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The title compound, C12H8N4, was obtained by thermal treatment of 3-cyano­pyridine in the presence of magnesium phthalocyanine as catalyst. The X-ray structure analysis, in direct contrast to molecular orbital calculations corresponding to the gas phase, shows the mol­ecule to be non-planar in the solid state, with an interplanar angle between the pyridine and 1,3,8-tri­aza­naphthalene rings of 13.33 (9)°. Mol­ecules related to one another by cell translation, and positioned at intervals consistent with π–π intermolecular interactions, form stacks in the b direction.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103015701/gd1264sup1.cif
Contains datablocks dim3cnpy, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103015701/gd1264Isup2.hkl
Contains datablock I

CCDC reference: 221077

Comment top

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 ππ 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 ππ stacking and clearly accommodates the 3.4 Å distance required for overlapping π-aromatic ring systems (Pauling, 1967).

Experimental top

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).

Refinement top

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].

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecule of (I), showing the labelling scheme. Non-H atoms are shown as 50% probability displacement ellipsoids and H atoms are shown as spheres of arbitrary radii.
[Figure 2] Fig. 2. Part of a stack of molecules of (I), propagated in the b direction (left to right across the page). Non-H atoms are shown as 50% probability displacement ellipsoids and H atoms have been omitted for clarity; selected atoms are labelled. Dashed lines indicate two of the shorter contacts between ring centroids, which are themselves shown as small dots. [Symmetry code: (i) x, y + 1, z; (ii) x, y − 1, z.]
2-(3-pyridyl)-1,3,8-triazanaphthalene top
Crystal data top
C12H8N4F(000) = 432
Mr = 208.22Dx = 1.449 Mg m3
Dm = 1.445 Mg m3
Dm measured by floatation
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 1322 reflections
a = 21.627 (4) Åθ = 2.6–27.9°
b = 3.804 (1) ŵ = 0.09 mm1
c = 11.605 (2) ÅT = 293 K
V = 954.7 (3) Å3Parallelepiped, colourless
Z = 40.38 × 0.12 × 0.08 mm
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
2107 independent reflections
Radiation source: fine-focus sealed tube1322 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.036
Detector resolution: 1024x1024 with blocks 2x2 pixels mm-1θmax = 27.9°, θmin = 2.6°
ω scanh = 2727
Absorption correction: analytical
face-indexed, SHELXTL (Sheldrick, 1990)
k = 44
Tmin = 0.959, Tmax = 0.984l = 1514
5415 measured reflections
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)] = 0.051H-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 reflectionsΔρmax = 0.15 e Å3
145 parametersΔρmin = 0.15 e Å3
0 restraintsAbsolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.2 (2), 928 Friedel pairs
Crystal data top
C12H8N4V = 954.7 (3) Å3
Mr = 208.22Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 21.627 (4) ŵ = 0.09 mm1
b = 3.804 (1) ÅT = 293 K
c = 11.605 (2) Å0.38 × 0.12 × 0.08 mm
Data collection top
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 = 0.984Rint = 0.036
5415 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.075Δρmax = 0.15 e Å3
S = 0.99Δρmin = 0.15 e Å3
2107 reflectionsAbsolute structure: Flack (1983)
145 parametersAbsolute structure parameter: 0.2 (2), 928 Friedel pairs
0 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
N10.73090 (13)0.3877 (7)0.1125 (2)0.0535 (7)
C20.78534 (14)0.2616 (7)0.1584 (3)0.0464 (8)
H20.79010.26710.23800.060*
C30.83356 (11)0.1269 (7)0.0928 (2)0.0415 (6)
C40.82762 (12)0.1306 (6)0.02531 (19)0.0358 (6)
H40.85940.04830.07200.043*
C50.77375 (12)0.2581 (8)0.0735 (2)0.0473 (7)
H50.76830.26520.15290.057*
C60.72867 (15)0.3737 (8)0.0000 (3)0.0503 (8)
H60.69220.45140.03400.060*
C70.89007 (11)0.0159 (7)0.14897 (19)0.0349 (7)
N80.93792 (9)0.0730 (5)0.08373 (18)0.0317 (5)
C90.98851 (12)0.2087 (7)0.13493 (17)0.0341 (7)
N101.03788 (9)0.2679 (6)0.0651 (2)0.0412 (5)
C111.08655 (14)0.4069 (8)0.1170 (3)0.0444 (7)
H111.12090.44630.07060.056*
C121.09266 (12)0.5008 (7)0.2312 (2)0.0429 (7)
H121.12900.60250.25820.051*
C131.04380 (14)0.4405 (8)0.3042 (2)0.0504 (8)
H131.04570.49470.38230.060*
C140.98998 (13)0.2898 (8)0.2532 (2)0.0429 (7)
C150.93725 (13)0.2028 (7)0.3138 (2)0.0471 (7)
H150.93710.24540.39270.056*
N160.88618 (11)0.0610 (6)0.26712 (18)0.0434 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0477 (14)0.0557 (16)0.0570 (15)0.0073 (15)0.0000 (12)0.0038 (13)
C20.052 (2)0.0435 (17)0.0430 (15)0.001 (2)0.0015 (14)0.0013 (14)
C30.0387 (12)0.0403 (15)0.0465 (16)0.0015 (16)0.0013 (12)0.0014 (14)
C40.0375 (14)0.0346 (14)0.0353 (14)0.0018 (16)0.0013 (15)0.0017 (14)
C50.0385 (15)0.0456 (16)0.0578 (18)0.0013 (15)0.0020 (13)0.0017 (14)
C60.0525 (19)0.0445 (17)0.0540 (19)0.0014 (16)0.0021 (14)0.0015 (15)
C70.0366 (15)0.0372 (15)0.0308 (15)0.0016 (12)0.0021 (10)0.0018 (12)
N80.0306 (10)0.0272 (12)0.0372 (14)0.0022 (9)0.0021 (9)0.0014 (10)
C90.0402 (16)0.0367 (16)0.0255 (11)0.0016 (17)0.0022 (15)0.0013 (16)
N100.0377 (10)0.0453 (12)0.0405 (12)0.0015 (10)0.0012 (9)0.0011 (11)
C110.0460 (15)0.0437 (18)0.0435 (16)0.0020 (15)0.0009 (12)0.0012 (15)
C120.0338 (11)0.0433 (17)0.0515 (19)0.0013 (15)0.0014 (12)0.0001 (14)
C130.0589 (19)0.051 (2)0.0414 (17)0.0004 (17)0.0020 (14)0.0009 (15)
C140.0453 (16)0.0432 (18)0.0401 (13)0.0019 (16)0.0021 (14)0.0015 (15)
C150.0521 (16)0.0425 (19)0.0466 (17)0.0019 (15)0.0003 (13)0.0013 (15)
N160.0468 (13)0.0455 (14)0.0379 (13)0.0002 (12)0.0021 (11)0.0020 (12)
Geometric parameters (Å, º) top
N1—C61.307 (3)N8—C91.348 (3)
N1—C21.378 (4)C9—N101.359 (3)
C2—C31.389 (4)C9—C141.407 (3)
C2—H20.9300N10—C111.323 (4)
C3—C41.377 (3)C11—C121.380 (4)
C3—C71.488 (3)C11—H110.9300
C4—C51.380 (4)C12—C131.374 (4)
C4—H40.9300C12—H120.9300
C5—C61.368 (4)C13—C141.426 (4)
C5—H50.9300C13—H130.9300
C6—H60.9300C14—C151.380 (4)
C7—N81.301 (3)C15—N161.343 (3)
C7—N161.384 (3)C15—H150.9300
C6—N1—C2113.8 (3)N8—C9—N10116.0 (2)
N1—C2—C3123.9 (3)N8—C9—C14122.2 (2)
N1—C2—H2118.0N10—C9—C14121.9 (3)
C3—C2—H2118.0C11—N10—C9114.8 (3)
C4—C3—C2118.1 (3)N10—C11—C12128.1 (3)
C4—C3—C7121.1 (2)N10—C11—H11115.9
C2—C3—C7120.8 (2)C12—C11—H11115.9
C5—C4—C3119.0 (3)C13—C12—C11118.4 (3)
C5—C4—H4120.5C13—C12—H12120.8
C3—C4—H4120.5C11—C12—H12120.8
C6—C5—C4117.5 (3)C12—C13—C14116.0 (3)
C6—C5—H5121.2C12—C13—H13122.0
C4—C5—H5121.2C14—C13—H13122.0
N1—C6—C5127.5 (3)C15—C14—C9115.2 (3)
N1—C6—H6116.2C15—C14—C13124.0 (3)
C5—C6—H6116.2C9—C14—C13120.8 (3)
N8—C7—N16127.2 (2)N16—C15—C14124.8 (3)
N8—C7—C3117.4 (2)N16—C15—H15117.6
N16—C7—C3115.4 (2)C14—C15—H15117.6
C7—N8—C9117.0 (2)C15—N16—C7113.5 (2)

Experimental details

Crystal data
Chemical formulaC12H8N4
Mr208.22
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)293
a, b, c (Å)21.627 (4), 3.804 (1), 11.605 (2)
V3)954.7 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.38 × 0.12 × 0.08
Data collection
DiffractometerKuma KM-4 CCD area-detector
diffractometer
Absorption correctionAnalytical
face-indexed, SHELXTL (Sheldrick, 1990)
Tmin, Tmax0.959, 0.984
No. of measured, independent and
observed [I > 2σ(I)] reflections
5415, 2107, 1322
Rint0.036
(sin θ/λ)max1)0.658
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.075, 0.99
No. of reflections2107
No. of parameters145
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.15, 0.15
Absolute structureFlack (1983)
Absolute structure parameter0.2 (2), 928 Friedel pairs

Computer programs: KM-4 Software (Kuma, 2000, KM-4 Software, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), SHELXTL (Sheldrick, 1990).

Selected X-ray structural and MO-calculated geometric parameters (Å, °) for (I) top
X-rayMO (calc)
N1—C61.307 (3)1.321
N1—C21.378 (4)1.320
C2—C31.389 (4)1.391
C3—C41.377 (3)1.390
C3—C71.488 (3)1.483
C4—C51.380 (4)1.379
C5—C61.368 (4)1.386
C7—N81.301 (3)1.306
C7—N161.384 (3)1.359
C8—C91.348 (3)1.354
C9—N101.359 (3)1.349
C9—C141.407 (3)1.402
N10—C111.323 (4)1.315
C11—C121.380 (4)1.408
C12—C131.374 (4)1.356
C13—C141.426 (4)1.412
C14—C151.380 (4)1.413
C15—N161.343 (3)1.289
C6—N1—C2113.8 (3)117.9
N1—C2—C3123.9 (3)123.6
C4—C3—C2118.1 (3)117.7
C4—C3—C7121.1 (2)120.9
C2—C3—C7120.8 (2)121.5
C5—C4—C3119.0 (3)118.9
C6—C5—C4117.5 (3)118.3
N1—C6—C5127.5 (3)123.6
N8—C7—N16127.2 (2)125.6
N8—C7—C3117.4 (2)118.0
N16—C7—-C3115.4 (2)116.3
C7—N8—C9117.0 (2)118.2
N8—C9—N10116.0 (2)117.5
N8—C9—C14122.2 (2)120.5
N10—C9—C14121.9 (3)121.9
C11—N10—C9114.8 (3)115.8
N10—C11—C12128.1 (3)125.1
C13—C12—C11118.4 (3)118.1
C12—C13—C14116.0 (3)118.6
C15—C14—C9115.2 (3)115.8
C13—C14—C9120.8 (3)119.1
C15—C14—C13124.0 (3)125.1
N16—C15—C14124.8 (3)122.8
C15—N16—C7113.5 (2)117.0
C2—C3—C7—N16-11.1 (5)0
C2—C3—C7—N8166.7 (3)180
C4—C3—C7—N8-12.7 (5)0
C4—C3—C7—N16169.4 (3)180
 

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