Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802006220/ya6100sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536802006220/ya6100Isup2.hkl |
CCDC reference: 185789
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).
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.
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).
Fig. 1. The molecular structure and crystallographic numbering scheme for (I). Displacement ellipsoids are shown at the 50% probability level (Johnson, 1976). |
C13H14N4S | F(000) = 272 |
Mr = 258.34 | Dx = 1.338 Mg m−3 |
Monoclinic, Pc | Mo Kα radiation, λ = 0.71069 Å |
Hall symbol: P -2yc | Cell parameters from 5174 reflections |
a = 6.8629 (4) Å | θ = 2.2–30.0° |
b = 9.1707 (5) Å | µ = 0.24 mm−1 |
c = 10.7176 (6) Å | T = 223 K |
β = 108.048 (1)° | Block, colourless |
V = 641.35 (6) Å3 | 0.25 × 0.10 × 0.07 mm |
Z = 2 |
Bruker SMART CCD diffractometer | 3244 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.022 |
Graphite monochromator | θmax = 30.0°, θmin = 2.2° |
ω scans | h = −7→9 |
5174 measured reflections | k = −12→10 |
3298 independent reflections | l = −15→14 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.040 | H-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 reflections | Δρmax = 0.38 e Å−3 |
164 parameters | Δρmin = −0.22 e Å−3 |
2 restraints | Absolute structure: Flack (1983) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.31 (7) |
C13H14N4S | V = 641.35 (6) Å3 |
Mr = 258.34 | Z = 2 |
Monoclinic, Pc | Mo Kα radiation |
a = 6.8629 (4) Å | µ = 0.24 mm−1 |
b = 9.1707 (5) Å | T = 223 K |
c = 10.7176 (6) Å | 0.25 × 0.10 × 0.07 mm |
β = 108.048 (1)° |
Bruker SMART CCD diffractometer | 3244 reflections with I > 2σ(I) |
5174 measured reflections | Rint = 0.022 |
3298 independent reflections |
R[F2 > 2σ(F2)] = 0.040 | H-atom parameters constrained |
wR(F2) = 0.111 | Δρmax = 0.38 e Å−3 |
S = 1.08 | Δρmin = −0.22 e Å−3 |
3298 reflections | Absolute structure: Flack (1983) |
164 parameters | Absolute structure parameter: 0.31 (7) |
2 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.15633 (5) | 0.32084 (4) | 0.81908 (4) | 0.03044 (12) | |
N1 | −0.0159 (2) | 0.09931 (17) | 0.90656 (18) | 0.0316 (3) | |
H1 | −0.0972 | 0.0665 | 0.9483 | 0.0416 (18)* | |
N2 | 0.6533 (3) | −0.05525 (19) | 0.97908 (19) | 0.0366 (4) | |
N3 | −0.0752 (3) | 0.32339 (15) | 0.97735 (17) | 0.0313 (3) | |
H3 | −0.1440 | 0.2778 | 1.0212 | 0.0416 (18)* | |
N4 | −0.2743 (3) | 0.7118 (2) | 0.68184 (18) | 0.0360 (4) | |
C1 | 0.0145 (2) | 0.24361 (19) | 0.90540 (16) | 0.0246 (3) | |
C2 | 0.0801 (3) | −0.0058 (2) | 0.8415 (2) | 0.0335 (4) | |
H2A | 0.0978 | 0.0395 | 0.7629 | 0.052 (2)* | |
H2B | −0.0115 | −0.0897 | 0.8131 | 0.052 (2)* | |
C3 | 0.2854 (3) | −0.05898 (19) | 0.92800 (18) | 0.0275 (3) | |
C4 | 0.3034 (3) | −0.1567 (2) | 1.0300 (2) | 0.0337 (4) | |
H4 | 0.1859 | −0.1909 | 1.0482 | 0.0416 (18)* | |
C5 | 0.4966 (4) | −0.2032 (2) | 1.1048 (2) | 0.0390 (4) | |
H5 | 0.5120 | −0.2695 | 1.1741 | 0.0416 (18)* | |
C6 | 0.6653 (3) | −0.1505 (2) | 1.0756 (2) | 0.0360 (4) | |
H6 | 0.7957 | −0.1833 | 1.1262 | 0.0416 (18)* | |
C7 | 0.4659 (3) | −0.0122 (2) | 0.9072 (2) | 0.0326 (4) | |
H7 | 0.4554 | 0.0538 | 0.8384 | 0.0416 (18)* | |
C8 | −0.0639 (3) | 0.4815 (2) | 0.98613 (19) | 0.0318 (4) | |
H8A | 0.0748 | 0.5122 | 0.9904 | 0.052 (2)* | |
H8B | −0.0874 | 0.5119 | 1.0680 | 0.052 (2)* | |
C9 | −0.2162 (3) | 0.55904 (18) | 0.87265 (17) | 0.0268 (3) | |
C10 | −0.4249 (3) | 0.5543 (2) | 0.8535 (2) | 0.0365 (4) | |
H10 | −0.4771 | 0.5015 | 0.9112 | 0.0416 (18)* | |
C11 | −0.5555 (3) | 0.6283 (3) | 0.7485 (2) | 0.0421 (5) | |
H11 | −0.6979 | 0.6257 | 0.7333 | 0.0416 (18)* | |
C12 | −0.4743 (3) | 0.7061 (3) | 0.6660 (2) | 0.0377 (4) | |
H12 | −0.5643 | 0.7574 | 0.5955 | 0.0416 (18)* | |
C13 | −0.1495 (3) | 0.6390 (2) | 0.78398 (19) | 0.0304 (4) | |
H13 | −0.0079 | 0.6423 | 0.7962 | 0.0416 (18)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0291 (2) | 0.0323 (2) | 0.0336 (2) | −0.00423 (18) | 0.01526 (16) | 0.00084 (18) |
N1 | 0.0249 (7) | 0.0275 (7) | 0.0465 (9) | −0.0013 (6) | 0.0169 (7) | 0.0013 (6) |
N2 | 0.0268 (8) | 0.0384 (9) | 0.0464 (9) | −0.0013 (6) | 0.0141 (7) | −0.0004 (7) |
N3 | 0.0388 (9) | 0.0266 (7) | 0.0346 (8) | 0.0003 (6) | 0.0202 (7) | 0.0021 (5) |
N4 | 0.0376 (9) | 0.0389 (8) | 0.0349 (8) | 0.0025 (7) | 0.0162 (7) | 0.0051 (7) |
C1 | 0.0181 (8) | 0.0285 (8) | 0.0267 (7) | −0.0016 (5) | 0.0063 (6) | 0.0006 (6) |
C2 | 0.0285 (9) | 0.0275 (8) | 0.0414 (10) | 0.0001 (6) | 0.0062 (7) | −0.0059 (7) |
C3 | 0.0262 (8) | 0.0252 (7) | 0.0323 (8) | 0.0001 (6) | 0.0106 (7) | −0.0035 (6) |
C4 | 0.0324 (10) | 0.0359 (9) | 0.0384 (9) | −0.0034 (7) | 0.0191 (8) | −0.0002 (7) |
C5 | 0.0443 (12) | 0.0417 (10) | 0.0309 (9) | 0.0049 (9) | 0.0113 (8) | 0.0057 (8) |
C6 | 0.0288 (10) | 0.0402 (10) | 0.0355 (9) | 0.0024 (8) | 0.0047 (8) | −0.0022 (8) |
C7 | 0.0320 (10) | 0.0294 (8) | 0.0390 (9) | −0.0007 (7) | 0.0147 (8) | 0.0042 (7) |
C8 | 0.0393 (10) | 0.0283 (8) | 0.0287 (8) | −0.0011 (7) | 0.0119 (7) | −0.0037 (6) |
C9 | 0.0318 (9) | 0.0231 (7) | 0.0285 (7) | −0.0038 (6) | 0.0139 (6) | −0.0053 (6) |
C10 | 0.0369 (11) | 0.0377 (10) | 0.0416 (10) | −0.0073 (8) | 0.0219 (9) | −0.0009 (8) |
C11 | 0.0277 (10) | 0.0521 (12) | 0.0476 (12) | −0.0052 (9) | 0.0132 (9) | −0.0024 (10) |
C12 | 0.0335 (11) | 0.0444 (10) | 0.0333 (9) | 0.0027 (8) | 0.0075 (8) | −0.0008 (8) |
C13 | 0.0290 (9) | 0.0303 (8) | 0.0362 (9) | −0.0014 (7) | 0.0167 (7) | −0.0006 (7) |
S1—C1 | 1.6920 (17) | C4—H4 | 0.9400 |
N1—C1 | 1.340 (2) | C5—C6 | 1.377 (3) |
N1—C2 | 1.461 (3) | C5—H5 | 0.9400 |
N1—H1 | 0.8700 | C6—H6 | 0.9400 |
N2—C6 | 1.337 (3) | C7—H7 | 0.9400 |
N2—C7 | 1.337 (3) | C8—C9 | 1.513 (3) |
N3—C1 | 1.343 (2) | C8—H8A | 0.9800 |
N3—C8 | 1.453 (2) | C8—H8B | 0.9800 |
N3—H3 | 0.8700 | C9—C10 | 1.383 (3) |
N4—C12 | 1.331 (3) | C9—C13 | 1.386 (2) |
N4—C13 | 1.341 (3) | C10—C11 | 1.380 (3) |
C2—C3 | 1.508 (3) | C10—H10 | 0.9400 |
C2—H2A | 0.9800 | C11—C12 | 1.381 (3) |
C2—H2B | 0.9800 | C11—H11 | 0.9400 |
C3—C4 | 1.389 (3) | C12—H12 | 0.9400 |
C3—C7 | 1.392 (3) | C13—H13 | 0.9400 |
C4—C5 | 1.387 (3) | ||
C1—N1—C2 | 123.55 (16) | N2—C6—H6 | 118.3 |
C1—N1—H1 | 118.2 | C5—C6—H6 | 118.3 |
C2—N1—H1 | 118.2 | N2—C7—C3 | 124.15 (18) |
C7—N2—C6 | 117.15 (18) | N2—C7—H7 | 117.9 |
C1—N3—C8 | 123.78 (16) | C3—C7—H7 | 117.9 |
C1—N3—H3 | 118.1 | N3—C8—C9 | 114.01 (16) |
C8—N3—H3 | 118.1 | N3—C8—H8A | 108.7 |
C12—N4—C13 | 117.25 (19) | C9—C8—H8A | 108.7 |
N3—C1—N1 | 115.62 (15) | N3—C8—H8B | 108.7 |
N3—C1—S1 | 121.98 (13) | C9—C8—H8B | 108.7 |
N1—C1—S1 | 122.40 (14) | H8A—C8—H8B | 107.6 |
N1—C2—C3 | 113.15 (16) | C10—C9—C13 | 117.51 (18) |
N1—C2—H2A | 108.9 | C10—C9—C8 | 122.04 (17) |
C3—C2—H2A | 108.9 | C13—C9—C8 | 120.46 (17) |
N1—C2—H2B | 108.9 | C11—C10—C9 | 119.12 (19) |
C3—C2—H2B | 108.9 | C11—C10—H10 | 120.4 |
H2A—C2—H2B | 107.8 | C9—C10—H10 | 120.4 |
C7—C3—C4 | 117.25 (18) | C10—C11—C12 | 119.2 (2) |
C7—C3—C2 | 120.68 (18) | C10—C11—H11 | 120.4 |
C4—C3—C2 | 122.07 (18) | C12—C11—H11 | 120.4 |
C5—C4—C3 | 119.29 (19) | N4—C12—C11 | 122.9 (2) |
C5—C4—H4 | 120.4 | N4—C12—H12 | 118.6 |
C3—C4—H4 | 120.4 | C11—C12—H12 | 118.6 |
C6—C5—C4 | 118.77 (19) | N4—C13—C9 | 124.06 (18) |
C6—C5—H5 | 120.6 | N4—C13—H13 | 118.0 |
C4—C5—H5 | 120.6 | C9—C13—H13 | 118.0 |
N2—C6—C5 | 123.37 (19) |
Experimental details
Crystal data | |
Chemical formula | C13H14N4S |
Mr | 258.34 |
Crystal system, space group | Monoclinic, Pc |
Temperature (K) | 223 |
a, b, c (Å) | 6.8629 (4), 9.1707 (5), 10.7176 (6) |
β (°) | 108.048 (1) |
V (Å3) | 641.35 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.24 |
Crystal size (mm) | 0.25 × 0.10 × 0.07 |
Data collection | |
Diffractometer | Bruker SMART CCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5174, 3298, 3244 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.704 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.111, 1.08 |
No. of reflections | 3298 |
No. of parameters | 164 |
No. of restraints | 2 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.38, −0.22 |
Absolute structure | Flack (1983) |
Absolute structure parameter | 0.31 (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).
S1—C1 | 1.6920 (17) | N3—C1 | 1.343 (2) |
N1—C1 | 1.340 (2) | N3—C8 | 1.453 (2) |
N1—C2 | 1.461 (3) | N4—C12 | 1.331 (3) |
N2—C6 | 1.337 (3) | N4—C13 | 1.341 (3) |
N2—C7 | 1.337 (3) | ||
C1—N1—C2 | 123.55 (16) | N3—C1—S1 | 121.98 (13) |
C1—N3—C8 | 123.78 (16) | N1—C1—S1 | 122.40 (14) |
N3—C1—N1 | 115.62 (15) |
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 C1═S1 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°.