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The structure of 2,6-bis­(2-pyridyltsulfanyl­methyl)pyridine (pytmp), (I), C17H15N3S2, presents a twisted conformation, with the three planar moieties almost perpendicular to each other. The structures of two related derivatives, namely 2,6-bis­(6-methyl-2-pyridylsulfanyl­methyl)pyridine (mpytmp), (II), C19H19N3S2, and 2,6-bis­(4-methyl-2-pyrimidylsulfanyl­methyl)­pyridine (mprtmp) n-pentane hemisolvate, (III), C17H17N5S2·0.5C5H12, present extended planar fragments with just one quasi-perpendicular aryl­sulfanyl­methyl side arm, such that the mol­ecules are folded in an L-shaped conformation. All three conformations appear different from those adopted by similar compounds, demonstrating the great flexibility of such species, although such differences in conformational behaviour might drive specific coordination modes.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270109051543/ku3018sup1.cif
Contains datablocks global, I, II, III

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270109051543/ku3018Isup2.hkl
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270109051543/ku3018IIsup3.hkl
Contains datablock II

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270109051543/ku3018IIIsup4.hkl
Contains datablock III

CCDC references: 765466; 765467; 765468

Comment top

The coordination chemistry of chelate ligands containing mixed functionalities in transition metal complexes is an active area of research. In particular, the chemistry of hemilabile ligands, which contain both inert and labile groups, has received considerable attention (Slone et al., 1999; Vagg, 1987; Heard, 2007). Some years ago, while studying thioether ligands with aromatic N-heterocycles, we found that these usually N,N-bidentate donors often show N,S-chelation towards congested ruthenium substrates (Scopelliti et al., 2001; Tresoldi et al., 2008). The resultant complexes display dynamic stereochemical rearrangements, which involve inversion at the S atom coordinated to ruthenium (Tresoldi et al., 2002), restricted rotation of the pendant ring (Baradello et al., 2004) and exchange between N,N-chelation, N,S-chelation with the formation of a five-membered ring and N,S-chelation with the formation of a four-membered ring (Tresoldi et al., 2002). However, species containing the last coordination type are, generally, low-concentration isomers in mixtures containing five-membered N,S-chelate species. Furthermore, the exchange processes between four- and five-membered N,S-chelated species show high energy barriers (Tresoldi et al., 2008).

With the aim of favouring the formation of four-membered N,S-chelated species and as an extension of our stereodynamic studies, we embarked on a programme which uses dithioether ligands containing a 2,6-substituted pyridine linker with two thioether-heterocycle arms to prepare fluxional transition metal complexes. These dithioether compounds can also be used as antiviral compounds (Joseph-McCarthy et al., 2001; Tsang et al., 2001). Furthermore, compounds bearing S and N donor atoms tend to form a great variety of structurally interesting supramolecular entities, in particular with group 11 metals (Peng et al., 2006; Han et al., 2005; Amoore et al., 2005; Li et al., 2004; Park et al. 2005). Since the flexible backbone of these dithioethers allows great structural diversity, we first investigated the Cambridge Structural Database (CSD, Version?; Allen, 2002) in order to understand the influence of the chemical nature of the outer rings on the structural and conformational properties of the dithioether ligands. It must be mentioned that the X-ray determination of 2,6-bis(2-pyrimidylthiomethyl)pyridine (prtmp) has already been reported (Peng et al., 2006). We prepared the dithioethers by the reaction of the pyridine or pyrimidine thiolate, formed in situ from KOH and the appropriate thiol, and 2,6-bis(chloromethyl)pyridine in butan-1-ol at high temperature. In this way, we were able to obtain the new ligand 2,6-bis(6-methyl-2-pyridylthiomethyl)pyridine (mpytmp). Colourless crystals of the title compounds 2,6-bis(2-pyridylthiomethyl)pyridine, pytmp, (I), 2,6-bis(6-methyl-2-pyridylthiomethyl)pyridine, mpytmp, (II), and 2,6-bis(4-methyl-2-pyrimidylthiomethyl)pyridine, mprtmp, as the n-pentane hemisolvate, (III), were obtained by slow evaporation of solvent mixtures and we present here their crystallographic characterization.

In (I), the pytmp molecule exists in a closed conformation (Figs. 1 and 2). Indeed, the approximately planar 2-pyridylthiomethylene moieties [maximum deviation from the mean N1/C2–C6/S8/C9 plane of 0.176 (2) Å for atom C3 and from the mean C16/S17/N19/C18–C23 plane of 0.106 (1) Å for atom C16] are both almost perpendicular with respect to the 2,6-dimethylpyridine core [angles between the mean planes 75.88 (2) and 70.25 (3)°, respectively]. This arrangement, with a pseudo-Cs symmetry (Figs. 1 and 2; Table 1), is also stabilized by dipolar intramolecular interactions between the methylene groups and the nearby pyridine N atoms (C9···N1 = 2.91, H9A···N1 = 2.39 Å and C9—H9A···N1 = 113°, and C16···N19 = 2.93, H16B···N19 = 2.44 Å and C16—H16B···N19 = 111°). The overall three-dimensional packing is stabilized by hydrophobic interactions and by a weak dipolar intermolecular interaction aligning molecules along the crystallographic screw b axis [C9···S17i = 3.76 Å and C9—H9B···S17i = 144°; symmetry code: (i) -x + 3/2, y + 1/2, -z + 1/2] (Fig. 5).

In the structure of (II), the central pyridyl ring of the mpytmp molecule is roughly coplanar with one of the side arms [Fig. 3; angle between mean planes 6.90 (3)°], so that an extended part of the molecule is roughly planar, with a maximum overall deviation from the N1/C2–C6/S8/C9/C10/C15 mean plane (but excluding C7) of 0.405 (2) Å for atom C4. Because of steric reasons, the other methylthioether group is tilted out of this plane; the angle between the N1/C2–C6/S8/C9/C10/C15 (excluding C7) and C16/S17/N19/C18–C23 mean planes is 64° (see also the comparison of selected parameters in Table 1). The crystal packing is mainly supported by non-polar interactions, such as head-to-tail ππ staggered stacking between homologous extended N1/C2–C6/S8/C9/C10/C15 planar moieties related by the the symmetry operator (-x + 1, -y + 1, -z + 1) [interplanar distance = 3.503 (3) Å, centroid-to-centroid distance = 4.234 (3) Å, and angle between the centroid line and the planes = 34°]. The whole crystal packing is made up of stacked L-shaped molecules (Fig. 2) filling the three-dimensional space (Fig. 6).

The asymmetric unit of (III) is composed of one mprtmp molecule (Fig. 4) and one-half of an n-pentane molecule disordered around the crystallographic inversion centre. Again, the mprtmp molecule shows an extended planar moiety for atoms N1/C2/N3/C4–C6/S8/C9/C10/C15 (excluding C7) [maximum deviation from the mean plane of 0.259 (3) Å for atom C9], whereas the other `arm' is out of the plane (angle between the mean planes of the extended group and C16/S17/C18/N19/C20–C22/N23 = 80°; see also dihedral angles in Table 1]. This time, the mutual orientation of the planar fragments is different from (II), as can be deduced from the selected dihedral angles, but again the conformation of the molecule resembles an L-shaped building block (Fig. 2) for the crystal packing.

Because of some weak dipolar intermolecular interactions [C15···N1i = 3.70, H15···N1i = 2.79 Å and C15—H15···N1= 165°; C15···S8i = 3.83, H15···S8I = 3.19 Å and C15—H15···S8i = 128 °; C14···S17i = 3.86, H14···S17i = 3.17 Å and C15—H15···S8i = 132 °; symmetry code: (i) x - 1, y, z], the mprtmp units of (III) are arrayed along the crystallographic a axis. The L-shaped conformation allows a brick-like filling of the other two space directions, further supported by ππ staggered interactions between the single pyridyl fragments related by the symmetry operator (-x + 2, -y, -z + 2) [with a mean interplanar distance of 3.472 (3) Å, a centroid-to-centroid distance of 3.521 (3) Å, and an angle between the centroid line and the planes of 1.3 (2) °]. Channels of n-pentane solvent run along the crystallographic a axis (Fig. 7).

It is well known that 2,6-bis(arylthiomethyl)pyridines, because of the orientation of the S lone pairs, drastically change their conformation to bind to transition metals (Teixidor et al., 2001). The conformations of (I)–(III) seem to be unique among uncoordinated 2,6-bis(arylthiomethyl)pyridines (Luo et al., 2006; Sillanpää et al., 1994). This is likely allowed by the presence of ortho aromatic N atoms over the pendant side chains. However, the large deviation from the quasi-C2 symmetric conformation of the very similar prtmp (Peng et al., 2006; comparable with Luo et al., 2006) confirms the high flexibility of such substrates, the major conformations of which are established only by weak inter- and intramolecular forces.

Experimental top

2,6-Bis(2-pyridylthiomethyl)pyridine, pytmp, (I), was prepared by the following procedure. A stirred mixture of KOH (2.17 g, 38.7 mmol) and 2-mercaptopyridine (4.30 g, 38.7 mmol) in butan-1-ol (60 ml) was heated to reflux for 1 h under N2. To the resulting thiolate solution, cooled to room temperature and stirred, were added slowly (over ca 30 min) and alternately small portions (ca 50 mg) of 2,6-bis(chloromethyl)pyridine (3.41 g, 19.4 mmol) and small aliquots (ca 1 ml) of butan-1-ol (20 ml). The solution was then heated to 363–373 K for 3 h. The solvent was removed and the residue extracted with CH2Cl2 (160 ml). Crystals suitable for X-ray analysis were obtained by slow evaporation of of a solution in a mixture of CH2Cl2 and n-heptane (50 ml) [Solvent ratio?]. Pytmp is very soluble in CHCl3 and CH2Cl2, moderately soluble in acetone and sparingly soluble in diethyl ether.

2,6-Bis(6-methyl-2-pyridylthiomethyl)pyridine, mpytmp, (II), was prepared in a similar manner to (I), using KOH (2.17 g, 38.7 mmol), 2-mercapto-6-methylpyridine (4.85 g, 38.7 mmol) and 2,6-bis(chloromethyl)pyridine (3.41 g, 19.4 mmol). The product obtained by extraction with CH2Cl2 and slow evaporation was an oil, which was dissolved in a mixture of diethyl ether (50 ml) and pentane (100 ml) and allowed to stand until colourless crystals of (II) suitable for X-ray analysis were formed. Mpytmp is soluble in most common solvents.

2,6-Bis(4-methyl-2-pyrimidylthiomethyl)pyridine n-pentane hemisolvate, mprtmp n-pentane hemisolvate, (III), was prepared in a similar manner to (I), using 2-mercapto-4-methylpyrimidine hydrochloride (6.29 g, 38.7 mmol), KOH (4.34 g, 77.4 mmol) and 2,6-bis(chloromethyl)pyridine (3.41 g, 19.4 mmol). Crystals suitable for X-ray analysis were obtained by slow evaporation (ca 2 d) of a solution in a mixture of CH2Cl2, n-heptane and n-pentane (2:1:1 v/v).

Spectroscopic and analytical data for compounds (I) and (II) are extensively reported in the archived CIF. [No data are included for (III) - do you wish to add any?]

Refinement top

All H atoms were located in difference Fourier maps and refined in ideal positions using the riding and rigid model technique, with C—H distances in the range 0.93 (aromatic H) to 0.97 Å (methylene H), and with Uiso(H) = 1.5Ueq(C) for methyl H and 1.2Ueq(C) for aromatic and methylene H. In (II) and (III), dynamic or statistical disorder of the methyl groups was treated as two totally staggered conformations with site-occupancy factors of 0.5. The half n-pentane solvent in (III) was treated as a rigid group with a site occupancy factor of 0.5 by restraining both displacement parameters and distances. The components of the anisotropic displacement parameters in the direction of the bonds were restrained to be equal within an effective standard deviation of 0.001, and additionally the Uij components were restrained to approximate isotropic behaviour. Distance 1–2 [Please clarify] was restrained to 1.540 (5) Å and distance 1–3 [Please clarify] was restrained to 2.52 (1) Å. Because of the disorder around the inversion centre, the parameters were set free from the symmetry operation (Ng, 2005).

Computing details top

For all compounds, data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Bruker, 2007), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999), PARST (Nardelli, 1995), enCIFer (Allen et al., 2004) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. Space-filling views of the molecular conformations of (I), (II) and (III).
[Figure 3] Fig. 3. The molecular structure of (II), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 4] Fig. 4. The molecular structure of (III), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 5] Fig. 5. The crystal packing of (I). S atoms are shown with larger radii.
[Figure 6] Fig. 6. The crystal packing of (II). S atoms are shown with larger radii.
[Figure 7] Fig. 7. The crystal packing of (III). S atoms are shown with larger radii. The n-pentane molecules are embedded in channels along the crystallographic a axis.
(I) 2,6-bis(2-pyridylthiomethyl)pyridine top
Crystal data top
C17H15N3S2F(000) = 680
Mr = 325.44Dx = 1.388 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9457 reflections
a = 10.696 (1) Åθ = 2.6–27.6°
b = 9.281 (1) ŵ = 0.34 mm1
c = 16.741 (1) ÅT = 296 K
β = 110.39 (2)°Irregular, colourless
V = 1557.7 (3) Å30.38 × 0.26 × 0.14 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
3188 independent reflections
Graphite monochromator2886 reflections with I > 2σ(I)
Detector resolution: 9 pixels mm-1Rint = 0.026
ϕ and ω scansθmax = 26.4°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
h = 1313
Tmin = 0.856, Tmax = 1k = 1111
46596 measured reflectionsl = 2020
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)] = 0.028H-atom parameters constrained
wR(F2) = 0.080 w = 1/[σ2(Fo2) + (0.037P)2 + 0.4485P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max = 0.001
3188 reflectionsΔρmax = 0.25 e Å3
200 parametersΔρmin = 0.26 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0249 (13)
Crystal data top
C17H15N3S2V = 1557.7 (3) Å3
Mr = 325.44Z = 4
Monoclinic, P21/cMo Kα radiation
a = 10.696 (1) ŵ = 0.34 mm1
b = 9.281 (1) ÅT = 296 K
c = 16.741 (1) Å0.38 × 0.26 × 0.14 mm
β = 110.39 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
3188 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
2886 reflections with I > 2σ(I)
Tmin = 0.856, Tmax = 1Rint = 0.026
46596 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0280 restraints
wR(F2) = 0.080H-atom parameters constrained
S = 1.08Δρmax = 0.25 e Å3
3188 reflectionsΔρmin = 0.26 e Å3
200 parameters
Special details top

Experimental. IR spectrum for (I) (KBr nujol): 1590 s, 1575 vs, 1555 vs, 1455 vs, 1411 vs, 1396 s, 1377 s, 1288 s, 1282 s, 1234 m, 1244 s, 1154 s, 1148 s, 1143 s, 1120 vs, 1118 vs, 1084 s, 1044 s, 1004 s, 992 s, 984 s, 960 m, 891 s, 852 ms, 838 m, 822 s, 763 s, 752 s, 732 ms, 720 s, 718 vs, 679 s, 668 m, 638 ms, 620 ms, 575 s, 559 m, 520 ms, 480 s, 428 ms and 418 ms cm-1. Analysis for C17H15N3S2, calculated: C 62.74, H 4.64, N 12.91, S 19.70%; found: C 62.70, H 4.50, N 12.80, S 19.50%. In the 1H NMR spectrum (300 MHz, acetone-d6, 298 K) of pytmp, the pyridine protons of the outer rings give an ABMX system: the ddd signals of H6 protons are observed at δ 8.43 (J6,5 = 5.0, J6,4 = 1.9, J6,3 = 1.0 Hz), of H4 at δ 7.60 (J4,3 = 8.1, J4,5 = 7.3), H3 at δ 7.31 and H5 at δ 7.08. The H4 proton of the central pyridine ring is observed as triplet at δ 7.62 (J = 7.8 Hz) and the H3 and H5 protons of the same ring as doublet at δ 7.36. The methylene protons give a singlet at δ 4.53. In the 13C{1H} NMR spectrum (75.56 MHz, CDCl3, 298 K), the signals are observed at δ 158.7 (CS), 158.0 (C—CH2), 149.6 (C6 of outer rings), 137.5 (C4 of central ring), 136.3 (C4 of outer rings), 122.2 (C3 and C5 of central ring), 121.7 (C3 of outer rings), 119.8 (C5 of outer rings), 36.2 (methylene).

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
N10.07422 (11)0.33303 (13)0.00009 (7)0.0418 (3)
C20.00576 (14)0.23799 (14)0.01690 (8)0.0395 (3)
C30.03597 (19)0.14644 (19)0.08643 (11)0.0619 (4)
H30.02230.07960.09580.074*
C40.1653 (2)0.1566 (2)0.14124 (11)0.0705 (5)
H40.19610.09620.18840.085*
C50.24879 (17)0.25643 (19)0.12605 (10)0.0573 (4)
H50.33650.26620.16290.069*
C60.19935 (15)0.34137 (17)0.05501 (9)0.0479 (3)
H60.25610.40860.04440.057*
S80.17558 (4)0.22973 (5)0.04864 (2)0.05169 (13)
C90.17723 (14)0.32782 (15)0.14236 (8)0.0418 (3)
H9A0.10640.3990.12590.05*
H9B0.26140.37870.1660.05*
C100.15926 (12)0.23172 (13)0.20955 (8)0.0350 (3)
N110.27108 (10)0.18329 (11)0.26887 (6)0.0344 (2)
C120.25921 (12)0.09780 (13)0.33057 (7)0.0348 (3)
C130.13728 (14)0.05761 (15)0.33481 (9)0.0435 (3)
H130.13250.00160.37850.052*
C140.02257 (14)0.10748 (17)0.27261 (10)0.0493 (3)
H140.06090.08160.27360.059*
C150.03319 (13)0.19568 (16)0.20928 (9)0.0440 (3)
H150.04280.23060.1670.053*
C160.38791 (14)0.04827 (15)0.39571 (8)0.0424 (3)
H16A0.44350.13150.41890.051*
H16B0.36920.00150.44210.051*
S170.47857 (3)0.07550 (4)0.35245 (2)0.04766 (12)
C180.42567 (13)0.24729 (14)0.37354 (8)0.0387 (3)
N190.34812 (13)0.25832 (13)0.42010 (9)0.0481 (3)
C200.31193 (17)0.39164 (17)0.43422 (11)0.0558 (4)
H200.25840.40140.46730.067*
C210.34906 (18)0.51399 (17)0.40285 (11)0.0585 (4)
H210.32060.60410.41370.07*
C220.42995 (17)0.50018 (17)0.35462 (11)0.0564 (4)
H220.45690.58140.33230.068*
C230.47021 (14)0.36587 (17)0.33986 (9)0.0476 (3)
H230.52580.35410.30820.057*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0424 (6)0.0448 (6)0.0374 (6)0.0008 (5)0.0130 (5)0.0012 (5)
C20.0459 (7)0.0390 (7)0.0343 (6)0.0006 (5)0.0149 (5)0.0057 (5)
C30.0733 (11)0.0555 (10)0.0524 (9)0.0078 (8)0.0164 (8)0.0129 (7)
C40.0844 (13)0.0660 (11)0.0475 (9)0.0107 (10)0.0058 (9)0.0173 (8)
C50.0517 (9)0.0691 (10)0.0415 (8)0.0106 (8)0.0042 (7)0.0073 (7)
C60.0441 (7)0.0559 (9)0.0424 (7)0.0034 (6)0.0134 (6)0.0091 (6)
S80.0434 (2)0.0709 (3)0.0423 (2)0.01074 (17)0.01705 (16)0.00431 (17)
C90.0396 (7)0.0432 (7)0.0384 (7)0.0041 (5)0.0083 (5)0.0052 (6)
C100.0371 (6)0.0318 (6)0.0340 (6)0.0009 (5)0.0097 (5)0.0015 (5)
N110.0357 (5)0.0321 (5)0.0329 (5)0.0021 (4)0.0087 (4)0.0022 (4)
C120.0423 (6)0.0284 (6)0.0314 (6)0.0000 (5)0.0100 (5)0.0043 (5)
C130.0521 (8)0.0407 (7)0.0409 (7)0.0016 (6)0.0202 (6)0.0033 (6)
C140.0404 (7)0.0544 (8)0.0580 (9)0.0016 (6)0.0232 (6)0.0056 (7)
C150.0350 (6)0.0470 (7)0.0473 (7)0.0033 (6)0.0109 (6)0.0065 (6)
C160.0477 (7)0.0371 (7)0.0351 (6)0.0002 (6)0.0055 (5)0.0007 (5)
S170.0412 (2)0.0466 (2)0.0572 (2)0.00423 (14)0.01957 (16)0.00929 (16)
C180.0337 (6)0.0421 (7)0.0356 (6)0.0033 (5)0.0062 (5)0.0006 (5)
N190.0532 (7)0.0401 (6)0.0581 (7)0.0008 (5)0.0282 (6)0.0051 (5)
C200.0646 (10)0.0455 (8)0.0671 (10)0.0066 (7)0.0355 (8)0.0062 (7)
C210.0692 (10)0.0398 (8)0.0685 (10)0.0059 (7)0.0266 (8)0.0071 (7)
C220.0634 (10)0.0455 (8)0.0591 (9)0.0061 (7)0.0197 (7)0.0143 (7)
C230.0445 (7)0.0544 (9)0.0437 (7)0.0068 (6)0.0150 (6)0.0062 (6)
Geometric parameters (Å, º) top
N1—C21.3255 (18)C13—C141.383 (2)
N1—C61.3360 (18)C13—H130.93
C2—C31.384 (2)C14—C151.375 (2)
C2—S81.7663 (14)C14—H140.93
C3—C41.371 (3)C15—H150.93
C3—H30.93C16—S171.8093 (15)
C4—C51.371 (3)C16—H16A0.97
C4—H40.93C16—H16B0.97
C5—C61.370 (2)S17—C181.7681 (14)
C5—H50.93C18—N191.3254 (18)
C6—H60.93C18—C231.3941 (19)
S8—C91.8086 (14)N19—C201.3418 (19)
C9—C101.4995 (17)C20—C211.367 (2)
C9—H9A0.97C20—H200.93
C9—H9B0.97C21—C221.380 (2)
C10—N111.3382 (16)C21—H210.93
C10—C151.3877 (18)C22—C231.369 (2)
N11—C121.3432 (16)C22—H220.93
C12—C131.3818 (19)C23—H230.93
C12—C161.4997 (18)
C2—N1—C6117.27 (12)C12—C13—H13120.8
N1—C2—C3122.99 (14)C14—C13—H13120.8
N1—C2—S8119.80 (10)C15—C14—C13119.32 (13)
C3—C2—S8117.16 (12)C15—C14—H14120.3
C4—C3—C2118.38 (16)C13—C14—H14120.3
C4—C3—H3120.8C14—C15—C10118.83 (13)
C2—C3—H3120.8C14—C15—H15120.6
C3—C4—C5119.54 (15)C10—C15—H15120.6
C3—C4—H4120.2C12—C16—S17112.81 (9)
C5—C4—H4120.2C12—C16—H16A109
C6—C5—C4118.07 (15)S17—C16—H16A109
C6—C5—H5121C12—C16—H16B109
C4—C5—H5121S17—C16—H16B109
N1—C6—C5123.72 (15)H16A—C16—H16B107.8
N1—C6—H6118.1C18—S17—C16103.84 (7)
C5—C6—H6118.1N19—C18—C23123.30 (13)
C2—S8—C9102.36 (6)N19—C18—S17119.77 (10)
C10—C9—S8112.72 (10)C23—C18—S17116.93 (11)
C10—C9—H9A109C18—N19—C20116.93 (12)
S8—C9—H9A109N19—C20—C21123.93 (15)
C10—C9—H9B109N19—C20—H20118
S8—C9—H9B109C21—C20—H20118
H9A—C9—H9B107.8C20—C21—C22118.23 (15)
N11—C10—C15122.52 (12)C20—C21—H21120.9
N11—C10—C9116.19 (11)C22—C21—H21120.9
C15—C10—C9121.29 (12)C23—C22—C21119.41 (14)
C10—N11—C12118.01 (11)C23—C22—H22120.3
N11—C12—C13122.87 (12)C21—C22—H22120.3
N11—C12—C16115.57 (11)C22—C23—C18118.19 (14)
C13—C12—C16121.57 (12)C22—C23—H23120.9
C12—C13—C14118.45 (12)C18—C23—H23120.9
C6—N1—C2—C31.9 (2)C16—C12—C13—C14179.91 (13)
C6—N1—C2—S8175.53 (10)C12—C13—C14—C150.5 (2)
N1—C2—C3—C41.3 (3)C13—C14—C15—C100.2 (2)
S8—C2—C3—C4176.14 (14)N11—C10—C15—C140.4 (2)
C2—C3—C4—C50.2 (3)C9—C10—C15—C14179.81 (13)
C3—C4—C5—C61.0 (3)N11—C12—C16—S1768.29 (13)
C2—N1—C6—C51.0 (2)C13—C12—C16—S17111.93 (12)
C4—C5—C6—N10.5 (2)C12—C16—S17—C1893.36 (10)
N1—C2—S8—C916.27 (12)C16—S17—C18—N196.38 (13)
C3—C2—S8—C9166.19 (12)C16—S17—C18—C23174.14 (10)
C2—S8—C9—C1092.31 (10)C23—C18—N19—C200.2 (2)
S8—C9—C10—N1192.78 (12)S17—C18—N19—C20179.67 (12)
S8—C9—C10—C1587.05 (14)C18—N19—C20—C210.7 (3)
C15—C10—N11—C120.69 (18)N19—C20—C21—C220.8 (3)
C9—C10—N11—C12179.48 (11)C20—C21—C22—C230.1 (3)
C10—N11—C12—C130.43 (18)C21—C22—C23—C180.9 (2)
C10—N11—C12—C16179.35 (10)N19—C18—C23—C221.0 (2)
N11—C12—C13—C140.1 (2)S17—C18—C23—C22179.49 (12)
(II) 2,6-bis(6-methyl-2-pyridylthiomethyl)pyridine top
Crystal data top
C19H19N3S2Z = 2
Mr = 353.49F(000) = 372
Triclinic, P1Dx = 1.328 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.946 (1) ÅCell parameters from 9973 reflections
b = 9.842 (1) Åθ = 2.2–27.5°
c = 12.503 (1) ŵ = 0.31 mm1
α = 69.829 (2)°T = 296 K
β = 75.053 (2)°Irregular, colourless
γ = 80.807 (2)°0.36 × 0.28 × 0.16 mm
V = 884.06 (16) Å3
Data collection top
Bruker APEXII CCD
diffractometer
3351 independent reflections
Radiation source: sealed tube3133 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
Detector resolution: 9 pixels mm-1θmax = 25.7°, θmin = 3.1°
ϕ and ω scansh = 99
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
k = 1111
Tmin = 0.934, Tmax = 1l = 1515
25682 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.089H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0473P)2 + 0.2366P]
where P = (Fo2 + 2Fc2)/3
3351 reflections(Δ/σ)max = 0.028
219 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = 0.3 e Å3
Crystal data top
C19H19N3S2γ = 80.807 (2)°
Mr = 353.49V = 884.06 (16) Å3
Triclinic, P1Z = 2
a = 7.946 (1) ÅMo Kα radiation
b = 9.842 (1) ŵ = 0.31 mm1
c = 12.503 (1) ÅT = 296 K
α = 69.829 (2)°0.36 × 0.28 × 0.16 mm
β = 75.053 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
3351 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
3133 reflections with I > 2σ(I)
Tmin = 0.934, Tmax = 1Rint = 0.020
25682 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.089H-atom parameters constrained
S = 1.05Δρmax = 0.21 e Å3
3351 reflectionsΔρmin = 0.3 e Å3
219 parameters
Special details top

Experimental. IR spectrum for (II) (KBr nujol): 1595 vs, 1556 br, 1434 br, 1403 br, 1376 vs, 1257 s, 1241 s, 1204 s, 1176 s, 1144 br, 1086 vs, 1034 s, 1004 s, 992 s, 973 s, 914 s, 898 s, 879 s, 869 vs, 798 vs, 788 vs, 775 vs, 758 vs, 729 s, 678 s, 611 ms, 593 ms, 561 ms, 546 ms, 538 ms, 448 m and 421 m cm-1. Analysis for C19H19N3S2, calculated: C 64.55, H 5.42, N 11.89, S 18.14%; found: C 64.70, H 5.50, N 11.80, S 18.00%. The 1H NMR spectrum (300 MHz, acetone-d6, 298 K) of mpytmp shows the deshielded H4 proton of the central pyridine ring as triplet at δ 7.63 (J = 7.7 Hz) and the H3 and H5 protons of the same ring as doublet at δ 7.38. Furthermore, the H3 and H5 protons of the outer pyridine rings give two doublets at δ 7.10 (J = 7.7 Hz) and δ 6.94 (J = 7.5 Hz), respectively, and the H4 protons of the same rings give a triplet at δ 7.48. The methylene protons give a signal at δ 4.53 and the methyl protons at δ 2.47. In the 13C{1H} NMR spectrum (75.56 MHz, acetone-d6, 298 K), the signals are observed at δ 158.2 (CS), 158.1 (C—CH2), 157.4 (C—CH3), 137.1 (C4 of central ring), 136.7 (C4 of outer rings), 121.3 (C3 and C5 of central ring), 118.8 (C3 of outer rings), 118.5 (C5 of outer rings), 35.3 (methylene), 23.5 (methyl).

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*/UeqOcc. (<1)
N10.15192 (15)0.73317 (13)0.34857 (10)0.0453 (3)
C20.18078 (18)0.76129 (16)0.43887 (12)0.0443 (3)
C30.1820 (2)0.90043 (19)0.44210 (16)0.0610 (4)
H30.2020.91560.5070.073*
C40.1527 (3)1.0150 (2)0.34676 (18)0.0715 (5)
H40.15241.10990.3460.086*
C50.1240 (2)0.98853 (19)0.25281 (16)0.0635 (5)
H50.10511.06530.18730.076*
C60.12338 (19)0.84690 (18)0.25572 (13)0.0509 (4)
C70.0880 (2)0.8118 (2)0.15658 (15)0.0675 (5)
H7A0.05230.71470.18390.101*0.5
H7B0.19220.81930.09610.101*0.5
H7C0.00330.87890.12620.101*0.5
H7D0.10850.89390.08690.101*0.5
H7E0.03140.78930.17470.101*0.5
H7F0.16410.72970.14460.101*0.5
S80.21766 (6)0.61694 (4)0.56417 (3)0.05140 (13)
C90.2615 (2)0.46735 (16)0.50711 (12)0.0474 (3)
H9A0.15860.45550.48410.057*
H9B0.35590.48840.43820.057*
C100.31068 (17)0.32936 (15)0.59557 (11)0.0395 (3)
N110.35095 (15)0.33797 (12)0.68983 (9)0.0400 (3)
C120.39592 (17)0.21472 (15)0.76910 (11)0.0387 (3)
C130.4027 (2)0.08040 (16)0.75665 (13)0.0495 (3)
H130.4330.00340.81360.059*
C140.3632 (3)0.07289 (18)0.65737 (15)0.0592 (4)
H140.3690.01640.64590.071*
C150.3154 (2)0.19789 (17)0.57619 (13)0.0520 (4)
H150.28680.19480.50950.062*
C160.44125 (19)0.23169 (16)0.87307 (12)0.0438 (3)
H16A0.53030.30.84720.053*
H16B0.48710.1390.91970.053*
S170.24729 (5)0.29707 (5)0.95997 (3)0.04965 (13)
C180.33537 (18)0.33080 (15)1.06356 (11)0.0394 (3)
N190.50405 (15)0.29498 (12)1.06317 (10)0.0403 (3)
C200.56814 (19)0.32481 (15)1.14166 (12)0.0419 (3)
C210.4649 (2)0.38725 (17)1.22219 (13)0.0496 (4)
H210.51240.40541.27610.06*
C220.2897 (2)0.42230 (18)1.22144 (13)0.0522 (4)
H220.21790.46441.2750.063*
C230.2223 (2)0.39458 (17)1.14103 (12)0.0478 (3)
H230.10490.41771.13850.057*
C240.7600 (2)0.2881 (2)1.13566 (15)0.0562 (4)
H24A0.81020.24921.07270.084*0.5
H24B0.77780.21731.20790.084*0.5
H24C0.81510.37421.12250.084*0.5
H24D0.79180.31121.19610.084*0.5
H24E0.82420.34321.06080.084*0.5
H24F0.78690.18631.14620.084*0.5
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0418 (6)0.0519 (7)0.0407 (6)0.0013 (5)0.0131 (5)0.0120 (5)
C20.0414 (7)0.0490 (8)0.0405 (7)0.0001 (6)0.0089 (6)0.0133 (6)
C30.0747 (11)0.0545 (9)0.0573 (10)0.0019 (8)0.0169 (8)0.0216 (8)
C40.0861 (14)0.0479 (9)0.0752 (12)0.0027 (9)0.0190 (10)0.0132 (9)
C50.0585 (10)0.0554 (10)0.0592 (10)0.0021 (8)0.0142 (8)0.0017 (8)
C60.0365 (7)0.0644 (10)0.0439 (8)0.0031 (7)0.0111 (6)0.0089 (7)
C70.0594 (10)0.0913 (14)0.0498 (9)0.0050 (9)0.0260 (8)0.0145 (9)
S80.0700 (3)0.0508 (2)0.0360 (2)0.00278 (18)0.01756 (17)0.01596 (16)
C90.0588 (9)0.0513 (8)0.0365 (7)0.0001 (7)0.0180 (6)0.0158 (6)
C100.0390 (7)0.0474 (8)0.0342 (6)0.0051 (6)0.0089 (5)0.0141 (6)
N110.0447 (6)0.0430 (6)0.0351 (6)0.0042 (5)0.0127 (5)0.0126 (5)
C120.0375 (7)0.0440 (7)0.0354 (7)0.0042 (5)0.0098 (5)0.0118 (5)
C130.0610 (9)0.0417 (8)0.0471 (8)0.0031 (7)0.0179 (7)0.0115 (6)
C140.0833 (12)0.0458 (9)0.0590 (10)0.0072 (8)0.0233 (9)0.0230 (7)
C150.0674 (10)0.0556 (9)0.0427 (8)0.0092 (7)0.0190 (7)0.0208 (7)
C160.0475 (8)0.0480 (8)0.0392 (7)0.0002 (6)0.0178 (6)0.0135 (6)
S170.0425 (2)0.0747 (3)0.0408 (2)0.00877 (17)0.01323 (15)0.02466 (18)
C180.0449 (7)0.0425 (7)0.0322 (6)0.0101 (6)0.0121 (5)0.0082 (5)
N190.0446 (6)0.0428 (6)0.0363 (6)0.0063 (5)0.0141 (5)0.0107 (5)
C200.0489 (8)0.0414 (7)0.0375 (7)0.0085 (6)0.0175 (6)0.0074 (6)
C210.0612 (9)0.0549 (9)0.0408 (7)0.0082 (7)0.0203 (7)0.0171 (6)
C220.0601 (9)0.0595 (9)0.0414 (8)0.0038 (7)0.0101 (7)0.0229 (7)
C230.0447 (8)0.0588 (9)0.0410 (7)0.0052 (7)0.0101 (6)0.0163 (7)
C240.0519 (9)0.0654 (10)0.0573 (9)0.0046 (7)0.0252 (7)0.0174 (8)
Geometric parameters (Å, º) top
N1—C21.3317 (18)C13—C141.384 (2)
N1—C61.3455 (19)C13—H130.93
C2—C31.385 (2)C14—C151.370 (2)
C2—S81.768 (1)C14—H140.93
C3—C41.371 (3)C15—H150.93
C3—H30.93C16—S171.809 (1)
C4—C51.367 (3)C16—H16A0.97
C4—H40.93C16—H16B0.97
C5—C61.383 (3)S17—C181.765 (1)
C5—H50.93C18—N191.3294 (18)
C6—C71.497 (2)C18—C231.389 (2)
C7—H7A0.96N19—C201.3465 (17)
C7—H7B0.96C20—C211.380 (2)
C7—H7C0.96C20—C241.498 (2)
C7—H7D0.96C21—C221.381 (2)
C7—H7E0.96C21—H210.93
C7—H7F0.96C22—C231.373 (2)
S8—C91.797 (1)C22—H220.93
C9—C101.4959 (19)C23—H230.93
C9—H9A0.97C24—H24A0.96
C9—H9B0.97C24—H24B0.96
C10—N111.3307 (17)C24—H24C0.96
C10—C151.389 (2)C24—H24D0.96
N11—C121.3404 (17)C24—H24E0.96
C12—C131.375 (2)C24—H24F0.96
C12—C161.5026 (18)
C2—N1—C6117.66 (13)C12—C13—H13120.8
N1—C2—C3123.54 (14)C14—C13—H13120.8
N1—C2—S8120.02 (11)C15—C14—C13119.51 (14)
C3—C2—S8116.44 (12)C15—C14—H14120.2
C4—C3—C2118.04 (17)C13—C14—H14120.2
C4—C3—H3121C14—C15—C10118.59 (13)
C2—C3—H3121C14—C15—H15120.7
C5—C4—C3119.36 (17)C10—C15—H15120.7
C5—C4—H4120.3C12—C16—S17109.25 (9)
C3—C4—H4120.3C12—C16—H16A109.8
C4—C5—C6119.61 (16)S17—C16—H16A109.8
C4—C5—H5120.2C12—C16—H16B109.8
C6—C5—H5120.2S17—C16—H16B109.8
N1—C6—C5121.80 (15)H16A—C16—H16B108.3
N1—C6—C7116.38 (15)C18—S17—C16101.30 (6)
C5—C6—C7121.81 (15)N19—C18—C23123.83 (12)
C6—C7—H7A109.5N19—C18—S17118.93 (10)
C6—C7—H7B109.5C23—C18—S17117.25 (11)
H7A—C7—H7B109.5C18—N19—C20117.52 (12)
C6—C7—H7C109.5N19—C20—C21122.44 (14)
H7A—C7—H7C109.5N19—C20—C24116.02 (13)
H7B—C7—H7C109.5C21—C20—C24121.54 (13)
C6—C7—H7D109.5C20—C21—C22118.90 (13)
H7A—C7—H7D141.1C20—C21—H21120.5
H7B—C7—H7D56.3C22—C21—H21120.5
H7C—C7—H7D56.3C23—C22—C21119.56 (14)
C6—C7—H7E109.5C23—C22—H22120.2
H7A—C7—H7E56.3C21—C22—H22120.2
H7B—C7—H7E141.1C22—C23—C18117.74 (14)
H7C—C7—H7E56.3C22—C23—H23121.1
H7D—C7—H7E109.5C18—C23—H23121.1
C6—C7—H7F109.5C20—C24—H24A109.5
H7A—C7—H7F56.3C20—C24—H24B109.5
H7B—C7—H7F56.3H24A—C24—H24B109.5
H7C—C7—H7F141.1C20—C24—H24C109.5
H7D—C7—H7F109.5H24A—C24—H24C109.5
H7E—C7—H7F109.5H24B—C24—H24C109.5
C2—S8—C9100.32 (7)C20—C24—H24D109.5
C10—C9—S8111.36 (9)H24A—C24—H24D141.1
C10—C9—H9A109.4H24B—C24—H24D56.3
S8—C9—H9A109.4H24C—C24—H24D56.3
C10—C9—H9B109.4C20—C24—H24E109.5
S8—C9—H9B109.4H24A—C24—H24E56.3
H9A—C9—H9B108H24B—C24—H24E141.1
N11—C10—C15122.38 (13)H24C—C24—H24E56.3
N11—C10—C9118.17 (12)H24D—C24—H24E109.5
C15—C10—C9119.45 (12)C20—C24—H24F109.5
C10—N11—C12118.42 (12)H24A—C24—H24F56.3
N11—C12—C13122.69 (12)H24B—C24—H24F56.3
N11—C12—C16115.89 (12)H24C—C24—H24F141.1
C13—C12—C16121.42 (12)H24D—C24—H24F109.5
C12—C13—C14118.40 (14)H24E—C24—H24F109.5
C6—N1—C2—C30.3 (2)C16—C12—C13—C14178.51 (15)
C6—N1—C2—S8179.54 (10)C12—C13—C14—C151.3 (3)
N1—C2—C3—C40.4 (3)C13—C14—C15—C100.9 (3)
S8—C2—C3—C4179.59 (14)N11—C10—C15—C140.1 (2)
C2—C3—C4—C50.1 (3)C9—C10—C15—C14179.08 (15)
C3—C4—C5—C60.6 (3)N11—C12—C16—S1767.25 (14)
C2—N1—C6—C50.2 (2)C13—C12—C16—S17113.44 (14)
C2—N1—C6—C7178.87 (13)C12—C16—S17—C18172.7 (1)
C4—C5—C6—N10.6 (3)C16—S17—C18—N194.75 (12)
C4—C5—C6—C7178.35 (17)C16—S17—C18—C23174.99 (11)
N1—C2—S8—C915.15 (13)C23—C18—N19—C201.1 (2)
C3—C2—S8—C9165.59 (13)S17—C18—N19—C20178.66 (10)
C2—S8—C9—C10175.9 (1)C18—N19—C20—C211.4 (2)
S8—C9—C10—N1113.66 (17)C18—N19—C20—C24177.77 (12)
S8—C9—C10—C15167.31 (12)N19—C20—C21—C220.9 (2)
C15—C10—N11—C120.7 (2)C24—C20—C21—C22178.25 (14)
C9—C10—N11—C12179.68 (12)C20—C21—C22—C230.0 (2)
C10—N11—C12—C130.2 (2)C21—C22—C23—C180.4 (2)
C10—N11—C12—C16179.55 (12)N19—C18—C23—C220.2 (2)
N11—C12—C13—C140.8 (2)S17—C18—C23—C22179.53 (12)
(III) 2,6-bis(4-methyl-2-pyrimidylthiomethyl)pyridine n-pentane hemisolvate top
Crystal data top
C17H17N5S2·0.5C5H12Z = 2
Mr = 391.57F(000) = 414
Triclinic, P1Dx = 1.313 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.407 (1) ÅCell parameters from 9954 reflections
b = 11.100 (1) Åθ = 2.7–29.9°
c = 12.428 (1) ŵ = 0.28 mm1
α = 95.91 (1)°T = 296 K
β = 99.80 (1)°Laminar, colourless
γ = 97.31 (1)°0.36 × 0.3 × 0.12 mm
V = 990.6 (2) Å3
Data collection top
Bruker APEXII CCD
diffractometer
3758 independent reflections
Graphite monochromator3265 reflections with I > 2σ(I)
Detector resolution: 9 pixels mm-1Rint = 0.052
ϕ and ω scansθmax = 25.7°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
h = 99
Tmin = 0.898, Tmax = 1k = 1313
33717 measured reflectionsl = 1515
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.135H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0726P)2 + 0.4726P]
where P = (Fo2 + 2Fc2)/3
3758 reflections(Δ/σ)max < 0.001
264 parametersΔρmax = 0.39 e Å3
40 restraintsΔρmin = 0.52 e Å3
Crystal data top
C17H17N5S2·0.5C5H12γ = 97.31 (1)°
Mr = 391.57V = 990.6 (2) Å3
Triclinic, P1Z = 2
a = 7.407 (1) ÅMo Kα radiation
b = 11.100 (1) ŵ = 0.28 mm1
c = 12.428 (1) ÅT = 296 K
α = 95.91 (1)°0.36 × 0.3 × 0.12 mm
β = 99.80 (1)°
Data collection top
Bruker APEXII CCD
diffractometer
3758 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
3265 reflections with I > 2σ(I)
Tmin = 0.898, Tmax = 1Rint = 0.052
33717 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.04440 restraints
wR(F2) = 0.135H-atom parameters constrained
S = 1.06Δρmax = 0.39 e Å3
3758 reflectionsΔρmin = 0.52 e Å3
264 parameters
Special details top

Experimental. 2,6-bis-[2-(4-methyl)pyrimidylthiomethyl]pyridine (mprtmp, II) was prepared as I, from 2-mercapto-4-methylpyrimidine hydrochloride (6.29 g, 38.7 mmol), KOH 4.34 g (77.4 mmol) and 2,6-bis(chloromethyl)pyridine (3.41 g 19.4 mmol). Crystals suitable for X-ray analysis were obtained by slow evaporation (ca. 2 d) of CH2Cl2, n-heptane and n-pentane mixture (2:1:1). Mprtmp is very soluble in CHCl3 and CH2Cl2, moderately in acetone and sparingly in diethyl ether. IR spectra (KBr nujol) 1591vs, 1562br, 1543vs, 1453br, 1435vs, 1415br, 1377vs, 1336br, 1267s, 1197vs, 1168s, 1125s, 1085s, 1035s, 994s, 976s, 879s, 856s, 839s, 827vs, 769s, 747s, 714s, 684ms, 634ms, 592ms, 580ms, 561ms, 543s, 526ms, 440m and 418ms cm-1. Analysis C39H46N10S4 calculated: C 59.82, H 5.92, N 17.89, S 16.38%; found: C 60.00, H 5.90, N 17.80, S 16.00%. The 1H NMR spectrum (300 MHz, acetone-d6, 298 K) of mprtmp shows the deshielded H6 protons of the outer pyrimidine rings as doublet at δ 8.42 (J = 5.1 Hz), the H5 protons of the same rings as doublet at δ 7.02, the H4 proton of the central pyridine ring as triplet at δ 7.64 (J = 7.8 Hz) and the H3 and H5 protons of the same ring as doublet at δ 7.41. The methylene protons give a signal at δ 4.51 and the methyl protons at δ 2.42. The 13C{1H} NMR spectrum (300 MHz, acetone-d6, 298 K) gives signals at δ 168.6 (CS), 158.6 (C-CH3), 158.0 (C-CH2 and C6 of outer rings), 138.1 (C4 of central ring), 122.3 (C3 and C5 of central ring), 117.4 (C5 of outer rings), 37.2 (methylene), 24.0 (methyl).

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*/UeqOcc. (<1)
N10.9382 (3)0.15960 (19)0.96401 (15)0.0510 (5)
C20.7564 (3)0.1613 (2)0.94648 (17)0.0460 (5)
N30.6503 (3)0.1712 (3)1.02074 (16)0.0697 (7)
C40.7405 (4)0.1821 (4)1.1251 (2)0.0837 (10)
H40.67250.19011.18120.1*
C50.9245 (4)0.1822 (3)1.1531 (2)0.0683 (7)
H50.98260.19071.22650.082*
C61.0234 (3)0.1695 (2)1.06967 (18)0.0521 (5)
C71.2256 (4)0.1672 (3)1.0913 (2)0.0745 (8)
H7A1.26850.15781.02270.112*0.5
H7B1.2520.09991.13110.112*0.5
H7C1.28760.24261.13420.112*0.5
H7D1.27020.17571.16930.112*0.5
H7E1.28670.23361.06090.112*0.5
H7F1.25110.09091.05780.112*0.5
S80.65672 (8)0.14776 (6)0.80548 (4)0.05184 (19)
C90.4180 (3)0.1429 (3)0.8144 (2)0.0722 (8)
H9A0.37630.06790.84250.087*
H9B0.4050.21120.86650.087*
C100.2970 (3)0.1484 (2)0.70631 (17)0.0443 (5)
N110.3650 (2)0.12554 (16)0.61433 (14)0.0402 (4)
C120.2550 (3)0.13007 (16)0.51799 (15)0.0354 (4)
C130.0777 (3)0.15861 (19)0.51114 (18)0.0441 (5)
H130.00580.16340.44310.053*
C140.0084 (3)0.1799 (2)0.60647 (19)0.0478 (5)
H140.11140.19780.60350.057*
C150.1189 (3)0.1742 (2)0.70537 (19)0.0483 (5)
H150.07510.18750.77080.058*
C160.3296 (3)0.09541 (19)0.41621 (16)0.0413 (5)
H16A0.23940.10630.35290.05*
H16B0.34030.00890.41160.05*
S170.54963 (7)0.17802 (5)0.40567 (4)0.04757 (19)
C180.4948 (3)0.3233 (2)0.37982 (16)0.0421 (5)
N190.6433 (3)0.4008 (2)0.37106 (19)0.0613 (5)
C200.6088 (4)0.5123 (3)0.3541 (3)0.0736 (8)
H200.70720.57050.34780.088*
C210.4365 (4)0.5465 (2)0.3455 (2)0.0660 (7)
H210.41740.62580.33410.079*
C220.2928 (3)0.4590 (2)0.35437 (19)0.0513 (5)
N230.3217 (2)0.34502 (16)0.37121 (14)0.0433 (4)
C240.0991 (4)0.4863 (3)0.3481 (3)0.0794 (9)
H24A0.01950.41390.35640.119*0.5
H24B0.05720.51240.27810.119*0.5
H24C0.09620.55010.40590.119*0.5
H24D0.09580.57040.33710.119*0.5
H24E0.05810.47180.41550.119*0.5
H24F0.01910.43410.28770.119*0.5
C250.5713 (13)0.4956 (16)0.9793 (11)0.152 (4)0.5
H25A0.47270.49581.02050.229*0.5
H25B0.55840.41760.93530.229*0.5
H25C0.56570.5590.93230.229*0.5
C260.7596 (16)0.519 (2)1.0596 (11)0.207 (5)0.5
H26A0.7820.6021.09640.248*0.5
H26B0.75830.46341.11520.248*0.5
C270.9128 (14)0.498 (2)0.9949 (13)0.205 (4)0.5
H27A0.88090.41650.95340.246*0.5
H27B0.91450.55610.94220.246*0.5
C281.1064 (15)0.5078 (19)1.0615 (12)0.208 (4)0.5
H28A1.10850.44571.1110.25*0.5
H28B1.13770.58721.10610.25*0.5
C291.2531 (16)0.493 (2)0.9900 (14)0.192 (6)0.5
H29A1.25250.55430.94110.288*0.5
H29B1.22590.4130.94780.288*0.5
H29C1.3730.50141.03630.288*0.5
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0465 (11)0.0737 (13)0.0333 (9)0.0131 (9)0.0070 (8)0.0050 (8)
C20.0457 (12)0.0617 (13)0.0315 (10)0.0122 (10)0.0074 (9)0.0048 (9)
N30.0522 (12)0.128 (2)0.0320 (10)0.0237 (12)0.0111 (9)0.0081 (11)
C40.0640 (17)0.161 (3)0.0328 (13)0.0314 (18)0.0161 (12)0.0122 (16)
C50.0644 (16)0.112 (2)0.0297 (12)0.0239 (15)0.0047 (11)0.0084 (12)
C60.0507 (13)0.0695 (14)0.0356 (11)0.0124 (11)0.0039 (9)0.0068 (10)
C70.0509 (15)0.120 (2)0.0512 (15)0.0198 (15)0.0008 (12)0.0118 (15)
S80.0445 (3)0.0845 (4)0.0276 (3)0.0154 (3)0.0071 (2)0.0044 (2)
C90.0467 (14)0.135 (3)0.0371 (13)0.0138 (15)0.0108 (10)0.0176 (14)
C100.0402 (11)0.0574 (12)0.0352 (11)0.0034 (9)0.0091 (8)0.0060 (9)
N110.0378 (9)0.0515 (9)0.0329 (9)0.0090 (7)0.0077 (7)0.0082 (7)
C120.0377 (10)0.0346 (9)0.0334 (10)0.0040 (7)0.0053 (8)0.0055 (7)
C130.0390 (11)0.0526 (12)0.0403 (11)0.0093 (9)0.0031 (9)0.0081 (9)
C140.0364 (11)0.0551 (12)0.0538 (13)0.0097 (9)0.0115 (9)0.0063 (10)
C150.0431 (12)0.0597 (13)0.0433 (12)0.0048 (10)0.0165 (9)0.0012 (10)
C160.0444 (11)0.0479 (11)0.0321 (10)0.0114 (9)0.0053 (8)0.0042 (8)
S170.0394 (3)0.0677 (4)0.0422 (3)0.0191 (2)0.0128 (2)0.0152 (2)
C180.0395 (11)0.0561 (12)0.0304 (10)0.0046 (9)0.0079 (8)0.0045 (8)
N190.0443 (11)0.0716 (13)0.0689 (14)0.0012 (9)0.0177 (10)0.0135 (11)
C200.0645 (17)0.0692 (17)0.085 (2)0.0136 (14)0.0222 (15)0.0135 (15)
C210.0741 (18)0.0509 (13)0.0738 (18)0.0044 (12)0.0171 (14)0.0115 (12)
C220.0542 (13)0.0512 (12)0.0489 (13)0.0103 (10)0.0092 (10)0.0053 (10)
N230.0388 (9)0.0512 (10)0.0407 (9)0.0083 (7)0.0079 (7)0.0064 (7)
C240.0649 (18)0.0712 (17)0.108 (3)0.0282 (14)0.0162 (17)0.0167 (16)
C250.153 (4)0.151 (4)0.153 (4)0.0223 (12)0.0280 (13)0.0195 (12)
C260.208 (4)0.206 (5)0.206 (5)0.0305 (12)0.0384 (13)0.0265 (12)
C270.207 (4)0.204 (5)0.205 (5)0.0298 (12)0.0379 (12)0.0266 (12)
C280.208 (4)0.208 (5)0.208 (5)0.0307 (12)0.0379 (12)0.0267 (12)
C290.193 (6)0.191 (6)0.192 (6)0.0283 (14)0.0359 (15)0.0249 (13)
Geometric parameters (Å, º) top
N1—C21.329 (3)S17—C181.760 (2)
N1—C61.343 (3)C18—N231.323 (3)
C2—N31.315 (3)C18—N191.334 (3)
C2—S81.765 (2)N19—C201.326 (4)
N3—C41.340 (3)C20—C211.367 (4)
C4—C51.348 (4)C20—H200.93
C4—H40.93C21—C221.374 (4)
C5—C61.374 (3)C21—H210.93
C5—H50.93C22—N231.341 (3)
C6—C71.480 (4)C22—C241.494 (4)
C7—H7A0.96C24—H24A0.96
C7—H7B0.96C24—H24B0.96
C7—H7C0.96C24—H24C0.96
C7—H7D0.96C24—H24D0.96
C7—H7E0.96C24—H24E0.96
C7—H7F0.96C24—H24F0.96
S8—C91.785 (3)C25—C261.546 (5)
C9—C101.494 (3)C25—H25A0.96
C9—H9A0.97C25—H25B0.96
C9—H9B0.97C25—H25C0.96
C10—N111.339 (3)C26—C271.525 (5)
C10—C151.384 (3)C26—H26A0.97
N11—C121.338 (2)C26—H26B0.97
C12—C131.381 (3)C27—C281.513 (5)
C12—C161.498 (3)C27—H27A0.97
C13—C141.379 (3)C27—H27B0.97
C13—H130.93C28—C291.531 (5)
C14—C151.368 (3)C28—H28A0.97
C14—H140.93C28—H28B0.97
C15—H150.93C29—H29A0.96
C16—S171.798 (2)C29—H29B0.96
C16—H16A0.97C29—H29C0.96
C16—H16B0.97
C2—N1—C6116.3 (2)C12—C16—H16A108.1
N3—C2—N1127.4 (2)S17—C16—H16A108.1
N3—C2—S8119.47 (17)C12—C16—H16B108.1
N1—C2—S8113.09 (16)S17—C16—H16B108.1
C2—N3—C4114.5 (2)H16A—C16—H16B107.3
N3—C4—C5123.4 (2)C18—S17—C16102.86 (10)
N3—C4—H4118.3N23—C18—N19127.6 (2)
C5—C4—H4118.3N23—C18—S17120.06 (16)
C4—C5—C6117.8 (2)N19—C18—S17112.35 (17)
C4—C5—H5121.1C20—N19—C18114.3 (2)
C6—C5—H5121.1N19—C20—C21123.6 (2)
N1—C6—C5120.4 (2)N19—C20—H20118.2
N1—C6—C7117.3 (2)C21—C20—H20118.2
C5—C6—C7122.2 (2)C20—C21—C22117.3 (2)
C6—C7—H7A109.5C20—C21—H21121.4
C6—C7—H7B109.5C22—C21—H21121.4
H7A—C7—H7B109.5N23—C22—C21121.0 (2)
C6—C7—H7C109.5N23—C22—C24116.9 (2)
H7A—C7—H7C109.5C21—C22—C24122.0 (2)
H7B—C7—H7C109.5C18—N23—C22116.20 (19)
C6—C7—H7D109.5C22—C24—H24A109.5
H7A—C7—H7D141.1C22—C24—H24B109.5
H7B—C7—H7D56.3H24A—C24—H24B109.5
H7C—C7—H7D56.3C22—C24—H24C109.5
C6—C7—H7E109.5H24A—C24—H24C109.5
H7A—C7—H7E56.3H24B—C24—H24C109.5
H7B—C7—H7E141.1C22—C24—H24D109.5
H7C—C7—H7E56.3H24A—C24—H24D141.1
H7D—C7—H7E109.5H24B—C24—H24D56.3
C6—C7—H7F109.5H24C—C24—H24D56.3
H7A—C7—H7F56.3C22—C24—H24E109.5
H7B—C7—H7F56.3H24A—C24—H24E56.3
H7C—C7—H7F141.1H24B—C24—H24E141.1
H7D—C7—H7F109.5H24C—C24—H24E56.3
H7E—C7—H7F109.5H24D—C24—H24E109.5
C2—S8—C9100.22 (11)C22—C24—H24F109.5
C10—C9—S8113.04 (17)H24A—C24—H24F56.3
C10—C9—H9A109H24B—C24—H24F56.3
S8—C9—H9A109H24C—C24—H24F141.1
C10—C9—H9B109H24D—C24—H24F109.5
S8—C9—H9B109H24E—C24—H24F109.5
H9A—C9—H9B107.8C27—C26—C25109.0 (7)
N11—C10—C15122.91 (19)C27—C26—H26A109.9
N11—C10—C9118.33 (19)C25—C26—H26A109.9
C15—C10—C9118.8 (2)C27—C26—H26B109.9
C12—N11—C10117.80 (17)C25—C26—H26B109.9
N11—C12—C13122.35 (18)H26A—C26—H26B108.3
N11—C12—C16116.63 (17)C28—C27—C26116.4 (7)
C13—C12—C16120.93 (17)C28—C27—H27A108.2
C14—C13—C12119.20 (19)C26—C27—H27A108.2
C14—C13—H13120.4C28—C27—H27B108.2
C12—C13—H13120.4C26—C27—H27B108.2
C15—C14—C13118.9 (2)H27A—C27—H27B107.3
C15—C14—H14120.5C27—C28—C29113.1 (7)
C13—C14—H14120.5C27—C28—H28A109
C14—C15—C10118.8 (2)C29—C28—H28A109
C14—C15—H15120.6C27—C28—H28B109
C10—C15—H15120.6C29—C28—H28B109
C12—C16—S17116.60 (14)H28A—C28—H28B107.8
C6—N1—C2—N30.1 (4)C12—C13—C14—C151.1 (3)
C6—N1—C2—S8179.98 (17)C13—C14—C15—C100.6 (3)
N1—C2—N3—C40.8 (4)N11—C10—C15—C141.8 (3)
S8—C2—N3—C4179.4 (2)C9—C10—C15—C14179.7 (2)
C2—N3—C4—C50.4 (5)N11—C12—C16—S1755.3 (2)
N3—C4—C5—C60.5 (6)C13—C12—C16—S17128.07 (18)
C2—N1—C6—C50.9 (4)C12—C16—S17—C1872.42 (16)
C2—N1—C6—C7179.7 (2)C16—S17—C18—N231.20 (19)
C4—C5—C6—N11.2 (4)C16—S17—C18—N19178.87 (16)
C4—C5—C6—C7179.4 (3)N23—C18—N19—C201.6 (4)
N3—C2—S8—C93.6 (3)S17—C18—N19—C20178.5 (2)
N1—C2—S8—C9176.2 (2)C18—N19—C20—C210.4 (4)
C2—S8—C9—C10172.2 (2)N19—C20—C21—C220.4 (5)
S8—C9—C10—N1116.4 (3)C20—C21—C22—N230.3 (4)
S8—C9—C10—C15165.0 (2)C20—C21—C22—C24179.0 (3)
C15—C10—N11—C121.1 (3)N19—C18—N23—C221.8 (3)
C9—C10—N11—C12179.6 (2)S17—C18—N23—C22178.31 (16)
C10—N11—C12—C130.8 (3)C21—C22—N23—C180.7 (3)
C10—N11—C12—C16175.79 (18)C24—C22—N23—C18178.0 (2)
N11—C12—C13—C141.9 (3)C25—C26—C27—C28176.1 (13)
C16—C12—C13—C14174.53 (19)C26—C27—C28—C29177 (2)

Experimental details

(I)(II)(III)
Crystal data
Chemical formulaC17H15N3S2C19H19N3S2C17H17N5S2·0.5C5H12
Mr325.44353.49391.57
Crystal system, space groupMonoclinic, P21/cTriclinic, P1Triclinic, P1
Temperature (K)296296296
a, b, c (Å)10.696 (1), 9.281 (1), 16.741 (1)7.946 (1), 9.842 (1), 12.503 (1)7.407 (1), 11.100 (1), 12.428 (1)
α, β, γ (°)90, 110.39 (2), 9069.829 (2), 75.053 (2), 80.807 (2)95.91 (1), 99.80 (1), 97.31 (1)
V3)1557.7 (3)884.06 (16)990.6 (2)
Z422
Radiation typeMo KαMo KαMo Kα
µ (mm1)0.340.310.28
Crystal size (mm)0.38 × 0.26 × 0.140.36 × 0.28 × 0.160.36 × 0.3 × 0.12
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Bruker APEXII CCD
diffractometer
Bruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2007)
Multi-scan
(SADABS; Bruker, 2007)
Multi-scan
(SADABS; Bruker, 2007)
Tmin, Tmax0.856, 10.934, 10.898, 1
No. of measured, independent and
observed [I > 2σ(I)] reflections
46596, 3188, 2886 25682, 3351, 3133 33717, 3758, 3265
Rint0.0260.0200.052
(sin θ/λ)max1)0.6250.6100.610
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.028, 0.080, 1.08 0.032, 0.089, 1.05 0.044, 0.135, 1.06
No. of reflections318833513758
No. of parameters200219264
No. of restraints0040
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.25, 0.260.21, 0.30.39, 0.52

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP (Bruker, 2007), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006), WinGX (Farrugia, 1999), PARST (Nardelli, 1995), enCIFer (Allen et al., 2004) and PLATON (Spek, 2009).

Comparison of selected geometric parameters (Å, °) for (I), (II) and (III) top
Parameters(I)(II)(III)
C2-S81.766 (1)1.768 (1)1.763 (2)
S8-C91.809 (1)1.797 (1)1.781 (2)
C16-S171.809 (1)1.809 (1)1.797 (2)
S17-C181.768 (1)1.765 (1)1.759 (2)
C2-S8-C9102.4 (1)100.3 (1)100.1 (1)
C18-S17-C16103.8 (1)101.3 (1)102.9 (1)
N1-C2-S8-C9-16.3 (1)15.1 (1)-3.8 (2)
C3-C2-S8-C9166.19 (12)-165.6 (1)176.3 (2)
C2-S8-C9-C10-92.3 (1)175.9 (1)172.4 (2)
C12-C16-S17-C1893.4 (1)-172.7 (1)-55.4 (2)
C16-S17-C18-N196.4 (1)-4.7 (1)128.0 (2)
C16-S17-C18-C23-174.1 (1)175.0 (1)-72.3 (1)
 

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