Literature DB >> 25309209

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

Joel T Mague1, Shaaban K Mohamed2, Mehmet Akkurt3, Bahgat R M Hussein4, Mustafa R Albayati5.   

Abstract

In the title mol-ecule, C15H20N4OS2, the acetamido fragment is nearly coplanar with the pyridyl ring [C-N-C-C torsion angle = -4.1 (2)°], while the cyclo-hexyl-sulfanyl portion protrudes from this plane [N-C-C-S torsion angle = -40.8 (6)°]. In the crystal, alternating pairwise N-H⋯O and N-H⋯N hydrogen bonds across inversion centres form chains along [101], which are associated into stepped layers via offset π-π stacking between pyridyl rings [centroid-centroid distance = 3.566 (1) Å]. The cyclo-hexyl group and the two atoms of the S-C bond attached to it are disordered over two sets of sites with site-occupancy factors of 0.8845 (18) and 0.1155 (18).

Entities:  

Keywords:  acetamido; crystal structure; cyclo­hexyl­sulfan­yl; hydrogen bonds; π–π stacking

Year:  2014        PMID: 25309209      PMCID: PMC4186101          DOI: 10.1107/S1600536814018534

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the diverse biological properties of pyridine-containing compounds see: Patrick & Kinsman (1996 ▶); Hishmat et al. (1990 ▶); Paronikyan et al. (2002 ▶); Bernardino et al. (2007 ▶); Doshi et al. (1999 ▶); Jemmezi et al. (2014 ▶); Mamolo et al. (2004 ▶); Bhatt et al. (2001 ▶). For the structure of a related compound, see: Akkurt et al. (2014 ▶).

Experimental

Crystal data

C15H20N4OS2 M = 336.47 Monoclinic, a = 7.2269 (8) Å b = 24.655 (3) Å c = 9.6933 (11) Å β = 92.5330 (17)° V = 1725.5 (3) Å3 Z = 4 Mo Kα radiation μ = 0.32 mm−1 T = 150 K 0.23 × 0.18 × 0.08 mm

Data collection

Bruker SMART APEX CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2013 ▶) T min = 0.93, T max = 0.97 31462 measured reflections 4538 independent reflections 3713 reflections with I > 2σ(I) R int = 0.047

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.106 S = 1.02 4538 reflections 225 parameters 68 restraints H-atom parameters constrained Δρmax = 0.36 e Å−3 Δρmin = −0.26 e Å−3

Data collection: APEX2 (Bruker, 2013 ▶); cell refinement: SAINT (Bruker, 2013 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814018534/bh2502sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814018534/bh2502Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814018534/bh2502Isup3.cml Click here for additional data file. . DOI: 10.1107/S1600536814018534/bh2502fig1.tif The title mol­ecule showing displacement ellipsoids at the 50% probability level. Only the major component of the disorder is shown. Click here for additional data file. . DOI: 10.1107/S1600536814018534/bh2502fig2.tif Perspective view of a portion of the hydrogen-bonded chain. Click here for additional data file. c . DOI: 10.1107/S1600536814018534/bh2502fig3.tif Packing viewed down the c axis, showing the pairwise N—H⋯O hydrogen bonding and the offset π-stacking inter­actions as dashed lines. CCDC reference: 1019463 Additional supporting information: crystallographic information; 3D view; checkCIF report
C15H20N4OS2Dx = 1.295 Mg m3
Mr = 336.47Melting point: 463 K
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.2269 (8) ÅCell parameters from 9975 reflections
b = 24.655 (3) Åθ = 2.3–29.0°
c = 9.6933 (11) ŵ = 0.32 mm1
β = 92.5330 (17)°T = 150 K
V = 1725.5 (3) Å3Plate, colourless
Z = 40.23 × 0.18 × 0.08 mm
F(000) = 712
Bruker SMART APEX CCD diffractometer4538 independent reflections
Radiation source: fine-focus sealed tube3713 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
Detector resolution: 8.3660 pixels mm-1θmax = 29.0°, θmin = 2.3°
φ and ω scansh = −9→9
Absorption correction: multi-scan (SADABS; Bruker, 2013)k = −33→33
Tmin = 0.93, Tmax = 0.97l = −13→13
31462 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: mixed
wR(F2) = 0.106H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0492P)2 + 0.7171P] where P = (Fo2 + 2Fc2)/3
4538 reflections(Δ/σ)max = 0.006
225 parametersΔρmax = 0.36 e Å3
68 restraintsΔρmin = −0.26 e Å3
0 constraints
Experimental. The diffraction data were obtained from 3 sets of 400 frames, each of width 0.5° in ω, collected at φ = 0.00, 90.00 and 180.00° and 2 sets of 800 frames, each of width 0.45° in φ, collected at ω = -30.00 and 210.00°. The scan time was 40 sec/frame.
xyzUiso*/UeqOcc. (<1)
S10.12721 (5)0.61034 (2)0.34743 (4)0.03110 (11)
O10.91811 (16)0.53918 (5)0.71493 (12)0.0356 (3)
N10.3292 (2)0.54925 (6)0.04030 (14)0.0378 (3)
N20.41788 (16)0.59429 (5)0.52327 (12)0.0235 (2)
N30.72278 (17)0.50958 (5)0.23714 (13)0.0287 (3)
H3A0.67730.49940.15200.034*
H3B0.83630.49400.25140.034*
N40.64424 (17)0.58430 (5)0.69315 (12)0.0264 (3)
H4A0.56800.60650.73970.032*
C10.35074 (19)0.58641 (5)0.39522 (15)0.0227 (3)
C20.44875 (19)0.55937 (5)0.29318 (14)0.0218 (3)
C30.62544 (18)0.53707 (5)0.32894 (14)0.0222 (3)
C40.69559 (19)0.54512 (6)0.46531 (14)0.0237 (3)
H40.81370.53140.49480.028*
C50.58845 (19)0.57337 (6)0.55479 (14)0.0226 (3)
C60.37713 (19)0.55438 (6)0.15424 (15)0.0258 (3)
C70.0634 (2)0.64195 (7)0.50548 (17)0.0332 (3)
H7A0.07920.61600.58170.050*
H7B−0.06640.65350.49680.050*
H7C0.14250.67360.52420.050*
C80.8003 (2)0.56755 (6)0.76461 (15)0.0258 (3)
S20.74307 (10)0.65352 (3)0.94799 (6)0.03506 (15)0.8845 (18)
C90.8162 (10)0.5850 (2)0.9147 (11)0.0327 (9)0.8845 (18)
H9A0.94700.58110.94810.039*0.8845 (18)
H9B0.74130.56000.96930.039*0.8845 (18)
C100.9173 (2)0.69109 (7)0.85620 (18)0.0303 (4)0.8845 (18)
H100.93780.67170.76750.036*0.8845 (18)
C110.8422 (3)0.74748 (9)0.8213 (3)0.0504 (6)0.8845 (18)
H11A0.81430.76670.90750.061*0.8845 (18)
H11B0.72550.74410.76450.061*0.8845 (18)
C120.9827 (4)0.78041 (10)0.7421 (3)0.0535 (6)0.8845 (18)
H12A1.00400.76250.65270.064*0.8845 (18)
H12B0.93230.81710.72250.064*0.8845 (18)
C131.1633 (4)0.78515 (11)0.8244 (3)0.0600 (7)0.8845 (18)
H13A1.14370.80530.91100.072*0.8845 (18)
H13B1.25320.80570.77070.072*0.8845 (18)
C141.2412 (3)0.72892 (12)0.8587 (3)0.0629 (7)0.8845 (18)
H14A1.35740.73270.91590.075*0.8845 (18)
H14B1.27080.71020.77210.075*0.8845 (18)
C151.1027 (3)0.69463 (11)0.9368 (3)0.0555 (6)0.8845 (18)
H15A1.15340.65770.95170.067*0.8845 (18)
H15B1.08420.71111.02840.067*0.8845 (18)
S2A0.6907 (8)0.6447 (2)0.9744 (5)0.03506 (15)0.1155 (18)
C9A0.833 (9)0.589 (2)0.918 (9)0.0327 (9)0.1155 (18)
H9A10.96380.60070.93020.039*0.1155 (18)
H9A20.81510.55840.98170.039*0.1155 (18)
C10A0.8290 (17)0.7034 (5)0.9292 (12)0.0303 (4)0.1155 (18)
H10A0.75260.73520.95600.036*0.1155 (18)
C11A0.854 (3)0.7113 (6)0.7781 (15)0.0504 (6)0.1155 (18)
H11C0.73170.71200.72830.061*0.1155 (18)
H11D0.92590.68060.74200.061*0.1155 (18)
C12A0.955 (3)0.7639 (8)0.753 (3)0.0535 (6)0.1155 (18)
H12C0.88180.79450.78790.064*0.1155 (18)
H12D0.96640.76900.65240.064*0.1155 (18)
C13A1.148 (3)0.7645 (10)0.8242 (19)0.0600 (7)0.1155 (18)
H13C1.21630.79800.80130.072*0.1155 (18)
H13D1.22140.73260.79710.072*0.1155 (18)
C14A1.109 (2)0.7627 (8)0.9781 (18)0.0629 (7)0.1155 (18)
H14C1.22650.76511.03370.075*0.1155 (18)
H14D1.03080.79411.00180.075*0.1155 (18)
C15A1.009 (2)0.7104 (8)1.013 (2)0.0555 (6)0.1155 (18)
H15C1.09120.67920.99470.067*0.1155 (18)
H15D0.98360.71021.11200.067*0.1155 (18)
U11U22U33U12U13U23
S10.02353 (18)0.0410 (2)0.0283 (2)0.00880 (15)−0.00329 (14)−0.00609 (15)
O10.0297 (6)0.0485 (7)0.0281 (6)0.0102 (5)−0.0041 (4)−0.0026 (5)
N10.0409 (8)0.0456 (8)0.0261 (7)0.0097 (6)−0.0061 (6)−0.0053 (6)
N20.0222 (6)0.0265 (6)0.0217 (6)0.0017 (4)−0.0002 (4)−0.0023 (5)
N30.0253 (6)0.0402 (7)0.0206 (6)0.0068 (5)−0.0003 (5)−0.0054 (5)
N40.0270 (6)0.0320 (6)0.0201 (6)0.0037 (5)−0.0010 (5)−0.0048 (5)
C10.0201 (6)0.0235 (6)0.0245 (7)−0.0005 (5)0.0002 (5)−0.0004 (5)
C20.0222 (6)0.0233 (6)0.0199 (6)0.0000 (5)−0.0004 (5)−0.0003 (5)
C30.0216 (6)0.0239 (6)0.0212 (6)−0.0013 (5)0.0023 (5)0.0002 (5)
C40.0195 (6)0.0288 (7)0.0226 (7)0.0012 (5)−0.0007 (5)−0.0013 (5)
C50.0225 (6)0.0248 (6)0.0204 (6)−0.0018 (5)−0.0012 (5)−0.0007 (5)
C60.0242 (7)0.0277 (7)0.0253 (7)0.0043 (5)−0.0006 (5)−0.0019 (5)
C70.0285 (7)0.0363 (8)0.0353 (8)0.0062 (6)0.0058 (6)−0.0048 (7)
C80.0280 (7)0.0270 (7)0.0221 (7)−0.0040 (5)−0.0021 (5)0.0018 (5)
S20.0358 (3)0.0437 (3)0.0258 (3)0.0014 (2)0.0031 (2)−0.0104 (2)
C90.0430 (19)0.0336 (14)0.0210 (10)−0.0013 (13)−0.0052 (14)0.0001 (11)
C100.0315 (9)0.0308 (8)0.0283 (9)0.0031 (7)−0.0019 (7)−0.0059 (7)
C110.0486 (12)0.0362 (10)0.0669 (15)0.0101 (9)0.0078 (11)−0.0019 (10)
C120.0639 (16)0.0350 (14)0.0615 (15)0.0021 (12)0.0024 (12)0.0057 (13)
C130.0766 (17)0.0525 (16)0.0504 (13)−0.0250 (15)−0.0012 (12)−0.0093 (13)
C140.0373 (12)0.0873 (19)0.0622 (16)−0.0158 (12)−0.0173 (11)0.0164 (14)
C150.0405 (12)0.0721 (16)0.0521 (14)−0.0090 (11)−0.0170 (10)0.0152 (12)
S2A0.0358 (3)0.0437 (3)0.0258 (3)0.0014 (2)0.0031 (2)−0.0104 (2)
C9A0.0430 (19)0.0336 (14)0.0210 (10)−0.0013 (13)−0.0052 (14)0.0001 (11)
C10A0.0315 (9)0.0308 (8)0.0283 (9)0.0031 (7)−0.0019 (7)−0.0059 (7)
C11A0.0486 (12)0.0362 (10)0.0669 (15)0.0101 (9)0.0078 (11)−0.0019 (10)
C12A0.0639 (16)0.0350 (14)0.0615 (15)0.0021 (12)0.0024 (12)0.0057 (13)
C13A0.0766 (17)0.0525 (16)0.0504 (13)−0.0250 (15)−0.0012 (12)−0.0093 (13)
C14A0.0373 (12)0.0873 (19)0.0622 (16)−0.0158 (12)−0.0173 (11)0.0164 (14)
C15A0.0405 (12)0.0721 (16)0.0521 (14)−0.0090 (11)−0.0170 (10)0.0152 (12)
S1—C11.7624 (14)C12—C131.505 (4)
S1—C71.7972 (16)C12—H12A0.9900
O1—C81.2173 (18)C12—H12B0.9900
N1—C61.150 (2)C13—C141.527 (4)
N2—C11.3269 (18)C13—H13A0.9900
N2—C51.3586 (18)C13—H13B0.9900
N3—C31.3422 (18)C14—C151.535 (3)
N3—H3A0.9101C14—H14A0.9900
N3—H3B0.9104C14—H14B0.9900
N4—C81.3616 (19)C15—H15A0.9900
N4—C51.4093 (18)C15—H15B0.9900
N4—H4A0.9098S2A—C9A1.807 (18)
C1—C21.4094 (19)S2A—C10A1.823 (12)
C2—C31.4190 (19)C9A—H9A10.9900
C2—C61.427 (2)C9A—H9A20.9900
C3—C41.4087 (19)C10A—C11A1.496 (13)
C4—C51.3770 (19)C10A—C15A1.511 (12)
C4—H40.9500C10A—H10A1.0000
C7—H7A0.9800C11A—C12A1.512 (13)
C7—H7B0.9800C11A—H11C0.9900
C7—H7C0.9800C11A—H11D0.9900
C8—C91.516 (10)C12A—C13A1.529 (14)
C8—C9A1.59 (8)C12A—H12C0.9900
S2—C91.803 (4)C12A—H12D0.9900
S2—C101.826 (2)C13A—C14A1.533 (14)
C9—H9A0.9900C13A—H13C0.9900
C9—H9B0.9900C13A—H13D0.9900
C10—C151.523 (3)C14A—C15A1.520 (13)
C10—C111.525 (3)C14A—H14C0.9900
C10—H101.0000C14A—H14D0.9900
C11—C121.532 (4)C15A—H15C0.9900
C11—H11A0.9900C15A—H15D0.9900
C11—H11B0.9900
C1—S1—C7100.83 (7)C12—C13—H13A109.6
C1—N2—C5116.45 (12)C14—C13—H13A109.6
C3—N3—H3A124.2C12—C13—H13B109.6
C3—N3—H3B127.4C14—C13—H13B109.6
H3A—N3—H3B107.9H13A—C13—H13B108.1
C8—N4—C5128.45 (12)C13—C14—C15111.4 (2)
C8—N4—H4A115.9C13—C14—H14A109.3
C5—N4—H4A115.6C15—C14—H14A109.3
N2—C1—C2123.46 (13)C13—C14—H14B109.3
N2—C1—S1119.33 (10)C15—C14—H14B109.3
C2—C1—S1117.21 (11)H14A—C14—H14B108.0
C1—C2—C3119.11 (12)C10—C15—C14110.86 (18)
C1—C2—C6122.05 (12)C10—C15—H15A109.5
C3—C2—C6118.83 (12)C14—C15—H15A109.5
N3—C3—C4121.05 (13)C10—C15—H15B109.5
N3—C3—C2121.74 (13)C14—C15—H15B109.5
C4—C3—C2117.21 (12)H15A—C15—H15B108.1
C5—C4—C3118.24 (13)C9A—S2A—C10A102 (3)
C5—C4—H4120.9C8—C9A—S2A118 (4)
C3—C4—H4120.9C8—C9A—H9A1107.7
N2—C5—C4125.47 (13)S2A—C9A—H9A1107.7
N2—C5—N4111.10 (12)C8—C9A—H9A2107.7
C4—C5—N4123.44 (13)S2A—C9A—H9A2107.7
N1—C6—C2176.06 (16)H9A1—C9A—H9A2107.1
S1—C7—H7A109.5C11A—C10A—C15A111.7 (13)
S1—C7—H7B109.5C11A—C10A—S2A115.5 (9)
H7A—C7—H7B109.5C15A—C10A—S2A115.5 (9)
S1—C7—H7C109.5C11A—C10A—H10A104.2
H7A—C7—H7C109.5C15A—C10A—H10A104.2
H7B—C7—H7C109.5S2A—C10A—H10A104.2
O1—C8—N4123.44 (14)C10A—C11A—C12A110.5 (17)
O1—C8—C9121.2 (3)C10A—C11A—H11C109.6
N4—C8—C9115.3 (3)C12A—C11A—H11C109.6
O1—C8—C9A119.2 (18)C10A—C11A—H11D109.6
N4—C8—C9A117.3 (17)C12A—C11A—H11D109.6
C9—S2—C10100.0 (3)H11C—C11A—H11D108.1
C8—C9—S2115.3 (6)C11A—C12A—C13A111.9 (17)
C8—C9—H9A108.4C11A—C12A—H12C109.2
S2—C9—H9A108.4C13A—C12A—H12C109.2
C8—C9—H9B108.4C11A—C12A—H12D109.2
S2—C9—H9B108.4C13A—C12A—H12D109.2
H9A—C9—H9B107.5H12C—C12A—H12D107.9
C15—C10—C11110.98 (18)C12A—C13A—C14A103 (2)
C15—C10—S2112.88 (14)C12A—C13A—H13C111.1
C11—C10—S2108.92 (14)C14A—C13A—H13C111.1
C15—C10—H10108.0C12A—C13A—H13D111.1
C11—C10—H10108.0C14A—C13A—H13D111.1
S2—C10—H10108.0H13C—C13A—H13D109.0
C10—C11—C12110.92 (19)C15A—C14A—C13A110.5 (17)
C10—C11—H11A109.5C15A—C14A—H14C109.6
C12—C11—H11A109.5C13A—C14A—H14C109.6
C10—C11—H11B109.5C15A—C14A—H14D109.6
C12—C11—H11B109.5C13A—C14A—H14D109.6
H11A—C11—H11B108.0H14C—C14A—H14D108.1
C13—C12—C11110.7 (2)C10A—C15A—C14A112.5 (13)
C13—C12—H12A109.5C10A—C15A—H15C109.1
C11—C12—H12A109.5C14A—C15A—H15C109.1
C13—C12—H12B109.5C10A—C15A—H15D109.1
C11—C12—H12B109.5C14A—C15A—H15D109.1
H12A—C12—H12B108.1H15C—C15A—H15D107.8
C12—C13—C14110.3 (2)
C5—N2—C1—C2−1.8 (2)C10—S2—C9—C8−65.2 (5)
C5—N2—C1—S1177.97 (10)C9—S2—C10—C15−78.6 (4)
C7—S1—C1—N21.40 (13)C9—S2—C10—C11157.7 (4)
C7—S1—C1—C2−178.84 (11)C15—C10—C11—C1256.0 (3)
N2—C1—C2—C32.8 (2)S2—C10—C11—C12−179.18 (18)
S1—C1—C2—C3−176.92 (10)C10—C11—C12—C13−57.8 (3)
N2—C1—C2—C6−176.20 (13)C11—C12—C13—C1457.8 (3)
S1—C1—C2—C64.05 (18)C12—C13—C14—C15−56.8 (3)
C1—C2—C3—N3178.10 (13)C11—C10—C15—C14−54.6 (3)
C6—C2—C3—N3−2.8 (2)S2—C10—C15—C14−177.19 (19)
C1—C2—C3—C4−2.14 (19)C13—C14—C15—C1055.2 (3)
C6—C2—C3—C4176.93 (13)O1—C8—C9A—S2A164 (3)
N3—C3—C4—C5−179.59 (13)N4—C8—C9A—S2A−13 (6)
C2—C3—C4—C50.6 (2)C10A—S2A—C9A—C8−90 (5)
C1—N2—C5—C40.1 (2)C9A—S2A—C10A—C11A65 (3)
C1—N2—C5—N4−179.93 (12)C9A—S2A—C10A—C15A−68 (3)
C3—C4—C5—N20.4 (2)C15A—C10A—C11A—C12A−51 (2)
C3—C4—C5—N4−179.53 (13)S2A—C10A—C11A—C12A174.6 (14)
C8—N4—C5—N2176.01 (14)C10A—C11A—C12A—C13A61 (3)
C8—N4—C5—C4−4.1 (2)C11A—C12A—C13A—C14A−65 (3)
C5—N4—C8—O1−0.2 (2)C12A—C13A—C14A—C15A62 (2)
C5—N4—C8—C9−178.1 (4)C11A—C10A—C15A—C14A51 (2)
C5—N4—C8—C9A176 (3)S2A—C10A—C15A—C14A−174.9 (14)
O1—C8—C9—S2141.3 (3)C13A—C14A—C15A—C10A−58 (2)
N4—C8—C9—S2−40.8 (6)
D—H···AD—HH···AD···AD—H···A
N3—H3B···O1i0.911.972.8792 (17)179
N3—H3A···N1ii0.912.223.0640 (19)155
C4—H4···O10.952.242.8493 (18)121
C7—H7A···O1iii0.982.603.440 (2)144
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N3—H3B⋯O1i 0.911.972.8792 (17)179
N3—H3A⋯N1ii 0.912.223.0640 (19)155

Symmetry codes: (i) ; (ii) .

  3 in total

1.  Synthesis and antimicrobial activity of new benzofuranylpyridine derivatives.

Authors:  O H Hishmat; F M Abdel Galil; D S Farrag
Journal:  Pharmazie       Date:  1990-10       Impact factor: 1.267

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Ethyl 2-[({[4-amino-5-cyano-6-(methyl-sulfan-yl)pyridin-2-yl]carbamo-yl}meth-yl)sulfan-yl]acetate monohydrate.

Authors:  Mehmet Akkurt; Joel T Mague; Shaaban K Mohamed; Bahgat R M Hussein; Mustafa R Albayati
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-06-04
  3 in total

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