Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103015701/gd1264sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270103015701/gd1264Isup2.hkl |
CCDC reference: 221077
Crystals of (I) were obtained directly during the thermal annealing of 3-cyanopyridine in the presence of magnesium phthalocyanine as catalyst at 453–473 °K. Below 453°K, the (4 + 1)-coordination complex of magnesium phthalocyanine with a 3-cyanopyridine molecule axially coordinated to the central Mg atom is stable (Janczak & Kubiak, 2003). Above 453°K, the 3-cyanopyridine molecules are released from the MgPc[3-CN(C5H4N)] complex in an activated state and the title complex forms from two 3-cyanopyridine molecules. In one of the molecules, the H atom ortho to both the CN group and the pyridine N atom is transfered to the C atom of the CN group, and then the activated 3-cyanopyridine molecules react and form crystalline (I).
The Friedel equivalents were not merged; however, in the absence of significant anomalous scattering, the value of the Flack (1983) parameter [0.2 (2)] was only weakly indicative of the correct orientation of the structure relative to the polar axis. In the final stages of refinement, H atoms were introduced in calculated positions [C—H = 0.93 Å] and refined using a riding model [Uiso = 1.2Ueq of the parent C atom].
Data collection: KM-4 Software (Kuma, 2000; cell refinement: KM-4 Software; data reduction: KM-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1990); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).
C12H8N4 | F(000) = 432 |
Mr = 208.22 | Dx = 1.449 Mg m−3 Dm = 1.445 Mg m−3 Dm measured by floatation |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 1322 reflections |
a = 21.627 (4) Å | θ = 2.6–27.9° |
b = 3.804 (1) Å | µ = 0.09 mm−1 |
c = 11.605 (2) Å | T = 293 K |
V = 954.7 (3) Å3 | Parallelepiped, colourless |
Z = 4 | 0.38 × 0.12 × 0.08 mm |
Kuma KM-4 CCD area-detector diffractometer | 2107 independent reflections |
Radiation source: fine-focus sealed tube | 1322 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.036 |
Detector resolution: 1024x1024 with blocks 2x2 pixels mm-1 | θmax = 27.9°, θmin = 2.6° |
ω scan | h = −27→27 |
Absorption correction: analytical face-indexed, SHELXTL (Sheldrick, 1990) | k = −4→4 |
Tmin = 0.959, Tmax = 0.984 | l = −15→14 |
5415 measured reflections |
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)] = 0.051 | H-atom parameters constrained |
wR(F2) = 0.075 | w = 1/[σ2(Fo2) + (0.025P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.99 | (Δ/σ)max = 0.002 |
2107 reflections | Δρmax = 0.15 e Å−3 |
145 parameters | Δρmin = −0.15 e Å−3 |
0 restraints | Absolute structure: Flack (1983) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.2 (2), 928 Friedel pairs |
C12H8N4 | V = 954.7 (3) Å3 |
Mr = 208.22 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 21.627 (4) Å | µ = 0.09 mm−1 |
b = 3.804 (1) Å | T = 293 K |
c = 11.605 (2) Å | 0.38 × 0.12 × 0.08 mm |
Kuma KM-4 CCD area-detector diffractometer | 2107 independent reflections |
Absorption correction: analytical face-indexed, SHELXTL (Sheldrick, 1990) | 1322 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.984 | Rint = 0.036 |
5415 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | H-atom parameters constrained |
wR(F2) = 0.075 | Δρmax = 0.15 e Å−3 |
S = 0.99 | Δρmin = −0.15 e Å−3 |
2107 reflections | Absolute structure: Flack (1983) |
145 parameters | Absolute structure parameter: 0.2 (2), 928 Friedel pairs |
0 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 | ||
N1 | 0.73090 (13) | −0.3877 (7) | 0.1125 (2) | 0.0535 (7) | |
C2 | 0.78534 (14) | −0.2616 (7) | 0.1584 (3) | 0.0464 (8) | |
H2 | 0.7901 | −0.2671 | 0.2380 | 0.060* | |
C3 | 0.83356 (11) | −0.1269 (7) | 0.0928 (2) | 0.0415 (6) | |
C4 | 0.82762 (12) | −0.1306 (6) | −0.02531 (19) | 0.0358 (6) | |
H4 | 0.8594 | −0.0483 | −0.0720 | 0.043* | |
C5 | 0.77375 (12) | −0.2581 (8) | −0.0735 (2) | 0.0473 (7) | |
H5 | 0.7683 | −0.2652 | −0.1529 | 0.057* | |
C6 | 0.72867 (15) | −0.3737 (8) | 0.0000 (3) | 0.0503 (8) | |
H6 | 0.6922 | −0.4514 | −0.0340 | 0.060* | |
C7 | 0.89007 (11) | 0.0159 (7) | 0.14897 (19) | 0.0349 (7) | |
N8 | 0.93792 (9) | 0.0730 (5) | 0.08373 (18) | 0.0317 (5) | |
C9 | 0.98851 (12) | 0.2087 (7) | 0.13493 (17) | 0.0341 (7) | |
N10 | 1.03788 (9) | 0.2679 (6) | 0.0651 (2) | 0.0412 (5) | |
C11 | 1.08655 (14) | 0.4069 (8) | 0.1170 (3) | 0.0444 (7) | |
H11 | 1.1209 | 0.4463 | 0.0706 | 0.056* | |
C12 | 1.09266 (12) | 0.5008 (7) | 0.2312 (2) | 0.0429 (7) | |
H12 | 1.1290 | 0.6025 | 0.2582 | 0.051* | |
C13 | 1.04380 (14) | 0.4405 (8) | 0.3042 (2) | 0.0504 (8) | |
H13 | 1.0457 | 0.4947 | 0.3823 | 0.060* | |
C14 | 0.98998 (13) | 0.2898 (8) | 0.2532 (2) | 0.0429 (7) | |
C15 | 0.93725 (13) | 0.2028 (7) | 0.3138 (2) | 0.0471 (7) | |
H15 | 0.9371 | 0.2454 | 0.3927 | 0.056* | |
N16 | 0.88618 (11) | 0.0610 (6) | 0.26712 (18) | 0.0434 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0477 (14) | 0.0557 (16) | 0.0570 (15) | −0.0073 (15) | 0.0000 (12) | 0.0038 (13) |
C2 | 0.052 (2) | 0.0435 (17) | 0.0430 (15) | 0.001 (2) | 0.0015 (14) | 0.0013 (14) |
C3 | 0.0387 (12) | 0.0403 (15) | 0.0465 (16) | 0.0015 (16) | 0.0013 (12) | 0.0014 (14) |
C4 | 0.0375 (14) | 0.0346 (14) | 0.0353 (14) | 0.0018 (16) | 0.0013 (15) | 0.0017 (14) |
C5 | 0.0385 (15) | 0.0456 (16) | 0.0578 (18) | −0.0013 (15) | 0.0020 (13) | −0.0017 (14) |
C6 | 0.0525 (19) | 0.0445 (17) | 0.0540 (19) | 0.0014 (16) | −0.0021 (14) | −0.0015 (15) |
C7 | 0.0366 (15) | 0.0372 (15) | 0.0308 (15) | −0.0016 (12) | −0.0021 (10) | 0.0018 (12) |
N8 | 0.0306 (10) | 0.0272 (12) | 0.0372 (14) | 0.0022 (9) | −0.0021 (9) | 0.0014 (10) |
C9 | 0.0402 (16) | 0.0367 (16) | 0.0255 (11) | 0.0016 (17) | 0.0022 (15) | 0.0013 (16) |
N10 | 0.0377 (10) | 0.0453 (12) | 0.0405 (12) | 0.0015 (10) | −0.0012 (9) | 0.0011 (11) |
C11 | 0.0460 (15) | 0.0437 (18) | 0.0435 (16) | −0.0020 (15) | 0.0009 (12) | 0.0012 (15) |
C12 | 0.0338 (11) | 0.0433 (17) | 0.0515 (19) | 0.0013 (15) | −0.0014 (12) | −0.0001 (14) |
C13 | 0.0589 (19) | 0.051 (2) | 0.0414 (17) | −0.0004 (17) | −0.0020 (14) | 0.0009 (15) |
C14 | 0.0453 (16) | 0.0432 (18) | 0.0401 (13) | 0.0019 (16) | 0.0021 (14) | 0.0015 (15) |
C15 | 0.0521 (16) | 0.0425 (19) | 0.0466 (17) | 0.0019 (15) | 0.0003 (13) | −0.0013 (15) |
N16 | 0.0468 (13) | 0.0455 (14) | 0.0379 (13) | −0.0002 (12) | 0.0021 (11) | −0.0020 (12) |
N1—C6 | 1.307 (3) | N8—C9 | 1.348 (3) |
N1—C2 | 1.378 (4) | C9—N10 | 1.359 (3) |
C2—C3 | 1.389 (4) | C9—C14 | 1.407 (3) |
C2—H2 | 0.9300 | N10—C11 | 1.323 (4) |
C3—C4 | 1.377 (3) | C11—C12 | 1.380 (4) |
C3—C7 | 1.488 (3) | C11—H11 | 0.9300 |
C4—C5 | 1.380 (4) | C12—C13 | 1.374 (4) |
C4—H4 | 0.9300 | C12—H12 | 0.9300 |
C5—C6 | 1.368 (4) | C13—C14 | 1.426 (4) |
C5—H5 | 0.9300 | C13—H13 | 0.9300 |
C6—H6 | 0.9300 | C14—C15 | 1.380 (4) |
C7—N8 | 1.301 (3) | C15—N16 | 1.343 (3) |
C7—N16 | 1.384 (3) | C15—H15 | 0.9300 |
C6—N1—C2 | 113.8 (3) | N8—C9—N10 | 116.0 (2) |
N1—C2—C3 | 123.9 (3) | N8—C9—C14 | 122.2 (2) |
N1—C2—H2 | 118.0 | N10—C9—C14 | 121.9 (3) |
C3—C2—H2 | 118.0 | C11—N10—C9 | 114.8 (3) |
C4—C3—C2 | 118.1 (3) | N10—C11—C12 | 128.1 (3) |
C4—C3—C7 | 121.1 (2) | N10—C11—H11 | 115.9 |
C2—C3—C7 | 120.8 (2) | C12—C11—H11 | 115.9 |
C5—C4—C3 | 119.0 (3) | C13—C12—C11 | 118.4 (3) |
C5—C4—H4 | 120.5 | C13—C12—H12 | 120.8 |
C3—C4—H4 | 120.5 | C11—C12—H12 | 120.8 |
C6—C5—C4 | 117.5 (3) | C12—C13—C14 | 116.0 (3) |
C6—C5—H5 | 121.2 | C12—C13—H13 | 122.0 |
C4—C5—H5 | 121.2 | C14—C13—H13 | 122.0 |
N1—C6—C5 | 127.5 (3) | C15—C14—C9 | 115.2 (3) |
N1—C6—H6 | 116.2 | C15—C14—C13 | 124.0 (3) |
C5—C6—H6 | 116.2 | C9—C14—C13 | 120.8 (3) |
N8—C7—N16 | 127.2 (2) | N16—C15—C14 | 124.8 (3) |
N8—C7—C3 | 117.4 (2) | N16—C15—H15 | 117.6 |
N16—C7—C3 | 115.4 (2) | C14—C15—H15 | 117.6 |
C7—N8—C9 | 117.0 (2) | C15—N16—C7 | 113.5 (2) |
Experimental details
Crystal data | |
Chemical formula | C12H8N4 |
Mr | 208.22 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 293 |
a, b, c (Å) | 21.627 (4), 3.804 (1), 11.605 (2) |
V (Å3) | 954.7 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.38 × 0.12 × 0.08 |
Data collection | |
Diffractometer | Kuma KM-4 CCD area-detector diffractometer |
Absorption correction | Analytical face-indexed, SHELXTL (Sheldrick, 1990) |
Tmin, Tmax | 0.959, 0.984 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5415, 2107, 1322 |
Rint | 0.036 |
(sin θ/λ)max (Å−1) | 0.658 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.075, 0.99 |
No. of reflections | 2107 |
No. of parameters | 145 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.15, −0.15 |
Absolute structure | Flack (1983) |
Absolute structure parameter | 0.2 (2), 928 Friedel pairs |
Computer programs: KM-4 Software (Kuma, 2000, KM-4 Software, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), SHELXTL (Sheldrick, 1990).
X-ray | MO (calc) | |
N1—C6 | 1.307 (3) | 1.321 |
N1—C2 | 1.378 (4) | 1.320 |
C2—C3 | 1.389 (4) | 1.391 |
C3—C4 | 1.377 (3) | 1.390 |
C3—C7 | 1.488 (3) | 1.483 |
C4—C5 | 1.380 (4) | 1.379 |
C5—C6 | 1.368 (4) | 1.386 |
C7—N8 | 1.301 (3) | 1.306 |
C7—N16 | 1.384 (3) | 1.359 |
C8—C9 | 1.348 (3) | 1.354 |
C9—N10 | 1.359 (3) | 1.349 |
C9—C14 | 1.407 (3) | 1.402 |
N10—C11 | 1.323 (4) | 1.315 |
C11—C12 | 1.380 (4) | 1.408 |
C12—C13 | 1.374 (4) | 1.356 |
C13—C14 | 1.426 (4) | 1.412 |
C14—C15 | 1.380 (4) | 1.413 |
C15—N16 | 1.343 (3) | 1.289 |
C6—N1—C2 | 113.8 (3) | 117.9 |
N1—C2—C3 | 123.9 (3) | 123.6 |
C4—C3—C2 | 118.1 (3) | 117.7 |
C4—C3—C7 | 121.1 (2) | 120.9 |
C2—C3—C7 | 120.8 (2) | 121.5 |
C5—C4—C3 | 119.0 (3) | 118.9 |
C6—C5—C4 | 117.5 (3) | 118.3 |
N1—C6—C5 | 127.5 (3) | 123.6 |
N8—C7—N16 | 127.2 (2) | 125.6 |
N8—C7—C3 | 117.4 (2) | 118.0 |
N16—C7—-C3 | 115.4 (2) | 116.3 |
C7—N8—C9 | 117.0 (2) | 118.2 |
N8—C9—N10 | 116.0 (2) | 117.5 |
N8—C9—C14 | 122.2 (2) | 120.5 |
N10—C9—C14 | 121.9 (3) | 121.9 |
C11—N10—C9 | 114.8 (3) | 115.8 |
N10—C11—C12 | 128.1 (3) | 125.1 |
C13—C12—C11 | 118.4 (3) | 118.1 |
C12—C13—C14 | 116.0 (3) | 118.6 |
C15—C14—C9 | 115.2 (3) | 115.8 |
C13—C14—C9 | 120.8 (3) | 119.1 |
C15—C14—C13 | 124.0 (3) | 125.1 |
N16—C15—C14 | 124.8 (3) | 122.8 |
C15—N16—C7 | 113.5 (2) | 117.0 |
C2—C3—C7—N16 | -11.1 (5) | 0 |
C2—C3—C7—N8 | 166.7 (3) | 180 |
C4—C3—C7—N8 | -12.7 (5) | 0 |
C4—C3—C7—N16 | 169.4 (3) | 180 |
The present study is a continuation of our investigations of the compounds formed during the transformation of organic cyano compounds in the presence of magnesium phthalocyanine as catalyst. In this context and to increase our understanding of the nature of the function of magnesium phthalocyanine during the transformation process of the cyano group, we have investigated the reactions of the 2- and 4-cyanopyridine isomers, finding that during thermal treatment in the presence of magnesium phthalocyanine a trimerization process takes place, resulting in the formation of 2,4,6-tris(2-pyridyl)-1,3,5-triazine and 2,4,6-tris(4-pyridyl)-1,3,5-triazine, respectively (Janczak & Kubiak, 2003). We now present the solid-state structure of the 2-(3-pyridyl)-1,3,8-triazanaphthalene, the product of the transformation of 3-cyanopyridine in the presence of magnesium phthalocyanine, and compare the result with that predicted for an isolated molecule by density function theory (DFT) fully optimized geometry calculation.
The molecule of the title compound, (I), with the labelling scheme used in the X-ray structure analysis, is shown in Fig. 1. Selected geometric parameters for this model, together with those corresponding to fully optimized geometry calculated at the B3LYP/6–31 G(d,p) level (Frisch et al. 1995) for an isolated (gas phase) molecule, are given in Table 1.
As revealed by X-ray structure analysis, the C—C and N—C bond lengths in (I) are entirely consistent with those found for molecules of this type (Allen, 2002). Furthermore, the pyridine and 1,3,8-triazanaphthalene ring systems, although planar, exhibit significant angular distortions. In both cases, the internal C—N—C and N—C—C angles are, respectively, less than and greater than 120°. These angular differences have been attributed to the steric effect of lone-pair electrons at the ring N atoms and are in agreement with the valence-shell electron-pair repulsion theory (VSEPR), which predicts the need for more space for non-bonding lone-pair electrons than for bonding electrons (Gillespie, 1963, 1992).
The optimized geometry of the molecule calculated by DFT methods gives values similar to those found in the crystal; however, the variation in the internal C—N—C and N—C—C angles is now less marked. Thus the distortion of the rings is perceived to result mainly from the steric effect of lone-pair electrons at the ring N atoms and in the crystal, augmented, to some extent, by π–π intermolecular interactions and crystal packing.
In complete contrast to the results of the crystal structure analysis, where the molecule is found to exhibit an angle of 13.33 (9)° between the planes of the pyridine ring and the 1,3,8-trazanaphthalene moiety by rotation about the C3—C7 bond joining them, the optimized molecule is completely planar. This planarity? was established by calculating potential energies for a series of conformations in which the pyridine ring was rotated in steps of 5° about the C3—C7 bond, while keeping the other optimized parameters, except the length of the C3—C7 bond, fixed. This process revealed a global minimum on the potential energy surface (PES) at 0° rotation (the planar equivalent of Fig. 1) and a further minimum, 1.5 kJ mol−1 higher than the first, at 180°, together with two equivalent energy maxima at 90 and 270°, both 34.84 kJ mol−1 higher than the energy at 0°. This energy value at the maxima is higher than the value at room temperature? (2.5 kJ mol−1). Thus, at ambient temperature, the change of conformation from that at 0° to that at the rotation angle of 180° is hindered. The energy barrier is nearly equivalent to he hydrogen-bond energy (Pauling, 1967). The 35 kJ mol−1 difference between the energy of the conformations of the molecule at 0 and at 90°, can be assigned to the π-delocalization energy of the π-electrons that are delocalized not only in the rings but also, at the rotation angle of 0°, over the inter-ring C3—C7 bond; at the rotation angle of 90°, the delocalization of the π-electrons over the inter-ring bond is impossible because of the symmetry of the orbitals. Further evidence for this hypothesis is the lengthening of the C3—C7 inter-ring bond from 1.483 (at 0°) to 1.504 Å (at 90°). Thus, in the molecule with lower energy, the inter-ring C3—C7 bond possesses a slight double-bond character as a result of delocalization of the π electrons between the rings and along the bond (Allen et al., 1987).
In the crystal of (I), a major feature is the face-to-face stacking of molecules related to one another by a cell translation, thus forming columns that propagate in the b direction (Fig. 2). Taking account of the tilt of the planes relative to the b cell edge, of the order of 66°, the repeat distance of 3.804 (1) Å corresponds to an interplanar separation of approximately 3.5 Å, which is consistant with the requirements of π–π stacking and clearly accommodates the 3.4 Å distance required for overlapping π-aromatic ring systems (Pauling, 1967).