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Acta Crystallogr Sect E Struct Rep Online. 2008 May 1; 64(Pt 5): o858.
Published online 2008 April 16. doi:  10.1107/S1600536808009768
PMCID: PMC2961226

1-[3,5-Bis(trifluoro­meth­yl)phen­yl]-3-(2-pyrid­yl)thio­urea

Abstract

The title compound, C14H9F6N3S, exhibits a nearly planar conformation in the solid state, with a dihedral angle between the planes of the benzene and pyridine rings of 14.86 (3)°. The pyridine N atom allows for the formation of a six-membered N—H(...)Npy hydrogen-bonded ring, thus forcing the two amide H atoms of the thio­urea group to point in opposite directions. The second N—H group forms an inter­molecular N—H(...)S hydrogen bond with the S atom of an adjacent mol­ecule. The F atoms of the two trifluoro­methyl groups display rotational disorder around the C—CF3 axis, with an occupancy ratio of 0.54 (1):0.46 (1).

Related literature

For related literature, see: Akiyama et al. (2006 [triangle]); Struga et al. (2007 [triangle]).

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Object name is e-64-0o858-scheme1.jpg

Experimental

Crystal data

  • C14H9F6N3S
  • M r = 365.30
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o858-efi1.jpg
  • a = 15.0907 (17) Å
  • b = 7.7491 (9) Å
  • c = 26.709 (3) Å
  • V = 3123.3 (6) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.27 mm−1
  • T = 293 (2) K
  • 0.41 × 0.31 × 0.17 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.873, T max = 0.962
  • 17235 measured reflections
  • 3406 independent reflections
  • 2585 reflections with I > 2σ(I)
  • R int = 0.102

Refinement

  • R[F 2 > 2σ(F 2)] = 0.058
  • wR(F 2) = 0.151
  • S = 1.06
  • 3406 reflections
  • 280 parameters
  • 13 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.40 e Å−3
  • Δρmin = −0.30 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT-Plus (Bruker, 2000 [triangle]); data reduction: SAINT-Plus and SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808009768/zl2103sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808009768/zl2103Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We acknowledge the help of Professor Jie Sun of Shanghai Institute of Organic Chemistry.

supplementary crystallographic information

Comment

Thiourea compounds have been extensively studied over the last few years due to their pharmacological and biological activities (Struga et al., 2007). Recently, excellent results have been also achieved with the use of the bifunctional thiourea catalysts, which effectively activate carbonyl groups and imines through double hydrogen-bonding interactions in asymmetric synthesis (Akiyama et al., 2006). Herein, we synthesized the title compound (I) and determined its crystal structure (Fig.1). The benzene and pyridine rings in the structural unit of (I) are almost perfectly coplanar with a dihedral angle between their planes of only 14.86 (3)°. Like other 2-pyridyl thioureas, the title compound exhibits both intramolecular and intermolecular hydrogen bonding interactions. The pyridine nitrogen N3 allows for the formation of a six membered N—H···Npyr hydrogen bonded ring which forces the two amide hydrogen atoms of the thiourea group to point in opposite directions. At the same time, the N1—H1 and C9—H9 moieties of the pyridine ring form intermolecular N—H···S and C—H···S hydrogen bonds with the S atom of an adjacent molecule (Fig. 2). This weak hydrogen-bonding network leads to the formation of infinite chains of molecules thus stabilizing the crystal packing.

Experimental

The title compound was synthesized by treating 3,5-bis-trifluoromethyl-phenyl isothiocyanate (2.71 g, 10 mmol) with 2-amino pyridine (0.94 g, 10 mmol) in MeCN (30 ml) under stirring at room temperature for 24 h. Suitable crystals of the title compound were obtained by slow evaporation of an actonitrile solution at room temperature (3.28 g, 10 mmol). Yield 90%, m.p. 431–433 K, 1H NMR (500 MHz, CDCl3): 6.91 (d, J = 8 Hz, 1H), 7.08–7.11 (m, 1H), 7.73–7.77 (m, 2H), 8.27 (s, 1H), 8.29–8.31 (m, 2H), 8.95 (s, 1H), 14.17 (s, 1H).

Refinement

Large solvent accessible voids are found in the crystal. The volumes (31 Å3 per cavity, four equivalent cavities per unit cell) of these voids are not quite large enough to host acetonitrile molecules, the solvent of crystallization, and no significant residual electron density is seen in difference Fourier syntheses maps. The largest residual electron density peak and the deepest negative density in these voids are 0.40 (0.97 Å from S1) and -0.30 (1.30 Å from C4), respectively. Also, an attempted correction for the electron density within the voids using the Squeeze algorithm implemented in the program PLATON (Spek, 2003) does not significantly improve the quality of the dataset or refinement. The fluorine atoms of the two CF3 groups exhibit conformational disorder around the C4—C13 and C6—C14 bonds with an occupancy ratio of 0.54 (1) to 0.46 (1). They are refined with restraints for the C—F bond lengths and the F···F interatomic distances to maintain nearly tetrahedral geometry. All C—F bond lengths are restrained to 1.35 (5) Å and the displacement parameters of the disordered F atoms are restrained to an approximate isotropic behaviour. All carbon-bond H atoms are placed in calculated positions with C—H = 0.93 Å (aromatic) and refined using a riding model, with Uiso(H) = 1.2eq(C). N-bound H atoms are located in a difference map and refined with an N—H distance restraint of 0.83 (2) Å.

Figures

Fig. 1.
View of the structure of the title compound showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level. For the sake of clarity, only the major orientation of the CF3 group is shown.
Fig. 2.
The molecular packing of the title compound showing the intermolecular N—H···S and C—H···S hydrogen-bonding interactions (dashed lines).

Crystal data

C14H9F6N3SDx = 1.554 Mg m3
Mr = 365.30Mo Kα radiation λ = 0.71073 Å
Orthorhombic, PbcnCell parameters from 4062 reflections
a = 15.0907 (17) Åθ = 5.4–45.0º
b = 7.7491 (9) ŵ = 0.27 mm1
c = 26.709 (3) ÅT = 293 (2) K
V = 3123.3 (6) Å3Prismatic, colourless
Z = 80.41 × 0.31 × 0.18 mm
F000 = 1472

Data collection

Bruker SMART CCD area-detector diffractometer3406 independent reflections
Radiation source: fine-focus sealed tube2585 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.102
T = 293(2) Kθmax = 27.0º
[var phi] and ω scansθmin = 1.5º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −19→19
Tmin = 0.873, Tmax = 0.962k = −9→9
17235 measured reflectionsl = −26→34

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.058H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.151  w = 1/[σ2(Fo2) + (0.075P)2 + 0.3374P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.040
3406 reflectionsΔρmax = 0.40 e Å3
280 parametersΔρmin = −0.30 e Å3
13 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

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 (Å2)

xyzUiso*/UeqOcc. (<1)
S10.44883 (4)1.05153 (11)0.42753 (2)0.0699 (3)
N10.37456 (12)0.8647 (3)0.49769 (7)0.0499 (5)
N20.28358 (12)0.9220 (3)0.43161 (6)0.0468 (5)
N30.22735 (11)0.7940 (2)0.51757 (6)0.0480 (5)
C10.36381 (13)0.9414 (3)0.45239 (8)0.0456 (5)
C20.25117 (14)0.9797 (3)0.38500 (7)0.0406 (5)
C30.30288 (14)1.0050 (3)0.34296 (7)0.0435 (5)
H30.36400.98980.34450.052*
C40.26236 (15)1.0534 (3)0.29841 (7)0.0426 (5)
C50.17215 (15)1.0763 (3)0.29537 (8)0.0477 (5)
H50.14591.10920.26530.057*
C60.12109 (14)1.0495 (3)0.33762 (8)0.0472 (5)
C70.15999 (14)1.0010 (3)0.38225 (8)0.0451 (5)
H70.12510.98250.41040.054*
C80.31247 (13)0.7912 (3)0.53057 (7)0.0431 (5)
C90.34218 (16)0.7222 (3)0.57550 (8)0.0538 (6)
H90.40230.71890.58300.065*
C100.28091 (17)0.6595 (3)0.60830 (9)0.0575 (6)
H100.29890.61270.63870.069*
C110.19245 (17)0.6658 (3)0.59626 (9)0.0597 (6)
H110.14960.62600.61840.072*
C120.16964 (15)0.7320 (3)0.55103 (9)0.0565 (6)
H120.10980.73430.54270.068*
C130.31954 (17)1.0781 (3)0.25314 (8)0.0550 (6)
C140.02309 (17)1.0700 (4)0.33485 (10)0.0693 (8)
F10.3600 (6)1.2197 (7)0.2520 (3)0.092 (3)0.540 (15)
F20.3770 (6)0.9559 (14)0.2476 (4)0.106 (4)0.540 (15)
F30.2703 (4)1.0759 (17)0.21099 (16)0.105 (3)0.540 (15)
F4−0.0158 (11)0.927 (2)0.3219 (7)0.114 (5)0.540 (15)
F5−0.0038 (9)1.1890 (19)0.3061 (5)0.111 (6)0.540 (15)
F6−0.0122 (7)1.1014 (17)0.3796 (3)0.118 (4)0.540 (15)
F1'0.3995 (6)1.140 (2)0.2647 (2)0.112 (5)0.460 (15)
F2'0.3344 (11)0.9413 (13)0.2292 (4)0.116 (5)0.460 (15)
F3'0.2887 (7)1.1881 (17)0.2217 (4)0.117 (5)0.460 (15)
F4'−0.0137 (13)0.957 (3)0.3042 (8)0.115 (7)0.460 (15)
F5'0.0011 (10)1.2244 (16)0.3174 (6)0.111 (4)0.460 (15)
F6'−0.0171 (6)1.0587 (17)0.3773 (3)0.097 (4)0.460 (15)
H10.4219 (13)0.877 (3)0.5105 (9)0.065 (8)*
H20.2456 (16)0.882 (3)0.4511 (9)0.047 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0397 (3)0.1245 (7)0.0456 (4)−0.0239 (3)−0.0094 (2)0.0228 (3)
N10.0327 (9)0.0801 (14)0.0370 (9)−0.0038 (9)−0.0087 (7)0.0105 (9)
N20.0334 (9)0.0741 (13)0.0328 (9)−0.0062 (8)−0.0037 (7)0.0073 (8)
N30.0371 (9)0.0676 (12)0.0394 (9)−0.0050 (8)−0.0015 (7)0.0030 (8)
C10.0331 (10)0.0688 (15)0.0350 (11)−0.0001 (9)−0.0020 (8)0.0014 (9)
C20.0369 (10)0.0511 (12)0.0337 (10)−0.0034 (9)−0.0056 (8)−0.0019 (8)
C30.0377 (10)0.0552 (12)0.0376 (11)0.0001 (9)−0.0011 (8)−0.0029 (9)
C40.0482 (12)0.0452 (12)0.0345 (10)−0.0035 (9)−0.0018 (9)−0.0024 (8)
C50.0523 (13)0.0542 (13)0.0368 (11)−0.0019 (10)−0.0104 (9)0.0051 (9)
C60.0369 (11)0.0579 (14)0.0468 (12)−0.0021 (9)−0.0095 (9)0.0039 (10)
C70.0372 (11)0.0609 (13)0.0371 (11)−0.0041 (9)−0.0025 (8)0.0031 (9)
C80.0405 (11)0.0522 (12)0.0367 (10)−0.0028 (9)−0.0020 (8)−0.0010 (9)
C90.0520 (13)0.0655 (15)0.0440 (12)−0.0024 (11)−0.0084 (10)0.0098 (10)
C100.0692 (16)0.0621 (15)0.0410 (12)−0.0048 (12)−0.0018 (11)0.0076 (10)
C110.0642 (15)0.0647 (16)0.0502 (14)−0.0094 (12)0.0109 (11)0.0040 (11)
C120.0433 (12)0.0751 (17)0.0511 (13)−0.0084 (11)0.0034 (10)0.0018 (11)
C130.0656 (16)0.0613 (16)0.0380 (12)−0.0007 (13)0.0038 (10)0.0004 (11)
C140.0443 (14)0.103 (2)0.0601 (17)−0.0011 (15)−0.0095 (12)0.0122 (16)
F10.127 (6)0.066 (3)0.082 (5)−0.042 (3)0.050 (4)−0.018 (2)
F20.124 (6)0.103 (7)0.092 (5)0.055 (6)0.063 (4)0.033 (5)
F30.103 (3)0.140 (9)0.0328 (17)−0.036 (5)−0.0070 (17)0.001 (3)
F40.051 (5)0.135 (7)0.157 (13)−0.041 (4)−0.005 (6)−0.035 (8)
F50.058 (4)0.147 (15)0.089 (5)0.026 (7)−0.018 (3)0.067 (7)
F60.062 (5)0.144 (8)0.097 (6)0.044 (4)0.004 (3)−0.038 (5)
F1'0.081 (5)0.151 (15)0.065 (3)−0.077 (6)0.010 (3)0.009 (6)
F2'0.148 (12)0.070 (5)0.088 (7)−0.011 (7)0.077 (7)−0.023 (5)
F3'0.113 (9)0.121 (8)0.077 (6)0.054 (7)0.040 (6)0.066 (6)
F4'0.062 (7)0.147 (14)0.126 (11)0.003 (7)−0.056 (7)−0.076 (10)
F5'0.056 (5)0.098 (5)0.140 (11)0.031 (3)0.005 (5)0.042 (5)
F6'0.035 (3)0.138 (7)0.088 (6)−0.008 (4)−0.002 (3)0.066 (6)

Geometric parameters (Å, °)

S1—C11.678 (2)C8—C91.388 (3)
N1—C11.358 (3)C9—C101.363 (3)
N1—C81.405 (3)C9—H90.9300
N1—H10.798 (17)C10—C111.374 (3)
N2—C11.340 (3)C10—H100.9300
N2—C21.410 (3)C11—C121.357 (3)
N2—H20.83 (2)C11—H110.9300
N3—C81.331 (3)C12—H120.9300
N3—C121.337 (3)C13—F11.256 (5)
C2—C31.381 (3)C13—F2'1.259 (8)
C2—C71.388 (3)C13—F3'1.285 (5)
C3—C41.389 (3)C13—F21.292 (7)
C3—H30.9300C13—F1'1.335 (6)
C4—C51.375 (3)C13—F31.349 (5)
C4—C131.498 (3)C14—F51.268 (9)
C5—C61.382 (3)C14—F6'1.288 (8)
C5—H50.9300C14—F41.301 (13)
C6—C71.381 (3)C14—F4'1.319 (13)
C6—C141.489 (3)C14—F5'1.326 (10)
C7—H70.9300C14—F61.331 (8)
C1—N1—C8130.91 (18)N3—C12—C11124.4 (2)
C1—N1—H1116 (2)N3—C12—H12117.8
C8—N1—H1112.3 (19)C11—C12—H12117.8
C1—N2—C2130.04 (19)F1—C13—F2'129.6 (6)
C1—N2—H2113.9 (16)F1—C13—F3'65.2 (5)
C2—N2—H2115.5 (16)F2'—C13—F3'106.9 (6)
C8—N3—C12116.63 (19)F1—C13—F2108.1 (6)
N2—C1—N1115.33 (19)F3'—C13—F2130.9 (4)
N2—C1—S1125.73 (17)F2'—C13—F1'105.0 (6)
N1—C1—S1118.94 (15)F3'—C13—F1'103.9 (6)
C3—C2—C7120.02 (18)F2—C13—F1'71.5 (7)
C3—C2—N2124.51 (19)F1—C13—F3104.9 (4)
C7—C2—N2115.35 (18)F2'—C13—F370.3 (6)
C2—C3—C4119.1 (2)F2—C13—F3105.4 (5)
C2—C3—H3120.5F1'—C13—F3134.0 (4)
C4—C3—H3120.5F1—C13—C4114.3 (3)
C5—C4—C3121.40 (19)F2'—C13—C4113.9 (5)
C5—C4—C13120.41 (19)F3'—C13—C4113.8 (3)
C3—C4—C13118.2 (2)F2—C13—C4112.6 (4)
C4—C5—C6118.98 (19)F1'—C13—C4112.4 (3)
C4—C5—H5120.5F3—C13—C4110.8 (3)
C6—C5—H5120.5F5—C14—F6'115.6 (8)
C7—C6—C5120.6 (2)F5—C14—F4108.3 (11)
C7—C6—C14119.6 (2)F6'—C14—F487.9 (10)
C5—C6—C14119.8 (2)F5—C14—F4'88.3 (12)
C6—C7—C2119.97 (19)F6'—C14—F4'107.6 (11)
C6—C7—H7120.0F6'—C14—F5'104.6 (9)
C2—C7—H7120.0F4—C14—F5'124.2 (11)
N3—C8—C9122.95 (19)F4'—C14—F5'105.9 (12)
N3—C8—N1118.28 (18)F5—C14—F6106.4 (9)
C9—C8—N1118.76 (19)F4—C14—F6102.3 (10)
C10—C9—C8118.3 (2)F4'—C14—F6120.7 (11)
C10—C9—H9120.9F5'—C14—F692.8 (9)
C8—C9—H9120.9F5—C14—C6115.2 (7)
C9—C10—C11119.7 (2)F6'—C14—C6114.6 (5)
C9—C10—H10120.1F4—C14—C6111.8 (9)
C11—C10—H10120.1F4'—C14—C6112.2 (10)
C12—C11—C10117.9 (2)F5'—C14—C6111.2 (7)
C12—C11—H11121.0F6—C14—C6111.9 (5)
C10—C11—H11121.0
C2—N2—C1—N1−178.0 (2)C8—N3—C12—C11−0.8 (4)
C2—N2—C1—S12.6 (4)C10—C11—C12—N3−1.0 (4)
C8—N1—C1—N2−11.5 (4)C5—C4—C13—F1101.7 (6)
C8—N1—C1—S1167.9 (2)C3—C4—C13—F1−79.2 (6)
C1—N2—C2—C328.6 (4)C5—C4—C13—F2'−93.6 (10)
C1—N2—C2—C7−155.3 (2)C3—C4—C13—F2'85.6 (10)
C7—C2—C3—C40.7 (3)C5—C4—C13—F3'29.4 (9)
N2—C2—C3—C4176.6 (2)C3—C4—C13—F3'−151.5 (9)
C2—C3—C4—C5−0.1 (3)C5—C4—C13—F2−134.4 (7)
C2—C3—C4—C13−179.3 (2)C3—C4—C13—F244.7 (7)
C3—C4—C5—C6−0.3 (3)C5—C4—C13—F1'147.1 (10)
C13—C4—C5—C6178.9 (2)C3—C4—C13—F1'−33.7 (10)
C4—C5—C6—C70.1 (3)C5—C4—C13—F3−16.6 (7)
C4—C5—C6—C14−178.7 (2)C3—C4—C13—F3162.5 (6)
C5—C6—C7—C20.4 (3)C7—C6—C14—F5145.4 (9)
C14—C6—C7—C2179.3 (2)C5—C6—C14—F5−35.8 (10)
C3—C2—C7—C6−0.8 (3)C7—C6—C14—F6'7.6 (8)
N2—C2—C7—C6−177.1 (2)C5—C6—C14—F6'−173.6 (7)
C12—N3—C8—C92.4 (3)C7—C6—C14—F4−90.4 (9)
C12—N3—C8—N1−176.2 (2)C5—C6—C14—F488.4 (9)
C1—N1—C8—N3−0.6 (4)C7—C6—C14—F4'−115.6 (12)
C1—N1—C8—C9−179.3 (2)C5—C6—C14—F4'63.3 (12)
N3—C8—C9—C10−2.1 (4)C7—C6—C14—F5'126.0 (8)
N1—C8—C9—C10176.5 (2)C5—C6—C14—F5'−55.2 (8)
C8—C9—C10—C110.1 (4)C7—C6—C14—F623.7 (7)
C9—C10—C11—C121.4 (4)C5—C6—C14—F6−157.5 (7)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···N30.83 (2)1.92 (2)2.641 (3)144 (2)
N1—H1···S1i0.798 (17)2.617 (18)3.3931 (19)165 (3)

Symmetry codes: (i) −x+1, −y+2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZL2103).

References

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