Crystal structure of N-[4-amino-5-cyano-6-(methyl-sulfan-yl)pyridin-2-yl]acetamide hemihydrate.

The title compound, C9H10N4OS·0.5H2O, crystallizes with two independent mol-ecules (A and B) in the asymmetric unit, together with a water mol-ecule of crystallization. The acetamide moiety, which has an extended conformation, is inclined to the pyridine ring by 7.95 (16)° in mol-ecule A and by 1.77 (16)° in mol-ecule B. In the crystal, the A and B mol-ecules are linked by two N-H⋯Ocarbon-yl hydrogen bonds, forming a dimer. The dimers are linked via N-H⋯N hydrogen bonds, forming ribbons that are linked by N-H⋯Owater hydrogen bonds to form sheets parallel to (110). The sheets are linked by O-H⋯N hydrogen bonds, forming slabs, and between the slabs there are weak slipped parallel π-π inter-actions [inter-centroid distance = 3.734 (2) Å, inter-planar distance = 3.3505 (11) Å and slippage = 1.648 Å], forming a three-dimensional structure.

Related literature

For various applications of polyfunctional pyridines, see: Knyazhanskii et al. (1996 ▸); Kurfurst et al. (1989 ▸); Enyedy et al. (2003 ▸); Arora & Knaus (1999 ▸); Kim et al. 2004 ▸); Pillai et al. (2003 ▸).

Experimental

Crystal data

C9H10N4OS·0.5H2O

M = 231.28

Triclinic,

a = 8.229 (3) Å

b = 10.181 (4) Å

c = 13.198 (5) Å

α = 84.221 (10)°

β = 80.036 (10)°

γ = 82.136 (11)°

V = 1075.4 (7) Å3

Z = 4

Mo Kα radiation

μ = 0.29 mm−1

T = 200 K

0.40 × 0.40 × 0.40 mm

Data collection

Bruker SMART X2S benchtop diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T min = 0.813, T max = 1.000

19554 measured reflections

3775 independent reflections

2517 reflections with I > 2σ(I)

R int = 0.066

Refinement

R[F 2 > 2σ(F 2)] = 0.052

wR(F 2) = 0.150

S = 1.03

3775 reflections

305 parameters

9 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.63 e Å−3

Δρmin = −0.31 e Å−3

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: PLATON (Spek, 2009 ▸); software used to prepare material for publication: SHELXL2014 and PLATON.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S205698901500256X/su5077sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901500256X/su5077Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S205698901500256X/su5077Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S205698901500256X/su5077fig1.tif

Mol­ecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The N—H⋯O hydrogen bonds are shown as dashed lines (see Table 1 for details).

Click here for additional data file.

c . DOI: 10.1107/S205698901500256X/su5077fig2.tif

View along the c axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have been omitted for clarity).

CCDC reference: 1048267

Additional supporting information: crystallographic information; 3D view; checkCIF report

C9H10N4OS·0.5H2O	Z = 4
Mr = 231.28	F(000) = 484
Triclinic, P1	Dx = 1.428 Mg m−3
a = 8.229 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 10.181 (4) Å	Cell parameters from 4579 reflections
c = 13.198 (5) Å	θ = 2.5–25.1°
α = 84.221 (10)°	µ = 0.29 mm−1
β = 80.036 (10)°	T = 200 K
γ = 82.136 (11)°	Block, yellow
V = 1075.4 (7) Å3	0.40 × 0.40 × 0.40 mm

Bruker SMART X2S benchtop diffractometer	3775 independent reflections
Radiation source: XOS X-beam microfocus source	2517 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromator	Rint = 0.066
ω scans	θmax = 25.2°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −9→9
Tmin = 0.813, Tmax = 1.000	k = −12→12
19554 measured reflections	l = −15→15

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052	Hydrogen site location: mixed
wR(F2) = 0.150	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ2(Fo2) + (0.0859P)2 + 0.1759P] where P = (Fo2 + 2Fc2)/3
3775 reflections	(Δ/σ)max = 0.001
305 parameters	Δρmax = 0.63 e Å−3
9 restraints	Δρmin = −0.31 e Å−3

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

	x	y	z	Uiso*/Ueq	Occ. (<1)
S1	0.84898 (9)	−0.09268 (8)	−0.11814 (5)	0.0324 (2)
O1	0.3621 (3)	0.3985 (2)	0.14350 (16)	0.0444 (6)
N1	0.6422 (3)	0.1137 (2)	−0.04595 (17)	0.0243 (5)
N2	0.4586 (3)	0.2943 (2)	−0.00302 (17)	0.0263 (6)
H2N	0.4539	0.3015	−0.0695	0.032*
N3	0.7191 (3)	0.0201 (3)	0.25778 (18)	0.0369 (7)
H3AN	0.6676	0.0723	0.3056	0.044*
H3BN	0.7858	−0.0510	0.2744	0.044*
N4	0.9584 (4)	−0.2438 (3)	0.1290 (2)	0.0453 (7)
C1	0.5671 (3)	0.1876 (3)	0.0309 (2)	0.0234 (6)
C2	0.5899 (3)	0.1621 (3)	0.1320 (2)	0.0267 (7)
H2	0.5348	0.2200	0.1827	0.032*
C3	0.6957 (3)	0.0492 (3)	0.1588 (2)	0.0263 (7)
C4	0.7727 (3)	−0.0312 (3)	0.0799 (2)	0.0224 (6)
C5	0.7434 (3)	0.0062 (3)	−0.0213 (2)	0.0229 (6)
C6	0.7793 (4)	−0.0068 (3)	−0.2309 (2)	0.0440 (9)
H6A	0.8123	0.0831	−0.2403	0.066*
H6B	0.6579	−0.0013	−0.2227	0.066*
H6C	0.8295	−0.0553	−0.2914	0.066*
C7	0.3596 (3)	0.3882 (3)	0.0525 (2)	0.0286 (7)
C8	0.2446 (4)	0.4802 (3)	−0.0064 (2)	0.0359 (8)
H8A	0.1873	0.5507	0.0368	0.054*
H8B	0.1626	0.4302	−0.0258	0.054*
H8C	0.3088	0.5199	−0.0688	0.054*
C9	0.8785 (4)	−0.1495 (3)	0.1042 (2)	0.0290 (7)
S2	0.05057 (10)	0.70420 (8)	0.65341 (6)	0.0356 (3)
O2	0.5272 (3)	0.2080 (2)	0.39329 (15)	0.0378 (5)
N5	0.2537 (3)	0.4955 (2)	0.58226 (16)	0.0215 (5)
N6	0.4339 (3)	0.3125 (2)	0.53944 (17)	0.0255 (5)
H6N	0.4420	0.3077	0.6053	0.031*
N7	0.1738 (3)	0.5867 (3)	0.27873 (18)	0.0362 (7)
H7AN	0.1079	0.6583	0.2620	0.043*
H7BN	0.2260	0.5349	0.2308	0.043*
N8	−0.0881 (3)	0.8386 (3)	0.4093 (2)	0.0424 (7)
C10	0.3278 (3)	0.4203 (3)	0.5052 (2)	0.0236 (6)
C11	0.3036 (3)	0.4451 (3)	0.4037 (2)	0.0256 (6)
H11	0.3597	0.3881	0.3526	0.031*
C12	0.1947 (3)	0.5562 (3)	0.3782 (2)	0.0240 (6)
C13	0.1145 (3)	0.6354 (3)	0.4567 (2)	0.0251 (7)
C14	0.1495 (3)	0.6013 (3)	0.5577 (2)	0.0251 (6)
C15	0.1416 (4)	0.6296 (3)	0.7623 (2)	0.0427 (9)
H15C	0.0914	0.6770	0.8233	0.064*
H15B	0.2615	0.6348	0.7486	0.064*
H15A	0.1216	0.5362	0.7747	0.064*
C16	0.5260 (3)	0.2144 (3)	0.4854 (2)	0.0262 (7)
C17	0.6252 (4)	0.1123 (3)	0.5476 (2)	0.0337 (7)
H17A	0.5529	0.0487	0.5854	0.051*
H17B	0.6719	0.1564	0.5967	0.051*
H17C	0.7157	0.0652	0.5014	0.051*
C18	0.0001 (4)	0.7485 (3)	0.4338 (2)	0.0298 (7)
O3A	0.4983 (13)	0.2878 (10)	−0.2316 (7)	0.066 (3)	0.5
H3A1	0.541 (6)	0.223 (3)	−0.2637 (16)	0.099*	0.5
H3A2	0.555 (10)	0.352 (5)	−0.254 (6)	0.099*	0.5
O3B	0.4470 (11)	0.3490 (9)	−0.2356 (7)	0.052 (2)	0.5
H3B1	0.383 (8)	0.416 (5)	−0.255 (7)	0.077*	0.5
H3B2	0.386 (8)	0.289 (6)	−0.214 (2)	0.077*	0.5

	U11	U22	U33	U12	U13	U23
S1	0.0361 (5)	0.0342 (5)	0.0234 (4)	0.0139 (4)	−0.0053 (3)	−0.0092 (3)
O1	0.0625 (15)	0.0445 (15)	0.0215 (12)	0.0279 (12)	−0.0163 (10)	−0.0105 (10)
N1	0.0268 (12)	0.0269 (14)	0.0176 (12)	0.0047 (11)	−0.0036 (10)	−0.0051 (10)
N2	0.0342 (13)	0.0255 (14)	0.0165 (12)	0.0124 (11)	−0.0094 (10)	−0.0014 (10)
N3	0.0503 (16)	0.0343 (16)	0.0206 (13)	0.0244 (13)	−0.0121 (11)	−0.0046 (11)
N4	0.0523 (17)	0.0385 (18)	0.0426 (17)	0.0174 (15)	−0.0188 (14)	−0.0031 (14)
C1	0.0246 (14)	0.0214 (15)	0.0222 (14)	0.0048 (12)	−0.0043 (11)	−0.0014 (12)
C2	0.0325 (15)	0.0264 (17)	0.0194 (14)	0.0093 (13)	−0.0059 (12)	−0.0069 (12)
C3	0.0306 (15)	0.0257 (17)	0.0226 (15)	0.0035 (13)	−0.0098 (12)	−0.0014 (12)
C4	0.0235 (14)	0.0223 (15)	0.0199 (14)	0.0059 (12)	−0.0051 (11)	−0.0040 (11)
C5	0.0217 (14)	0.0245 (16)	0.0226 (15)	0.0017 (12)	−0.0060 (11)	−0.0042 (12)
C6	0.054 (2)	0.049 (2)	0.0224 (16)	0.0151 (17)	−0.0047 (15)	−0.0050 (15)
C7	0.0321 (16)	0.0274 (17)	0.0244 (16)	0.0072 (13)	−0.0079 (13)	−0.0014 (13)
C8	0.0411 (18)	0.0340 (19)	0.0298 (17)	0.0164 (15)	−0.0111 (14)	−0.0085 (14)
C9	0.0347 (16)	0.0286 (18)	0.0233 (15)	0.0044 (15)	−0.0085 (13)	−0.0046 (13)
S2	0.0450 (5)	0.0339 (5)	0.0249 (4)	0.0171 (4)	−0.0098 (3)	−0.0110 (3)
O2	0.0507 (13)	0.0362 (13)	0.0234 (11)	0.0194 (10)	−0.0134 (10)	−0.0081 (9)
N5	0.0245 (12)	0.0211 (13)	0.0185 (12)	0.0055 (10)	−0.0059 (9)	−0.0061 (10)
N6	0.0319 (13)	0.0292 (14)	0.0139 (11)	0.0102 (11)	−0.0090 (10)	−0.0042 (10)
N7	0.0516 (16)	0.0314 (15)	0.0213 (13)	0.0178 (13)	−0.0114 (12)	−0.0028 (11)
N8	0.0465 (16)	0.0372 (17)	0.0392 (16)	0.0147 (14)	−0.0137 (13)	0.0030 (13)
C10	0.0263 (15)	0.0249 (16)	0.0189 (14)	0.0021 (13)	−0.0042 (11)	−0.0042 (12)
C11	0.0324 (15)	0.0262 (16)	0.0174 (14)	0.0078 (13)	−0.0071 (12)	−0.0072 (12)
C12	0.0286 (15)	0.0252 (16)	0.0184 (14)	0.0013 (13)	−0.0078 (11)	−0.0016 (12)
C13	0.0284 (15)	0.0213 (16)	0.0241 (15)	0.0080 (13)	−0.0084 (12)	−0.0030 (12)
C14	0.0279 (15)	0.0246 (16)	0.0222 (15)	0.0042 (13)	−0.0072 (12)	−0.0041 (12)
C15	0.056 (2)	0.046 (2)	0.0249 (16)	0.0141 (17)	−0.0152 (15)	−0.0120 (15)
C16	0.0281 (15)	0.0284 (17)	0.0219 (15)	0.0018 (13)	−0.0066 (12)	−0.0028 (13)
C17	0.0413 (18)	0.0279 (17)	0.0300 (17)	0.0108 (14)	−0.0107 (14)	−0.0044 (13)
C18	0.0358 (17)	0.0283 (18)	0.0238 (15)	0.0029 (15)	−0.0052 (13)	−0.0039 (13)
O3A	0.077 (7)	0.086 (8)	0.031 (3)	−0.003 (5)	0.002 (4)	−0.017 (5)
O3B	0.050 (5)	0.072 (6)	0.029 (3)	0.004 (4)	−0.006 (3)	−0.005 (4)

S1—C5	1.743 (3)	O2—C16	1.222 (3)
S1—C6	1.790 (3)	N5—C14	1.332 (3)
O1—C7	1.219 (3)	N5—C10	1.345 (3)
N1—C5	1.330 (4)	N6—C16	1.353 (3)
N1—C1	1.336 (4)	N6—C10	1.394 (3)
N2—C7	1.356 (4)	N6—H6N	0.8800
N2—C1	1.398 (3)	N7—C12	1.353 (3)
N2—H2N	0.8800	N7—H7AN	0.8800
N3—C3	1.350 (3)	N7—H7BN	0.8800
N3—H3AN	0.8800	N8—C18	1.145 (4)
N3—H3BN	0.8800	C10—C11	1.381 (4)
N4—C9	1.140 (4)	C11—C12	1.395 (4)
C1—C2	1.374 (4)	C11—H11	0.9500
C2—C3	1.399 (4)	C12—C13	1.395 (4)
C2—H2	0.9500	C13—C14	1.411 (4)
C3—C4	1.399 (4)	C13—C18	1.427 (4)
C4—C5	1.403 (4)	C15—H15C	0.9800
C4—C9	1.430 (4)	C15—H15B	0.9800
C6—H6A	0.9800	C15—H15A	0.9800
C6—H6B	0.9800	C16—C17	1.500 (4)
C6—H6C	0.9800	C17—H17A	0.9800
C7—C8	1.497 (4)	C17—H17B	0.9800
C8—H8A	0.9800	C17—H17C	0.9800
C8—H8B	0.9800	O3A—H3A1	0.823 (18)
C8—H8C	0.9800	O3A—H3A2	0.85 (2)
S2—C14	1.742 (3)	O3B—H3B1	0.85 (2)
S2—C15	1.789 (3)	O3B—H3B2	0.84 (2)
C5—S1—C6	102.00 (14)	C14—N5—C10	116.8 (2)
C5—N1—C1	116.9 (2)	C16—N6—C10	129.0 (2)
C7—N2—C1	128.8 (2)	C16—N6—H6N	115.5
C7—N2—H2N	115.6	C10—N6—H6N	115.5
C1—N2—H2N	115.6	C12—N7—H7AN	120.0
C3—N3—H3AN	120.0	C12—N7—H7BN	120.0
C3—N3—H3BN	120.0	H7AN—N7—H7BN	120.0
H3AN—N3—H3BN	120.0	N5—C10—C11	124.8 (3)
N1—C1—C2	124.8 (3)	N5—C10—N6	111.9 (2)
N1—C1—N2	112.0 (2)	C11—C10—N6	123.2 (2)
C2—C1—N2	123.2 (3)	C10—C11—C12	118.2 (2)
C1—C2—C3	118.7 (3)	C10—C11—H11	120.9
C1—C2—H2	120.6	C12—C11—H11	120.9
C3—C2—H2	120.6	N7—C12—C13	122.0 (3)
N3—C3—C2	120.2 (3)	N7—C12—C11	119.7 (3)
N3—C3—C4	122.4 (3)	C13—C12—C11	118.3 (2)
C2—C3—C4	117.3 (2)	C12—C13—C14	118.7 (2)
C3—C4—C5	119.1 (2)	C12—C13—C18	119.8 (2)
C3—C4—C9	119.3 (2)	C14—C13—C18	121.5 (2)
C5—C4—C9	121.6 (2)	N5—C14—C13	123.2 (2)
N1—C5—C4	123.1 (2)	N5—C14—S2	119.3 (2)
N1—C5—S1	119.3 (2)	C13—C14—S2	117.6 (2)
C4—C5—S1	117.6 (2)	S2—C15—H15C	109.5
S1—C6—H6A	109.5	S2—C15—H15B	109.5
S1—C6—H6B	109.5	H15C—C15—H15B	109.5
H6A—C6—H6B	109.5	S2—C15—H15A	109.5
S1—C6—H6C	109.5	H15C—C15—H15A	109.5
H6A—C6—H6C	109.5	H15B—C15—H15A	109.5
H6B—C6—H6C	109.5	O2—C16—N6	122.9 (2)
O1—C7—N2	123.4 (2)	O2—C16—C17	122.4 (3)
O1—C7—C8	121.8 (3)	N6—C16—C17	114.8 (2)
N2—C7—C8	114.8 (2)	C16—C17—H17A	109.5
C7—C8—H8A	109.5	C16—C17—H17B	109.5
C7—C8—H8B	109.5	H17A—C17—H17B	109.5
H8A—C8—H8B	109.5	C16—C17—H17C	109.5
C7—C8—H8C	109.5	H17A—C17—H17C	109.5
H8A—C8—H8C	109.5	H17B—C17—H17C	109.5
H8B—C8—H8C	109.5	N8—C18—C13	176.0 (3)
N4—C9—C4	176.3 (3)	H3A1—O3A—H3A2	108 (3)
C14—S2—C15	101.47 (14)	H3B1—O3B—H3B2	106 (3)
C5—N1—C1—C2	1.5 (4)	C14—N5—C10—C11	0.1 (4)
C5—N1—C1—N2	−177.4 (2)	C14—N5—C10—N6	−180.0 (2)
C7—N2—C1—N1	178.7 (3)	C16—N6—C10—N5	178.3 (3)
C7—N2—C1—C2	−0.2 (5)	C16—N6—C10—C11	−1.7 (4)
N1—C1—C2—C3	−1.7 (4)	N5—C10—C11—C12	0.0 (4)
N2—C1—C2—C3	177.1 (3)	N6—C10—C11—C12	−179.9 (2)
C1—C2—C3—N3	−179.1 (3)	C10—C11—C12—N7	177.1 (3)
C1—C2—C3—C4	0.1 (4)	C10—C11—C12—C13	−0.8 (4)
N3—C3—C4—C5	−179.5 (3)	N7—C12—C13—C14	−176.5 (3)
C2—C3—C4—C5	1.4 (4)	C11—C12—C13—C14	1.3 (4)
N3—C3—C4—C9	0.8 (4)	N7—C12—C13—C18	3.2 (4)
C2—C3—C4—C9	−178.4 (2)	C11—C12—C13—C18	−179.0 (3)
C1—N1—C5—C4	0.1 (4)	C10—N5—C14—C13	0.5 (4)
C1—N1—C5—S1	−178.62 (19)	C10—N5—C14—S2	−179.4 (2)
C3—C4—C5—N1	−1.6 (4)	C12—C13—C14—N5	−1.2 (4)
C9—C4—C5—N1	178.2 (3)	C18—C13—C14—N5	179.1 (3)
C3—C4—C5—S1	177.2 (2)	C12—C13—C14—S2	178.7 (2)
C9—C4—C5—S1	−3.1 (4)	C18—C13—C14—S2	−1.1 (4)
C6—S1—C5—N1	0.3 (3)	C15—S2—C14—N5	3.4 (3)
C6—S1—C5—C4	−178.5 (2)	C15—S2—C14—C13	−176.4 (2)
C1—N2—C7—O1	6.3 (5)	C10—N6—C16—O2	0.0 (5)
C1—N2—C7—C8	−173.6 (3)	C10—N6—C16—C17	−179.2 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3AN···O2	0.88	2.00	2.870 (3)	169
N7—H7BN···O1	0.88	1.99	2.860 (3)	170
N3—H3BN···N8i	0.88	2.33	3.080 (4)	143
N7—H7AN···N4ii	0.88	2.38	3.116 (4)	142
N2—H2N···O3A	0.88	2.12	2.984 (10)	166
N2—H2N···O3B	0.88	2.21	3.079 (9)	172
N6—H6N···O3Aiii	0.88	2.26	3.138 (10)	173
N6—H6N···O3Biii	0.88	2.19	3.051 (9)	166
O3A—H3A2···N7iv	0.85 (2)	2.36 (6)	3.083 (12)	143 (9)
O3B—H3B1···N5v	0.85 (2)	2.57 (6)	3.239 (8)	137 (8)

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N3H3ANO2	0.88	2.00	2.870(3)	169
N7H7BNO1	0.88	1.99	2.860(3)	170
N3H3BNN8i	0.88	2.33	3.080(4)	143
N7H7ANN4ii	0.88	2.38	3.116(4)	142
N2H2NO3A	0.88	2.12	2.984(10)	166
N2H2NO3B	0.88	2.21	3.079(9)	172
N6H6NO3A iii	0.88	2.26	3.138(10)	173
N6H6NO3B iii	0.88	2.19	3.051(9)	166
O3AH3A2N7iv	0.85(2)	2.36(6)	3.083(12)	143(9)
O3BH3B1N5v	0.85(2)	2.57(6)	3.239(8)	137(8)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .