Crystal structure of 4,6-di-amino-2-(methyl-sulfan-yl)pyridine-3-carbo-nitrile.

The title pyrimidine derivative, C7H8N4S, is essentially planar, with a maximum deviation of 0.029 (2) Å from the mean plane of the non-H atoms. In the crystal, mol-ecules are linked by an inter-molecular bifurcated N-H⋯N hydrogen bond between the cyano N atom and the two amino groups, an N-H⋯N hydrogen bond between the two amino groups and a weak C-H⋯π inter-action, forming a three-dimensional network.

Related literature

For the abundance of pyridines in pharmaceuticals and natural products, see: Zhang et al. (2010 ▸). For various applications of pyridine-containing compounds, see: Murata et al. (2003 ▸). For the use of polyfunctional pyridines in preparing a variety of heterocyclic compounds, see: Al-Haiza et al. (2003 ▸). For the synthesis of the title compound, see: Abu-Shanab (1999 ▸). For a similar structure, see: Mohamed et al. (2014 ▸).

Experimental

Crystal data

C7H8N4S

M = 180.23

Orthorhombic,

a = 5.0863 (7) Å

b = 12.698 (2) Å

c = 13.069 (2) Å

V = 844.1 (2) Å3

Z = 4

Mo Kα radiation

μ = 0.33 mm−1

T = 200 K

0.40 × 0.09 × 0.05 mm

Data collection

Bruker SMART X2S benchtop diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2008 ▸) T min = 0.833, T max = 0.984

9083 measured reflections

1487 independent reflections

1353 reflections with I > 2σ(I)

R int = 0.037

Refinement

R[F 2 > 2σ(F 2)] = 0.026

wR(F 2) = 0.062

S = 1.06

1487 reflections

122 parameters

6 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.20 e Å−3

Δρmin = −0.13 e Å−3

Absolute structure: Flack (1983 ▸)

Absolute structure parameter: 0.01 (4)

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT (Bruker, 2009 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸); software used to prepare material for publication: PLATON (Spek, 2009 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015003114/is5390sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015003114/is5390Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989015003114/is5390Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S2056989015003114/is5390fig1.tif

The mol­ecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level.

Click here for additional data file.

a . DOI: 10.1107/S2056989015003114/is5390fig2.tif

The hydrogen bonding (dashed lines) and packing of the title compound viewed down the a axis.

CCDC reference: 1049335

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

C7H8N4S	F(000) = 376
Mr = 180.23	Dx = 1.418 Mg m−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 3713 reflections
a = 5.0863 (7) Å	θ = 2.2–25.0°
b = 12.698 (2) Å	µ = 0.33 mm−1
c = 13.069 (2) Å	T = 200 K
V = 844.1 (2) Å3	Needle, yellow
Z = 4	0.40 × 0.09 × 0.05 mm

Bruker SMART X2S benchtop diffractometer	1487 independent reflections
Radiation source: XOS X-beam microfocus source	1353 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromator	Rint = 0.037
ω scans	θmax = 25.0°, θmin = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −6→6
Tmin = 0.833, Tmax = 0.984	k = −15→12
9083 measured reflections	l = −15→15

Refinement on F2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.026	w = 1/[σ2(Fo2) + (0.0294P)2 + 0.1689P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.062	(Δ/σ)max < 0.001
S = 1.06	Δρmax = 0.20 e Å−3
1487 reflections	Δρmin = −0.13 e Å−3
122 parameters	Absolute structure: Flack (1983)
6 restraints	Absolute structure parameter: 0.01 (4)

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

Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

	x	y	z	Uiso*/Ueq
S1	1.05518 (13)	0.80355 (6)	0.72687 (5)	0.0304 (2)
N1	0.8883 (4)	0.62615 (18)	0.63890 (15)	0.0256 (7)
N2	0.7653 (6)	0.4785 (2)	0.55086 (19)	0.0410 (9)
N3	0.3276 (4)	0.5616 (2)	0.86570 (18)	0.0282 (7)
N4	0.6450 (4)	0.7998 (2)	0.94969 (16)	0.0322 (7)
C1	0.7297 (5)	0.5407 (2)	0.6340 (2)	0.0277 (8)
C2	0.5369 (5)	0.5181 (2)	0.70666 (18)	0.0268 (8)
C3	0.5066 (4)	0.5834 (2)	0.79017 (17)	0.0222 (8)
C4	0.6745 (5)	0.67178 (19)	0.79768 (17)	0.0217 (8)
C5	0.8576 (4)	0.6892 (2)	0.71847 (18)	0.0238 (7)
C6	0.6581 (5)	0.7431 (2)	0.88141 (19)	0.0242 (8)
C7	1.2520 (6)	0.7927 (3)	0.6128 (2)	0.0387 (10)
H2	0.42720	0.45820	0.69870	0.0320*
H2A	0.894 (5)	0.487 (3)	0.509 (2)	0.0620*
H2B	0.682 (6)	0.4202 (18)	0.545 (3)	0.0620*
H3A	0.210 (5)	0.5167 (19)	0.849 (2)	0.0420*
H3B	0.286 (6)	0.6117 (17)	0.9060 (19)	0.0420*
H7A	1.32830	0.72190	0.60900	0.0580*
H7B	1.39330	0.84510	0.61490	0.0580*
H7C	1.14140	0.80510	0.55260	0.0580*

	U11	U22	U33	U12	U13	U23
S1	0.0274 (3)	0.0303 (4)	0.0334 (3)	−0.0054 (3)	0.0014 (3)	−0.0023 (3)
N1	0.0259 (13)	0.0261 (12)	0.0249 (11)	0.0002 (10)	0.0014 (9)	−0.0017 (10)
N2	0.0562 (18)	0.0331 (16)	0.0338 (14)	−0.0117 (13)	0.0185 (12)	−0.0121 (12)
N3	0.0290 (13)	0.0291 (13)	0.0266 (12)	−0.0026 (11)	0.0033 (10)	−0.0050 (10)
N4	0.0355 (12)	0.0340 (14)	0.0270 (11)	−0.0016 (12)	−0.0010 (10)	−0.0054 (12)
C1	0.0328 (15)	0.0254 (15)	0.0248 (13)	0.0026 (12)	0.0010 (11)	−0.0012 (12)
C2	0.0305 (14)	0.0224 (14)	0.0275 (13)	−0.0049 (12)	0.0014 (12)	−0.0042 (11)
C3	0.0222 (15)	0.0245 (14)	0.0200 (12)	0.0035 (10)	−0.0029 (10)	0.0026 (11)
C4	0.0213 (12)	0.0242 (15)	0.0195 (12)	0.0044 (10)	−0.0036 (9)	−0.0002 (10)
C5	0.0207 (12)	0.0268 (13)	0.0240 (11)	0.0031 (11)	−0.0051 (10)	0.0041 (13)
C6	0.0207 (12)	0.0261 (14)	0.0258 (14)	0.0003 (11)	−0.0032 (11)	0.0034 (12)
C7	0.0364 (15)	0.045 (2)	0.0347 (15)	−0.0091 (15)	0.0057 (12)	0.0038 (15)

S1—C5	1.769 (3)	N2—H2B	0.86 (2)
S1—C7	1.801 (3)	N3—H3A	0.86 (2)
N1—C1	1.354 (3)	C3—C4	1.414 (3)
N1—C5	1.322 (3)	N3—H3B	0.85 (2)
N2—C1	1.355 (4)	C4—C5	1.410 (3)
N3—C3	1.371 (3)	C4—C6	1.423 (3)
N4—C6	1.149 (3)	C2—H2	0.9500
C1—C2	1.395 (4)	C7—H7A	0.9800
C2—C3	1.379 (3)	C7—H7B	0.9800
N2—H2A	0.86 (3)	C7—H7C	0.9800
C5—S1—C7	101.63 (14)	C5—C4—C6	120.2 (2)
C1—N1—C5	116.9 (2)	C3—C4—C5	118.2 (2)
N1—C1—N2	115.2 (2)	C3—C4—C6	121.6 (2)
N1—C1—C2	123.5 (2)	N1—C5—C4	124.1 (2)
N2—C1—C2	121.3 (2)	S1—C5—N1	118.61 (17)
C1—C2—C3	119.6 (2)	S1—C5—C4	117.28 (18)
C1—N2—H2A	123 (2)	N4—C6—C4	179.3 (3)
C1—N2—H2B	121 (3)	C1—C2—H2	120.00
H2A—N2—H2B	115 (3)	C3—C2—H2	120.00
N3—C3—C2	121.5 (2)	S1—C7—H7A	109.00
N3—C3—C4	120.8 (2)	S1—C7—H7B	109.00
C2—C3—C4	117.7 (2)	S1—C7—H7C	109.00
C3—N3—H3A	114.6 (18)	H7A—C7—H7B	109.00
C3—N3—H3B	117.3 (18)	H7A—C7—H7C	110.00
H3A—N3—H3B	119 (3)	H7B—C7—H7C	110.00
C7—S1—C5—C4	180.0 (2)	C1—C2—C3—N3	−177.1 (2)
C7—S1—C5—N1	−0.5 (2)	N3—C3—C4—C5	179.0 (2)
C1—N1—C5—C4	0.9 (4)	N3—C3—C4—C6	−2.3 (4)
C1—N1—C5—S1	−178.60 (18)	C2—C3—C4—C5	1.5 (3)
C5—N1—C1—C2	1.2 (4)	C2—C3—C4—C6	−179.7 (2)
C5—N1—C1—N2	179.4 (2)	C3—C4—C5—N1	−2.3 (4)
N2—C1—C2—C3	−179.9 (2)	C6—C4—C5—S1	−1.6 (3)
N1—C1—C2—C3	−1.8 (4)	C6—C4—C5—N1	179.0 (2)
C1—C2—C3—C4	0.4 (3)	C3—C4—C5—S1	177.24 (18)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N3i	0.86 (3)	2.43 (3)	3.225 (4)	155 (3)
N2—H2B···N4ii	0.86 (2)	2.26 (3)	3.083 (4)	161 (3)
N3—H3B···N4iii	0.85 (2)	2.31 (2)	3.128 (3)	161 (2)
C7—H7A···Cg1iv	0.98	2.77	3.552 (4)	137

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N2H2AN3i	0.86(3)	2.43(3)	3.225(4)	155(3)
N2H2BN4ii	0.86(2)	2.26(3)	3.083(4)	161(3)
N3H3BN4iii	0.85(2)	2.31(2)	3.128(3)	161(2)
C7H7A Cg1iv	0.98	2.77	3.552(4)	137

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .