H5A	0.9800
S3—C8	1.8224 (17)	C5—H5B	0.9800
N1—C1	1.3438 (17)	C6—C7	1.514 (2)
N1—C1ⁱ	1.3438 (17)	C6—H6A	0.9800
N2—C2	1.3387 (17)	C6—H6B	0.9800
N2—C2ⁱ	1.3388 (17)	C7—H7A	0.9800
C1—C2	1.400 (2)	C7—H7B	0.9800
C1—C3	1.503 (2)	C8—H8A	0.9800
C2—C8	1.497 (2)	C8—H8B	0.9800
C3—H3A	0.9800

C4—S1—C3	100.87 (7)	C4—C5—H5A	109.0
C5—S2—C6	100.49 (7)	S2—C5—H5A	109.0
C7ⁱ—S3—C8	103.79 (7)	C4—C5—H5B	109.0
C1—N1—C1ⁱ	119.07 (18)	S2—C5—H5B	109.0
C2—N2—C2ⁱ	118.69 (18)	H5A—C5—H5B	107.8
N1—C1—C2	119.85 (14)	C7—C6—S2	112.64 (11)
N1—C1—C3	116.11 (14)	C7—C6—H6A	109.1
C2—C1—C3	124.04 (14)	S2—C6—H6A	109.1
N2—C2—C1	120.57 (14)	C7—C6—H6B	109.1
N2—C2—C8	115.52 (14)	S2—C6—H6B	109.1
C1—C2—C8	123.88 (14)	H6A—C6—H6B	107.8
C1—C3—S1	114.28 (11)	C6—C7—S3ⁱ	111.45 (11)
C1—C3—H3A	108.7	C6—C7—H7A	109.3
S1—C3—H3A	108.7	S3ⁱ—C7—H7A	109.3
C1—C3—H3B	108.7	C6—C7—H7B	109.3
S1—C3—H3B	108.7	S3ⁱ—C7—H7B	109.3
H3A—C3—H3B	107.6	H7A—C7—H7B	108.0
C5—C4—S1	111.90 (11)	C2—C8—S3	112.36 (11)
C5—C4—H4A	109.2	C2—C8—H8A	109.1
S1—C4—H4A	109.2	S3—C8—H8A	109.1
C5—C4—H4B	109.2	C2—C8—H8B	109.1
S1—C4—H4B	109.2	S3—C8—H8B	109.1
H4A—C4—H4B	107.9	H8A—C8—H8B	107.9
C4—C5—S2	112.78 (12)

C1ⁱ—N1—C1—C2	5.44 (9)	C4—S1—C3—C1	−49.44 (14)
C1ⁱ—N1—C1—C3	−174.39 (14)	C3—S1—C4—C5	108.79 (12)
C2ⁱ—N2—C2—C1	5.52 (9)	S1—C4—C5—S2	−179.11 (8)
C2ⁱ—N2—C2—C8	−172.62 (14)	C6—S2—C5—C4	82.34 (13)
N1—C1—C2—N2	−11.29 (19)	C5—S2—C6—C7	76.92 (13)
C3—C1—C2—N2	168.54 (12)	S2—C6—C7—S3ⁱ	175.79 (8)
N1—C1—C2—C8	166.69 (12)	N2—C2—C8—S3	106.65 (12)
C3—C1—C2—C8	−13.5 (2)	C1—C2—C8—S3	−71.42 (17)
N1—C1—C3—S1	116.25 (12)	C7ⁱ—S3—C8—C2	−42.15 (14)
C2—C1—C3—S1	−63.58 (18)

Symmetry code: (i) −x+2, y, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4A···S3ⁱⁱ	0.98	2.83	3.581 (2)	134

Symmetry code: (ii) x−1/2, −y+1/2, −z+1.

Table 3. Short interatomic contacts^a (Å) for I (m-bis L1) and II (p-bis L1) top

Atom1···Atom2	Length	Length-VdW	Symm. op. 1	Symm. op. 2
I
S1···S1	3.3938 (11)	-0.206	-x, -y, 1 - z	-1 + x, y, z
S3···S1	3.5135 (11)	-0.086	x, y, z	-1 + x, y, z
H3A···S2	2.969	-0.031	-x, -y, 1 - z	-1/2 + x, -1/2 - y, -1/2 + z
H8A···S1	3.007	0.007	x, y, z	-1 + x, y, z
H6A···H7A	2.415	0.015	-x, -y, 1-z	x, y, -1 + z
H4A2···H5A2	2.487	0.087	-x, -y, 1-z	-1/2 + x, -1/2 - y, -1/2 + z

II
H4A···S3	2.828	-0.172	-1 + x, y, z	-3/2 + x, 1/2 - y, 1 - z
C3···H7A	2.842	-0.058	1 - x, y, 3/2 - z	1/2 - x, -1/2 + y, z
H3A···H7A	2.345	-0.055	1 - x, y, 3/2 - z	1/2 - x, -1/2 + y, z
N1···H7A	2.700	-0.050	-1 + x, y, z	1/2 - x, -1/2 + y, z
S1···S3	3.6360 (6)	0.036	-1 + x, y, z	-3/2 + x, 1/2 - y, 1 - z
H8B···H8B	2.444	0.044	-1 + x, y, z	1 - x, 1 - y, 1 - z
S3···H5A	3.072	0.072	-1 + x, y, z	1 - x, 1 - y, 1 - z
C1···H7A	2.976	0.076	1 - x, y, 3/2 - z	1/2 - x, -1/2 + y, z
C4···S3	3.5806 (16)	0.081	-1 + x, y, z	-3/2 + x, 1/2 - y, 1 - z

Note: (a) Values were calculated using Mercury (Macrae et al., 2020).

Acknowledgements

HSE is grateful to the University of Neuchâtel for their support over the years.

Funding information

Funding for this research was provided by: Swiss National Science Foundation and the University of Neuchâtel.

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CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 76| Part 7| July 2020| Pages 977-983

https://doi.org/10.1107/S2056989020007057

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

The crystal structures, Hirshfeld surface analyses and energy frameworks of two hexa­thia­pyrazino­phane regioisomers; 2,5,8,11,14,17-hexa­thia-[9.9](2,6,3,5)-pyrazino­phane and 2,5,8,11,14,17-hexa­thia-[9.9](2,5,3,6)-pyrazino­phane

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Hirshfeld surface analyses, two-dimensional fingerprint plots and energy frameworks for I (m-bis L1) and II (p-bis L1).

5. Database survey

6. Synthesis and crystallization

7. Refinement

Supporting information

Acknowledgements

Funding information

References

research communications

The crystal structures, Hirshfeld surface analyses and energy frameworks of two hexathiapyrazinophane regioisomers; 2,5,8,11,14,17-hexathia-[9.9](2,6,3,5)-pyrazinophane and 2,5,8,11,14,17-hexathia-[9.9](2,5,3,6)-pyrazinophane

3. Supramolecular features