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

Mohamed, S.K.; Knight, K.S.; Akkurt, M.; Hussein, B.R.M.; Albayati, M.R.

doi:10.1107/S2056989015003114

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 71| Part 3| March 2015| Pages o197-o198

doi:10.1107/S2056989015003114

Open

access

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 and Mustafa R. Albayati ^f ^*

^aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, ^bChemistry Department, Faculty of Science, Mini University, 61519 El-Minia, Egypt, ^cDepartment of Chemistry, The University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA, ^dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, ^eChemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt, and ^fKirkuk University, College of Science, Department of Chemistry, Kirkuk, Iraq
^*Correspondence e-mail: shaabankamel@yahoo.com

Edited by H. Ishida, Okayama University, Japan (Received 3 February 2015; accepted 13 February 2015; online 21 February 2015)

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.

CCDC reference: 1049335

1. 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 ).

2. Experimental

2.1. Crystal data

C₇H₈N₄S
M_r = 180.23
Orthorhombic, P 2₁ 2₁ 2₁
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

2.2. 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

2.3. Refinement

R[F² > 2σ(F²)] = 0.026
wR(F²) = 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)

Table 1
Hydrogen-bond geometry (Å, °)

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⋯Cg1^iv	0.98	2.77	3.552 (4)	137
Symmetry codes: (i) $[-x+{\script{3\over 2}}, -y+1, z-{\script{1\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ ; (iv) x+1, y, z.

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 ).

Supporting information

CCDC reference: 1049335

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015003114/is5390sup1.cif

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

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

checkCIF report

Comment top

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).

Related literature top

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 top

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).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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).

Figures top

	Fig. 1. 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.
	Fig. 2. The hydrogen bonding (dashed lines) and packing of the title compound viewed down the a axis.

4,6-Diamino-2-(methylsulfanyl)pyridine-3-carbonitrile top

Crystal data top

C₇H₈N₄S	F(000) = 376
M_r = 180.23	D_x = 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

Data collection top

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	R_int = 0.037
ω scans	θ_max = 25.0°, θ_min = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −6→6
T_min = 0.833, T_max = 0.984	k = −15→12
9083 measured reflections	l = −15→15

Refinement top

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(F_o²) + (0.0294P)² + 0.1689P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.062	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.20 e Å⁻³
1487 reflections	Δρ_min = −0.13 e Å⁻³
122 parameters	Absolute structure: Flack (1983)
6 restraints	Absolute structure parameter: 0.01 (4)

Crystal data top

C₇H₈N₄S	V = 844.1 (2) Å³
M_r = 180.23	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.0863 (7) Å	µ = 0.33 mm⁻¹
b = 12.698 (2) Å	T = 200 K
c = 13.069 (2) Å	0.40 × 0.09 × 0.05 mm

Data collection top

Bruker SMART X2S benchtop diffractometer	1487 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	1353 reflections with I > 2σ(I)
T_min = 0.833, T_max = 0.984	R_int = 0.037
9083 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.026	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.062	Δρ_max = 0.20 e Å⁻³
S = 1.06	Δρ_min = −0.13 e Å⁻³
1487 reflections	Absolute structure: Flack (1983)
122 parameters	Absolute structure parameter: 0.01 (4)
6 restraints

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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···Cg1^iv	0.98	2.77	3.552 (4)	137

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

Hydrogen-bond geometry (Å, º) top

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···Cg1^iv	0.98	2.77	3.552 (4)	137

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

Acknowledgements

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

References

Abu-Shanab, F. A. (1999). J. Chem. Res. (S), 7, 430–431. Google Scholar
Al-Haiza, M. A., Mostafa1, M. S. & El-Kady, M. Y. (2003). Molecules, 8, 275–286. Google Scholar
Bruker (2008). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Flack, H. D. (1983). Acta Cryst. A39, 876–881. CrossRef CAS Web of Science IUCr Journals Google Scholar
Mohamed, S. K., Akkurt, M., Singh, K., Hussein, B. R. M. & Albayati, M. R. (2014). Acta Cryst. E70, o993–o994. CSD CrossRef IUCr Journals Google Scholar
Murata, T., Shimada, M., Sakakibara, S., Yoshino, T., Kadono, H., Masuda, T., Shimazaki, M., Shintani, T., Fuchikami, K., Sakai, K., Inbe, H., Takeshita, K., Niki, T., Umeda, M., Bacon, K. B., Ziegelbauer, K. B. & Lowinger, T. B. (2003). Bioorg. Med. Chem. Lett. 13, 913–918. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhang, X., Li, D., Fan, X., Wang, X., Li, X., Qu, G. & Wang, J. (2010). Mol. Divers. 14, 159–167. CrossRef PubMed CAS Google Scholar