organic compounds
of 4,6-diamino-2-sulfanylidene-1,2-dihydropyridine-3-carbonitrile
aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, bChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, cDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, dDepartment of Chemistry, University of Leicester, Leicester, England, 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 compound, C6H6N4S, crystallizes with two independent molecules, A and B, in the Both independent molecules are almost planar [maximum deviations of 0.068 (6) Å in molecule A and 0.079 (6) Å in molecule B]. In the crystal, molecules A and B are linked by N—H⋯S, N—H⋯N and C—H⋯S hydrogen bonds, forming a three-dimensional network.
Keywords: crystal structure; polyfuntional pyridines; 3-cyanopyridine-2(1H)-thiones; hydrogen bonding.
CCDC reference: 1018166
1. Related literature
For the synthesis of polyfuntional pyridines, see: Attaby et al. (1995); Asadov et al. (2003). For various biological properties of pyridine scaffold compounds, see: Abdel-Rahman et al. (2002); Rao et al. (2006). For the synthesis of 3-cyanopyridine-2(1H)-thiones, see: Fahmy & Mohareb (1986); Schmidt & Kubitzek (1960). For the use of 3-cyanopyridine-2(1H)-thiones in the synthesis of bio-active compounds, see: Taylor et al. (1983); Gangiee et al. (1991); Amr et al. (2003); Abu-Shanab et al. (2002); Awad et al. (1962); El-Gaby (2004); Miky & Zahkoug (1997; Guerrera et al. (1993); Krauze et al. (1999). For a similar see: Eyduran et al. (2007). For the synthesis of the title compound, see: Abu-Shanab (1999). For standard bond-length data, see: Allen et al. (1987).
2. Experimental
2.1. Crystal data
|
Data collection: SMART (Bruker, 2011); cell SAINT (Bruker, 2011); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
CCDC reference: 1018166
10.1107/S1600536814018029/hg5399sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814018029/hg5399Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814018029/hg5399Isup3.cml
The title compound was prepared according to the reported method (Abu-Shanab, 1999). Crystals of the product were obtained in excellent yield (79%) and recrystallized from butanol to afford yellow needles (M.p. 583 K) in a sufficient quality for X-ray diffraction studies.
H-atoms were placed in calculated positions (C—H = 0.95 and N—H = 0.88 Å and were included as riding contributions with isotropic displacement parameters 1.2 times those of the attached atoms.
Data collection: SMART (Bruker, 2011); cell
SAINT (Bruker, 2011); data reduction: SAINT (Bruker, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).Fig. 1. The title molecule showing the numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. Packing viewed down the b axis showing the hydrogen bonding as dashed lines. |
C6H6N4S | F(000) = 688 |
Mr = 166.21 | Dx = 1.538 Mg m−3 |
Orthorhombic, Pca21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2ac | Cell parameters from 748 reflections |
a = 26.252 (8) Å | θ = 2.3–23.4° |
b = 4.3670 (14) Å | µ = 0.38 mm−1 |
c = 12.523 (4) Å | T = 150 K |
V = 1435.7 (8) Å3 | Needle, pale yellow |
Z = 8 | 0.32 × 0.12 × 0.04 mm |
Bruker APEX 2000 CCD area-detector diffractometer | 3412 independent reflections |
Radiation source: fine-focus sealed tube | 2027 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.137 |
phi and ω scans | θmax = 28.7°, θmin = 1.6° |
Absorption correction: multi-scan (SADABS: Bruker, 2011) | h = −34→33 |
Tmin = 0.518, Tmax = 0.928 | k = −5→5 |
11662 measured reflections | l = −16→16 |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.064 | w = 1/[σ2(Fo2) + (0.0282P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.117 | (Δ/σ)max < 0.001 |
S = 0.87 | Δρmax = 0.42 e Å−3 |
3412 reflections | Δρmin = −0.34 e Å−3 |
199 parameters | Absolute structure: Flack (1983), 1573 Friedel pairs |
1 restraint | Absolute structure parameter: 0.01 (13) |
C6H6N4S | V = 1435.7 (8) Å3 |
Mr = 166.21 | Z = 8 |
Orthorhombic, Pca21 | Mo Kα radiation |
a = 26.252 (8) Å | µ = 0.38 mm−1 |
b = 4.3670 (14) Å | T = 150 K |
c = 12.523 (4) Å | 0.32 × 0.12 × 0.04 mm |
Bruker APEX 2000 CCD area-detector diffractometer | 3412 independent reflections |
Absorption correction: multi-scan (SADABS: Bruker, 2011) | 2027 reflections with I > 2σ(I) |
Tmin = 0.518, Tmax = 0.928 | Rint = 0.137 |
11662 measured reflections |
R[F2 > 2σ(F2)] = 0.064 | H-atom parameters constrained |
wR(F2) = 0.117 | Δρmax = 0.42 e Å−3 |
S = 0.87 | Δρmin = −0.34 e Å−3 |
3412 reflections | Absolute structure: Flack (1983), 1573 Friedel pairs |
199 parameters | Absolute structure parameter: 0.01 (13) |
1 restraint |
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 | 0.27967 (6) | 0.5692 (5) | 0.10895 (15) | 0.0332 (6) | |
S1A | 0.59399 (6) | 0.7628 (4) | 0.41599 (15) | 0.0279 (5) | |
N1 | 0.28114 (18) | 0.2124 (13) | −0.0607 (4) | 0.027 (2) | |
N2 | 0.1365 (2) | 0.4860 (15) | 0.1504 (5) | 0.039 (2) | |
N3 | 0.1288 (2) | 0.0258 (14) | −0.0735 (5) | 0.037 (2) | |
N4 | 0.2980 (2) | −0.1066 (15) | −0.2027 (5) | 0.040 (2) | |
C1 | 0.2513 (3) | 0.3403 (15) | 0.0166 (5) | 0.026 (2) | |
C2 | 0.1995 (2) | 0.2719 (16) | 0.0115 (5) | 0.025 (2) | |
C3 | 0.1797 (2) | 0.0835 (15) | −0.0684 (5) | 0.025 (2) | |
C4 | 0.2122 (2) | −0.0471 (17) | −0.1416 (6) | 0.030 (3) | |
C5 | 0.2637 (2) | 0.0167 (17) | −0.1372 (6) | 0.027 (3) | |
C6 | 0.1661 (2) | 0.3946 (18) | 0.0905 (6) | 0.031 (3) | |
N1A | 0.59425 (19) | 1.1254 (12) | 0.5874 (4) | 0.0230 (17) | |
N2A | 0.4628 (2) | 0.4521 (15) | 0.4637 (5) | 0.038 (2) | |
N3A | 0.45527 (19) | 0.8585 (13) | 0.7032 (4) | 0.0327 (19) | |
N4A | 0.6065 (2) | 1.4593 (13) | 0.7299 (4) | 0.0277 (19) | |
C1A | 0.5677 (3) | 0.9133 (16) | 0.5295 (5) | 0.025 (2) | |
C2A | 0.5201 (2) | 0.8249 (16) | 0.5670 (5) | 0.023 (2) | |
C3A | 0.5005 (3) | 0.9504 (16) | 0.6643 (5) | 0.022 (2) | |
C4A | 0.5300 (2) | 1.1636 (15) | 0.7195 (6) | 0.026 (2) | |
C5A | 0.5760 (2) | 1.2555 (16) | 0.6797 (5) | 0.026 (2) | |
C6A | 0.4896 (2) | 0.6151 (16) | 0.5089 (6) | 0.025 (2) | |
H1 | 0.31370 | 0.25940 | −0.06120 | 0.0320* | |
H4 | 0.19930 | −0.18060 | −0.19500 | 0.0360* | |
H31 | 0.11670 | −0.09500 | −0.12370 | 0.0450* | |
H32 | 0.10800 | 0.10930 | −0.02670 | 0.0450* | |
H41 | 0.33050 | −0.06070 | −0.19550 | 0.0480* | |
H42 | 0.28820 | −0.23400 | −0.25310 | 0.0480* | |
H1A | 0.62450 | 1.18140 | 0.56440 | 0.0270* | |
H4A | 0.51800 | 1.24540 | 0.78520 | 0.0310* | |
H33 | 0.44400 | 0.93300 | 0.76400 | 0.0400* | |
H34 | 0.43690 | 0.72390 | 0.66770 | 0.0400* | |
H43 | 0.59690 | 1.53930 | 0.79120 | 0.0330* | |
H44 | 0.63580 | 1.51200 | 0.70130 | 0.0330* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0253 (9) | 0.0437 (12) | 0.0307 (10) | −0.0029 (9) | −0.0017 (8) | −0.0139 (10) |
S1A | 0.0223 (8) | 0.0385 (10) | 0.0229 (8) | 0.0018 (9) | 0.0020 (8) | 0.0010 (9) |
N1 | 0.016 (3) | 0.037 (4) | 0.027 (4) | −0.001 (3) | −0.001 (2) | −0.005 (3) |
N2 | 0.026 (3) | 0.054 (5) | 0.037 (4) | 0.002 (3) | −0.001 (3) | −0.011 (3) |
N3 | 0.024 (3) | 0.054 (4) | 0.034 (4) | −0.004 (3) | −0.002 (3) | −0.020 (4) |
N4 | 0.029 (3) | 0.057 (5) | 0.034 (4) | −0.009 (3) | 0.004 (3) | −0.020 (3) |
C1 | 0.031 (4) | 0.025 (4) | 0.021 (4) | 0.003 (3) | 0.000 (3) | −0.001 (3) |
C2 | 0.023 (4) | 0.031 (4) | 0.021 (4) | 0.005 (3) | −0.003 (3) | −0.006 (3) |
C3 | 0.022 (3) | 0.028 (4) | 0.025 (4) | −0.002 (3) | 0.001 (3) | −0.001 (4) |
C4 | 0.025 (4) | 0.034 (5) | 0.030 (4) | −0.005 (3) | 0.000 (3) | −0.017 (4) |
C5 | 0.026 (4) | 0.036 (5) | 0.020 (4) | −0.003 (3) | 0.001 (3) | −0.008 (3) |
C6 | 0.023 (4) | 0.040 (5) | 0.031 (5) | 0.001 (3) | −0.001 (3) | −0.007 (4) |
N1A | 0.022 (3) | 0.027 (3) | 0.020 (3) | −0.003 (3) | −0.001 (2) | 0.002 (3) |
N2A | 0.035 (4) | 0.042 (4) | 0.036 (4) | −0.009 (3) | 0.001 (3) | −0.003 (3) |
N3A | 0.021 (3) | 0.049 (4) | 0.028 (3) | −0.004 (3) | 0.005 (3) | −0.012 (3) |
N4A | 0.026 (3) | 0.032 (4) | 0.025 (3) | −0.003 (3) | −0.002 (2) | 0.000 (3) |
C1A | 0.028 (4) | 0.023 (4) | 0.023 (4) | 0.004 (3) | −0.003 (3) | 0.001 (3) |
C2A | 0.019 (3) | 0.026 (4) | 0.025 (4) | 0.002 (3) | −0.002 (3) | 0.004 (3) |
C3A | 0.018 (3) | 0.026 (4) | 0.023 (4) | 0.006 (3) | 0.000 (3) | 0.003 (3) |
C4A | 0.027 (4) | 0.025 (4) | 0.026 (4) | 0.002 (3) | 0.001 (3) | −0.001 (3) |
C5A | 0.023 (4) | 0.026 (4) | 0.030 (4) | 0.000 (3) | −0.008 (3) | 0.009 (4) |
C6A | 0.020 (4) | 0.024 (4) | 0.032 (4) | 0.006 (3) | 0.005 (3) | 0.007 (4) |
S1—C1 | 1.700 (7) | N1A—C5A | 1.374 (8) |
S1A—C1A | 1.711 (7) | N1A—C1A | 1.367 (9) |
N1—C1 | 1.365 (9) | N2A—C6A | 1.150 (9) |
N1—C5 | 1.363 (9) | N3A—C3A | 1.345 (9) |
N2—C6 | 1.151 (9) | C4—H4 | 0.9500 |
N3—C3 | 1.361 (7) | N4A—C5A | 1.352 (8) |
N4—C5 | 1.332 (9) | C1A—C2A | 1.390 (9) |
C1—C2 | 1.394 (9) | N1A—H1A | 0.8800 |
N1—H1 | 0.8800 | C2A—C3A | 1.432 (9) |
C2—C3 | 1.396 (9) | C2A—C6A | 1.418 (9) |
C2—C6 | 1.426 (9) | C3A—C4A | 1.394 (10) |
C3—C4 | 1.376 (9) | N3A—H34 | 0.8800 |
N3—H31 | 0.8800 | N3A—H33 | 0.8800 |
N3—H32 | 0.8800 | C4A—C5A | 1.367 (8) |
N4—H41 | 0.8800 | N4A—H43 | 0.8800 |
N4—H42 | 0.8800 | N4A—H44 | 0.8800 |
C4—C5 | 1.382 (8) | C4A—H4A | 0.9500 |
C1—N1—C5 | 124.2 (5) | C5—C4—H4 | 120.00 |
S1—C1—N1 | 118.1 (6) | S1A—C1A—N1A | 119.7 (5) |
S1—C1—C2 | 125.8 (5) | S1A—C1A—C2A | 122.5 (5) |
N1—C1—C2 | 116.1 (6) | N1A—C1A—C2A | 117.9 (6) |
C1—N1—H1 | 118.00 | C1A—N1A—H1A | 118.00 |
C5—N1—H1 | 118.00 | C5A—N1A—H1A | 118.00 |
C1—C2—C3 | 121.5 (6) | C1A—C2A—C3A | 120.3 (6) |
C1—C2—C6 | 119.2 (6) | C1A—C2A—C6A | 120.9 (6) |
C3—C2—C6 | 119.3 (5) | C3A—C2A—C6A | 118.8 (6) |
N3—C3—C2 | 120.6 (5) | N3A—C3A—C2A | 120.8 (6) |
C3—N3—H31 | 120.00 | C3A—N3A—H33 | 120.00 |
C3—N3—H32 | 120.00 | C3A—N3A—H34 | 120.00 |
H31—N3—H32 | 120.00 | H33—N3A—H34 | 120.00 |
C2—C3—C4 | 119.4 (5) | C2A—C3A—C4A | 118.6 (6) |
N3—C3—C4 | 120.0 (6) | N3A—C3A—C4A | 120.7 (6) |
C5—N4—H42 | 120.00 | C5A—N4A—H44 | 120.00 |
C5—N4—H41 | 120.00 | C5A—N4A—H43 | 120.00 |
C3—C4—C5 | 119.8 (6) | C3A—C4A—C5A | 120.4 (7) |
H41—N4—H42 | 120.00 | H43—N4A—H44 | 120.00 |
N1—C5—N4 | 117.3 (5) | N1A—C5A—N4A | 117.2 (5) |
N4—C5—C4 | 123.8 (7) | N4A—C5A—C4A | 123.2 (6) |
N1—C5—C4 | 118.9 (6) | N1A—C5A—C4A | 119.6 (6) |
N2—C6—C2 | 175.5 (7) | N2A—C6A—C2A | 176.7 (6) |
C1A—N1A—C5A | 123.3 (5) | C3A—C4A—H4A | 120.00 |
C3—C4—H4 | 120.00 | C5A—C4A—H4A | 120.00 |
C5—N1—C1—S1 | 177.7 (5) | C5A—N1A—C1A—S1A | −179.5 (5) |
C5—N1—C1—C2 | −3.0 (10) | C5A—N1A—C1A—C2A | −0.5 (10) |
C1—N1—C5—C4 | 3.5 (10) | C1A—N1A—C5A—C4A | 2.6 (9) |
C1—N1—C5—N4 | −175.4 (6) | C1A—N1A—C5A—N4A | 179.1 (6) |
S1—C1—C2—C6 | −1.5 (10) | S1A—C1A—C2A—C6A | −3.5 (10) |
S1—C1—C2—C3 | 179.3 (5) | S1A—C1A—C2A—C3A | 178.0 (5) |
N1—C1—C2—C3 | 0.0 (10) | N1A—C1A—C2A—C3A | −1.1 (10) |
N1—C1—C2—C6 | 179.2 (6) | N1A—C1A—C2A—C6A | 177.5 (6) |
C1—C2—C3—N3 | −178.3 (6) | C1A—C2A—C3A—N3A | −177.7 (6) |
C6—C2—C3—C4 | −176.9 (7) | C6A—C2A—C3A—C4A | −178.1 (6) |
C1—C2—C3—C4 | 2.4 (10) | C1A—C2A—C3A—C4A | 0.5 (10) |
C6—C2—C3—N3 | 2.4 (10) | C6A—C2A—C3A—N3A | 3.7 (10) |
N3—C3—C4—C5 | 178.8 (7) | N3A—C3A—C4A—C5A | 179.8 (6) |
C2—C3—C4—C5 | −1.9 (10) | C2A—C3A—C4A—C5A | 1.6 (10) |
C3—C4—C5—N4 | 177.9 (7) | C3A—C4A—C5A—N4A | −179.4 (6) |
C3—C4—C5—N1 | −0.9 (11) | C3A—C4A—C5A—N1A | −3.2 (10) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···S1Ai | 0.88 | 2.44 | 3.293 (5) | 163 |
N1A—H1A···S1ii | 0.88 | 2.80 | 3.579 (5) | 149 |
N3—H31···N4Aiii | 0.88 | 2.44 | 3.300 (8) | 165 |
N3—H32···N2Aiv | 0.88 | 2.39 | 3.077 (8) | 135 |
N3A—H33···S1Aii | 0.88 | 2.53 | 3.392 (6) | 168 |
N3A—H34···N2v | 0.88 | 2.20 | 2.981 (8) | 148 |
N4—H41···S1Ai | 0.88 | 2.75 | 3.536 (6) | 149 |
N4—H42···S1vi | 0.88 | 2.63 | 3.424 (6) | 151 |
N4—H42···N2vi | 0.88 | 2.62 | 3.083 (9) | 114 |
N4A—H44···S1ii | 0.88 | 2.53 | 3.353 (6) | 157 |
C4—H4···S1vi | 0.95 | 2.74 | 3.551 (8) | 143 |
Symmetry codes: (i) −x+1, −y+1, z−1/2; (ii) −x+1, −y+2, z+1/2; (iii) x−1/2, −y+1, z−1; (iv) −x+1/2, y, z−1/2; (v) −x+1/2, y, z+1/2; (vi) −x+1/2, y−1, z−1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···S1Ai | 0.88 | 2.44 | 3.293 (5) | 163 |
N1A—H1A···S1ii | 0.88 | 2.80 | 3.579 (5) | 149 |
N3—H31···N4Aiii | 0.88 | 2.44 | 3.300 (8) | 165 |
N3—H32···N2Aiv | 0.88 | 2.39 | 3.077 (8) | 135 |
N3A—H33···S1Aii | 0.88 | 2.53 | 3.392 (6) | 168 |
N3A—H34···N2v | 0.88 | 2.20 | 2.981 (8) | 148 |
N4—H41···S1Ai | 0.88 | 2.75 | 3.536 (6) | 149 |
N4—H42···S1vi | 0.88 | 2.63 | 3.424 (6) | 151 |
N4—H42···N2vi | 0.88 | 2.62 | 3.083 (9) | 114 |
N4A—H44···S1ii | 0.88 | 2.53 | 3.353 (6) | 157 |
C4—H4···S1vi | 0.95 | 2.74 | 3.551 (8) | 143 |
Symmetry codes: (i) −x+1, −y+1, z−1/2; (ii) −x+1, −y+2, z+1/2; (iii) x−1/2, −y+1, z−1; (iv) −x+1/2, y, z−1/2; (v) −x+1/2, y, z+1/2; (vi) −x+1/2, y−1, z−1/2. |
Acknowledgements
Manchester Metropolitan University, Erciyes University and the University of Leicester are gratefully acknowledged for supporting this study.
References
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Polyfunctional pyridines are highly reactive reagents that have been used extensively in heterocyclic synthesis (Attaby et al., 1995; Asadov et al., 2003). 3-Cyano-pyridine-2(1H)-thiones compounds (Fahmy & Mohareb 1986; Schmidt & Kubitzek, 1960) have also gained considerable interest due to their importance as intermediates for the synthesis of the biologically active deazafolic acid and deaza amino protein ring system (Taylor et al., 1983; Gangiee et al., 1991). In addition, 3-Cyano-2(1H)-pyridinethiones and their related compounds were found to be very reactive substances for the synthesis of many different heterocyclic systems which exhibited biological activities such as antibacterial, pesticidal, antifungal, acaricidal and neurotropic activities (Amr et al., 2003; Abu-Shanab et al., 2002; Awad et al., 1962; El-Gaby, 2004; Miky & Zahkoug, 1997; Guerrera et al., 1993; Krauze et al., 1999; Abdel-Rahman et al., 2002; Rao et al., 2006). In light of these observations we report in this study the synthesis and crystal structure of the title compound.
In the title compound (Fig. 1), the asymmetric unit contains two independent molecules (A and B). Molecules A and B both are almost planar (Fig. 3), with the maximum deviations of -0.068 (6) Å for N4 in molecule A and 0.079 (6) Å for N2A in molecule B. The bond lengths of molecules A and B are comparable to those of the previously published structures (Eyduran et al., 2007; Allen et al., 1987).
In the crystal, the N—H···S, N—H···N and C—H···S hydrogen bonds connect the molecules, forming a three dimensional network (Table 1, Fig. 2). In addition, C—H···π interactions and π-π stacking interactions are not observed.