Download citation
Download citation
link to html
The mol­ecule of 1,3-bis(3-pyridyl­methyl)-2-thio­urea, C13H14N4S, has approximate C2 symmetry, implying a syn relationship between the two N—H groups. The mol­ecules associate via N—H...Npyridyl interactions to form a two-dimensional arrangement with adjacent layers connected via C—H...π contacts.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802006220/ya6100sup1.cif
Contains datablocks general, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536802006220/ya6100Isup2.hkl
Contains datablock I

CCDC reference: 185789

Key indicators

  • Single-crystal X-ray study
  • T = 223 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.040
  • wR factor = 0.111
  • Data-to-parameter ratio = 20.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
STRVAL_01 From the CIF: _refine_ls_abs_structure_Flack 0.310 From the CIF: _refine_ls_abs_structure_Flack_su 0.070 Alert C Flack test results are ambiguous. General Notes
REFLT_03 From the CIF: _diffrn_reflns_theta_max 30.00 From the CIF: _reflns_number_total 3298 Count of symmetry unique reflns 1871 Completeness (_total/calc) 176.27% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 1427 Fraction of Friedel pairs measured 0.763 Are heavy atom types Z>Si present yes Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check

Comment top

Thiourea compounds are well known to possess biological activity (Schroeder, 1955). Thus, various derivatives display antituberculous, antithyroid, antibacterial, insecticidal, hypnotic and anaesthetic properties (e.g. Liu et al., 1998; Tobe et al., 1998; D'Cruz et al., 2000).

The title compound, 1,3-bis(3-pyridylmethyl)-2-thiourea, (I), represents a symmetrically substituted species that is commercially available. The molecular structure of (I) is shown in Fig. 1 in which it is apparent that there is molecular C2 symmetry such that the C1S1 bond lies on the non-crystallographic twofold axis. This implies that the amine N—H atoms are syn with respect to each other. Deviations from the ideal symmetry (Table 1) are most apparent in the magnitudes of the respective N1—C2—C3—C4 and N1—C2—C3—C7 torsion angles of 73.9 (2) and -106.7 (2)°, respectively, which may be compared with the related angles involving the second 3-pyridylmethyl residue, i.e. N3—C8—C9—C10 and N3—C8—C9—C13 of 68.1 (2) and -112.4 (2)°, respectively. The central S1/N1/N3/C1/C2/C8 moiety is essentially planar, with the maximum deviations being 0.011 (2) Å for N3 and -0.034 (2) Å for N1. The pyridyl groups lie above and below the central chromophore plane so that the dihedral angles between this plane and the N2- and N4-pyridyl rings are 68.84 (8) and 70.35 (8)°, respectively. The dihedral angle formed by the two pyridyl residues is 4.95 (10)°. As noted from the above description, the deviations from crystallographic twofold symmetry in the molecular structure are not dramatic. The crystal packing, however, as well as the intermolecular hydrogen-bond system lack the C2 symmetry, which accounts for the absence of a twofold axis in the crystal.

Each of the N—H atoms forms a donor hydrogen-bonding interaction to a pyridyl N atom of a symmetry-related molecule. In this way, the N1—H1 atom forms a hydrogen bond to N2i such that H1···N2i is 2.15 Å, N1···N2i is 2.977 (3) Å and the angle subtended at H1 is 158° [symmetry code: (i) x - 1, y, z]. These interactions occur between translationally related molecules along the a axis, leading to the formation of a chain. Similarly, the N3—H3 atom is 2.17 Å from N4ii so that N3···N4ii is 2.938 (3) Å and the angle at H3 is 146° [symmetry code: (ii) x, 1 - y, 1/2 + z]. These interactions, generated by the c-glide, coupled with those described above lead to a corrugated two-dimensional structure. Cohesion between the layers is afforded by C—H···π interactions (Steiner & Koellner, 2001) occurring between C12—H12 and the ring centroid of the pyridyl ring containing N2iii [symmetry code: (iii) -1 + x, 1 - y, -1/2 + z]. Thus, the distance between H12 and the ring centroid is 3.38 Å, and the angle subtended at H12 is 128°.

Experimental top

Crystals of (I) were obtained from slow evaporation of an acetonitrile/chloroform solution (1:1) of the commerically available sample (Aldrich) (m.p. 430–431 K).

Refinement top

The C-bound and N-bound H atoms were placed in their geometrically calculated positions and included in the final refinement with an overall refined displacement parameter Uiso for pyridyl and nitrogen-H, and 1.25Uiso for methylene H. The unambiguous determination of the absolute structure proved to be impossible.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SHELXTL (Bruker, 2000); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2000).

Figures top
[Figure 1] Fig. 1. The molecular structure and crystallographic numbering scheme for (I). Displacement ellipsoids are shown at the 50% probability level (Johnson, 1976).
(I) top
Crystal data top
C13H14N4SF(000) = 272
Mr = 258.34Dx = 1.338 Mg m3
Monoclinic, PcMo Kα radiation, λ = 0.71069 Å
Hall symbol: P -2ycCell parameters from 5174 reflections
a = 6.8629 (4) Åθ = 2.2–30.0°
b = 9.1707 (5) ŵ = 0.24 mm1
c = 10.7176 (6) ÅT = 223 K
β = 108.048 (1)°Block, colourless
V = 641.35 (6) Å30.25 × 0.10 × 0.07 mm
Z = 2
Data collection top
Bruker SMART CCD
diffractometer
3244 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.022
Graphite monochromatorθmax = 30.0°, θmin = 2.2°
ω scansh = 79
5174 measured reflectionsk = 1210
3298 independent reflectionsl = 1514
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.111 w = 1/[σ2(Fo2) + (0.0697P)2 + 0.0997P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001'
3298 reflectionsΔρmax = 0.38 e Å3
164 parametersΔρmin = 0.22 e Å3
2 restraintsAbsolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.31 (7)
Crystal data top
C13H14N4SV = 641.35 (6) Å3
Mr = 258.34Z = 2
Monoclinic, PcMo Kα radiation
a = 6.8629 (4) ŵ = 0.24 mm1
b = 9.1707 (5) ÅT = 223 K
c = 10.7176 (6) Å0.25 × 0.10 × 0.07 mm
β = 108.048 (1)°
Data collection top
Bruker SMART CCD
diffractometer
3244 reflections with I > 2σ(I)
5174 measured reflectionsRint = 0.022
3298 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.111Δρmax = 0.38 e Å3
S = 1.08Δρmin = 0.22 e Å3
3298 reflectionsAbsolute structure: Flack (1983)
164 parametersAbsolute structure parameter: 0.31 (7)
2 restraints
Special details top

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) top
xyzUiso*/Ueq
S10.15633 (5)0.32084 (4)0.81908 (4)0.03044 (12)
N10.0159 (2)0.09931 (17)0.90656 (18)0.0316 (3)
H10.09720.06650.94830.0416 (18)*
N20.6533 (3)0.05525 (19)0.97908 (19)0.0366 (4)
N30.0752 (3)0.32339 (15)0.97735 (17)0.0313 (3)
H30.14400.27781.02120.0416 (18)*
N40.2743 (3)0.7118 (2)0.68184 (18)0.0360 (4)
C10.0145 (2)0.24361 (19)0.90540 (16)0.0246 (3)
C20.0801 (3)0.0058 (2)0.8415 (2)0.0335 (4)
H2A0.09780.03950.76290.052 (2)*
H2B0.01150.08970.81310.052 (2)*
C30.2854 (3)0.05898 (19)0.92800 (18)0.0275 (3)
C40.3034 (3)0.1567 (2)1.0300 (2)0.0337 (4)
H40.18590.19091.04820.0416 (18)*
C50.4966 (4)0.2032 (2)1.1048 (2)0.0390 (4)
H50.51200.26951.17410.0416 (18)*
C60.6653 (3)0.1505 (2)1.0756 (2)0.0360 (4)
H60.79570.18331.12620.0416 (18)*
C70.4659 (3)0.0122 (2)0.9072 (2)0.0326 (4)
H70.45540.05380.83840.0416 (18)*
C80.0639 (3)0.4815 (2)0.98613 (19)0.0318 (4)
H8A0.07480.51220.99040.052 (2)*
H8B0.08740.51191.06800.052 (2)*
C90.2162 (3)0.55904 (18)0.87265 (17)0.0268 (3)
C100.4249 (3)0.5543 (2)0.8535 (2)0.0365 (4)
H100.47710.50150.91120.0416 (18)*
C110.5555 (3)0.6283 (3)0.7485 (2)0.0421 (5)
H110.69790.62570.73330.0416 (18)*
C120.4743 (3)0.7061 (3)0.6660 (2)0.0377 (4)
H120.56430.75740.59550.0416 (18)*
C130.1495 (3)0.6390 (2)0.78398 (19)0.0304 (4)
H130.00790.64230.79620.0416 (18)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0291 (2)0.0323 (2)0.0336 (2)0.00423 (18)0.01526 (16)0.00084 (18)
N10.0249 (7)0.0275 (7)0.0465 (9)0.0013 (6)0.0169 (7)0.0013 (6)
N20.0268 (8)0.0384 (9)0.0464 (9)0.0013 (6)0.0141 (7)0.0004 (7)
N30.0388 (9)0.0266 (7)0.0346 (8)0.0003 (6)0.0202 (7)0.0021 (5)
N40.0376 (9)0.0389 (8)0.0349 (8)0.0025 (7)0.0162 (7)0.0051 (7)
C10.0181 (8)0.0285 (8)0.0267 (7)0.0016 (5)0.0063 (6)0.0006 (6)
C20.0285 (9)0.0275 (8)0.0414 (10)0.0001 (6)0.0062 (7)0.0059 (7)
C30.0262 (8)0.0252 (7)0.0323 (8)0.0001 (6)0.0106 (7)0.0035 (6)
C40.0324 (10)0.0359 (9)0.0384 (9)0.0034 (7)0.0191 (8)0.0002 (7)
C50.0443 (12)0.0417 (10)0.0309 (9)0.0049 (9)0.0113 (8)0.0057 (8)
C60.0288 (10)0.0402 (10)0.0355 (9)0.0024 (8)0.0047 (8)0.0022 (8)
C70.0320 (10)0.0294 (8)0.0390 (9)0.0007 (7)0.0147 (8)0.0042 (7)
C80.0393 (10)0.0283 (8)0.0287 (8)0.0011 (7)0.0119 (7)0.0037 (6)
C90.0318 (9)0.0231 (7)0.0285 (7)0.0038 (6)0.0139 (6)0.0053 (6)
C100.0369 (11)0.0377 (10)0.0416 (10)0.0073 (8)0.0219 (9)0.0009 (8)
C110.0277 (10)0.0521 (12)0.0476 (12)0.0052 (9)0.0132 (9)0.0024 (10)
C120.0335 (11)0.0444 (10)0.0333 (9)0.0027 (8)0.0075 (8)0.0008 (8)
C130.0290 (9)0.0303 (8)0.0362 (9)0.0014 (7)0.0167 (7)0.0006 (7)
Geometric parameters (Å, º) top
S1—C11.6920 (17)C4—H40.9400
N1—C11.340 (2)C5—C61.377 (3)
N1—C21.461 (3)C5—H50.9400
N1—H10.8700C6—H60.9400
N2—C61.337 (3)C7—H70.9400
N2—C71.337 (3)C8—C91.513 (3)
N3—C11.343 (2)C8—H8A0.9800
N3—C81.453 (2)C8—H8B0.9800
N3—H30.8700C9—C101.383 (3)
N4—C121.331 (3)C9—C131.386 (2)
N4—C131.341 (3)C10—C111.380 (3)
C2—C31.508 (3)C10—H100.9400
C2—H2A0.9800C11—C121.381 (3)
C2—H2B0.9800C11—H110.9400
C3—C41.389 (3)C12—H120.9400
C3—C71.392 (3)C13—H130.9400
C4—C51.387 (3)
C1—N1—C2123.55 (16)N2—C6—H6118.3
C1—N1—H1118.2C5—C6—H6118.3
C2—N1—H1118.2N2—C7—C3124.15 (18)
C7—N2—C6117.15 (18)N2—C7—H7117.9
C1—N3—C8123.78 (16)C3—C7—H7117.9
C1—N3—H3118.1N3—C8—C9114.01 (16)
C8—N3—H3118.1N3—C8—H8A108.7
C12—N4—C13117.25 (19)C9—C8—H8A108.7
N3—C1—N1115.62 (15)N3—C8—H8B108.7
N3—C1—S1121.98 (13)C9—C8—H8B108.7
N1—C1—S1122.40 (14)H8A—C8—H8B107.6
N1—C2—C3113.15 (16)C10—C9—C13117.51 (18)
N1—C2—H2A108.9C10—C9—C8122.04 (17)
C3—C2—H2A108.9C13—C9—C8120.46 (17)
N1—C2—H2B108.9C11—C10—C9119.12 (19)
C3—C2—H2B108.9C11—C10—H10120.4
H2A—C2—H2B107.8C9—C10—H10120.4
C7—C3—C4117.25 (18)C10—C11—C12119.2 (2)
C7—C3—C2120.68 (18)C10—C11—H11120.4
C4—C3—C2122.07 (18)C12—C11—H11120.4
C5—C4—C3119.29 (19)N4—C12—C11122.9 (2)
C5—C4—H4120.4N4—C12—H12118.6
C3—C4—H4120.4C11—C12—H12118.6
C6—C5—C4118.77 (19)N4—C13—C9124.06 (18)
C6—C5—H5120.6N4—C13—H13118.0
C4—C5—H5120.6C9—C13—H13118.0
N2—C6—C5123.37 (19)

Experimental details

Crystal data
Chemical formulaC13H14N4S
Mr258.34
Crystal system, space groupMonoclinic, Pc
Temperature (K)223
a, b, c (Å)6.8629 (4), 9.1707 (5), 10.7176 (6)
β (°) 108.048 (1)
V3)641.35 (6)
Z2
Radiation typeMo Kα
µ (mm1)0.24
Crystal size (mm)0.25 × 0.10 × 0.07
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5174, 3298, 3244
Rint0.022
(sin θ/λ)max1)0.704
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.111, 1.08
No. of reflections3298
No. of parameters164
No. of restraints2
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.38, 0.22
Absolute structureFlack (1983)
Absolute structure parameter0.31 (7)

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXTL (Bruker, 2000), SIR92 (Altomare et al., 1994), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976), SHELXTL and PLATON (Spek, 2000).

Selected geometric parameters (Å, º) top
S1—C11.6920 (17)N3—C11.343 (2)
N1—C11.340 (2)N3—C81.453 (2)
N1—C21.461 (3)N4—C121.331 (3)
N2—C61.337 (3)N4—C131.341 (3)
N2—C71.337 (3)
C1—N1—C2123.55 (16)N3—C1—S1121.98 (13)
C1—N3—C8123.78 (16)N1—C1—S1122.40 (14)
N3—C1—N1115.62 (15)
 

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds