Crystal structure of 4,6-di­amino-2-(methyl­sulfan­yl)pyridine-3-carbo­nitrile

Shaaban K Mohamed; Kyle S Knight; Mehmet Akkurt; Bahgat R M Hussein; Mustafa R Albayati

doi:10.1107/S2056989015003114

. 2015 Feb 21;71(Pt 3):o197–o198. doi: 10.1107/S2056989015003114

Crystal structure of 4,6-diamino-2-(methylsulfanyl)pyridine-3-carbonitrile

Shaaban K Mohamed ^a,^b, Kyle S Knight ^c, Mehmet Akkurt ^d, Bahgat R M Hussein ^e, Mustafa R Albayati ^f,^*

PMCID: PMC4350697 PMID: 25844246

Abstract

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, molecules are linked by an intermolecular 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 interaction, forming a three-dimensional network.

Keywords: crystal structure; 4,6-diamino-2-(methylsulfanyl)pyridine-3-carbonitrile; multifunctional pyridines

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 _r = 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
Δρ_max = 0.20 e Å⁻³
Δρ_min = −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 ▸).

Supplementary Material

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

e-71-0o197-sup1.cif^{(18.5KB, cif)}

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

e-71-0o197-Isup2.hkl^{(82.1KB, hkl)}

Click here for additional data file.^{(3.3KB, cml)}

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

Click here for additional data file.^{(1.4MB, tif)}

. 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.^{(2.5MB, tif)}

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

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 Cg1^iv	0.98	2.77	3.552(4)	137

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

Acknowledgments

The authors would like express their gratitude to the University of Tennessee for providing the X-ray data.

supplementary crystallographic information

S1. Comment

The pyridine ring is a core structure in a number of pharmaceuticals and natural products (Zhang et al., 2010). 2-Amino-3-cyanopyridines have been identified as IKK-β inhibitors (Murata et al., 2003). Besides this, they are important and useful intermediates in preparing variety of heterocyclic compounds (Al-Haiza et al., 2003). Such findings and following to our on-going study on synthesis of bio-active heterocyclic molecules we report in this study the synthesis and crystal structure determination of the title compound.

The molecule of the title compound, Fig. 1, is a tetra-substituted pyrimidine derivative, which is essentially planar with C7–S1–C5–C4, C3–C2–C1–N2, N3–C3–C4–C5 and C6–C4–C3–C2 torsion angles being 180.0 (2), 179.9 (2), 179.0 (2) and 179.7 (2)°, respectively. All bond lengths and bond angles are normal and comparable to those observed in a similar structure (Mohamed et al., 2014). In the crystal structure, intermolecular N—H···N hydrogen bonds and a weak C—H···π interaction feature in the crystal packing (Table 1, Fig. 2).

S2. Experimental

The title compound was prepared according to the reported method (Abu-Shanab, 1999). Crystals of the product were obtained in a good yield (77%) and were suitable for X-ray diffraction (M.p. 426–428 K).