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

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

doi:10.1107/S2056989015002431

organic compounds

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

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, 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).

Keywords: crystal structure; N-[4-amino-5-cyano-6-(methylsulfanyl)pyridin-2-yl]-2-chloroacetamide; polyfunctional pyridines; hydrogen bonding.

CCDC reference: 1047552

1. Related literature

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 ).

2. Experimental

2.1. Crystal data

C₉H₉ClN₄OS
M_r = 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 ) T_min = 0.756, T_max = 0.951
11998 measured reflections
1960 independent reflections
1634 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.41 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

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

Supporting information

CCDC reference: 1047552

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015002431/hb7362sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015002431/hb7362Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015002431/hb7362Isup3.cml

checkCIF report

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.

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

	Fig. 1. Perspective view of the title compound with displacement ellipsoids drawn at the 50% probability level.
	Fig. 2. View of the hydrogen bonding and packing of the title compound viewed along the a axis.
	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

C₉H₉ClN₄OS	F(000) = 528
M_r = 256.71	D_x = 1.514 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3684 reflections
a = 5.1654 (7) Å	θ = 2.8–24.9°
b = 20.483 (3) Å	µ = 0.51 mm⁻¹
c = 10.9489 (14) Å	T = 200 K
β = 103.562 (5)°	Needle, yellow
V = 1126.1 (3) Å³	0.50 × 0.16 × 0.10 mm
Z = 4

Data collection top

Bruker SMART X2S benchtop diffractometer	1960 independent reflections
Radiation source: XOS X-beam microfocus source	1634 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromator	R_int = 0.043
ω scans	θ_max = 25.0°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −6→6
T_min = 0.756, T_max = 0.951	k = −24→24
11998 measured reflections	l = −12→10

Refinement top

Refinement on F²	3 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.035	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.096	w = 1/[σ²(F_o²) + (0.0489P)² + 0.4578P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
1960 reflections	Δρ_max = 0.34 e Å⁻³
152 parameters	Δρ_min = −0.41 e Å⁻³

Crystal data top

C₉H₉ClN₄OS	V = 1126.1 (3) Å³
M_r = 256.71	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 5.1654 (7) Å	µ = 0.51 mm⁻¹
b = 20.483 (3) Å	T = 200 K
c = 10.9489 (14) Å	0.50 × 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)
T_min = 0.756, T_max = 0.951	R_int = 0.043
11998 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	3 restraints
wR(F²) = 0.096	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.34 e Å⁻³
1960 reflections	Δρ_min = −0.41 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Cl1	0.63935 (18)	−0.00064 (3)	0.86334 (7)	0.0591 (3)
S1	0.99138 (10)	0.34034 (2)	0.48516 (6)	0.0319 (2)
O1	0.7921 (4)	0.02162 (8)	0.61866 (18)	0.0494 (6)
N1	0.8476 (3)	0.22309 (8)	0.55160 (16)	0.0229 (5)
N2	1.2836 (4)	0.11962 (8)	0.34016 (18)	0.0302 (6)
N3	1.4013 (3)	0.28346 (9)	0.27223 (18)	0.0341 (6)
N4	0.7070 (3)	0.13030 (8)	0.62971 (16)	0.0251 (5)
C1	0.8574 (4)	0.15744 (9)	0.55067 (18)	0.0220 (6)
C2	0.9959 (4)	0.12055 (10)	0.48191 (18)	0.0246 (6)
C3	1.1424 (4)	0.15360 (9)	0.40844 (18)	0.0226 (6)
C4	1.1368 (4)	0.22219 (10)	0.40856 (19)	0.0228 (6)
C5	0.9869 (4)	0.25440 (10)	0.48268 (19)	0.0227 (6)
C6	1.2825 (4)	0.25766 (9)	0.3341 (2)	0.0249 (6)
C7	0.7603 (4)	0.35817 (11)	0.5806 (2)	0.0355 (7)
C8	0.6819 (4)	0.06691 (10)	0.6581 (2)	0.0304 (7)
C9	0.4941 (5)	0.05515 (11)	0.7435 (2)	0.0416 (8)
H2	0.99210	0.07420	0.48430	0.0300*
H2A	1.358 (6)	0.1378 (14)	0.287 (2)	0.0890*
H2B	1.269 (7)	0.0780 (5)	0.339 (3)	0.0890*
H4	0.61790	0.15830	0.66520	0.0300*
H7A	0.57850	0.34940	0.53250	0.0530*
H7B	0.77610	0.40420	0.60550	0.0530*
H7C	0.80060	0.33060	0.65590	0.0530*
H9A	0.32330	0.03740	0.69400	0.0500*
H9B	0.45690	0.09690	0.78160	0.0500*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.1097 (6)	0.0365 (4)	0.0449 (4)	0.0030 (3)	0.0458 (4)	0.0068 (3)
S1	0.0342 (3)	0.0178 (3)	0.0481 (4)	−0.0007 (2)	0.0187 (3)	0.0002 (2)
O1	0.0775 (12)	0.0217 (8)	0.0684 (13)	0.0051 (8)	0.0560 (10)	0.0063 (8)
N1	0.0238 (8)	0.0210 (8)	0.0258 (9)	−0.0004 (6)	0.0098 (7)	−0.0004 (7)
N2	0.0379 (10)	0.0258 (9)	0.0344 (11)	0.0008 (8)	0.0236 (8)	−0.0009 (8)
N3	0.0357 (10)	0.0333 (10)	0.0374 (11)	−0.0070 (8)	0.0168 (9)	0.0024 (9)
N4	0.0313 (9)	0.0204 (8)	0.0299 (10)	0.0014 (7)	0.0198 (7)	0.0009 (7)
C1	0.0225 (9)	0.0230 (10)	0.0221 (11)	0.0007 (8)	0.0086 (8)	0.0021 (8)
C2	0.0299 (10)	0.0201 (10)	0.0274 (11)	−0.0009 (8)	0.0139 (9)	0.0005 (8)
C3	0.0221 (9)	0.0233 (10)	0.0238 (11)	0.0013 (8)	0.0085 (8)	0.0005 (8)
C4	0.0224 (10)	0.0226 (10)	0.0252 (11)	−0.0024 (7)	0.0095 (8)	0.0017 (8)
C5	0.0204 (9)	0.0200 (10)	0.0280 (11)	−0.0008 (7)	0.0063 (8)	0.0004 (8)
C6	0.0263 (10)	0.0223 (10)	0.0275 (11)	−0.0013 (8)	0.0093 (9)	0.0001 (9)
C7	0.0363 (12)	0.0281 (12)	0.0445 (14)	0.0043 (9)	0.0141 (10)	−0.0061 (10)
C8	0.0380 (11)	0.0239 (11)	0.0354 (13)	0.0009 (9)	0.0209 (10)	0.0022 (9)
C9	0.0536 (14)	0.0309 (12)	0.0516 (16)	0.0008 (11)	0.0353 (12)	0.0055 (11)

Geometric parameters (Å, º) top

Cl1—C9	1.769 (2)	N2—H2B	0.856 (11)
S1—C5	1.761 (2)	C3—C4	1.405 (3)
S1—C7	1.799 (2)	N4—H4	0.8800
O1—C8	1.219 (3)	C4—C5	1.410 (3)
N1—C1	1.346 (2)	C4—C6	1.431 (3)
N1—C5	1.324 (3)	C8—C9	1.516 (3)
N2—C3	1.353 (3)	C2—H2	0.9500
N3—C6	1.144 (3)	C7—H7A	0.9800
N4—C1	1.406 (3)	C7—H7B	0.9800
N4—C8	1.348 (3)	C7—H7C	0.9800
C1—C2	1.379 (3)	C9—H9A	0.9900
C2—C3	1.401 (3)	C9—H9B	0.9900
N2—H2A	0.85 (3)

C5—S1—C7	101.76 (10)	S1—C5—C4	118.02 (16)
C1—N1—C5	116.95 (17)	N3—C6—C4	177.0 (2)
C1—N4—C8	128.28 (17)	N4—C8—C9	113.90 (18)
N1—C1—N4	111.30 (17)	O1—C8—N4	125.0 (2)
N1—C1—C2	125.23 (19)	O1—C8—C9	121.1 (2)
N4—C1—C2	123.48 (17)	Cl1—C9—C8	109.80 (17)
C1—C2—C3	117.89 (18)	C1—C2—H2	121.00
C3—N2—H2B	118 (2)	C3—C2—H2	121.00
H2A—N2—H2B	118 (3)	S1—C7—H7A	109.00
C3—N2—H2A	122.6 (19)	S1—C7—H7B	110.00
C2—C3—C4	117.94 (18)	S1—C7—H7C	109.00
N2—C3—C4	121.91 (18)	H7A—C7—H7B	109.00
N2—C3—C2	120.15 (17)	H7A—C7—H7C	110.00
C3—C4—C5	118.85 (19)	H7B—C7—H7C	109.00
C3—C4—C6	119.57 (18)	Cl1—C9—H9A	110.00
C5—C4—C6	121.58 (18)	Cl1—C9—H9B	110.00
C1—N4—H4	116.00	C8—C9—H9A	110.00
C8—N4—H4	116.00	C8—C9—H9B	110.00
S1—C5—N1	118.85 (15)	H9A—C9—H9B	108.00
N1—C5—C4	123.13 (19)

C7—S1—C5—N1	−4.84 (19)	C1—C2—C3—N2	179.40 (19)
C7—S1—C5—C4	176.27 (17)	C1—C2—C3—C4	−0.6 (3)
C5—N1—C1—N4	178.53 (17)	N2—C3—C4—C5	−179.5 (2)
C1—N1—C5—S1	−177.61 (15)	C2—C3—C4—C6	−179.61 (19)
C1—N1—C5—C4	1.2 (3)	N2—C3—C4—C6	0.4 (3)
C5—N1—C1—C2	−1.4 (3)	C2—C3—C4—C5	0.5 (3)
C1—N4—C8—O1	0.6 (4)	C6—C4—C5—N1	179.3 (2)
C8—N4—C1—N1	−175.96 (19)	C3—C4—C5—S1	178.04 (16)
C8—N4—C1—C2	4.0 (3)	C3—C4—C5—N1	−0.8 (3)
C1—N4—C8—C9	−177.90 (19)	C6—C4—C5—S1	−1.9 (3)
N4—C1—C2—C3	−178.82 (18)	O1—C8—C9—Cl1	46.4 (3)
N1—C1—C2—C3	1.1 (3)	N4—C8—C9—Cl1	−135.06 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1	0.95	2.26	2.863 (3)	121
N2—H2B···O1ⁱ	0.856 (11)	2.132 (14)	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+1/2, z+1/2.

Acknowledgements

We thank the University of Tennessee for supporting this study.

References

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doi:10.1107/S2056989015002431

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

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

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

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