In the crystal structure, intermolecular N—H⋯N hydrogen bonds link the molecules into infinite ribbons extending along the [100] direction.
Keywords: crystal structure; 1,2,4,5-tetrazine; hydrogen bond
Abstract
The structure of the title compound, C12H10N6, at 100 K has monoclinic (P21/n) symmetry. Crystals were obtained as a yellow solid by reduction of 3,6-bis(pyridin-2-yl)-1,2,4,5-tetrazine. The structure displays intermolecular hydrogen bonding of the N—H⋯N type, ordering molecules into infinite ribbons extending along the [100] direction.
Chemical context
s-Tetrazines represent a class of heterocyclic compounds. The substitution of four nitrogen atoms in a six-membered benzene-like ring results in strong π-electron deficiency and concentration of negative charge on the heteroatoms. As a result of these properties, s-tetrazines are used in organic synthesis (Saracoglu, 2007 ▸; Šečkutė & Deveraj et al., 2013 ▸; Churakov et al., 2004 ▸) as well as bridging ligands in metal complexes (Kaim, 2002 ▸; Clavier & Audebert, 2010 ▸). Moreover, their derivatives are often among biologically active compounds (Saghatforoush et al., 2016 ▸) and play an important role in anti-inflammatory (Kamal et al., 2006 ▸), anticancer, antiviral drugs (Rao & Hu, 2006 ▸; Neunhoeffer et al., 1984 ▸) or as insecticidal products (Sauer et al.,1996 ▸; Brooker et al., 1987 ▸).
The title compound 3,6-bis(pyridin-2-yl)-1,4-dihydro-1,2,4,5-tetrazine (I) was obtained as a yellow solid by reduction of 3,6-bis(pyridin-2-yl)-1,2,4,5-tetrazine (II) during its crystallization with 2-mercaptopyridine N-oxide (III) in ethanol solution (Fig. 1 ▸).
Figure 1.
Molecular formulae of: 3,6-bis(pyridin-2-yl)-1,4-dihydro-1,2,4,5-tetrazine (I), 3,6-bis(pyridin-2-yl)-1,2,4,5-tetrazine (II) and 2-mercaptopyridine N-oxide (III).
Structural commentary
Compound (I) crystallizes in the monoclinic space group P21/n. The atomic labelling scheme is shown in Fig. 2 ▸. In (I), being a reduced form of (II), there are two hydrogen atoms at the 1 and 4 positions and two 2-pyridyl substituents at the 3 and 6 positions.
Figure 2.
The molecular structure of (I), showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
The C—C bond lengths are within the expected values known for aromatic systems (Allen et al., 1987 ▸). However, there is a fluctuation of bond distances involving nitrogen atoms. The N—N bonds within the central (A) ring are of almost equal length, being 1.4285 (15) and 1.4306 (16) Å. The C6—N1 and C3—N4 [1.3953 (17) and 1.4051 (17) Å] bond lengths are longer than those for C6—N5 and C3—N2 [1.2848 (17) Å, 1.2809 (18) Å], respectively. This is the result of the protonation of the N1 and N4 atoms. The C—N bond lengths in the B and C rings are comparable within 3σ, varying from 1.3384 (18) Å to 1.3416 (17) Å.
The central tetrazine ring (A) shows a boat conformation with pseudo-symmetry mirror planes passing through bonds N2—C3 and N5—C6 [ΔCs = 1.30 (16)°] and atoms N1, N4 [ΔCs = 2.00 (14)°]. In this conformation, hydrogen atoms are located in the equatorial positions of the ring and the N—H bonds are directed to the bottom of the boat (compare torsion angles in Table 1 ▸). The planes of the aromatic pirydyl rings (B and C) are not to parallel to each other. The dihedral angles between these rings and central tetrazine ring are 22.43 (7)° (A and B) and 25.71 (6)° (A and C). The dihedral angle between rings B and C is 27.13 (7)°. The overall molecular structure could be recognized as a butterfly-like conformation as shown in Fig. 3 ▸.
Table 1. Selected torsion angles (°).
| N2—C3—N4—H4 | 164.1 (13) | C3—N2—N1—H1 | −168.4 (12) |
| C6—N5—N4—H4 | −165.2 (14) | N5—C6—N1—H1 | 164.3 (13) |
Figure 3.
The butterfly-like molecular conformation of (I).
Supramolecular features
The crystal packing of (I) is mainly determined by intermolecular hydrogen bonds of the N—H⋯N type (Table 2 ▸). Firstly, two similar hydrogen bonds (N1—H1⋯N5 and N4—H4⋯N2) between the 1,2,4,5-tetrazine rings of neighbouring molecules form a chain with an R 2 2(6) ring motif (Etter et al., 1990 ▸) (see Fig. 4 ▸). As a result, the molecules are ordered into infinite ribbons extending along the [100] direction. This parallel arrangement of the ribbons is additionally stabilized by further interactions between adjacent molecules [N5⋯C33(1 − x, 1 − y, 1 − z) = 3.2418 (18) Å and C34⋯C61(1 − x, 1 − y, 1 − z) = 3.3334 (19) Å], as shown in Fig. 5 ▸.
Table 2. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| N4—H4⋯N2i | 0.89 (2) | 2.56 (2) | 3.3017 (16) | 142.5 (17) |
| N1—H1⋯N5ii | 0.880 (17) | 2.415 (17) | 3.1321 (16) | 138.9 (15) |
Symmetry codes: (i) 
; (ii) 
.
Figure 4.
N—H ⋯ N hydrogen bonds between rings of 1,2,4,5-tetrazine of adjacent molecules forming a chain of cyclic dimers.
Figure 5.
A view of the unit-cell packing, showing the ribbon-like arrangement of molecules. Short C⋯N and C⋯C intermolecular contacts between adjacent molecular ribbons are shown as dashed blue lines.
Database survey
A search of the Cambridge Structure Database (CSD version 5.39, update of February 2018; Groom et al., 2016 ▸) results in 76 derivatives of 3,6-bis(pyridin-2-yl)-1,2,4,5-tetrazine, among them compound (II) (refcode JUMXAQ; Klein et al., 1998 ▸), which is the oxidated form of (I). Even tought (II) crystallizes in the smae monoclinic space group as (I), its molecular and crystal structures show completely different features.
Synthesis and crystallization
Crystals suitable for X-ray measurements were obtained from a commercially available reagent (Aldrich Chemical Co.) and used without further purification. 0.5 mmol of 3,6-bis(pyridin-2-yl)-1,2,4,5-tetrazine and 0.5 mmol of 2-mercaptopyridine N-oxide (in a 1:1 molar ratio) were mixed in ethanol (4 ml). The resulting solution was warmed to 343 K and then kept at room temperature. Within two weeks, after slow evaporation of the solvent, two kinds of crystal were obtained in a crystallizer. X-ray studies confirmed that the pink crystals were of the known structure (II), while the yellow crystals were identified as being of a previously unreported structure, i.e. (I).
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. Hydrogen atoms of aromatic rings were introduced in calculated positions with idealized geometry and constrained using a rigid body model with isotropic displacement parameters equal to 1.2 the equivalent displacement parameters of the parent atoms. The H atoms of the NH groups, in 1,2,4,5-tetrazine ring, were located in a difference Fourier map and freely refined.
Table 3. Experimental details.
| Crystal data | |
| Chemical formula | C12H10N6 |
| M r | 238.26 |
| Crystal system, space group | Monoclinic, P21/n |
| Temperature (K) | 100 |
| a, b, c (Å) | 5.4603 (1), 12.7845 (3), 15.6474 (4) |
| β (°) | 97.281 (2) |
| V (Å3) | 1083.49 (4) |
| Z | 4 |
| Radiation type | Cu Kα |
| μ (mm−1) | 0.78 |
| Crystal size (mm) | 0.11 × 0.10 × 0.08 |
| Data collection | |
| Diffractometer | Rigaku Oxford Diffraction SuperNova, Dual, Cu at zero, Atlas |
| Absorption correction | Multi-scan (CrysAlis PRO; Rigaku OD, 2015 ▸) |
| T min, T max | 0.958, 1.000 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 8686, 2004, 1767 |
| R int | 0.027 |
| (sin θ/λ)max (Å−1) | 0.603 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.035, 0.095, 1.12 |
| No. of reflections | 2004 |
| No. of parameters | 171 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.14, −0.24 |
Supplementary Material
Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698901801753X/ff2157sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901801753X/ff2157Isup2.hkl
Supporting information file. DOI: 10.1107/S205698901801753X/ff2157Isup3.cml
CCDC reference: 1884403
Additional supporting information: crystallographic information; 3D view; checkCIF report
supplementary crystallographic information
Crystal data
| C12H10N6 | F(000) = 496 |
| Mr = 238.26 | Dx = 1.461 Mg m−3 |
| Monoclinic, P21/n | Cu Kα radiation, λ = 1.54184 Å |
| a = 5.4603 (1) Å | Cell parameters from 3734 reflections |
| b = 12.7845 (3) Å | θ = 4.5–76.4° |
| c = 15.6474 (4) Å | µ = 0.78 mm−1 |
| β = 97.281 (2)° | T = 100 K |
| V = 1083.49 (4) Å3 | Plate, yellow |
| Z = 4 | 0.11 × 0.10 × 0.08 mm |
Data collection
| Rigaku Oxford Diffraction SuperNova, Dual, Cu at zero, Atlas diffractometer | 2004 independent reflections |
| Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source | 1767 reflections with I > 2σ(I) |
| Detector resolution: 10.4052 pixels mm-1 | Rint = 0.027 |
| ω scans | θmax = 68.5°, θmin = 4.5° |
| Absorption correction: multi-scan (CrysAlisPRO; Rigaku OD, 2015) | h = −6→6 |
| Tmin = 0.958, Tmax = 1.000 | k = −15→14 |
| 8686 measured reflections | l = −18→17 |
Refinement
| Refinement on F2 | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.035 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.095 | w = 1/[σ2(Fo2) + (0.051P)2 + 0.2596P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.12 | (Δ/σ)max < 0.001 |
| 2004 reflections | Δρmax = 0.14 e Å−3 |
| 171 parameters | Δρmin = −0.24 e Å−3 |
Special details
| 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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| N5 | 0.3304 (2) | 0.59460 (9) | 0.30162 (7) | 0.0159 (3) | |
| N1 | 0.7587 (2) | 0.61063 (9) | 0.30346 (7) | 0.0167 (3) | |
| N66 | 0.7195 (2) | 0.45247 (9) | 0.18218 (7) | 0.0178 (3) | |
| N4 | 0.3800 (2) | 0.66133 (9) | 0.37517 (7) | 0.0162 (3) | |
| N2 | 0.7969 (2) | 0.61146 (9) | 0.39548 (7) | 0.0166 (3) | |
| N36 | 0.4117 (2) | 0.70258 (9) | 0.54575 (7) | 0.0196 (3) | |
| C3 | 0.6017 (2) | 0.63816 (10) | 0.42759 (9) | 0.0151 (3) | |
| C31 | 0.6094 (2) | 0.65389 (10) | 0.52161 (8) | 0.0159 (3) | |
| C6 | 0.5274 (2) | 0.57389 (10) | 0.26787 (8) | 0.0150 (3) | |
| C61 | 0.5133 (2) | 0.50651 (10) | 0.19059 (8) | 0.0153 (3) | |
| C62 | 0.2981 (2) | 0.49884 (11) | 0.13279 (8) | 0.0183 (3) | |
| H62 | 0.1608 | 0.5397 | 0.1394 | 0.022* | |
| C65 | 0.7096 (2) | 0.38393 (10) | 0.11717 (9) | 0.0191 (3) | |
| H65 | 0.8497 | 0.3444 | 0.1116 | 0.023* | |
| C64 | 0.5020 (3) | 0.36871 (11) | 0.05778 (9) | 0.0194 (3) | |
| H64 | 0.5020 | 0.3195 | 0.0140 | 0.023* | |
| C34 | 0.6135 (3) | 0.69920 (11) | 0.69170 (9) | 0.0201 (3) | |
| H34 | 0.6106 | 0.7167 | 0.7493 | 0.024* | |
| C32 | 0.8134 (3) | 0.62397 (11) | 0.57895 (9) | 0.0196 (3) | |
| H32 | 0.9460 | 0.5895 | 0.5596 | 0.024* | |
| C63 | 0.2943 (3) | 0.42869 (11) | 0.06517 (9) | 0.0201 (3) | |
| H63 | 0.1539 | 0.4219 | 0.0252 | 0.024* | |
| C33 | 0.8137 (3) | 0.64675 (11) | 0.66537 (9) | 0.0215 (3) | |
| H33 | 0.9465 | 0.6272 | 0.7054 | 0.026* | |
| C35 | 0.4179 (3) | 0.72475 (11) | 0.62978 (9) | 0.0211 (3) | |
| H35 | 0.2832 | 0.7593 | 0.6476 | 0.025* | |
| H1 | 0.886 (3) | 0.5796 (14) | 0.2850 (11) | 0.022 (4)* | |
| H4 | 0.253 (4) | 0.6611 (15) | 0.4051 (13) | 0.030 (5)* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| N5 | 0.0158 (5) | 0.0169 (5) | 0.0144 (5) | 0.0008 (4) | −0.0001 (4) | −0.0012 (4) |
| N1 | 0.0134 (5) | 0.0221 (6) | 0.0148 (5) | −0.0014 (5) | 0.0020 (4) | −0.0020 (4) |
| N66 | 0.0154 (5) | 0.0182 (6) | 0.0198 (6) | 0.0000 (4) | 0.0025 (4) | −0.0009 (4) |
| N4 | 0.0138 (5) | 0.0196 (6) | 0.0150 (6) | 0.0025 (4) | 0.0007 (4) | −0.0025 (4) |
| N2 | 0.0159 (5) | 0.0191 (6) | 0.0145 (5) | −0.0009 (4) | 0.0003 (4) | −0.0013 (4) |
| N36 | 0.0174 (6) | 0.0229 (6) | 0.0181 (6) | 0.0010 (4) | 0.0009 (4) | −0.0024 (4) |
| C3 | 0.0138 (6) | 0.0136 (6) | 0.0173 (7) | −0.0002 (5) | −0.0001 (5) | 0.0003 (5) |
| C31 | 0.0161 (6) | 0.0144 (6) | 0.0170 (7) | −0.0025 (5) | 0.0015 (5) | 0.0009 (5) |
| C6 | 0.0137 (6) | 0.0149 (6) | 0.0162 (6) | 0.0006 (5) | 0.0007 (5) | 0.0022 (5) |
| C61 | 0.0151 (6) | 0.0144 (6) | 0.0166 (6) | −0.0010 (5) | 0.0032 (5) | 0.0015 (5) |
| C62 | 0.0153 (6) | 0.0211 (7) | 0.0185 (7) | 0.0017 (5) | 0.0018 (5) | 0.0005 (5) |
| C65 | 0.0168 (6) | 0.0175 (6) | 0.0236 (7) | 0.0007 (5) | 0.0055 (5) | −0.0018 (5) |
| C64 | 0.0223 (7) | 0.0183 (6) | 0.0181 (7) | −0.0027 (5) | 0.0049 (5) | −0.0025 (5) |
| C34 | 0.0253 (7) | 0.0193 (7) | 0.0155 (6) | −0.0053 (5) | 0.0017 (5) | −0.0006 (5) |
| C32 | 0.0180 (7) | 0.0204 (7) | 0.0203 (7) | 0.0013 (5) | 0.0019 (5) | 0.0023 (5) |
| C63 | 0.0175 (6) | 0.0237 (7) | 0.0183 (7) | −0.0024 (5) | −0.0005 (5) | 0.0002 (5) |
| C33 | 0.0212 (7) | 0.0231 (7) | 0.0190 (7) | −0.0019 (5) | −0.0024 (5) | 0.0038 (5) |
| C35 | 0.0209 (7) | 0.0226 (7) | 0.0202 (7) | 0.0000 (5) | 0.0040 (5) | −0.0033 (5) |
Geometric parameters (Å, º)
| N5—C6 | 1.2848 (17) | C61—C62 | 1.3926 (18) |
| N5—N4 | 1.4306 (16) | C62—C63 | 1.385 (2) |
| N1—C6 | 1.3953 (17) | C62—H62 | 0.9300 |
| N1—N2 | 1.4285 (15) | C65—C64 | 1.386 (2) |
| N1—H1 | 0.880 (19) | C65—H65 | 0.9300 |
| N66—C65 | 1.3384 (18) | C64—C63 | 1.386 (2) |
| N66—C61 | 1.3416 (17) | C64—H64 | 0.9300 |
| N4—C3 | 1.4051 (17) | C34—C35 | 1.387 (2) |
| N4—H4 | 0.88 (2) | C34—C33 | 1.389 (2) |
| N2—C3 | 1.2809 (18) | C34—H34 | 0.9300 |
| N36—C35 | 1.3412 (18) | C32—C33 | 1.383 (2) |
| N36—C31 | 1.3415 (18) | C32—H32 | 0.9300 |
| C3—C31 | 1.4800 (18) | C63—H63 | 0.9300 |
| C31—C32 | 1.3922 (19) | C33—H33 | 0.9300 |
| C6—C61 | 1.4786 (18) | C35—H35 | 0.9300 |
| C6—N5—N4 | 111.75 (11) | C63—C62—H62 | 120.9 |
| C6—N1—N2 | 114.45 (10) | C61—C62—H62 | 120.9 |
| C6—N1—H1 | 115.4 (12) | N66—C65—C64 | 123.53 (12) |
| N2—N1—H1 | 108.3 (12) | N66—C65—H65 | 118.2 |
| C65—N66—C61 | 117.28 (12) | C64—C65—H65 | 118.2 |
| C3—N4—N5 | 113.90 (10) | C65—C64—C63 | 118.36 (13) |
| C3—N4—H4 | 111.4 (13) | C65—C64—H64 | 120.8 |
| N5—N4—H4 | 110.1 (13) | C63—C64—H64 | 120.8 |
| C3—N2—N1 | 112.02 (11) | C35—C34—C33 | 118.16 (13) |
| C35—N36—C31 | 116.93 (12) | C35—C34—H34 | 120.9 |
| N2—C3—N4 | 121.69 (12) | C33—C34—H34 | 120.9 |
| N2—C3—C31 | 120.37 (12) | C33—C32—C31 | 118.30 (13) |
| N4—C3—C31 | 117.75 (12) | C33—C32—H32 | 120.9 |
| N36—C31—C32 | 123.55 (12) | C31—C32—H32 | 120.9 |
| N36—C31—C3 | 114.85 (12) | C62—C63—C64 | 119.26 (13) |
| C32—C31—C3 | 121.54 (12) | C62—C63—H63 | 120.4 |
| N5—C6—N1 | 121.95 (12) | C64—C63—H63 | 120.4 |
| N5—C6—C61 | 119.77 (12) | C32—C33—C34 | 119.21 (13) |
| N1—C6—C61 | 118.25 (11) | C32—C33—H33 | 120.4 |
| N66—C61—C62 | 123.33 (12) | C34—C33—H33 | 120.4 |
| N66—C61—C6 | 115.02 (11) | N36—C35—C34 | 123.82 (13) |
| C62—C61—C6 | 121.63 (12) | N36—C35—H35 | 118.1 |
| C63—C62—C61 | 118.13 (12) | C34—C35—H35 | 118.1 |
| N2—C3—N4—H4 | 164.1 (13) | C3—N2—N1—H1 | −168.4 (12) |
| C6—N5—N4—H4 | −165.2 (14) | N5—C6—N1—H1 | 164.3 (13) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N4—H4···N2i | 0.89 (2) | 2.56 (2) | 3.3017 (16) | 142.5 (17) |
| N1—H1···N5ii | 0.880 (17) | 2.415 (17) | 3.1321 (16) | 138.9 (15) |
Symmetry codes: (i) x−1, y, z; (ii) x+1, y, z.
Funding Statement
This work was funded by Narodowe Centrum Nauki grant 2015/19/B/ST4/01773. EFRD in Operational Programme Development of Eastern Poland 2007–2013, the Oxford Diffraction SuperNova DualSource diffractometer grant POPW.01.03.00-20-004/11.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698901801753X/ff2157sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901801753X/ff2157Isup2.hkl
Supporting information file. DOI: 10.1107/S205698901801753X/ff2157Isup3.cml
CCDC reference: 1884403
Additional supporting information: crystallographic information; 3D view; checkCIF report