organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 71| Part 3| March 2015| Pages o169-o170

Crystal structure of N-[4-amino-5-cyano-6-(methyl­sulfan­yl)pyridin-2-yl]-2-chloro­acetamide

CROSSMARK_Color_square_no_text.svg

aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, bChemistry Department, Faculty of Science, Minia 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 W. T. A. Harrison, University of Aberdeen, Scotland (Received 4 February 2015; accepted 4 February 2015; online 13 February 2015)

In the title compound, C9H9ClN4OS, the dihedral angle between the acetamide moiety and the pyridine ring is 4.83 (12)°. The O=C—C—Cl torsion angle is 46.4 (3)° and an intra­molecular C—H⋯O inter­action generates an S(6) ring. In the crystal, mol­ecules are linked by N—H⋯O, N—H⋯N and C—H⋯N hydrogen bonds, generating sheets lying parallel to (120).

1. Related literature

For medicinal and industrial applications of pyridine-containing compounds, see: Boger & Nakahara (1991[Boger, D. L. & Nakahara, S. (1991). J. Org. Chem. 56, 880-884.]); Zhang et al. (1995[Zhang, T. Y., Stout, J. R., Keay, J. G., Scriven, E. F. V., Toomey, J. E. & Goe, G. L. (1995). Tetrahedron, 51, 13177-13184.]); Castedo et al. (1984[Castedo, L., Quintela, J. M. & Riguers, R. (1984). Eur. J. Med. Chem., 19, 555-557.]); Latif et al. (1981[Latif, N., Mishrky, N. & Girgis, N. S. (1981). Indian J. Chem. Sect. B, 20, 147-149.]), Mamolo et al. (2001[Mamolo, M. G., Zampieri, D., Falagiani, V., Vio, E. & Banfi, E. (2001). II Farmaco, 56, 593-599.]); Gachet et al. (1995[Gachet, C., Cattaneo, M., Ohlmann, P., Hechler, B., Lecchi, A., Chevalier, J., Cassel, D., Mannucci, P. M. & Cazenave, J.-P. (1995). Br. J. Haematol. 91, 434-444.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C9H9ClN4OS

  • Mr = 256.71

  • Monoclinic, P 21 /c

  • a = 5.1654 (7) Å

  • b = 20.483 (3) Å

  • c = 10.9489 (14) Å

  • β = 103.562 (5)°

  • V = 1126.1 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.51 mm−1

  • T = 200 K

  • 0.50 × 0.16 × 0.10 mm

2.2. Data collection

  • Bruker SMART X2S benchtop diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.756, Tmax = 0.951

  • 11998 measured reflections

  • 1960 independent reflections

  • 1634 reflections with I > 2σ(I)

  • Rint = 0.043

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.096

  • S = 1.05

  • 1960 reflections

  • 152 parameters

  • 3 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.34 e Å−3

  • Δρmin = −0.41 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯O1 0.95 2.26 2.863 (3) 121
N2—H2B⋯O1i 0.86 (1) 2.13 (1) 2.968 (2) 165 (3)
N4—H4⋯N3ii 0.88 2.16 3.034 (2) 172
C9—H9B⋯N3ii 0.99 2.47 3.366 (3) 151
Symmetry codes: (i) -x+2, -y, -z+1; (ii) [x-1, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. A71, 3-8.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyridine compounds have occupied a unique position in medicinal and industrial chemistry. Some polyfuctional pyridines constitute an important class of antitumor compounds (Boger & Nakahara, 1991; Zhang et al., 1995). They also show antibacterial (Castedo et al., 1984), antifungal (Latif et al., 1981), antimyotic (Mamolo et al., 2001) and antidepressant (Gachet et al., 1995) activities. In this respect, and also in continuation of our study on synthesis of different heterocyclic system that containing highly biological activity, we report here the synthesis and crystal structur of the title compound.

In the title compound (Fig. 1), the chloroacetamide moiety has an extended conformation, as indicated by the torsion angles around the C8—N4 [C9—C8—N4—C1 = 177.90 (19)°] and N4—C1 [C8—N4—C1—C2 = 4.0 (3)°] bonds. The sum of the angles around atom N4 (360.28°) suggests sp2-hybridization. The dihedral angle between the pyridine ring (N1/C1–C5) and the chloroacetamide moiety is 22.36 (6)°.

Molecular structure is stabilized by a weak intramolecular C—H···O interaction (Table 1). In the crystal, molecules are linked via intermolecular N—H···O, N—H···N and C—H···N hydrogen bonds (Table 1, Figs. 2 & 3), forming two dimensional networks paralel to the (120) planes.

Related literature top

For medicinal and industrial applications of pyridine-containing compounds, see: Boger & Nakahara (1991); Zhang et al. (1995); Castedo et al. (1984); Latif et al. (1981), Mamolo et al. (2001); Gachet et al. (1995).

Experimental top

In an ice bath, to a solution of 4,6-Diamino-3-cyano-2-methylthiopyridine-2(1H)-thione (0.5 g, 2.7 mmol) in 30 ml dioxane, chloroacetyl chloride (0.31 g, 2.7 mmol) was added drop by drop with stirring at 273 K over 30 min. The resulting solid product was filtered off under vacuum, washed with cold ethanol, dried and recrystallized from ethanol to furnish colourless crystals (yield 0.65 g, 91%) Mp. 529 – 531 K.

Refinement top

H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.99 Å). They were included as riding contributions with isotropic displacement parameters 1.2 or 1.5 times those of the attached atoms. The hydrogen atoms attached to N2 were found from difference Fourier maps and their Uiso were refined riding contributions with isotropic displacement parameters 1.5 times those of the attached atom, with N2—H2A = 0.85 (3) and N2—H2B = 0.856 (11) Å.

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, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Perspective view of the title compound with displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. View of the hydrogen bonding and packing of the title compound viewed along the a axis.
[Figure 3] Fig. 3. Packing of the title compound viewed along the b axis.
N-[4-Amino-5-cyano-6-(methylsulfanyl)pyridin-2-yl]-2-chloroacetamide top
Crystal data top
C9H9ClN4OSF(000) = 528
Mr = 256.71Dx = 1.514 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3684 reflections
a = 5.1654 (7) Åθ = 2.8–24.9°
b = 20.483 (3) ŵ = 0.51 mm1
c = 10.9489 (14) ÅT = 200 K
β = 103.562 (5)°Needle, yellow
V = 1126.1 (3) Å30.50 × 0.16 × 0.10 mm
Z = 4
Data collection top
Bruker SMART X2S benchtop
diffractometer
1960 independent reflections
Radiation source: XOS X-beam microfocus source1634 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromatorRint = 0.043
ω scansθmax = 25.0°, θmin = 2.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 66
Tmin = 0.756, Tmax = 0.951k = 2424
11998 measured reflectionsl = 1210
Refinement top
Refinement on F23 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.096 w = 1/[σ2(Fo2) + (0.0489P)2 + 0.4578P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1960 reflectionsΔρmax = 0.34 e Å3
152 parametersΔρmin = 0.41 e Å3
Crystal data top
C9H9ClN4OSV = 1126.1 (3) Å3
Mr = 256.71Z = 4
Monoclinic, P21/cMo Kα radiation
a = 5.1654 (7) ŵ = 0.51 mm1
b = 20.483 (3) ÅT = 200 K
c = 10.9489 (14) Å0.50 × 0.16 × 0.10 mm
β = 103.562 (5)°
Data collection top
Bruker SMART X2S benchtop
diffractometer
1960 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
1634 reflections with I > 2σ(I)
Tmin = 0.756, Tmax = 0.951Rint = 0.043
11998 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0353 restraints
wR(F2) = 0.096H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.34 e Å3
1960 reflectionsΔρmin = 0.41 e Å3
152 parameters
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
xyzUiso*/Ueq
Cl10.63935 (18)0.00064 (3)0.86334 (7)0.0591 (3)
S10.99138 (10)0.34034 (2)0.48516 (6)0.0319 (2)
O10.7921 (4)0.02162 (8)0.61866 (18)0.0494 (6)
N10.8476 (3)0.22309 (8)0.55160 (16)0.0229 (5)
N21.2836 (4)0.11962 (8)0.34016 (18)0.0302 (6)
N31.4013 (3)0.28346 (9)0.27223 (18)0.0341 (6)
N40.7070 (3)0.13030 (8)0.62971 (16)0.0251 (5)
C10.8574 (4)0.15744 (9)0.55067 (18)0.0220 (6)
C20.9959 (4)0.12055 (10)0.48191 (18)0.0246 (6)
C31.1424 (4)0.15360 (9)0.40844 (18)0.0226 (6)
C41.1368 (4)0.22219 (10)0.40856 (19)0.0228 (6)
C50.9869 (4)0.25440 (10)0.48268 (19)0.0227 (6)
C61.2825 (4)0.25766 (9)0.3341 (2)0.0249 (6)
C70.7603 (4)0.35817 (11)0.5806 (2)0.0355 (7)
C80.6819 (4)0.06691 (10)0.6581 (2)0.0304 (7)
C90.4941 (5)0.05515 (11)0.7435 (2)0.0416 (8)
H20.992100.074200.484300.0300*
H2A1.358 (6)0.1378 (14)0.287 (2)0.0890*
H2B1.269 (7)0.0780 (5)0.339 (3)0.0890*
H40.617900.158300.665200.0300*
H7A0.578500.349400.532500.0530*
H7B0.776100.404200.605500.0530*
H7C0.800600.330600.655900.0530*
H9A0.323300.037400.694000.0500*
H9B0.456900.096900.781600.0500*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.1097 (6)0.0365 (4)0.0449 (4)0.0030 (3)0.0458 (4)0.0068 (3)
S10.0342 (3)0.0178 (3)0.0481 (4)0.0007 (2)0.0187 (3)0.0002 (2)
O10.0775 (12)0.0217 (8)0.0684 (13)0.0051 (8)0.0560 (10)0.0063 (8)
N10.0238 (8)0.0210 (8)0.0258 (9)0.0004 (6)0.0098 (7)0.0004 (7)
N20.0379 (10)0.0258 (9)0.0344 (11)0.0008 (8)0.0236 (8)0.0009 (8)
N30.0357 (10)0.0333 (10)0.0374 (11)0.0070 (8)0.0168 (9)0.0024 (9)
N40.0313 (9)0.0204 (8)0.0299 (10)0.0014 (7)0.0198 (7)0.0009 (7)
C10.0225 (9)0.0230 (10)0.0221 (11)0.0007 (8)0.0086 (8)0.0021 (8)
C20.0299 (10)0.0201 (10)0.0274 (11)0.0009 (8)0.0139 (9)0.0005 (8)
C30.0221 (9)0.0233 (10)0.0238 (11)0.0013 (8)0.0085 (8)0.0005 (8)
C40.0224 (10)0.0226 (10)0.0252 (11)0.0024 (7)0.0095 (8)0.0017 (8)
C50.0204 (9)0.0200 (10)0.0280 (11)0.0008 (7)0.0063 (8)0.0004 (8)
C60.0263 (10)0.0223 (10)0.0275 (11)0.0013 (8)0.0093 (9)0.0001 (9)
C70.0363 (12)0.0281 (12)0.0445 (14)0.0043 (9)0.0141 (10)0.0061 (10)
C80.0380 (11)0.0239 (11)0.0354 (13)0.0009 (9)0.0209 (10)0.0022 (9)
C90.0536 (14)0.0309 (12)0.0516 (16)0.0008 (11)0.0353 (12)0.0055 (11)
Geometric parameters (Å, º) top
Cl1—C91.769 (2)N2—H2B0.856 (11)
S1—C51.761 (2)C3—C41.405 (3)
S1—C71.799 (2)N4—H40.8800
O1—C81.219 (3)C4—C51.410 (3)
N1—C11.346 (2)C4—C61.431 (3)
N1—C51.324 (3)C8—C91.516 (3)
N2—C31.353 (3)C2—H20.9500
N3—C61.144 (3)C7—H7A0.9800
N4—C11.406 (3)C7—H7B0.9800
N4—C81.348 (3)C7—H7C0.9800
C1—C21.379 (3)C9—H9A0.9900
C2—C31.401 (3)C9—H9B0.9900
N2—H2A0.85 (3)
C5—S1—C7101.76 (10)S1—C5—C4118.02 (16)
C1—N1—C5116.95 (17)N3—C6—C4177.0 (2)
C1—N4—C8128.28 (17)N4—C8—C9113.90 (18)
N1—C1—N4111.30 (17)O1—C8—N4125.0 (2)
N1—C1—C2125.23 (19)O1—C8—C9121.1 (2)
N4—C1—C2123.48 (17)Cl1—C9—C8109.80 (17)
C1—C2—C3117.89 (18)C1—C2—H2121.00
C3—N2—H2B118 (2)C3—C2—H2121.00
H2A—N2—H2B118 (3)S1—C7—H7A109.00
C3—N2—H2A122.6 (19)S1—C7—H7B110.00
C2—C3—C4117.94 (18)S1—C7—H7C109.00
N2—C3—C4121.91 (18)H7A—C7—H7B109.00
N2—C3—C2120.15 (17)H7A—C7—H7C110.00
C3—C4—C5118.85 (19)H7B—C7—H7C109.00
C3—C4—C6119.57 (18)Cl1—C9—H9A110.00
C5—C4—C6121.58 (18)Cl1—C9—H9B110.00
C1—N4—H4116.00C8—C9—H9A110.00
C8—N4—H4116.00C8—C9—H9B110.00
S1—C5—N1118.85 (15)H9A—C9—H9B108.00
N1—C5—C4123.13 (19)
C7—S1—C5—N14.84 (19)C1—C2—C3—N2179.40 (19)
C7—S1—C5—C4176.27 (17)C1—C2—C3—C40.6 (3)
C5—N1—C1—N4178.53 (17)N2—C3—C4—C5179.5 (2)
C1—N1—C5—S1177.61 (15)C2—C3—C4—C6179.61 (19)
C1—N1—C5—C41.2 (3)N2—C3—C4—C60.4 (3)
C5—N1—C1—C21.4 (3)C2—C3—C4—C50.5 (3)
C1—N4—C8—O10.6 (4)C6—C4—C5—N1179.3 (2)
C8—N4—C1—N1175.96 (19)C3—C4—C5—S1178.04 (16)
C8—N4—C1—C24.0 (3)C3—C4—C5—N10.8 (3)
C1—N4—C8—C9177.90 (19)C6—C4—C5—S11.9 (3)
N4—C1—C2—C3178.82 (18)O1—C8—C9—Cl146.4 (3)
N1—C1—C2—C31.1 (3)N4—C8—C9—Cl1135.06 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O10.952.262.863 (3)121
N2—H2B···O1i0.86 (1)2.13 (1)2.968 (2)165 (3)
N4—H4···N3ii0.882.163.034 (2)172
C9—H9B···N3ii0.992.473.366 (3)151
Symmetry codes: (i) x+2, y, z+1; (ii) x1, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O10.952.262.863 (3)121
N2—H2B···O1i0.856 (11)2.132 (14)2.968 (2)165 (3)
N4—H4···N3ii0.882.163.034 (2)172
C9—H9B···N3ii0.992.473.366 (3)151
Symmetry codes: (i) x+2, y, z+1; (ii) x1, y+1/2, z+1/2.
 

Acknowledgements

We thank the University of Tennessee for supporting this study.

References

First citationBoger, D. L. & Nakahara, S. (1991). J. Org. Chem. 56, 880–884.  CrossRef CAS Web of Science Google Scholar
First citationBruker (2008). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCastedo, L., Quintela, J. M. & Riguers, R. (1984). Eur. J. Med. Chem., 19, 555–557.  CAS Google Scholar
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationGachet, C., Cattaneo, M., Ohlmann, P., Hechler, B., Lecchi, A., Chevalier, J., Cassel, D., Mannucci, P. M. & Cazenave, J.-P. (1995). Br. J. Haematol. 91, 434–444.  CrossRef CAS PubMed Web of Science Google Scholar
First citationLatif, N., Mishrky, N. & Girgis, N. S. (1981). Indian J. Chem. Sect. B, 20, 147–149.  Google Scholar
First citationMamolo, M. G., Zampieri, D., Falagiani, V., Vio, E. & Banfi, E. (2001). II Farmaco, 56, 593–599.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZhang, T. Y., Stout, J. R., Keay, J. G., Scriven, E. F. V., Toomey, J. E. & Goe, G. L. (1995). Tetrahedron, 51, 13177–13184.  CrossRef CAS Web of Science Google Scholar

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.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 71| Part 3| March 2015| Pages o169-o170
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds