The six-membered-ring azomethine N-((E)-{5-[(E)-(pyridin-3-yl­imino)­meth­yl]thio­phen-2-yl}methyl­idene)pyridin-3-amine

The title compound, C₁₆H₁₂N₄S, forms a three-dimensional layered network structure via inter­molecular hydrogen bonding and π-stacking. The azomethine molecule adopts the thermodynamically stable E regioisomer and the pyridine substituents are antiperi­planar. The mean planes of the pyridine rings and the azomethine group to which they are connected are twisted by 27.27 (5) and 33.60 (5)°. The electrochemical energy gap of 2.3 eV based on the HOMO–LUMO energy difference is in agreement with the spectroscopically derived value.

S1. Introduction

Various azomethines (–N═CH–) have been prepared owing in part to their straightforward preparation by condensing complementary amines and aldehydes. The resulting heteroatomic bonds have been extensively used to coordinate various metals for obtaining optically and electrochemically active metal-coordinated compounds. It has also recently been demonstrated that metal-free azomethines similarly possess optical and electrochemical properties that are compatible for use as heteroatomic conjugated systems in plastic devices (Bolduc et al., 2013). It was shown that both the optical and electrochemical properties of the metal-free azomethines are highly contingent on the type of the aromatic rings and amines used for their preparation (Dufresne & Skene, 2008a,b).The variable properties were attributed not only to the different electron densities of the aromatics, but also to the different mean plane angles between of the aromatics and the azomethines (Dufresne & Skene, 2010a,b, 2012; Dufresne et al., 2010). For example, the mean plane angle between the aryl–azomethine bond for six-membered aromatics in aryl–azomethine–aryl–azomethine–aryl triads [compound (3) in the Scheme] is twisted by up to 65° (Bürgi & Dunitz, 1970). This is a result of steric hindrance between the azomethine and ortho-aromatic H atoms. In contrast, relatively low aryl–azomethine twist angles, ranging between 0 and 25°, were observed for triads consisting of five-membered aromatics (Bolduc et al., 2010, 2012, 2013; Guarin et al., 2007). Despite the plethora of azomethine crystallographic studies, crystal structures of azomethine triads consisting of mixed six- or five-membered rings have not been reported. The crystal structures of such triads would provide important information about the different twisting angles between the aryl-azomethine planes allowing for correlation with the optical and electrochemical properties. Additionally, a crystal structure is pivotal for determining the absolute E or Z orientation of the azomethine bond that cannot be assigned with conventional characterization techniques, such as NMR. The title compound was synthesized during the course of our on-going conjugated azomethine research for the purpose of providing the important crystallographic data.

S2. Experimental

S2.1. Synthesis and crystallization

All chemicals were purchased from Sigma–Aldrich. Anhydrous and deaerated solvents were obtained from an activated alumina solvent purification system.

For the synthesis of (1), DABCO (1,4-di­aza­bicyclo­[2.2.2]o­ctane; 0.47 g, 4.27 mmol) was dissolved in anhydrous toluene in a round-bottomed flask, followed by the addition of thio­phene-2,5-dicarboxaldehyde (0.10 g, 0.71 mmol). Then TiCl₄ (0.1 M in toluene, 1.4 ml, 0.14 mmol) was added dropwise at 273 K. 3-Amino­pyridine (0.13 g, 1.42 mmol) was dissolved separately in anhydrous toluene. This solution was added to the TiCl₄ containing reaction mixture and the resulting mixture was refluxed for 2 d. The solvent was then removed from the crude reaction mixture and the solid was redissolved in acetone. The undissolved solids were filtered. The solvent from the filtrate was then removed under reduced pressure. Purification by flash-column chromatography (80/20 hexanes/ethyl acetate) gave the title compound as a yellow powder (yield 0.21 mmol, 30%). Single crystals were obtained by slow evaporation of acetone at room temperature over a period of 3 weeks.

S2.2. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. H atoms were placed in calculated positions (C—H = 0.95 Å) and included in the refinement in the riding-model approximation, with U_iso(H) values refined freely.

S3. Results and discussion

The crystal structure of the title compound N-((E)-{5-[(E)-(pyridin-3-yl­imino)­methyl]­thio­phen-2-yl}methyl­idene)pyridin-3-amine, (1), reveals that the compound adopts the thermodynamically stable E regioisomer. The molecule is not planar as the dihedral angles between mean planes of the central thio­phene and the adjacent pyridines are 27.27 (5) and 33.60 (5)°. This twisting can be attributed to the steric hindrance between the hydrogen of the imine bond and the hydrogen on the adjacent pyridine ring, as previously reported for six-membered heterocycles (Dufresne et al., 2008). This is in part responsible for the observed hypsochromic shifts in the absorbance spectra of (1) relative to its all-thio­phene analogue [compound (2) in the Scheme]. The mean plane dihedral angles of the aryl–azomethines bonds of (2) are 9.04 (4) and 25.07 (6)° (Skene et al., 2006) and they are also smaller than for the analogous six-membered homo­aryl azomethine triad, (E)-N-benzyl­idene-4-[(E)-(phenyl­imino)­methyl]­aniline [renamed to match scheme; please check that scheme shows correct structure], (3), whose mean plane torsion angle is 46 (3)° (Thyen & Zugenmaier, 1994). It is further evident from Fig. 1 that in (1) the pyridines are anti­planar.

Another point of inter­est is the bond length in the azomethines. The bond lengths for C6—N5, N5—C5 and C5—C1, as well as the bond lengths for C12—N11, N11—C11 and C11—C4 (see Table 2), are consistent with those of analogous triads consisting uniquely of thio­phenes. The analogous bond lengths for (2) are 1.439 (4), 1.278 (3) and 1.397 (3) Å (Skene et al., 2006). The azomethine bond lengths are 0.053 Å shorter than the C═C bond of analogous vinyl­enes (Hoekstra et al., 1975). The different bond lengths confirm that the N═CH and CH═CH bonds are not isoelectronic in terms of bond distances, contrary to what is generally understood (Yang & Jenekhe, 1991).

The three-dimensional network of (1) is governed by multiple weak inter­actions. Fig. 2 shows those inter­actions with π-stacking occurring between inter­calated thio­phenes and azomethine bonds. The mean plane determined by atoms N5, C5, C1, C2, C3, C4, S1, C11 and N11 is at an acceptable π-stacking distance (Janiak, 2000) from the mean plane determined by the same atoms of the anti­periplanar molecule at (-x+1, -y+1, -z) (Fig. 2 and Table 3). π-stacking can also be observed between the central molecule and the syn molecule at (-x+1, y, -z+1/2) (Fig. 2), and between the aforementioned molecule at (-x+1, -y+1, -z) and the syn molecule at (x, -y+1, z-1/2) [-z-1/2 in Table 3] (Fig. 2). The molecules are oriented in anti or syn orientations owing to their hydrogen bonding in the crystal lattice. Table 4 and Fig. 3 describe the hydrogen-bonding pattern and the three-dimensional network of the molecules in (1).

The optical and electrochemical properties of the title compound are reported in Fig. 4. It can be seen that (1) has a maximum absorbance and emission wavelength of 365 and 495 nm, respectively. The conjugated nature of (1) is confirmed by the low optical energy gap of 2.8 eV, suggesting low twisting angles between the aryl and azomethine mean planes. However, the absorbance and fluorescence spectra of all-thio­phene analogue (2) are red shifted by 75 and 39 nm, respectively, relative to (1) (Bourgeaux et al., 2007). The degree of conjugation of (1) is further confirmed by the electrochemical properties found in the inset of Fig. 4. The oxidation at 1.06 V versus Ag/AgCl is irreversible because the resulting pyridine radical cation undergoes anodic polymerization. The reduction at -1.17 V versus Ag/AgCl is similarly irreversible. The HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) levels can be calculated from the oxidation and reduction onsets, respectively, resulting in HOMO = -5.4 eV and LUMO = -3.1 eV. The electrochemical energy gap (2.3 eV) is derived from the HOMO–LUMO energy difference and it is in agreement with the spectroscopically derived value.

Related literature

For related literature, see: Bürgi & Dunitz (1970); Bolduc et al. (2010, 2012, 2013); Bourgeaux et al. (2007); Dufresne & Skene (2008a, 2008b, 2012); Dufresne et al. (2008, 2010); Guarin et al. (2007); Janiak (2000); Skene et al. (2006); Thyen & Zugenmaier (1994); Yang & Jenekhe (1991).

Computing details

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Bruker, 2001) and ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: UdMX (Maris, 2004).

Figures

	Fig. 1. The molecular structure of (1), showing the atom-numbering scheme adopted. Displacement ellipsoids are drawn at 30% probability level.
	Fig. 2. Three-dimensional structure of (1) shown along the b axis, illustrating the π-stacking within the crystal lattice.[Symmetry codes: (i) 1 - x, y, 0.5 - z ii)1 - x, 1 - y, -z iii) x, 1 - y, -0.5 + z].
	Fig. 3. Three dimensional structure of 1 shown along the c axis illustrating the hydrogen-bond interactions within the crystal lattice. Only the atoms involved in hydrogen bonds are numbered and only the hydrogen involved are shown for clarity. [Symmetry codes: (i) -x+1/2, y-1/2, -z-1/2; (ii) -x+1, y+1, -z+1/2.]
	Fig. 4. Normalized absorbance (black dot) and emission (square) of (1) in dichloromethane. Inset: cyclic voltammogram of (1) in 0.1 M TBAPF6 in anhydrous and deaerated dichloromethane.

N-((E)-{5-[(E)-(Pyridin-3-ylimino)methyl]thiophen-2-yl}methylidene)pyridin-3-amine

Crystal data

C16H12N4S	F(000) = 1216
Mr = 292.36	Dx = 1.383 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 9039 reflections
a = 33.4368 (5) Å	θ = 2.8–72.1°
b = 6.0490 (1) Å	µ = 0.23 mm^−1
c = 14.6066 (2) Å	T = 150 K
β = 108.034 (1)°	Plate, yellow
V = 2809.18 (7) Å^3	0.12 × 0.08 × 0.05 mm
Z = 8

Data collection

Bruker SMART 6000 diffractometer	2773 independent reflections
Radiation source: Rotating Anode	2581 reflections with I > 2σ(I)
Montel 200 optics monochromator	Rint = 0.043
Detector resolution: 5.5 pixels mm^-1	θmax = 26.1°, θmin = 1.3°
ω scans	h = −40→40
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −7→7
Tmin = 0.827, Tmax = 1.000	l = −17→17
18280 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.036	Only H-atom displacement parameters refined
wR(F^2) = 0.094	w = 1/[σ^2(Fo^2) + (0.0575P)^2 + 1.3506P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max = 0.001
2773 reflections	Δρmax = 0.23 e Å^−3
203 parameters	Δρmin = −0.32 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0082 (6)

Special details

Experimental. X-ray crystallographic data for I were collected from a single-crystal sample, which was mounted on a loop fiber. Data were collected using a Bruker Platform diffractometer, equipped with a Bruker SMART 4 K Charged-Coupled Device (CCD) Area Detector using the program 2 and a Nonius FR591 rotating anode equiped with a Montel 200 optics The crystal-to-detector distance was 5.0 cm, and the data collection was carried out in 512 x 512 pixel mode. The initial unit-cell parameters were determined by a least-squares fit of the angular setting of strong reflections, collected by a 10.0 degree scan in 33 frames over four different parts of the reciprocal space (132 frames total). One complete sphere of data was collected, to better than 0.80 Å resolution.

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.494790 (9)	0.43847 (5)	0.12073 (2)	0.02215 (13)
C1	0.46157 (4)	0.6498 (2)	0.06511 (9)	0.0245 (3)
C2	0.48038 (4)	0.8538 (2)	0.08655 (9)	0.0270 (3)
H2	0.4668	0.9891	0.0621	0.039 (4)*
C3	0.52212 (4)	0.8394 (2)	0.14898 (9)	0.0272 (3)
H3	0.5397	0.9640	0.1716	0.040 (5)*
C4	0.53440 (4)	0.6242 (2)	0.17338 (9)	0.0245 (3)
C5	0.41971 (4)	0.6033 (2)	0.00183 (9)	0.0250 (3)
H5	0.4020	0.7222	−0.0285	0.034 (4)*
C6	0.36502 (4)	0.3683 (2)	−0.07637 (9)	0.0253 (3)
C7	0.33116 (4)	0.5106 (2)	−0.08330 (10)	0.0296 (3)
H7	0.3361	0.6391	−0.0440	0.038 (4)*
C8	0.28572 (4)	0.2909 (3)	−0.19639 (10)	0.0352 (3)
H8	0.2584	0.2648	−0.2397	0.046 (5)*
C9	0.31693 (5)	0.1366 (3)	−0.19210 (10)	0.0337 (3)
H9	0.3108	0.0068	−0.2306	0.048 (5)*
C10	0.35708 (4)	0.1747 (2)	−0.13088 (9)	0.0291 (3)
H10	0.3789	0.0706	−0.1260	0.036 (4)*
C11	0.57432 (4)	0.5450 (2)	0.23643 (9)	0.0246 (3)
H11	0.5956	0.6479	0.2680	0.035 (4)*
C12	0.61990 (4)	0.2621 (2)	0.31301 (9)	0.0242 (3)
C13	0.61887 (4)	0.0623 (2)	0.36000 (10)	0.0283 (3)
H13	0.5923	−0.0072	0.3490	0.032 (4)*
C14	0.68957 (5)	0.0631 (3)	0.43387 (11)	0.0367 (4)
H14	0.7141	−0.0060	0.4750	0.051 (5)*
C15	0.69398 (4)	0.2638 (3)	0.39202 (10)	0.0351 (3)
H15	0.7209	0.3308	0.4057	0.041 (4)*
C16	0.65884 (4)	0.3655 (2)	0.33020 (9)	0.0294 (3)
H16	0.6612	0.5023	0.3003	0.029 (4)*
N5	0.40623 (3)	0.40443 (19)	−0.01400 (8)	0.0250 (3)
N7	0.29210 (4)	0.4748 (2)	−0.14263 (9)	0.0356 (3)
N11	0.58121 (3)	0.33688 (18)	0.24999 (7)	0.0248 (2)
N13	0.65245 (4)	−0.0382 (2)	0.41918 (9)	0.0349 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0232 (2)	0.0189 (2)	0.02419 (19)	−0.00122 (10)	0.00713 (14)	−0.00032 (11)
C1	0.0271 (6)	0.0234 (6)	0.0245 (6)	0.0006 (5)	0.0102 (5)	0.0002 (5)
C2	0.0282 (6)	0.0231 (7)	0.0301 (6)	0.0007 (5)	0.0096 (5)	0.0005 (5)
C3	0.0265 (6)	0.0227 (6)	0.0326 (7)	−0.0028 (5)	0.0094 (5)	−0.0020 (5)
C4	0.0242 (6)	0.0245 (6)	0.0267 (6)	−0.0026 (5)	0.0104 (5)	−0.0018 (5)
C5	0.0258 (6)	0.0256 (6)	0.0238 (6)	0.0013 (5)	0.0080 (5)	0.0016 (5)
C6	0.0279 (6)	0.0248 (6)	0.0231 (6)	−0.0032 (5)	0.0080 (5)	0.0016 (5)
C7	0.0274 (7)	0.0298 (7)	0.0304 (7)	−0.0018 (5)	0.0070 (5)	−0.0040 (6)
C8	0.0282 (7)	0.0432 (8)	0.0298 (7)	−0.0080 (6)	0.0029 (6)	−0.0016 (6)
C9	0.0392 (8)	0.0325 (7)	0.0286 (7)	−0.0085 (6)	0.0093 (6)	−0.0046 (6)
C10	0.0337 (7)	0.0248 (7)	0.0294 (7)	−0.0018 (5)	0.0106 (6)	0.0002 (5)
C11	0.0234 (6)	0.0251 (7)	0.0267 (6)	−0.0026 (5)	0.0098 (5)	−0.0025 (5)
C12	0.0247 (6)	0.0250 (6)	0.0237 (6)	0.0008 (5)	0.0086 (5)	−0.0033 (5)
C13	0.0313 (7)	0.0254 (7)	0.0285 (7)	−0.0005 (5)	0.0098 (6)	−0.0017 (5)
C14	0.0332 (8)	0.0416 (9)	0.0306 (7)	0.0099 (6)	0.0027 (6)	−0.0016 (6)
C15	0.0253 (7)	0.0429 (8)	0.0356 (7)	−0.0005 (6)	0.0073 (6)	−0.0063 (6)
C16	0.0269 (7)	0.0311 (7)	0.0306 (7)	−0.0021 (5)	0.0094 (5)	−0.0016 (6)
N5	0.0251 (6)	0.0264 (6)	0.0231 (5)	−0.0008 (4)	0.0070 (4)	0.0001 (4)
N7	0.0263 (6)	0.0403 (7)	0.0370 (7)	−0.0007 (5)	0.0050 (5)	−0.0025 (5)
N11	0.0227 (5)	0.0257 (6)	0.0263 (5)	−0.0012 (4)	0.0079 (4)	0.0003 (4)
N13	0.0403 (7)	0.0311 (6)	0.0306 (6)	0.0056 (5)	0.0072 (5)	0.0020 (5)

Geometric parameters (Å, º)

S1—C1	1.7231 (13)	C8—H8	0.95
S1—C4	1.7253 (13)	C9—C10	1.3828 (19)
C1—C2	1.3768 (18)	C9—H9	0.95
C1—C5	1.4459 (18)	C10—H10	0.95
C2—C3	1.4138 (19)	C11—N11	1.2839 (17)
C2—H2	0.95	C11—H11	0.95
C3—C4	1.3785 (18)	C12—C16	1.3953 (18)
C3—H3	0.95	C12—C13	1.3959 (18)
C4—C11	1.4486 (18)	C12—N11	1.4101 (16)
C5—N5	1.2805 (17)	C13—N13	1.3326 (18)
C5—H5	0.95	C13—H13	0.95
C6—C10	1.3947 (18)	C14—N13	1.340 (2)
C6—C7	1.4009 (19)	C14—C15	1.387 (2)
C6—N5	1.4141 (17)	C14—H14	0.95
C7—N7	1.3428 (17)	C15—C16	1.3850 (19)
C7—H7	0.95	C15—H15	0.95
C8—N7	1.340 (2)	C16—H16	0.95
C8—C9	1.387 (2)
C1—S1—C4	91.21 (6)	C8—C9—H9	120.5
C2—C1—C5	127.10 (12)	C9—C10—C6	118.95 (13)
C2—C1—S1	112.04 (10)	C9—C10—H10	120.5
C5—C1—S1	120.83 (10)	C6—C10—H10	120.5
C1—C2—C3	112.45 (12)	N11—C11—C4	120.56 (12)
C1—C2—H2	123.8	N11—C11—H11	119.7
C3—C2—H2	123.8	C4—C11—H11	119.7
C4—C3—C2	112.36 (12)	C16—C12—C13	117.62 (12)
C4—C3—H3	123.8	C16—C12—N11	126.16 (12)
C2—C3—H3	123.8	C13—C12—N11	116.19 (11)
C3—C4—C11	128.23 (12)	N13—C13—C12	124.72 (13)
C3—C4—S1	111.95 (10)	N13—C13—H13	117.6
C11—C4—S1	119.81 (10)	C12—C13—H13	117.6
N5—C5—C1	120.99 (12)	N13—C14—C15	123.27 (14)
N5—C5—H5	119.5	N13—C14—H14	118.4
C1—C5—H5	119.5	C15—C14—H14	118.4
C10—C6—C7	117.92 (12)	C16—C15—C14	119.46 (14)
C10—C6—N5	118.22 (12)	C16—C15—H15	120.3
C7—C6—N5	123.79 (12)	C14—C15—H15	120.3
N7—C7—C6	123.38 (13)	C15—C16—C12	118.30 (13)
N7—C7—H7	118.3	C15—C16—H16	120.9
C6—C7—H7	118.3	C12—C16—H16	120.9
N7—C8—C9	123.45 (13)	C5—N5—C6	118.69 (12)
N7—C8—H8	118.3	C8—N7—C7	117.31 (13)
C9—C8—H8	118.3	C11—N11—C12	119.99 (11)
C10—C9—C8	118.91 (13)	C13—N13—C14	116.62 (13)
C10—C9—H9	120.5
C4—S1—C1—C2	−0.03 (10)	S1—C4—C11—N11	3.27 (17)
C4—S1—C1—C5	178.12 (11)	C16—C12—C13—N13	−0.8 (2)
C5—C1—C2—C3	−178.22 (12)	N11—C12—C13—N13	177.35 (12)
S1—C1—C2—C3	−0.21 (15)	N13—C14—C15—C16	−1.4 (2)
C1—C2—C3—C4	0.42 (17)	C14—C15—C16—C12	0.6 (2)
C2—C3—C4—C11	−178.99 (12)	C13—C12—C16—C15	0.39 (19)
C2—C3—C4—S1	−0.44 (15)	N11—C12—C16—C15	−177.60 (12)
C1—S1—C4—C3	0.27 (10)	C1—C5—N5—C6	179.89 (11)
C1—S1—C4—C11	178.96 (11)	C10—C6—N5—C5	148.52 (12)
C2—C1—C5—N5	178.24 (13)	C7—C6—N5—C5	−34.63 (19)
S1—C1—C5—N5	0.40 (17)	C9—C8—N7—C7	1.3 (2)
C10—C6—C7—N7	−3.0 (2)	C6—C7—N7—C8	0.9 (2)
N5—C6—C7—N7	−179.88 (13)	C4—C11—N11—C12	−178.76 (11)
N7—C8—C9—C10	−1.4 (2)	C16—C12—N11—C11	−31.89 (19)
C8—C9—C10—C6	−0.8 (2)	C13—C12—N11—C11	150.10 (12)
C7—C6—C10—C9	2.84 (19)	C12—C13—N13—C14	0.2 (2)
N5—C6—C10—C9	179.88 (12)	C15—C14—N13—C13	0.9 (2)
C3—C4—C11—N11	−178.28 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8···N7^i	0.95	2.66	3.4881 (19)	146
C7—H7···N13^ii	0.95	2.62	3.5614 (19)	173

Symmetry codes: (i) −x+1/2, y−1/2, −z−1/2; (ii) −x+1, y+1, −z+1/2.