organic compounds
(5Z,7Z)-N5,N7-Bis(pyridin-2-yl)-5H-6,7-dihydropyrrolo[3,4-b]pyrazine-5,7-diimine
aInstitute of Chemistry, University of Neuchâtel, Av de Bellevaux 51, CH-2000 Neuchâtel, Switzerland, and bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
*Correspondence e-mail: helen.stoeckli-evans@unine.ch
The whole molecule of the title compound, C16H11N7, is relatively planar, with an r.m.s. deviation of 0.061 Å for all 23 heteroatoms. It exhibits symmetric three-centre (bifurcated) intramolecular hydrogen bonds. In the crystal, molecules are linked by C—H⋯N hydrogen bonds, forming 31 helices propagating along the c-axis direction. Within the helices, there is evidence of offset π–π stacking being present [intercentroid distances = 3.648 (6) and 3.832 (6) Å].
Keywords: crystal structure; pyrrolopyrazine; isoindoline analogue; three-centre (bifurcated) hydrogen bonds; 31 helix.
CCDC reference: 1841267
Structure description
Symmetrical isoindolines have been synthesized to study a number of properties, such as their birefringence (Wong et al., 2012). The isoindoline 1,3-bis(2-pyridylimino)isoindoline [systematic name: (1Z,3Z)-N1,N3-bis(pyridin-2-yl)isoindoline-1,3-diimine], possesses mirror symmetry and exhibits symmetric three-centre (bifurcated) intramolecular hydrogen bonds (Schilf, 2004). Such compounds are ideal tridentate ligands; for example, a series of six bis(pyridylimino)isoindolines with different substituents in the 4-position on the pyridine rings have been used to form homoleptic iron complexes for the study of their temperature-dependent spin and redox states (Scheja et al., 2015). The title compound, the pyrazine analogue of 1,3-bis(2-pyridylimino)isoindoline, was synthesized to study its coordination behaviour with transition metals (Posel, 1998).
The molecular structure of the title compound is illustrated in Fig. 1. The molecule is relatively planar (r.m.s. deviation of 0.061 Å for all 23 heteroatoms), with the two pyridine rings (N4/C6–C10) and (N7/C12–C16) being inclined to each other by 2.7 (5)° and to the central pyrrolopyrazine unit (N1/N2/N5/C1–C5/C11) by 4.0 (4) and 4.6 (4)°, respectively. As in 1,3-bis(2-pyridylimino)isoindoline (Schilf, 2004), the title compound exhibits three-centre (bifurcated) intramolecular hydrogen bonds (Fig. 1 and Table 1), and the configuration about the C=N bonds (C5=N3 and C11=N6) is Z.
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In the crystal, molecules are linked by C—H⋯N hydrogen bonds, forming 31 helices propagating along the c-axis direction (Fig. 2 and Table 1). Within the helices there is evidence of offset π–π stacking involving the pyrazine ring (N1/N2/C1–C4; centroid Cg2) and pyridine ring (N7/C12–C16; centroid Cg4), and the two pyridine rings (N4/C6–C10; centroid Cg3, and N7/C12–C16; centroid Cg4): Cg2⋯Cg4ii = 3.648 (6) Å, interplanar distance = 3.264 (4) Å, slippage = 1.63 Å, and Cg3⋯Cg4iii = 3.832 (6) Å, interplanar distance = 3.338 (4) Å, slippage = 1.884 Å; symmetry codes: (ii) x, x − y, z + , (iii) x, x − y, z − .
There are small channel-like cavities in the crystal, with a total potential solvent area volume of ca 72 Å3 (ca 1.1% of the unit-cell volume). They are represented in brown/yellow in Fig. 3. There is no evidence of any residual electron density being present in these cavities on examination of the final difference Fourier map (see Table 2).
Synthesis and crystallization
The title compound was synthesized by the reaction of pyrazine-2,3-dicarbonitrile with 2-aminopyridine.
Synthesis of pyrazine-2,3-dicarbonitrile (L). 12.5 ml of deionized water in a round-bottomed flask fitted with a reflux condenser was acidified with H2SO4 (tech.) to pH = 1, then with vigorous stirring 2.7 g (0.025 mol) of 2,3-diaminomaleonitrile were added. After it had dissolved (temp = 323 K), a suspension of 5.8 g (0.0 3 mol) of a 30% aqueous solution of glyoxal was added slowly dropwise. An orange precipitate was obtained and the suspension was warmed to 370 K and stirred at this temperature for 1.3 h. The suspension was then cooled to room temperature, and the orange product filtered off and washed several times with small amounts of deionized water. Immediately after, the product was purified by dissolving in a mixture of diluted oxalic acid (2–3% aqueous solution) and ethanol and heating it almost to boiling point, with the addition of active carbon; the mixture was then heated to reflux for 10 min and filtered immediately. The pale-yellow solution was left overnight in a refrigerator and the next day a white crystalline product was filtered off and washed several times with ethanol. The product was dried under vacuum in a desiccator over silica (yield 2.8 g, 86%; m.p. 404–405 K). IR (KBr pellet, cm−1): 3425, 3105, 3075, 3056, 2929, 2818, 2708, 2359, 2296, 2245, 2103, 1977, 1862, 1748, 1645, 1564, 1551, 1525, 1413, 1387, 1270, 1224, 1178, 1143, 1121, 1082, 1053, 990, 972, 876, 865, 695, 613, 574, 537, 470, 446. This compound (CAS-number 13481–25-9) is also available commercially.
Synthesis of the title compound. A round-bottomed flask was charged with 0.65 g (5 mmol) of L, 0.06 g (0.054 mmol) of anhydrous CaCl2 and 0.99 g (10.5 mmol) of 2-aminopyridine and 25 ml of dry 1-butanol. The mixture was heated for 48 h at 333 K to give a green product. The resulting solution was evaporated to dryness under reduced pressure, and the residue was dissolved in 40 ml of deionized water. The product was extracted several times with chloroform (4 × 100 ml), then the solution was again evaporated to dryness under reduced pressure and dried in a vacuum desiccator over silica (yield: 1.35 g, 89.6%). The pale-green–brown product was chromatographed over silica (Kieselgel 60 particle size 0.063–0.200, 70–230 Mesh ASTM, Merck) with chloroform as the yellow fraction was collected. After evaporated to dryness under reduced pressure, the yellow product obtained was dried in a vacuum desiccator over silica (yield 0.5 g, 37%; m.p. 547–548 K). Calculated for C16H11N7 (%): C 63.78, H 3.68, N 32.54; found: C 63.69, H 3.89, N 32.40%. IR (KBr pellet, cm−1): 3443, 3057, 1706, 1641, 1607, 1581, 1554, 1477, 1458, 1435, 1378, 1354, 1296, 1261, 1249, 1203, 1166, 1139, 1091, 1053, 998, 870, 790, 736, 725, 705, 538, 484, 431, 413.
Note: Despite many crystallization attempts, it was not possible to obtain suitable crystals of the yellow product. The only crystals of the title compound, suitable for analysis, were obtained from reactions of the title compound with metal salts.
Refinement
Crystal data, data collection and structure . The NH hydrogen was located in a difference Fourier map and freely refined.
details are summarized in Table 2Structural data
CCDC reference: 1841267
https://doi.org/10.1107/S241431461800682X/sj4178sup1.cif
contains datablocks I, Global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S241431461800682X/sj4178Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S241431461800682X/sj4178Isup3.cml
Data collection: STADI4 (Stoe & Cie, 1997); cell
STADI4 (Stoe & Cie, 1997); data reduction: X-RED (Stoe & Cie, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015), PLATON (Spek, 2009) and publCIF (Westrip, 2010).C16H11N7 | Dx = 1.398 Mg m−3 |
Mr = 301.32 | Mo Kα radiation, λ = 0.71069 Å |
Trigonal, R3c:H | Cell parameters from 17 reflections |
a = 29.781 (4) Å | θ = 12.8–19.2° |
c = 8.3901 (14) Å | µ = 0.09 mm−1 |
V = 6444.3 (19) Å3 | T = 293 K |
Z = 18 | Rod, brown |
F(000) = 2808 | 0.68 × 0.19 × 0.19 mm |
Stoe Siemens AED2 four-circle diffractometer | Rint = 0.115 |
Radiation source: fine-focus sealed tube | θmax = 25.5°, θmin = 2.4° |
Plane graphite monochromator | h = −35→36 |
ω/2θ scans | k = −18→36 |
7762 measured reflections | l = −10→9 |
2629 independent reflections | 3 standard reflections every 60 min |
1606 reflections with I > 2σ(I) | intensity decay: 2% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.066 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.147 | w = 1/[σ2(Fo2) + (0.0368P)2 + 9.7595P] where P = (Fo2 + 2Fc2)/3 |
S = 1.10 | (Δ/σ)max < 0.001 |
2629 reflections | Δρmax = 0.19 e Å−3 |
213 parameters | Δρmin = −0.18 e Å−3 |
2 restraints | Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0017 (2) |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.3344 (2) | 0.1923 (2) | 0.7094 (7) | 0.0466 (16) | |
N2 | 0.2900 (2) | 0.2525 (2) | 0.5971 (7) | 0.0469 (17) | |
N3 | 0.1969 (3) | 0.1841 (2) | 0.3886 (7) | 0.0461 (17) | |
N4 | 0.1451 (3) | 0.1023 (3) | 0.2631 (9) | 0.066 (2) | |
N5 | 0.2247 (2) | 0.1224 (2) | 0.4508 (7) | 0.0387 (15) | |
H5N | 0.201 (2) | 0.095 (2) | 0.399 (8) | 0.07 (3)* | |
N6 | 0.2733 (2) | 0.0847 (2) | 0.5673 (7) | 0.0405 (15) | |
N7 | 0.2067 (3) | 0.0269 (2) | 0.3879 (8) | 0.0466 (17) | |
C1 | 0.3524 (3) | 0.2415 (3) | 0.7485 (10) | 0.051 (2) | |
H1 | 0.3811 | 0.2573 | 0.8156 | 0.061* | |
C2 | 0.3310 (3) | 0.2710 (3) | 0.6946 (10) | 0.051 (2) | |
H2 | 0.3459 | 0.3053 | 0.7283 | 0.062* | |
C3 | 0.2718 (3) | 0.2029 (3) | 0.5587 (8) | 0.0383 (18) | |
C4 | 0.2929 (3) | 0.1738 (3) | 0.6132 (8) | 0.0369 (18) | |
C5 | 0.2269 (3) | 0.1699 (3) | 0.4560 (9) | 0.0412 (18) | |
C6 | 0.1564 (3) | 0.1507 (4) | 0.2875 (9) | 0.050 (2) | |
C7 | 0.1303 (4) | 0.1729 (4) | 0.2118 (11) | 0.064 (3) | |
H7 | 0.1391 | 0.2071 | 0.2320 | 0.077* | |
C8 | 0.0912 (4) | 0.1426 (5) | 0.1063 (12) | 0.078 (3) | |
H8 | 0.0734 | 0.1563 | 0.0530 | 0.093* | |
C9 | 0.0785 (4) | 0.0923 (5) | 0.0803 (12) | 0.087 (4) | |
H9 | 0.0519 | 0.0711 | 0.0106 | 0.105* | |
C10 | 0.1060 (4) | 0.0741 (4) | 0.1597 (14) | 0.090 (3) | |
H10 | 0.0975 | 0.0399 | 0.1417 | 0.108* | |
C11 | 0.2634 (3) | 0.1217 (3) | 0.5432 (8) | 0.0365 (17) | |
C12 | 0.2447 (3) | 0.0363 (3) | 0.4909 (9) | 0.0401 (17) | |
C13 | 0.2587 (3) | −0.0006 (3) | 0.5267 (11) | 0.054 (2) | |
H13 | 0.2854 | 0.0070 | 0.5984 | 0.065* | |
C14 | 0.2327 (4) | −0.0486 (3) | 0.4549 (11) | 0.065 (3) | |
H14 | 0.2411 | −0.0741 | 0.4785 | 0.078* | |
C15 | 0.1944 (4) | −0.0579 (3) | 0.3483 (11) | 0.063 (3) | |
H15 | 0.1767 | −0.0897 | 0.2962 | 0.075* | |
C16 | 0.1822 (3) | −0.0197 (3) | 0.3189 (11) | 0.054 (2) | |
H16 | 0.1557 | −0.0267 | 0.2473 | 0.064* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.043 (4) | 0.045 (4) | 0.050 (4) | 0.021 (3) | −0.007 (3) | −0.007 (3) |
N2 | 0.057 (4) | 0.035 (4) | 0.046 (4) | 0.021 (3) | 0.005 (4) | 0.000 (3) |
N3 | 0.054 (4) | 0.054 (4) | 0.041 (4) | 0.035 (4) | −0.002 (3) | 0.002 (3) |
N4 | 0.058 (5) | 0.059 (5) | 0.079 (6) | 0.027 (4) | −0.018 (4) | −0.007 (4) |
N5 | 0.040 (4) | 0.033 (4) | 0.042 (4) | 0.018 (3) | −0.008 (3) | −0.001 (3) |
N6 | 0.042 (4) | 0.037 (4) | 0.045 (4) | 0.021 (3) | −0.002 (3) | −0.003 (3) |
N7 | 0.050 (4) | 0.034 (4) | 0.052 (4) | 0.019 (3) | −0.003 (3) | −0.002 (3) |
C1 | 0.047 (5) | 0.049 (5) | 0.052 (5) | 0.021 (4) | −0.003 (4) | −0.006 (4) |
C2 | 0.057 (5) | 0.037 (5) | 0.052 (5) | 0.016 (4) | 0.001 (4) | −0.007 (4) |
C3 | 0.046 (5) | 0.036 (4) | 0.033 (4) | 0.021 (4) | 0.002 (3) | 0.004 (3) |
C4 | 0.037 (4) | 0.035 (4) | 0.036 (4) | 0.016 (4) | 0.007 (3) | 0.002 (3) |
C5 | 0.046 (5) | 0.037 (4) | 0.043 (5) | 0.023 (4) | 0.008 (4) | 0.002 (4) |
C6 | 0.048 (5) | 0.065 (6) | 0.044 (5) | 0.034 (5) | 0.006 (4) | 0.004 (4) |
C7 | 0.068 (6) | 0.103 (8) | 0.043 (5) | 0.059 (6) | 0.003 (5) | 0.000 (5) |
C8 | 0.075 (7) | 0.138 (10) | 0.054 (6) | 0.079 (8) | −0.001 (5) | 0.003 (7) |
C9 | 0.061 (7) | 0.136 (10) | 0.072 (7) | 0.055 (7) | −0.022 (5) | −0.023 (7) |
C10 | 0.074 (7) | 0.083 (8) | 0.100 (8) | 0.030 (6) | −0.034 (7) | −0.027 (7) |
C11 | 0.037 (4) | 0.038 (4) | 0.038 (4) | 0.021 (4) | 0.006 (3) | 0.003 (3) |
C12 | 0.045 (4) | 0.031 (4) | 0.044 (4) | 0.019 (4) | 0.010 (4) | 0.004 (3) |
C13 | 0.062 (5) | 0.050 (5) | 0.062 (5) | 0.038 (5) | 0.001 (4) | −0.001 (4) |
C14 | 0.087 (7) | 0.049 (6) | 0.071 (6) | 0.043 (6) | 0.012 (6) | 0.005 (5) |
C15 | 0.079 (7) | 0.038 (5) | 0.062 (6) | 0.023 (5) | 0.012 (5) | 0.003 (4) |
C16 | 0.056 (5) | 0.043 (5) | 0.055 (5) | 0.019 (4) | −0.006 (4) | −0.004 (4) |
N1—C1 | 1.324 (9) | C3—C5 | 1.477 (10) |
N1—C4 | 1.341 (9) | C4—C11 | 1.472 (9) |
N2—C3 | 1.335 (9) | C6—C7 | 1.400 (11) |
N2—C2 | 1.338 (10) | C7—C8 | 1.380 (13) |
N3—C5 | 1.293 (9) | C7—H7 | 0.9300 |
N3—C6 | 1.402 (10) | C8—C9 | 1.367 (14) |
N4—C6 | 1.319 (11) | C8—H8 | 0.9300 |
N4—C10 | 1.354 (11) | C9—C10 | 1.362 (14) |
N5—C5 | 1.384 (8) | C9—H9 | 0.9300 |
N5—C11 | 1.397 (9) | C10—H10 | 0.9300 |
N5—H5N | 0.88 (3) | C12—C13 | 1.389 (10) |
N6—C11 | 1.288 (9) | C13—C14 | 1.378 (11) |
N6—C12 | 1.410 (9) | C13—H13 | 0.9300 |
N7—C16 | 1.335 (9) | C14—C15 | 1.364 (12) |
N7—C12 | 1.340 (9) | C14—H14 | 0.9300 |
C1—C2 | 1.396 (11) | C15—C16 | 1.379 (11) |
C1—H1 | 0.9300 | C15—H15 | 0.9300 |
C2—H2 | 0.9300 | C16—H16 | 0.9300 |
C3—C4 | 1.377 (10) | ||
C1—N1—C4 | 112.6 (7) | C6—C7—H7 | 121.1 |
C3—N2—C2 | 112.6 (7) | C9—C8—C7 | 120.0 (9) |
C5—N3—C6 | 121.5 (7) | C9—C8—H8 | 120.0 |
C6—N4—C10 | 116.7 (8) | C7—C8—H8 | 120.0 |
C5—N5—C11 | 112.3 (6) | C10—C9—C8 | 117.8 (10) |
C5—N5—H5N | 123 (6) | C10—C9—H9 | 121.1 |
C11—N5—H5N | 124 (6) | C8—C9—H9 | 121.1 |
C11—N6—C12 | 121.6 (6) | N4—C10—C9 | 124.5 (10) |
C16—N7—C12 | 117.4 (7) | N4—C10—H10 | 117.7 |
N1—C1—C2 | 123.8 (8) | C9—C10—H10 | 117.7 |
N1—C1—H1 | 118.1 | N6—C11—N5 | 129.9 (6) |
C2—C1—H1 | 118.1 | N6—C11—C4 | 124.6 (6) |
N2—C2—C1 | 123.3 (7) | N5—C11—C4 | 105.5 (6) |
N2—C2—H2 | 118.3 | N7—C12—C13 | 122.2 (7) |
C1—C2—H2 | 118.3 | N7—C12—N6 | 121.4 (6) |
N2—C3—C4 | 123.8 (7) | C13—C12—N6 | 116.5 (7) |
N2—C3—C5 | 127.4 (7) | C14—C13—C12 | 119.4 (8) |
C4—C3—C5 | 108.7 (6) | C14—C13—H13 | 120.3 |
N1—C4—C3 | 123.9 (7) | C12—C13—H13 | 120.3 |
N1—C4—C11 | 127.9 (7) | C15—C14—C13 | 118.5 (8) |
C3—C4—C11 | 108.2 (6) | C15—C14—H14 | 120.8 |
N3—C5—N5 | 129.2 (7) | C13—C14—H14 | 120.8 |
N3—C5—C3 | 125.5 (7) | C14—C15—C16 | 119.2 (9) |
N5—C5—C3 | 105.2 (6) | C14—C15—H15 | 120.4 |
N4—C6—C7 | 123.1 (9) | C16—C15—H15 | 120.4 |
N4—C6—N3 | 121.9 (7) | N7—C16—C15 | 123.4 (8) |
C7—C6—N3 | 115.0 (8) | N7—C16—H16 | 118.3 |
C8—C7—C6 | 117.9 (10) | C15—C16—H16 | 118.3 |
C8—C7—H7 | 121.1 | ||
C4—N1—C1—C2 | −0.4 (11) | N3—C6—C7—C8 | 177.8 (7) |
C3—N2—C2—C1 | 0.6 (11) | C6—C7—C8—C9 | 0.9 (13) |
N1—C1—C2—N2 | −0.4 (13) | C7—C8—C9—C10 | −0.8 (16) |
C2—N2—C3—C4 | −0.1 (10) | C6—N4—C10—C9 | 0.3 (17) |
C2—N2—C3—C5 | 179.1 (7) | C8—C9—C10—N4 | 0.2 (19) |
C1—N1—C4—C3 | 0.9 (10) | C12—N6—C11—N5 | 2.8 (11) |
C1—N1—C4—C11 | 178.6 (7) | C12—N6—C11—C4 | −177.3 (6) |
N2—C3—C4—N1 | −0.8 (11) | C5—N5—C11—N6 | 179.8 (7) |
C5—C3—C4—N1 | 179.9 (7) | C5—N5—C11—C4 | −0.1 (8) |
N2—C3—C4—C11 | −178.8 (6) | N1—C4—C11—N6 | 1.0 (11) |
C5—C3—C4—C11 | 1.8 (7) | C3—C4—C11—N6 | 179.0 (7) |
C6—N3—C5—N5 | −3.1 (12) | N1—C4—C11—N5 | −179.1 (7) |
C6—N3—C5—C3 | 177.3 (6) | C3—C4—C11—N5 | −1.1 (7) |
C11—N5—C5—N3 | −178.4 (7) | C16—N7—C12—C13 | −0.2 (11) |
C11—N5—C5—C3 | 1.2 (8) | C16—N7—C12—N6 | 178.8 (7) |
N2—C3—C5—N3 | −1.5 (12) | C11—N6—C12—N7 | 1.2 (10) |
C4—C3—C5—N3 | 177.8 (7) | C11—N6—C12—C13 | −179.7 (7) |
N2—C3—C5—N5 | 178.8 (7) | N7—C12—C13—C14 | −0.2 (12) |
C4—C3—C5—N5 | −1.9 (8) | N6—C12—C13—C14 | −179.3 (7) |
C10—N4—C6—C7 | −0.2 (13) | C12—C13—C14—C15 | 1.1 (13) |
C10—N4—C6—N3 | −178.2 (8) | C13—C14—C15—C16 | −1.4 (13) |
C5—N3—C6—N4 | 3.7 (11) | C12—N7—C16—C15 | −0.2 (12) |
C5—N3—C6—C7 | −174.4 (7) | C14—C15—C16—N7 | 1.0 (13) |
N4—C6—C7—C8 | −0.4 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
N5—H5N···N4 | 0.88 (6) | 2.12 (7) | 2.653 (11) | 119 (5) |
N5—H5N···N7 | 0.88 (6) | 2.12 (6) | 2.670 (8) | 120 (5) |
C2—H2···N2i | 0.93 | 2.62 | 3.395 (11) | 141 |
Symmetry code: (i) −y+2/3, x−y+1/3, z+1/3. |
Funding information
Funding for this research was provided by: Swiss National Science Foundation; University of Neuchâtel.
References
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