S-Methyl 5-methyl­pyrazine-2-carbo­thioate

The title compound, C₇H₈N₂OS, can be a key synthetic inter­mediate for the preparation of various pyrazine compounds of biological inter­est. It was prepared by the hydrolysis of 2-tris­(methyl­sulfan­yl)methyl-5-methyl­pyrazine using the HgCl₂/CaCO₃ system. The mol­ecule is quasi-planar; the H atoms of the methyl group linked to the pyrazine ring break the mol­ecular mirror pseudosymmetry. One of these H atoms is involved in an inter­molecular hydrogen bond with the carbonyl group of a neighbouring mol­ecule. Two mol­ecules related by an inversion centre inter­act through C—H...N hydrogen bonds, forming R₂²(6) dimers. Neighbouring dimers inter­act through longer C—H...N contacts and form infinite planes parallel to (10). These planes inter­act together through C—H...O hydrogen bonds and π–π inter­actions (pyrazine centroids are separated by 3.99 Å and the inter­planar spacing is 3.38 Å).

Key indicators

• Single-crystal X-ray study
• T = 105 K
• Mean [sigma](C-C) = 0.001 Å
• R factor = 0.040
• wR factor = 0.109
• Data-to-parameter ratio = 33.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.70
PLAT480_ALERT_4_C Long H...A H-Bond Reported H9B    ..  N4      ..       2.65 Ang.

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

The title compound (I) (Fig. 1) is a pyrazine derivative (Sato, 1995), which has a quasi planar molecular structure with a r.m.s. deviation from planarity of 0.03 Å. Two molecules related by an inversion centre interact through C—H···N hydrogen bonds, forming R₂²(6) dimers (Bernstein et al., 1995) (Table 2). Neighbouring dimers interact through longer C—H···N contacts (H9B···N4 = 2.65 Å) and form infinite planes parallel to (1 0 3) (Fig. 2). The cohesion between these molecular planes is done through C—H···O hydrogen bonds (Table 2, Fig. 3), which induce a rotation of the methyl groups linked to the pyrazine rings (Fig. 1; the H7A—C7—C5—N4 torsion angle is -26.6°). π–π interactions are also present between these molecular planes (Figs. 3 and 4), the pyrazine centroids being separated by 3.99 Å (the interplane spacing is 3.38 Å).

Related literature

For the synthesis of the title compound, see: Mamane et al. (2007). For details of the pharmacological properties of pyrazine compounds, see: Sato (1995). For graph-set analysis, see: Bernstein et al. (1995).

S2. Experimental

The synthesis follows a published procedure (Mamane et al., 2007). HgCl₂ (3.3 mmol, 897 mg) and CaCO₃ (3.3 mmol, 330 mg) were added to a stirred solution of 2-tris(methylthio)methyl-5-methylpyrazine (1.5 mmol, 369 mg) in CH₃CN/H₂O (4/1, 15 ml) at 298 K. After stirring for 4 h., the mixture was filtered over celite and dichloromethane was added until no spot of product appeared on TLC. More water was added and the organic phase was separated and dried over MgSO₄. After solvent evaporation the residue was purified by chromatography on silica gel (hexanes/ethyl acetate, 4/1) to give 210 mg of a white powder (83%). M.p. 375 K. Single crystals were obtained by slow evaporation of a dilute solution of (I) in dichloromethane / hexane (1/1) at 298 K.

S3. Refinement

All H atoms were located in difference Fourier maps. The final structure was constructed using riding models for C—H bonds with interatomic distances fixed at 0.95 (aromatic C) and 0.98 Å (methyl C), and U_iso(H) fixed at 1.2U_eq(C) (aromatic C) and 1.5U_eq(C) (methyl C). At the end of the refinement, residuals in a difference map revealed that the most important electron density residues are associated with valence density.

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and POVRay (Persistence of Vision Development Team, 2005); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

	Fig. 1. Molecular structure of (I). Atomic displacement ellipsoids are plotted at the 50% probability level. Image rendered with PovRay (Persistence of Vision Development Team, 2005)
	Fig. 2. Molecules of (I) aggregate has infinite planes parallel to (1 0 3), interacting through C—H···N hydrogen bonds (displayed as dashed lines).
	Fig. 3. Crystal structure of (I) viewed along [0 1 0], displaying the C—H···O hydrogen bonds (dashed lines) linking the (1 0 3) planes.
	Fig. 4. View along [1 0 3]^* showing two (I) molecules belonging to two adjacent (1 0 3) planes. The distance between the pyrazine ring centroids (displayed as green spheres) is 3.99 Å, whereas the distance from one pyrazine centroid to the mean plane of the second pyrazine ring is 3.38 Å.

S-Methyl 5-methylpyrazine-2-carbothioate

Crystal data

C7H8N2OS	F(000) = 352
Mr = 168.21	Dx = 1.423 Mg m^−3
Monoclinic, P21/n	Melting point: 375.15 K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 3.9934 (2) Å	Cell parameters from 37490 reflections
b = 13.8082 (5) Å	θ = 3.3–34.7°
c = 14.3502 (4) Å	µ = 0.35 mm^−1
β = 97.008 (4)°	T = 105 K
V = 785.38 (5) Å^3	Block, pale brown
Z = 4	0.51 × 0.26 × 0.26 mm

Data collection

Oxford Diffraction XCalibur diffractometer	3362 independent reflections
Radiation source: Enhance (Mo) X-ray Source	3009 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
Detector resolution: 8.4221 pixels mm^-1	θmax = 34.7°, θmin = 3.3°
oscillation scans	h = −6→6
Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2007) using a multifaceted crystal (Clark & Reid, 1995)]	k = −22→21
Tmin = 0.900, Tmax = 0.941	l = −22→22
37490 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.109	H-atom parameters constrained
S = 1.14	w = 1/[σ^2(Fo^2) + (0.0569P)^2 + 0.29P] where P = (Fo^2 + 2Fc^2)/3
3362 reflections	(Δ/σ)max < 0.001
102 parameters	Δρmax = 0.68 e Å^−3
0 restraints	Δρmin = −0.25 e Å^−3

Special details

Refinement. The high ratio of maximum / minimum residual density (2.70) is explained by the accumulation of valence electron density in covalent chemical bonds and in non-spherical electron density of the S atoms, as evidenced in a final difference map.

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

	x	y	z	Uiso*/Ueq
S1	0.39777 (6)	0.269288 (17)	−0.055470 (16)	0.01819 (8)
O1	0.7218 (2)	0.36238 (5)	0.08893 (6)	0.02209 (15)
N4	1.1412 (2)	0.11198 (6)	0.22049 (6)	0.01882 (16)
N1	0.6955 (2)	0.10828 (6)	0.05344 (6)	0.01678 (15)
C8	0.6575 (2)	0.28398 (7)	0.05203 (6)	0.01546 (15)
C2	0.7927 (2)	0.19143 (7)	0.09611 (6)	0.01430 (15)
C7	1.1770 (3)	−0.06478 (8)	0.22269 (8)	0.02189 (18)
H7A	1.3923	−0.0524	0.2614	0.033*
H7B	1.2114	−0.1116	0.1734	0.033*
H7C	1.0148	−0.0910	0.2621	0.033*
C3	1.0136 (2)	0.19323 (7)	0.17937 (6)	0.01804 (16)
H3	1.0752	0.2539	0.2077	0.022*
C6	0.8185 (2)	0.02717 (7)	0.09494 (7)	0.01737 (16)
H6	0.7522	−0.0334	0.0671	0.021*
C5	1.0433 (2)	0.02814 (7)	0.17854 (6)	0.01624 (16)
C9	0.2807 (3)	0.39414 (8)	−0.07722 (7)	0.02153 (18)
H9A	0.1853	0.4204	−0.0227	0.032*
H9B	0.1124	0.3982	−0.1328	0.032*
H9C	0.4808	0.4317	−0.0879	0.032*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.01976 (12)	0.01688 (12)	0.01668 (12)	0.00107 (7)	−0.00283 (8)	0.00022 (7)
O1	0.0296 (4)	0.0141 (3)	0.0211 (3)	0.0002 (3)	−0.0029 (3)	−0.0018 (2)
N4	0.0213 (3)	0.0177 (4)	0.0161 (3)	−0.0004 (3)	−0.0034 (3)	0.0011 (3)
N1	0.0196 (3)	0.0141 (3)	0.0157 (3)	−0.0009 (3)	−0.0016 (2)	−0.0009 (2)
C8	0.0158 (3)	0.0153 (4)	0.0149 (3)	0.0001 (3)	0.0003 (3)	0.0002 (3)
C2	0.0156 (3)	0.0133 (3)	0.0138 (3)	0.0000 (3)	0.0007 (2)	0.0004 (3)
C7	0.0230 (4)	0.0184 (4)	0.0232 (4)	0.0023 (3)	−0.0011 (3)	0.0053 (3)
C3	0.0218 (4)	0.0154 (4)	0.0157 (4)	−0.0015 (3)	−0.0028 (3)	−0.0007 (3)
C6	0.0206 (4)	0.0146 (4)	0.0162 (4)	−0.0012 (3)	−0.0008 (3)	−0.0005 (3)
C5	0.0172 (3)	0.0157 (4)	0.0156 (3)	0.0005 (3)	0.0011 (3)	0.0023 (3)
C9	0.0221 (4)	0.0198 (4)	0.0219 (4)	0.0039 (3)	−0.0004 (3)	0.0045 (3)

Geometric parameters (Å, º)

S1—C8	1.7624 (9)	C7—H7A	0.9800
S1—C9	1.8035 (11)	C7—H7B	0.9800
O1—C8	1.2186 (12)	C7—H7C	0.9800
N4—C3	1.3390 (13)	C3—H3	0.9500
N4—C5	1.3409 (13)	C6—C5	1.4079 (13)
N1—C6	1.3338 (12)	C6—H6	0.9500
N1—C2	1.3363 (12)	C9—H9A	0.9800
C8—C2	1.4971 (13)	C9—H9B	0.9800
C2—C3	1.3963 (13)	C9—H9C	0.9800
C7—C5	1.5002 (14)
C8—S1—C9	98.85 (5)	N4—C3—C2	121.93 (9)
C3—N4—C5	116.81 (8)	N4—C3—H3	119.0
C6—N1—C2	116.51 (8)	C2—C3—H3	119.0
O1—C8—C2	121.92 (8)	N1—C6—C5	122.29 (9)
O1—C8—S1	123.57 (8)	N1—C6—H6	118.9
C2—C8—S1	114.51 (7)	C5—C6—H6	118.9
N1—C2—C3	121.68 (8)	N4—C5—C6	120.76 (9)
N1—C2—C8	118.05 (8)	N4—C5—C7	118.65 (8)
C3—C2—C8	120.26 (8)	C6—C5—C7	120.59 (9)
C5—C7—H7A	109.5	S1—C9—H9A	109.5
C5—C7—H7B	109.5	S1—C9—H9B	109.5
H7A—C7—H7B	109.5	H9A—C9—H9B	109.5
C5—C7—H7C	109.5	S1—C9—H9C	109.5
H7A—C7—H7C	109.5	H9A—C9—H9C	109.5
H7B—C7—H7C	109.5	H9B—C9—H9C	109.5
C9—S1—C8—O1	−2.37 (10)	C5—N4—C3—C2	−0.85 (14)
C9—S1—C8—C2	176.96 (7)	N1—C2—C3—N4	0.41 (15)
C6—N1—C2—C3	0.51 (14)	C8—C2—C3—N4	−179.58 (9)
C6—N1—C2—C8	−179.50 (8)	C2—N1—C6—C5	−0.95 (14)
O1—C8—C2—N1	176.54 (9)	C3—N4—C5—C6	0.41 (14)
S1—C8—C2—N1	−2.80 (11)	C3—N4—C5—C7	−179.37 (9)
O1—C8—C2—C3	−3.47 (14)	N1—C6—C5—N4	0.52 (15)
S1—C8—C2—C3	177.19 (7)	N1—C6—C5—C7	−179.71 (9)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···N1^i	0.95	2.55	3.344 (1)	141 (1)
C9—H9B···N4^ii	0.98	2.65	3.626 (1)	173 (1)
C7—H7C···O1^iii	0.98	2.52	3.451 (1)	158 (1)

Symmetry codes: (i) −x+1, −y, −z; (ii) x−3/2, −y+1/2, z−1/2; (iii) −x+3/2, y−1/2, −z+1/2.