5-Acetyl-4-amino-2-benzyl­sulfanyl-6-methyl­nicotinonitrile

In the title compound, C₁₆H₁₅N₃OS, the crystal packing is stabilized by inter- and intra­molecular N—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.063
• wR factor = 0.179
• Data-to-parameter ratio = 13.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        100 Deg.
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          4
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C3     -   C4      ..       5.27 su
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C10
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C12
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C13
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C2
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C11
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.76
PLAT331_ALERT_2_C Small Average Phenyl C-C Dist.   C11    -C16           1.36 Ang.
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          7
PLAT371_ALERT_2_C Long   C(sp2)-C(sp1) Bond  C7     -   C9     ...       1.42 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       N2     -   H2A    ...          ?

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
  14 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  10 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Pyridine derivatives are important compounds in terms of pesticides and medicines (Bretschneider et al., 1999; Hirano 2000; Hui et al., 2000; Nicholas et al., 2000). We report here the molecular structure of the title compound (I).

In the title compound (I), all bond lengths and angles are within normal ranges (Allen et al., 1987) and the crystal structure are stabilized by intra and intermolecular hydrogen bonds (Table 1).

Related literature

For biological and pharmaceutical activity of pyridines, see Psnreddy et al. (1987); Hui et al. (2000). Many derivatives of pyridines have been prepared by Bretschneider et al. (1999) and Hirano (2000). For related literature, see: Allen et al. (1987); Lin et al. (2002); Nicholas & Molinskiet (2000).

S2. Experimental

2-(Amino-benzylsulfanyl-methylene)-malononitrile (1.29 g, 10 mmol) and acetylacetone (0.72 g, 12 mmol) were added to a solution of zinc nitrate (3.56 g, 20 mmol) in ethanol (15 ml) at room temperature while stirring. The mixture was then refluxed for 12 h. The precipitate was filtered and washed with water, recrystallized from ethanol to give the title compound (yield 59%). Red crystals of (I) suitable for X-ray structure analysis were grown from ethanol.

S3. Refinement

All H atoms were placed in calculated positions, with N—H = 0.86 Å and C—H distances in the range 0.93–0.97 Å, and included in the final cycles of refinement using a riding-model approximation, with U_iso(H) = 1.2–1.5U_eq(carrier atom).

Computing details

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1997); software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The structure of (I). showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. Crystal packing diagram of (I). Hydrogen bonds are shown as dashed lines.

5-Acetyl-4-amino-2-benzylsulfanyl-6-methylnicotinonitrile

Crystal data

C16H15N3OS	Z = 2
Mr = 297.37	F(000) = 312
Triclinic, P1	Dx = 1.303 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.6850 (5) Å	Cell parameters from 822 reflections
b = 9.9127 (6) Å	θ = 2.5–19.2°
c = 10.3236 (7) Å	µ = 0.22 mm^−1
α = 111.007 (1)°	T = 295 K
β = 105.027 (1)°	Block, red
γ = 101.552 (1)°	0.16 × 0.10 × 0.10 mm
V = 757.78 (8) Å^3

Data collection

Bruker SMART CCD area-detector diffractometer	2621 independent reflections
Radiation source: fine-focus sealed tube	1413 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.025
φ and ω scans	θmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −10→8
Tmin = 0.966, Tmax = 0.979	k = −11→11
5133 measured reflections	l = −12→12

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.063	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.179	H-atom parameters constrained
S = 0.99	w = 1/[σ^2(Fo^2) + (0.0923P)^2] where P = (Fo^2 + 2Fc^2)/3
2621 reflections	(Δ/σ)max < 0.001
192 parameters	Δρmax = 0.17 e Å^−3
0 restraints	Δρmin = −0.16 e Å^−3

Special details

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.26894 (14)	0.45770 (11)	0.72133 (11)	0.0998 (5)
N1	0.2088 (4)	0.4459 (3)	0.9578 (3)	0.0936 (9)
C7	0.3932 (4)	0.6858 (4)	1.0011 (4)	0.0775 (10)
C3	0.3315 (4)	0.6554 (4)	1.2065 (4)	0.0775 (10)
C2	0.3636 (5)	0.7181 (5)	1.3694 (4)	0.0868 (11)
O1	0.3731 (4)	0.8483 (3)	1.4385 (3)	0.1101 (9)
N2	0.4994 (4)	0.8984 (4)	1.2380 (4)	0.1074 (10)
H2A	0.5474	0.9533	1.2021	0.129*
H2B	0.5093	0.9384	1.3299	0.129*
C4	0.2318 (5)	0.5065 (4)	1.1043 (5)	0.0885 (12)
C6	0.4095 (4)	0.7511 (4)	1.1507 (4)	0.0794 (10)
C8	0.2931 (5)	0.5339 (4)	0.9098 (4)	0.0840 (10)
C9	0.4776 (4)	0.7725 (4)	0.9408 (4)	0.0859 (10)
C11	0.0735 (5)	0.1891 (4)	0.4854 (5)	0.0885 (11)
N3	0.5430 (4)	0.8423 (4)	0.8923 (3)	0.1136 (11)
C5	0.1246 (5)	0.3945 (4)	1.1406 (5)	0.1151 (14)
H5A	0.0286	0.3247	1.0529	0.173*
H5B	0.0870	0.4495	1.2170	0.173*
H5C	0.1903	0.3385	1.1748	0.173*
C16	0.1482 (5)	0.0911 (4)	0.4183 (5)	0.0974 (11)
H16	0.2369	0.0740	0.4760	0.117*
C14	−0.0360 (7)	0.0392 (6)	0.1803 (6)	0.1275 (17)
H14	−0.0748	−0.0139	0.0772	0.153*
C10	0.1286 (6)	0.2644 (4)	0.6516 (5)	0.1131 (13)
H10A	0.1865	0.2071	0.6935	0.136*
H10B	0.0311	0.2668	0.6805	0.136*
C13	−0.1093 (6)	0.1380 (8)	0.2438 (8)	0.150 (2)
H13	−0.1965	0.1558	0.1851	0.180*
C15	0.0931 (6)	0.0166 (5)	0.2647 (6)	0.1173 (14)
H15	0.1457	−0.0494	0.2197	0.141*
C1	0.3932 (6)	0.6203 (5)	1.4510 (4)	0.1248 (16)
H1A	0.4878	0.6791	1.5428	0.187*
H1B	0.4159	0.5332	1.3902	0.187*
H1C	0.2946	0.5864	1.4716	0.187*
C12	−0.0554 (6)	0.2116 (7)	0.3942 (7)	0.1387 (19)
H12	−0.1072	0.2797	0.4372	0.166*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.1349 (10)	0.1084 (7)	0.1140 (8)	0.0544 (6)	0.0875 (8)	0.0726 (6)
N1	0.127 (3)	0.1003 (19)	0.125 (3)	0.0618 (18)	0.091 (2)	0.0806 (19)
C7	0.089 (2)	0.109 (3)	0.094 (3)	0.052 (2)	0.059 (2)	0.079 (2)
C3	0.096 (3)	0.103 (3)	0.103 (3)	0.063 (2)	0.067 (2)	0.081 (2)
C2	0.095 (3)	0.143 (3)	0.108 (3)	0.075 (2)	0.074 (2)	0.099 (3)
O1	0.153 (3)	0.129 (2)	0.109 (2)	0.071 (2)	0.0761 (19)	0.0827 (18)
N2	0.136 (3)	0.132 (3)	0.093 (2)	0.036 (2)	0.059 (2)	0.083 (2)
C4	0.121 (3)	0.112 (3)	0.125 (3)	0.080 (3)	0.094 (3)	0.095 (3)
C6	0.089 (3)	0.104 (3)	0.099 (3)	0.048 (2)	0.055 (2)	0.079 (2)
C8	0.103 (3)	0.110 (3)	0.109 (3)	0.065 (2)	0.075 (2)	0.079 (2)
C9	0.094 (3)	0.112 (2)	0.087 (2)	0.035 (2)	0.046 (2)	0.071 (2)
C11	0.090 (3)	0.113 (3)	0.115 (3)	0.045 (2)	0.063 (3)	0.080 (3)
N3	0.125 (3)	0.144 (3)	0.103 (2)	0.024 (2)	0.056 (2)	0.086 (2)
C5	0.155 (4)	0.122 (3)	0.146 (4)	0.062 (3)	0.108 (3)	0.096 (3)
C16	0.089 (3)	0.105 (3)	0.106 (3)	0.041 (2)	0.032 (3)	0.052 (3)
C14	0.092 (4)	0.168 (5)	0.118 (4)	−0.010 (3)	0.024 (3)	0.093 (4)
C10	0.156 (4)	0.107 (3)	0.128 (3)	0.052 (3)	0.089 (3)	0.075 (3)
C13	0.088 (4)	0.253 (7)	0.185 (6)	0.062 (4)	0.056 (4)	0.169 (6)
C15	0.114 (4)	0.126 (3)	0.112 (4)	0.033 (3)	0.049 (3)	0.049 (3)
C1	0.175 (4)	0.189 (4)	0.137 (3)	0.123 (4)	0.107 (3)	0.137 (3)
C12	0.124 (4)	0.224 (5)	0.191 (5)	0.112 (4)	0.109 (4)	0.155 (5)

Geometric parameters (Å, º)

S1—C8	1.752 (4)	C11—C10	1.497 (5)
S1—C10	1.815 (4)	C5—H5A	0.9600
N1—C8	1.336 (4)	C5—H5B	0.9600
N1—C4	1.353 (4)	C5—H5C	0.9600
C7—C8	1.395 (5)	C16—C15	1.383 (5)
C7—C6	1.399 (4)	C16—H16	0.9300
C7—C9	1.425 (4)	C14—C15	1.341 (6)
C3—C4	1.393 (5)	C14—C13	1.342 (7)
C3—C6	1.423 (4)	C14—H14	0.9300
C3—C2	1.494 (5)	C10—H10A	0.9700
C2—O1	1.203 (4)	C10—H10B	0.9700
C2—C1	1.512 (4)	C13—C12	1.355 (7)
N2—C6	1.338 (4)	C13—H13	0.9300
N2—H2A	0.8600	C15—H15	0.9300
N2—H2B	0.8600	C1—H1A	0.9600
C4—C5	1.519 (4)	C1—H1B	0.9600
C9—N3	1.136 (4)	C1—H1C	0.9600
C11—C16	1.359 (5)	C12—H12	0.9300
C11—C12	1.376 (6)
C8—S1—C10	101.86 (18)	C4—C5—H5C	109.5
C8—N1—C4	117.3 (3)	H5A—C5—H5C	109.5
C8—C7—C6	119.5 (3)	H5B—C5—H5C	109.5
C8—C7—C9	119.5 (3)	C11—C16—C15	120.4 (4)
C6—C7—C9	120.9 (3)	C11—C16—H16	119.8
C4—C3—C6	117.1 (3)	C15—C16—H16	119.8
C4—C3—C2	124.0 (3)	C15—C14—C13	120.4 (5)
C6—C3—C2	118.8 (4)	C15—C14—H14	119.8
O1—C2—C3	120.7 (3)	C13—C14—H14	119.8
O1—C2—C1	119.2 (3)	C11—C10—S1	108.9 (2)
C3—C2—C1	120.1 (4)	C11—C10—H10A	109.9
C6—N2—H2A	120.0	S1—C10—H10A	109.9
C6—N2—H2B	120.0	C11—C10—H10B	109.9
H2A—N2—H2B	120.0	S1—C10—H10B	109.9
N1—C4—C3	124.6 (3)	H10A—C10—H10B	108.3
N1—C4—C5	111.0 (4)	C14—C13—C12	119.5 (5)
C3—C4—C5	124.2 (3)	C14—C13—H13	120.3
N2—C6—C7	120.1 (3)	C12—C13—H13	120.3
N2—C6—C3	121.8 (3)	C14—C15—C16	120.3 (5)
C7—C6—C3	118.1 (4)	C14—C15—H15	119.8
N1—C8—C7	123.0 (3)	C16—C15—H15	119.8
N1—C8—S1	118.5 (3)	C2—C1—H1A	109.5
C7—C8—S1	118.4 (2)	C2—C1—H1B	109.5
N3—C9—C7	179.0 (4)	H1A—C1—H1B	109.5
C16—C11—C12	117.1 (4)	C2—C1—H1C	109.5
C16—C11—C10	120.3 (4)	H1A—C1—H1C	109.5
C12—C11—C10	122.6 (4)	H1B—C1—H1C	109.5
C4—C5—H5A	109.5	C13—C12—C11	122.2 (5)
C4—C5—H5B	109.5	C13—C12—H12	118.9
H5A—C5—H5B	109.5	C11—C12—H12	118.9
C4—C3—C2—O1	−143.0 (4)	C4—N1—C8—S1	178.9 (2)
C6—C3—C2—O1	38.4 (5)	C6—C7—C8—N1	0.8 (5)
C4—C3—C2—C1	40.0 (5)	C9—C7—C8—N1	−179.3 (3)
C6—C3—C2—C1	−138.5 (3)	C6—C7—C8—S1	177.6 (2)
C8—N1—C4—C3	2.7 (5)	C9—C7—C8—S1	−2.4 (4)
C8—N1—C4—C5	178.6 (3)	C10—S1—C8—N1	−1.9 (3)
C6—C3—C4—N1	2.2 (5)	C10—S1—C8—C7	−178.9 (3)
C2—C3—C4—N1	−176.4 (3)	C12—C11—C16—C15	−1.0 (6)
C6—C3—C4—C5	−173.2 (3)	C10—C11—C16—C15	177.4 (4)
C2—C3—C4—C5	8.3 (5)	C16—C11—C10—S1	100.1 (3)
C8—C7—C6—N2	−177.3 (3)	C12—C11—C10—S1	−81.6 (4)
C9—C7—C6—N2	2.8 (5)	C8—S1—C10—C11	171.6 (3)
C8—C7—C6—C3	4.2 (5)	C15—C14—C13—C12	−1.9 (8)
C9—C7—C6—C3	−175.7 (3)	C13—C14—C15—C16	2.2 (7)
C4—C3—C6—N2	176.0 (3)	C11—C16—C15—C14	−0.7 (6)
C2—C3—C6—N2	−5.4 (5)	C14—C13—C12—C11	0.2 (8)
C4—C3—C6—C7	−5.5 (4)	C16—C11—C12—C13	1.2 (7)
C2—C3—C6—C7	173.1 (3)	C10—C11—C12—C13	−177.1 (4)
C4—N1—C8—C7	−4.2 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2B···O1	0.86	2.11	2.726 (3)	129
N2—H2B···O1^i	0.86	2.34	3.105 (5)	148

Symmetry code: (i) −x+1, −y+2, −z+3.