2,3,5,6-Tetra­kis{[(pyridin-2-yl)sulfan­yl]meth­yl}pyrazine

Assoumatine, T.; Stoeckli-Evans, H.

doi:10.1107/S2414314616019775

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 12| December 2016| x161977

https://doi.org/10.1107/S2414314616019775

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2,3,5,6-Tetrakis{[(pyridin-2-yl)sulfanyl]methyl}pyrazine

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

^aCanAm Bioresearch Inc., 9-1250 Waverley Street, Winnipeg, Manitoba R3T 6C6, Canada, 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 W. T. A. Harrison, University of Aberdeen, Scotland (Received 10 December 2016; accepted 10 December 2016; online 16 December 2016)

The title compound, C₂₈H₂₄N₆S₄, synthesized by the reaction of 2,3,5,6-tetrakis(bromomethyl)pyrazine with 2-mercaptopyridine, crystallizes with one half-molecule in the asymmetric unit. The whole molecule is generated by inversion symmetry, the centre of the pyrazine ring being located about an inversion centre. The pyridine rings of the unique (pyridin-2-ylsulfanyl)methyl substituents are inclined to the pyrazine ring by 38.7 (3) and 75.6 (2)°, and by 66.0 (3)° to one another. In the crystal, molecules are linked via C—H⋯π interactions, forming chains along the b-axis direction. The chains are linked by offset π–π interactions [intercentroid distance = 3.682 (3) Å], forming layers lying parallel to the bc plane.

Keywords: crystal structure; tetrakis-substituted; pyrazine; pyridin-2-ylsulfanyl derivative; inversion symmetry; C—H⋯π interactions; offset π–π interactions.

CCDC reference: 1521950

Structure description

The title compound is one of a series of tetra-substituted pyrazine compounds (Pacifico & Stoeckli-Evans, 2004 ; Assoumatine et al., 2007 ; Assoumatine & Stoeckli-Evans, 2014a ), prepared in order to study their coordination behaviour with various transition metals (Assoumatine, 1999 ). It was synthesized by the reaction of 2,3,5,6-tetrakis(bromomethyl)pyrazine (Assoumatine & Stoeckli-Evans, 2014b ), with 2-mercaptopyridine. The synthesis and crystal structure of 2,3,5,6-tetrakis(bromomethyl)pyrazine have been reported (Assoumatine & Stoeckli-Evans, 2014b).

The title compound, crystallizes with one half-molecule in the asymmetric unit (Fig. 1). The whole molecule is generated by inversion symmetry, the centre of the pyrazine ring being located about an inversion centre. The pyridine rings (N2/C4–C8 and N3/C10–C14) of the unique (pyridin-2-ylsulfanyl)methyl substituents are inclined to the pyrazine ring by 38.7 (3) and 75.6 (2)°, respectively, and by 66.0 (3)° to one another. In the phenyl analogue of the title compound, viz. 2,3,5,6-tetrakis[(phenylsulfanyl)methyl]pyrazine (Assoumatine et al., 2007), the corresponding dihedral angles are 19.15 (7), 79.58 (7) and 60.45 (8)°, respectively.

Figure 1
A view of the molecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. Unlabelled atoms are related to labelled atoms by the symmetry operation (−x, 1 − y, 1 − z).

In the crystal, molecules are linked via C—H⋯π interactions, forming chains along [010]; see Table 1 and Fig. 2. The chains are linked by offset π–π interactions, forming layers lying parallel to the bc plane, as shown in Fig. 3. The intercentroid distances are Cg1⋯Cg3ⁱ = Cg1⋯Cg3ⁱⁱ = 3.682 (3) Å, interplanar distances = 3.554 (2) Å, offsets = 1.142 Å; Cg1 and Cg3 are the centroids of the pyrazine ring and the pyridine ring N3/C10–C14; symmetry codes: (i) −x + 2, y + $[{1\over 2}]$ , −z + $[{3\over 2}]$ ; (ii) x, −y + $[{1\over 2}]$ , z + $[{1\over 2}]$ . There are no other significant intermolecular interactions present in the crystal.

Table 1
Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of pyridine ring N2/C4–C8.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C11—H11⋯Cg2ⁱ	0.93	2.93	3.804 (6)	156
Symmetry code: (i) x, y-1, z.

Figure 2
A partial view along the a axis of the crystal packing of the title compound. The C—H⋯π interactions are represented by dashed lines (Table 1

), and, for clarity, only H atom H11 (grey ball) has been included.

Figure 3
A view along the a axis of the crystal packing of the title compound. The C—H⋯π interactions (Table 1

) are represented by cyan dashed lines, and examples of the π–π interactions by orange dashed lines. For clarity, only H atom H11 (grey ball) has been included.

Synthesis and crystallization

To a magnetically stirred solution of 2-mercaptopyridine (4 g, 35.4 mmol; Aldrich, 99%) in CH₂Cl₂ (100 ml), were added 2,3,5,6-tetrakis(bromomethyl)pyrazine (4 g, 8.85 mmol) and triethylamine (5 ml, 35.4 mmol; Fluka, 99.5%). The contents were heated at reflux for 30 min, cooled to room temperature, and diluted with CH₂Cl₂ (100 ml). The organic solution was washed with water (3 × 30 ml) and a saturated solution of NaCl (1 × 30 ml), dried over anhydrous MgSO₄ and evaporated to dryness on a rotary evaporator after filtration. The resultant yellowish residue was recrystallized from acetonitrile solution and dried under vacuum to afford the title compound (yield 4.56 g, 90%; m.p. 422–423 K). R_f 0.48 (solvent CH₂Cl₂, eluent CHCl₃/MeCO₂Et, 7/5 v/v). Pale-yellow blocks were prepared by diffusion of an equal volume of ethanol into a concentrated CHCl₃ (4 ml) solution of the title compound. Spectroscopic and analytical data: The principal peaks of the IR spectrum (KBr disc, cm⁻¹) are: ν = 1579 vs, 1556 s, 1453 s, 1414 vs, 1124 vs, 754 vs, 723 s. ¹H RMN (CDCl₃, 400 MHz): δ = 8.35 [ddd, ³J(6,5) = 4.9, ⁴J(6,4) = 1.8, ⁵J(6,3) = 0.9, 4H, 6-PyH], 7.44 [ddd, ³J(4,3) = 8.1, ³J(4,5) = 7.4, ⁴J(4,6) = 1.9, 4H, 4-PyH), 7.24 (ddd, ³J(3,4) = 8.1, ⁴J(3,5) = ⁵J(3,6) = 1.0, 4H, 3-PyH], 6.95 [ddd, ³J(5,4) = 7.3, ³J(5,6) = 4.9, ⁴J(5,3) = 1.0, 4H, 5-PyH], 4.80 (s, 8H, Pz—CH2—S) p.p.m. ¹³C RMN (CDCl₃, 100 MHz): δ = 159.01, 150.23, 149.88, 136.74, 122.65, 120.27, 33.88 p.p.m. Analysis for C₂₈H₂₄N₆S₄ (M_r = 572.82 g mol⁻¹); calculated: C 58.71, H 4.23, N 14.68, S 22.39%; found: C 58.76, H 4.23, N 14.68, S 22.25%. MS (EI, 70 eV), m/z (%): 572 ([M⁺], 5.2).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. No absorption correction was applied owing to the irregular shape of the crystal, and as there were no suitable reflections for ψ scans.

Table 2
Experimental details

Crystal data
Chemical formula	C₂₈H₂₄N₆S₄
M_r	572.77
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	11.8139 (12), 7.4803 (11), 15.5204 (10)
β (°)	96.766 (8)
V (Å³)	1362.0 (3)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.38
Crystal size (mm)	0.27 × 0.25 × 0.15

Data collection
Diffractometer	Stoe AED2 four-circle
No. of measured, independent and observed [I > 2σ(I)] reflections	3360, 2523, 1590
R_int	0.035
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.069, 0.130, 1.14
No. of reflections	2523
No. of parameters	173
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.31, −0.24
Computer programs: STADI4 and X-RED (Stoe & Cie, 1997 ), SHELXS97 (Sheldrick, 2008 ), Mercury (Macrae et al., 2008 ), SHELXL2014 (Sheldrick, 2015 ), PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1521950

Crystal structure: contains datablocks I, Global. DOI: https://doi.org/10.1107/S2414314616019775/hb4103sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616019775/hb4103Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019775/hb4103Isup3.cml

checkCIF report

Computing details top

Data collection: STADI4 (Stoe & Cie, 1997); cell refinement: STADI4 (Stoe & Cie, 1997); data reduction: X-RED (Stoe & Cie, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

2,3,5,6-Tetrakis{[(pyridin-2-yl)sulfanyl]methyl}pyrazine top

Crystal data top

C₂₈H₂₄N₆S₄	F(000) = 596
M_r = 572.77	D_x = 1.397 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 11.8139 (12) Å	Cell parameters from 28 reflections
b = 7.4803 (11) Å	θ = 14.0–19.6°
c = 15.5204 (10) Å	µ = 0.38 mm⁻¹
β = 96.766 (8)°	T = 293 K
V = 1362.0 (3) Å³	Block, pale yellow
Z = 2	0.27 × 0.25 × 0.15 mm

Data collection top

Stoe AED2 four-circle diffractometer	R_int = 0.035
Radiation source: fine-focus sealed tube	θ_max = 25.5°, θ_min = 2.6°
Graphite monochromator	h = −14→14
ω/2θ scans	k = 0→9
3360 measured reflections	l = −18→18
2523 independent reflections	3 standard reflections every 120 min
1590 reflections with I > 2σ(I)	intensity decay: 1%

Refinement top

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)] = 0.069	H-atom parameters constrained
wR(F²) = 0.130	w = 1/[σ²(F_o²) + (0.0077P)² + 2.2742P] where P = (F_o² + 2F_c²)/3
S = 1.14	(Δ/σ)_max < 0.001
2523 reflections	Δρ_max = 0.31 e Å⁻³
173 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0034 (4)

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	0.72006 (10)	0.7083 (2)	0.88691 (7)	0.0656 (5)
S2	0.87442 (11)	0.2016 (2)	0.80919 (7)	0.0579 (4)
N1	1.0653 (3)	0.3502 (5)	0.98745 (19)	0.0418 (9)
N2	0.6938 (3)	0.6825 (6)	0.7136 (2)	0.0646 (12)
N3	0.8849 (3)	0.3740 (6)	0.6582 (2)	0.0544 (11)
C1	0.9341 (3)	0.5756 (6)	0.9335 (2)	0.0372 (10)
C2	1.0000 (3)	0.4258 (6)	0.9210 (2)	0.0392 (11)
C3	0.8619 (3)	0.6669 (7)	0.8603 (2)	0.0473 (12)
H3A	0.8578	0.5926	0.8088	0.057*
H3B	0.8970	0.7794	0.8475	0.057*
C4	0.6412 (4)	0.7190 (7)	0.7825 (3)	0.0531 (13)
C5	0.5276 (4)	0.7658 (8)	0.7779 (4)	0.0784 (18)
H5	0.4942	0.7927	0.8277	0.094*
C6	0.4649 (5)	0.7715 (10)	0.6969 (5)	0.098 (2)
H6	0.3883	0.8033	0.6911	0.118*
C7	0.5171 (6)	0.7297 (10)	0.6251 (4)	0.104 (3)
H7	0.4760	0.7291	0.5702	0.125*
C8	0.6291 (5)	0.6895 (9)	0.6359 (3)	0.088 (2)
H8	0.6642	0.6651	0.5866	0.105*
C9	1.0016 (4)	0.3364 (7)	0.8342 (2)	0.0480 (12)
H9A	1.0687	0.2612	0.8354	0.058*
H9B	1.0052	0.4263	0.7896	0.058*
C10	0.8353 (4)	0.2440 (6)	0.6968 (2)	0.0441 (12)
C11	0.7524 (4)	0.1338 (7)	0.6552 (3)	0.0609 (14)
H11	0.7199	0.0431	0.6851	0.073*
C12	0.7194 (4)	0.1621 (8)	0.5681 (3)	0.0686 (16)
H12	0.6639	0.0902	0.5381	0.082*
C13	0.7684 (4)	0.2955 (8)	0.5268 (3)	0.0659 (15)
H13	0.7472	0.3164	0.4681	0.079*
C14	0.8497 (4)	0.3991 (8)	0.5729 (3)	0.0644 (15)
H14	0.8823	0.4914	0.5442	0.077*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0532 (7)	0.1041 (12)	0.0390 (6)	0.0141 (8)	0.0032 (5)	0.0054 (8)
S2	0.0748 (9)	0.0683 (9)	0.0284 (5)	−0.0127 (8)	−0.0025 (5)	−0.0026 (6)
N1	0.045 (2)	0.052 (2)	0.0272 (16)	0.0003 (18)	−0.0010 (14)	−0.0026 (17)
N2	0.063 (3)	0.087 (3)	0.040 (2)	0.011 (3)	−0.0095 (19)	0.001 (2)
N3	0.056 (2)	0.073 (3)	0.0325 (19)	−0.005 (2)	0.0009 (17)	0.001 (2)
C1	0.038 (2)	0.050 (3)	0.0222 (19)	−0.004 (2)	−0.0023 (16)	0.0036 (19)
C2	0.037 (2)	0.054 (3)	0.0246 (19)	−0.004 (2)	−0.0048 (17)	−0.001 (2)
C3	0.047 (3)	0.064 (3)	0.030 (2)	0.005 (2)	−0.0006 (18)	0.005 (2)
C4	0.048 (3)	0.057 (3)	0.050 (3)	0.004 (3)	−0.009 (2)	0.010 (3)
C5	0.051 (3)	0.100 (5)	0.082 (4)	0.017 (3)	−0.002 (3)	0.013 (4)
C6	0.054 (4)	0.111 (6)	0.121 (6)	0.013 (4)	−0.029 (4)	0.017 (5)
C7	0.084 (5)	0.133 (7)	0.083 (5)	0.011 (5)	−0.043 (4)	0.010 (5)
C8	0.090 (4)	0.115 (6)	0.049 (3)	0.013 (4)	−0.026 (3)	−0.005 (4)
C9	0.051 (3)	0.066 (3)	0.026 (2)	0.002 (2)	0.0009 (18)	−0.003 (2)
C10	0.046 (2)	0.057 (3)	0.028 (2)	0.008 (2)	−0.0018 (18)	−0.012 (2)
C11	0.068 (3)	0.067 (4)	0.045 (3)	−0.010 (3)	−0.004 (2)	−0.004 (3)
C12	0.068 (4)	0.089 (5)	0.044 (3)	−0.005 (3)	−0.014 (2)	−0.015 (3)
C13	0.065 (3)	0.098 (5)	0.032 (2)	0.006 (3)	−0.007 (2)	−0.005 (3)
C14	0.070 (3)	0.086 (4)	0.038 (2)	0.001 (3)	0.006 (2)	0.010 (3)

Geometric parameters (Å, º) top

S1—C4	1.773 (4)	C5—C6	1.383 (7)
S1—C3	1.799 (4)	C5—H5	0.9300
S2—C10	1.780 (4)	C6—C7	1.371 (9)
S2—C9	1.813 (4)	C6—H6	0.9300
N1—C2	1.339 (5)	C7—C8	1.349 (8)
N1—C1ⁱ	1.346 (5)	C7—H7	0.9300
N2—C4	1.328 (6)	C8—H8	0.9300
N2—C8	1.349 (5)	C9—H9A	0.9700
N3—C10	1.315 (6)	C9—H9B	0.9700
N3—C14	1.353 (5)	C10—C11	1.380 (6)
C1—N1ⁱ	1.346 (5)	C11—C12	1.379 (6)
C1—C2	1.390 (6)	C11—H11	0.9300
C1—C3	1.502 (5)	C12—C13	1.353 (7)
C2—C9	1.506 (5)	C12—H12	0.9300
C3—H3A	0.9700	C13—C14	1.368 (7)
C3—H3B	0.9700	C13—H13	0.9300
C4—C5	1.380 (6)	C14—H14	0.9300

C4—S1—C3	101.7 (2)	C8—C7—H7	120.7
C10—S2—C9	102.9 (2)	C6—C7—H7	120.7
C2—N1—C1ⁱ	117.9 (4)	N2—C8—C7	124.3 (6)
C4—N2—C8	116.3 (4)	N2—C8—H8	117.8
C10—N3—C14	116.5 (4)	C7—C8—H8	117.8
N1ⁱ—C1—C2	121.1 (3)	C2—C9—S2	109.9 (3)
N1ⁱ—C1—C3	116.3 (4)	C2—C9—H9A	109.7
C2—C1—C3	122.6 (3)	S2—C9—H9A	109.7
N1—C2—C1	120.9 (4)	C2—C9—H9B	109.7
N1—C2—C9	115.7 (4)	S2—C9—H9B	109.7
C1—C2—C9	123.3 (4)	H9A—C9—H9B	108.2
C1—C3—S1	111.5 (3)	N3—C10—C11	124.0 (4)
C1—C3—H3A	109.3	N3—C10—S2	120.0 (3)
S1—C3—H3A	109.3	C11—C10—S2	116.0 (4)
C1—C3—H3B	109.3	C12—C11—C10	118.0 (5)
S1—C3—H3B	109.3	C12—C11—H11	121.0
H3A—C3—H3B	108.0	C10—C11—H11	121.0
N2—C4—C5	123.7 (4)	C13—C12—C11	119.4 (5)
N2—C4—S1	118.8 (3)	C13—C12—H12	120.3
C5—C4—S1	117.5 (4)	C11—C12—H12	120.3
C4—C5—C6	117.9 (5)	C12—C13—C14	118.9 (4)
C4—C5—H5	121.1	C12—C13—H13	120.6
C6—C5—H5	121.1	C14—C13—H13	120.6
C7—C6—C5	119.2 (5)	N3—C14—C13	123.3 (5)
C7—C6—H6	120.4	N3—C14—H14	118.3
C5—C6—H6	120.4	C13—C14—H14	118.3
C8—C7—C6	118.6 (6)

C1ⁱ—N1—C2—C1	−0.5 (6)	C5—C6—C7—C8	−2.0 (12)
C1ⁱ—N1—C2—C9	−179.4 (4)	C4—N2—C8—C7	−0.3 (10)
N1ⁱ—C1—C2—N1	0.5 (7)	C6—C7—C8—N2	2.0 (12)
C3—C1—C2—N1	178.5 (4)	N1—C2—C9—S2	101.6 (4)
N1ⁱ—C1—C2—C9	179.4 (4)	C1—C2—C9—S2	−77.3 (5)
C3—C1—C2—C9	−2.6 (6)	C10—S2—C9—C2	139.0 (3)
N1ⁱ—C1—C3—S1	−49.8 (5)	C14—N3—C10—C11	0.8 (7)
C2—C1—C3—S1	132.0 (4)	C14—N3—C10—S2	−179.3 (4)
C4—S1—C3—C1	−155.3 (3)	C9—S2—C10—N3	−11.3 (4)
C8—N2—C4—C5	−1.4 (9)	C9—S2—C10—C11	168.6 (4)
C8—N2—C4—S1	178.8 (4)	N3—C10—C11—C12	−0.3 (7)
C3—S1—C4—N2	5.4 (5)	S2—C10—C11—C12	179.9 (4)
C3—S1—C4—C5	−174.4 (5)	C10—C11—C12—C13	−0.1 (8)
N2—C4—C5—C6	1.3 (9)	C11—C12—C13—C14	−0.1 (8)
S1—C4—C5—C6	−178.9 (5)	C10—N3—C14—C13	−1.1 (8)
C4—C5—C6—C7	0.5 (11)	C12—C13—C14—N3	0.7 (8)

Symmetry code: (i) −x+2, −y+1, −z+2.

Hydrogen-bond geometry (Å, º) top

Cg2 is the centroid of pyridine ring N2/C4–C8.

D—H···A	D—H	H···A	D···A	D—H···A
C11—H11···Cg2ⁱⁱ	0.93	2.93	3.804 (6)	156

Symmetry code: (ii) x, y−1, z.

Acknowledgements

This work was supported by the Swiss National Science Foundation and the University of Neuchâtel.

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Volume 1| Part 12| December 2016| x161977

https://doi.org/10.1107/S2414314616019775

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

2,3,5,6-Tetra­kis{[(pyridin-2-yl)sulfan­yl]meth­yl}pyrazine

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds

2,3,5,6-Tetrakis{[(pyridin-2-yl)sulfanyl]methyl}pyrazine