Crystal structure of 2,3,5,6-tetra­kis[(methyl­sulfan­yl)meth­yl]pyrazine

Abstract

The title compound, C₁₂H₂₀N₂S₄, synthesized by the reaction of 2,3,5,6-tetra­kis­(bromo­meth­yl)pyrazine with sodium methane­thiol­ate, crystallizes with a half -mol­ecule in the asymmetric unit. The whole mol­ecule is generated by inversion symmetry; the inversion centre being located in the centre of the pyrazine ring. The mol­ecule has an S-shaped conformation with two (methyl­sulfan­yl)methyl substituent arms directed above the plane of the pyrazine ring and two below. The C(H₃)—S—C(H₂)—C(aromatic) torsion angles are 70.47 (18) and −67.65 (17)°, respectively. In the crystal, mol­ecules are linked via weak C—H⋯S hydrogen bonds, forming chains along [001] and enclosing R ₂ ²(12) ring motifs. The chains are linked by further weak C—H⋯S hydrogen bonds, forming sheets lying parallel to (101).

Related literature  

For syntheses of the starting reagent, 2,3,5,6-tetra­kis­(bromo­meth­yl)pyrazine, see: Ferigo et al. (1994 ▶); Assoumatine (1999 ▶); Assoumatine & Stoeckli-Evans (2014 ▶). For the crystal structures of similar sulfanylmethyl derivatives of pyrazine, such as two triclinic polymorphs of 2,3,5,6 tetra­kis­(naphthalen-2-ylsulfanylmeth­yl)pyrazine both possessing inversion symmetry, see: Pacifico & Stoeckli-Evans (2004 ▶), and for 2,3,5,6-tetra­kis­(phenyl­sulfanylmeth­yl)pyrazine, which also crystallizes in space group P and possesses inversion symmetry, see: Assoumatine et al. (2007 ▶).

Experimental  

Crystal data  

• C₁₂H₂₀N₂S₄

• M _r = 320.54

• Triclinic,

• a = 6.6773 (6) Å

• b = 6.9433 (4) Å

• c = 9.5135 (5) Å

• α = 102.635 (6)°

• β = 107.539 (5)°

• γ = 99.462 (9)°

• V = 397.61 (5) ų

• Z = 1

• Mo Kα radiation

• μ = 0.58 mm⁻¹

• T = 293 K

• 0.40 × 0.40 × 0.23 mm

Data collection  

• Stoe AED2 four-circle diffractometer

• 2960 measured reflections

• 1478 independent reflections

• 1283 reflections with I > 2σ(I)

• R _int = 0.018

• 3 standard reflections every 60 min intensity decay: 1%

Refinement  

• R[F ² > 2σ(F ²)] = 0.032

• wR(F ²) = 0.088

• S = 1.08

• 1478 reflections

• 85 parameters

• H-atom parameters constrained

• Δρ_max = 0.24 e Å⁻³

• Δρ_min = −0.20 e Å⁻³

Data collection: STADI4 (Stoe & Cie, 1997 ▶); cell refinement: STADI4; data reduction: X-RED (Stoe & Cie, 1997 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL2013, PLATON (Spek, 2009 ▶) and publCIF (Westrip, 2010 ▶).

Supplementary Material

CCDC reference: 1004261

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3A⋯S2i	0.97	2.89	3.589 (2)	130
C5—H5B⋯S1ii	0.97	2.95	3.7395 (19)	139
C5—H5B⋯S1i	0.97	2.93	3.614 (2)	128

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

S1.1. Synthesis and crystallization

A mixture of sodium methane­thiol­ate (0.94 g, 13 mmol, Fluka 95%) in ethanol (50 ml) was added slowly and drop wise with stirring to a refluxed solution of 2,3,5,6-tetra­kis(bromo­methyl)­pyrazine [Assoumatine & Stoeckli-Evans, 2014], (1.5 g, 3.32 mmol) in ethanol (50 ml). Refluxing and stirring were continued for 4 h. The solvent was removed under reduced pressure and the resultant residue diluted with CH₂Cl₂ (200 ml). The organic layer was washed with water (3 × 30 ml) and saturated NaCl (30 ml), then dried over anhydrous MgSO₄ and evaporated to dryness after filtration. The brown residue obtained was washed with aceto­nitrile till this solvent became colourless, yielding the title compound which was further dried under vacuum [Yield 0.55 g (52%), M.p. 418-419 K]; Rf 0.48 (solvent : CH₂Cl₂, eluent : toluene/MeCO₂Et, 10/1 v/v). Diffusion of an equal volume of ethanol into a concentrated CHCl₃ (4 ml) solution of the title compound in a 16 mm diameter glass tube yielded suitable yellow plate-like crystals for X-ray diffraction analysis. Spectroscopic data: ¹H-NMR (CDCl₃, 400 MHz): δ = 3.97 (s, 8H, Pz—CH₂—S), 2.13 (s, 12H, S—CH₃) ppm. ¹³C-NMR (CDCl₃, 100 MHz): δ = 149.50, 35.89, 15.65 ppm. Anal. for C₁₂H₂₀N₂S₄ (Mr = 320.58 g/mol) Calc. (%): C 44.96; H 6.30; N 8.74; S 40.00. Found (%): C 44.65; H 6.24; N 8.76; S 40.03. MS (EI, 70 eV), m/z (%): 320 ([M⁺], 89.4), 274 (95.2), 257 (50.1), 227 (100), 210 (25.4), 194 (37.9), 181 (54.2), 164 (29.2), 135 (28.1), 97 (23.8). IR (KBr disc, cm^-1): 2967 w, 2915 w, 1425 ms, 1394 vs, 1311 w, 1248 w, 1218 s, 1120 ms, 988 ms, 903 w, 795 w, 754 w, 720 w, 679 w, 484 w.

S1.2. Refinement

The H atoms were included in calculated positions and treated as riding atoms: C—H = 0.96 - 0.97 Å with U_iso(H) = 1.5U_eq(C-methyl) and = 1.2U_eq(C) for other H atoms. No absorption correction was applied owing to the irregular shape of the crystal, and as there were no suitable reflections for psi scans.

Figures

Fig. 1.

A view of the molecular structure of the title molecule, with atom labelling (unlabelled atoms are generated by inversion symmetry with symmetry code: -x, -y+1, -z + 1). Displacement ellipsoids are drawn at the 50% probability level.

Fig. 2.

A partial view along the a axis of the crystal packing of the title compound, showing the formation of the C—H···S hydrogen-bonded chains along [001], enclosing R22(12) ring motifs (H atoms not involved in these hydrogen bonds have been omitted for clarity).

Crystal data

C12H20N2S4	Z = 1
Mr = 320.54	F(000) = 170
Triclinic, P1	Dx = 1.339 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.6773 (6) Å	Cell parameters from 33 reflections
b = 6.9433 (4) Å	θ = 14.2–18.8°
c = 9.5135 (5) Å	µ = 0.58 mm−1
α = 102.635 (6)°	T = 293 K
β = 107.539 (5)°	Plate, yellow
γ = 99.462 (9)°	0.40 × 0.40 × 0.23 mm
V = 397.61 (5) Å3

Data collection

Stoe AED2 four-circle diffractometer	Rint = 0.018
Radiation source: fine-focus sealed tube	θmax = 25.5°, θmin = 2.3°
Graphite monochromator	h = −8→7
2θ/ω scans	k = −8→8
2960 measured reflections	l = 0→11
1478 independent reflections	3 standard reflections every 60 min
1283 reflections with I > 2σ(I)	intensity decay: 1%

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032	H-atom parameters constrained
wR(F2) = 0.088	w = 1/[σ2(Fo2) + (0.0451P)2 + 0.1143P] where P = (Fo2 + 2Fc2)/3
S = 1.08	(Δ/σ)max < 0.001
1478 reflections	Δρmax = 0.24 e Å−3
85 parameters	Δρmin = −0.20 e Å−3
0 restraints	Extinction correction: SHELXL2013 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.064 (11)

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S1	0.10172 (10)	0.33963 (9)	0.10899 (6)	0.0509 (2)
S2	0.37011 (9)	0.28482 (9)	0.80525 (6)	0.0515 (2)
N1	−0.0169 (2)	0.2930 (2)	0.44718 (16)	0.0326 (4)
C1	−0.0580 (3)	0.4056 (3)	0.34870 (19)	0.0311 (5)
C2	0.0402 (3)	0.3854 (3)	0.59786 (19)	0.0313 (5)
C3	−0.1194 (3)	0.2955 (3)	0.1806 (2)	0.0390 (6)
C4	0.2772 (5)	0.2016 (4)	0.2027 (3)	0.0684 (10)
C5	0.0843 (3)	0.2519 (3)	0.7029 (2)	0.0376 (6)
C6	0.4534 (4)	0.1829 (4)	0.6484 (3)	0.0665 (9)
H3A	−0.23980	0.33950	0.12120	0.0470*
H3B	−0.16800	0.15040	0.16540	0.0470*
H4A	0.33380	0.26610	0.31160	0.1030*
H4B	0.39480	0.20040	0.16450	0.1030*
H4C	0.19730	0.06420	0.18230	0.1030*
H5A	0.02160	0.11060	0.64270	0.0450*
H5B	0.01290	0.28160	0.77720	0.0450*
H6A	0.36700	0.04660	0.59450	0.1000*
H6B	0.60330	0.18130	0.68720	0.1000*
H6C	0.43450	0.26620	0.57940	0.1000*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
S1	0.0731 (4)	0.0608 (4)	0.0394 (3)	0.0318 (3)	0.0335 (3)	0.0242 (3)
S2	0.0568 (4)	0.0584 (4)	0.0352 (3)	0.0256 (3)	0.0050 (2)	0.0128 (2)
N1	0.0386 (8)	0.0332 (8)	0.0285 (7)	0.0114 (6)	0.0133 (6)	0.0097 (6)
C1	0.0355 (9)	0.0350 (9)	0.0252 (8)	0.0112 (7)	0.0123 (7)	0.0092 (7)
C2	0.0340 (9)	0.0371 (9)	0.0272 (8)	0.0112 (7)	0.0134 (7)	0.0123 (7)
C3	0.0492 (11)	0.0408 (10)	0.0265 (9)	0.0141 (8)	0.0124 (8)	0.0076 (8)
C4	0.0750 (17)	0.0855 (19)	0.0741 (17)	0.0467 (15)	0.0399 (14)	0.0415 (15)
C5	0.0493 (11)	0.0384 (10)	0.0307 (9)	0.0154 (8)	0.0164 (8)	0.0145 (8)
C6	0.0570 (15)	0.0784 (18)	0.0633 (16)	0.0307 (13)	0.0207 (12)	0.0090 (13)

Geometric parameters (Å, º)

S1—C3	1.813 (2)	C3—H3B	0.9700
S1—C4	1.789 (3)	C4—H4A	0.9600
S2—C5	1.812 (2)	C4—H4B	0.9600
S2—C6	1.790 (3)	C4—H4C	0.9600
N1—C1	1.342 (2)	C5—H5A	0.9700
N1—C2	1.342 (2)	C5—H5B	0.9700
C1—C3	1.509 (2)	C6—H6A	0.9600
C1—C2i	1.401 (3)	C6—H6B	0.9600
C2—C5	1.504 (3)	C6—H6C	0.9600
C3—H3A	0.9700
C3—S1—C4	101.45 (13)	S1—C4—H4B	109.00
C5—S2—C6	100.09 (11)	S1—C4—H4C	109.00
C1—N1—C2	118.31 (16)	H4A—C4—H4B	109.00
N1—C1—C3	116.40 (17)	H4A—C4—H4C	109.00
N1—C1—C2i	120.78 (15)	H4B—C4—H4C	109.00
C2i—C1—C3	122.82 (17)	S2—C5—H5A	109.00
N1—C2—C5	116.03 (17)	S2—C5—H5B	109.00
N1—C2—C1i	120.91 (17)	C2—C5—H5A	109.00
C1i—C2—C5	123.05 (15)	C2—C5—H5B	109.00
S1—C3—C1	113.18 (14)	H5A—C5—H5B	108.00
S2—C5—C2	113.56 (15)	S2—C6—H6A	109.00
S1—C3—H3A	109.00	S2—C6—H6B	109.00
S1—C3—H3B	109.00	S2—C6—H6C	109.00
C1—C3—H3A	109.00	H6A—C6—H6B	110.00
C1—C3—H3B	109.00	H6A—C6—H6C	109.00
H3A—C3—H3B	108.00	H6B—C6—H6C	109.00
S1—C4—H4A	109.00
C4—S1—C3—C1	70.47 (18)	C2i—C1—C3—S1	77.1 (2)
C6—S2—C5—C2	−67.65 (17)	N1—C1—C2i—N1i	−0.5 (3)
C2—N1—C1—C3	179.41 (18)	N1—C1—C2i—C5i	−180.00 (19)
C2—N1—C1—C2i	0.4 (3)	C3—C1—C2i—N1i	−179.35 (18)
C1—N1—C2—C5	179.98 (18)	C3—C1—C2i—C5i	1.1 (3)
C1—N1—C2—C1i	−0.4 (3)	N1—C2—C5—S2	103.98 (18)
N1—C1—C3—S1	−101.84 (19)	C1i—C2—C5—S2	−75.6 (2)

Symmetry code: (i) −x, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3A···S2i	0.97	2.89	3.589 (2)	130
C5—H5B···S1ii	0.97	2.95	3.7395 (19)	139
C5—H5B···S1i	0.97	2.93	3.614 (2)	128

Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, y, z+1.