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organic compounds
of 4,6-diamino-2-(methylsulfanyl)pyridine-3-carbonitrile
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
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 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
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Data collection: APEX2 (Bruker, 2009); cell 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
10.1107/S2056989015003114/is5390sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989015003114/is5390Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989015003114/is5390Isup3.cml
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).
H-atoms attached to carbon were placed in calculated positions (C—H = 0.95–0.98 Å) and refined as riding with Uiso(H) = 1.2 or 1.5Ueq(C) . The H atoms attached to N2 and N3 were found in a difference Fourier map and their positions were refined with bond length and angle restraints of N—H = 0.86 (1) and H···H = 1.40 (3) Å, and with Uiso(H) = 1.5Ueq(N).
Data collection: APEX2 (Bruker, 2009); cell
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).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) |
C7H8N4S | V = 844.1 (2) Å3 |
Mr = 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 |
Bruker SMART X2S benchtop diffractometer | 1487 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 1353 reflections with I > 2σ(I) |
Tmin = 0.833, Tmax = 0.984 | Rint = 0.037 |
9083 measured reflections |
R[F2 > 2σ(F2)] = 0.026 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.062 | Δρmax = 0.20 e Å−3 |
S = 1.06 | Δρmin = −0.13 e Å−3 |
1487 reflections | Absolute structure: Flack (1983) |
122 parameters | Absolute structure parameter: 0.01 (4) |
6 restraints |
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 |
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. |
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 |
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
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).