The title compound can be described as a salt (HL)+(Gal)− (L = 1,3-bis(benzimidazol-2-yl)propane (L); HGal = gallic acid) co-crystallized with a neutral molecule L. The crystal also comprises disordered solvent ethyl acetate molecules.
Keywords: crystal structure, co-crystal, hydrogen bonds, supramolecular structure, solvent mask
Abstract
The chemical formula of the title compound, 2C17H17N4 +·2C7H5O5 −·C17H16N4·2.94C4H8O2, was established by X-ray diffraction of a single-crystal obtained by reacting 1,3-bis(benzimidazol-2-yl)propane (L) and gallic acid (HGal) in ethyl acetate. The molecular structure can be described as a salt (HL)+(Gal)− co-crystallized with a molecule L, with a stoichiometric relation of 2:1. Moreover, large voids in the crystal are filled with ethyl acetate, the amount of which was estimated by using a solvent mask during structure refinement, affording the chemical formula (HL +·Gal−)2·L·(C4H8O2)2.94. The arrangement of components in the crystal is driven by O—H⋯O, N—H⋯O and O—H⋯N hydrogen bonds rather than by π–π or C—H⋯π interactions. In the crystal, molecules and ions shape the boundary of cylindrical tunnels parallel to [100] via R (rings) and D (discrete) supramolecular motifs. These voids, which account for about 28% of the unit-cell volume, contain disordered solvent molecules.
1. Chemical context
Bis-imidazole and bis-benzimidazole ligands are frequently used in coordination chemistry because of their chelating properties. Moreover, the size and the nature of the bridge connecting the imidazole moieties can modify the spectroscopic and physicochemical properties of the resulting complexes (Pandiyan et al., 1997 ▸). Such behaviour is useful in bioinorganic chemistry, in particular for the design of models of active centres in metalloproteins. In the specific case of 1,3-bis(benzimidazol-2-yl)propane (C17H16N4, abbreviated L hereafter), coordination complexes with late transition metals have been reported (CoII, NiII, CuII, ZnII, AgI and CdII; see for example: van Albada et al., 1999 ▸).
Another salient aspect for these molecules is that they include both acidic protons and protonable sites, allowing the formation of cations or anions, for example by modifying the pH value of the medium. However, the symmetric character of L leads to a reasonable assumption that both benzimidazole moieties should behave similarly, so that a dicationic species H2
L
2+ is more readily available compared to the dissymmetric cation HL
+. We report herein the crystal structure of a compound overriding this rule of thumb, since it contains both neutral L and cationic HL
+ species, together with gallate anions Gal− (3,4,5-trihydroxybenzoate, C7H5O5
−, derived from gallic acid, HGal) for charge balancing. Moreover, disordered solvent molecules (ethyl acetate, C4H8O2) are present in the crystal, which can then be seen as an uncommon case of a solvated co-crystal between a salt and a molecule.
2. Structural commentary
The asymmetric unit of the compound under study contains one cation HL + and one anion Gal− in general positions, and one-half of a molecule L, placed on the twofold rotation axis of space group I2/a (Fig. 1 ▸). The molecular formula is then (HL +·Gal−)2·L. With this formula, the calculated Kitaigorodskii packing index (Kitaigorodskii, 1965 ▸), η = 0.534, is physically unreasonable, and the refinement can be greatly improved by considering the presence of disordered solvent molecules in the crystal. Large voids of ca 2000 Å3 per unit cell, which equals 28% of the cell volume, are actually present in the crystal structure, forming wide tunnels running along [100], which are filled with solvent molecules (Fig. 2 ▸). A solvent mask was calculated with OLEX2 (van der Sluis & Spek, 1990 ▸; Dolomanov et al., 2009 ▸), recovering a density of 564 electrons per unit cell. Since Z = 4 for the above-mentioned formula, and considering that only ethyl acetate was used as solvent during the synthesis and crystallization, the formula of the compound was derived as (HL +·Gal−)2·L·(C4H8O2)2.94. However, it must be noted that the determination of the solvent amount via a SQUEEZE-like procedure is always inaccurate (e.g. Hernández Linares et al., 2016 ▸). The given formula is thus not meant to be precise regarding the overall solvent content. It rather points out that the crystallized compound is a solvated co-crystal between a salt, HL +·Gal−, and a molecule, L.
Figure 1.
The structures of the molecular entities in the title compound, with displacement ellipsoids for non-H atoms at the 30% probability level. Non-labelled atoms in the neutral moiety (bottom molecule) are generated by symmetry
− x, y, 1 − z (twofold rotation).
Figure 2.
Part of the crystal structure of the title compound showing tunnels in which the disordered ethyl acetate solvent molecules are located (Macrae et al., 2020 ▸). The projection is almost normal to unit-cell axis a and the probe radius for the voids is 1.25 Å.
The presence of voids in the crystal is a consequence of the lack of efficient stacking interactions between the co-crystal components, although they contain aromatic heterocycles. This feature is, in turn, related to the different conformations observed for HL
+ and L. The molecule L displays a trans–trans conformation for the propane link bridging the benzimidazole heterocycles: torsion angles C18—C25—C26—C25i and C18i—C25i—C26i—C25 are equal by symmetry, 172.70 (12)° [symmetry code: (i) −x +
, y, −z + 1]. In contrast, the cation HL
+ is placed in a general position, and the propane chain displays a gauche–trans conformation, reflected in torsion angles C1—C8—C9—C10 = −63.93 (16)° and C11—C10—C9—C8 = 179.45 (11)°. Both L and HL
+ have a bent shape, with dihedral angles between the benzimidazole rings of 65.07 (2) and 37.58 (3)°, respectively. These twisted components do not stack with the gallate anions, probably because, in the first place, the crystal structure is stabilized via Coulombic attractions in the ionic part HL
+·Gal−. Only two significant π–π intermolecular contacts are calculated by PLATON (Spek, 2020 ▸), for benzimidazole rings in inversion-related L molecules [separation for π-stacked N5/N6/C18/C19/C24 rings: 3.6070 (8) Å, slippage 0.644 Å] and inversion-related HL
+ cations [separation for π stacking between N1/N2/C1/C2/C7 rings: 3.6672 (7) Å, slippage 0.720 Å]. The gallate anions Gal− are arranged in rows parallel to [100], and do not interact with neighbouring aromatic rings: the angles between the Gal− mean plane and surrounding benzimidazole rings are in the range 45.78 (7)–84.96 (6)°. No C—H⋯π interactions are observed in the crystal structure.
3. Supramolecular features
Notwithstanding the absence of well-organized stacks in the crystal structure, all N—H, O—H and C=O functional groups are engaged in hydrogen bonds (Table 1 ▸), forming a tri-periodic framework. This is confirmed in the Hirshfeld surface calculated for the expanded asymmetric unit represented in Fig. 1 ▸, that is (HL +·Gal−)·L. This map (Fig. 3 ▸) shows typical spots for regions where interatomic distances are shorter than the sum of the van der Waals radii of the atoms. O⋯H and H⋯O contacts account for 16.1% of the Hirshfeld surface, while N⋯H and H⋯N contacts account for 6.0% of the surface. Both kinds of hydrogen bonds generate well-defined spikes in the 2D fingerprint plot, at short (d i, d e) coordinates. Apart from these stabilizing interactions, the map is dominated by H⋯H contacts (49.3% of the surface) related to van der Waals contacts.
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| N2—H2⋯O2i | 0.936 (16) | 1.924 (17) | 2.8204 (14) | 159.7 (13) |
| N3—H3⋯O1 | 0.880 (16) | 1.832 (16) | 2.6433 (13) | 152.4 (14) |
| N4—H4⋯O30ii | 0.867 (16) | 2.043 (16) | 2.8509 (12) | 154.6 (14) |
| N4—H4⋯O31ii | 0.867 (16) | 2.394 (16) | 3.0199 (14) | 129.5 (13) |
| N6—H6A⋯O1iii | 0.893 (15) | 1.955 (16) | 2.8018 (12) | 157.9 (13) |
| O30—H30⋯N1iv | 0.946 (18) | 1.785 (18) | 2.7238 (12) | 171.3 (16) |
| O31—H31⋯O2i | 0.894 (18) | 1.882 (18) | 2.7314 (11) | 157.8 (16) |
| O32—H32⋯N5 | 0.948 (19) | 1.717 (19) | 2.6515 (14) | 167.9 (16) |
Symmetry codes: (i)
; (ii)
; (iii)
; (iv)
.
Figure 3.
Hirshfeld surface (Spackman et al., 2021 ▸) mapped over d norm in the range −0.5 Å (red) to 3.0 Å (blue). Labels 1–8 refer to entries in Table 1 ▸ for each hydrogen bond. Contact N3—H3⋯O1 (entry 2) is not visible, since it corresponds to an intramolecular hydrogen bond in the inside pocket limited by the Hirshfeld surface. The deep-blue surface at the top of the map is the boundary with the region containing disordered solvent molecules. The two-dimensional fingerprint plot including all contacts is shown in the inset.
Among the many motifs present in this supramolecular framework, four are of particular importance for the building of the crystal structure, as they provide the cavities that are filled with disordered solvent molecules. Ring motifs
(5),
(10) and
(15) along with discrete motifs D(2) link four HL
+ cations, six Gal− anions and two L molecules, forming a ring-shaped supramolecule (Fig. 4 ▸). Connecting these supramolecular rings along [100], the remaining hydrogen bonds (entries 3, 4 and 6 in Table 1 ▸, i.e. those including ‘−x + 1’ in their symmetry operator for the acceptor site) generate the tunnels depicted in Fig. 2 ▸. The boundary of the cavity is formed by a sequence of twelve elements, alternating anions, cations and molecules (Fig. 5 ▸).
Figure 4.
Supramolecular arrangement of HL +, Gal− and L, affording the boundary of the cavities containing the disordered solvent. HL + and L are coloured red, while Gal− anions are coloured green. Hydrogen bonds are shown as dashed purple lines. All rings (R) and discrete (D) motifs involved in the building of the supramolecular ring are indicated. All C-bound H atoms are omitted for clarity.
Figure 5.
The complete supramolecular framework enclosing the disordered ethyl acetate solvent, as viewed down the symmetry axis, parallel to [100] in the crystal. The colour code is as for Fig. 4 ▸. All C-bound H atoms are omitted for clarity. The inset is the same framework in a spacefill representation, and including H atoms, showing the real void space available for disordered ethyl acetate molecules. The crystallographic twofold rotation axis position is also shown.
The shape of this infinite supramolecule is close to cylindrical, and its point group is approximately C 2v , which is compatible with the space group, I2/a. However, the crystallographic twofold rotation axis of I2/a is parallel to [010], and thus it does not coincide with the symmetry axis of the cylindrical supramolecule, which is parallel to [100]. The most important feature for the crystallization of the title compound is depicted in Fig. 5 ▸: hydrophobic benzene rings of HL + and L point towards the inside of the cylindrical supramolecule. This arrangement prevents solvent molecules filling these cavities from forming hydrogen bonds with (HL +·Gal−)2·L, and, presumably, only weak C—H⋯O=C contacts are present. This explains why ethyl acetate is disordered in this solvated co-crystal.
4. Database survey
A search of the CSD (v. 5.43 with all updates; Groom et al., 2016 ▸) shows that crystal-structure determinations of compounds including cations H2 L 2+ or HL + are rather rare. Three salts of H2 L 2+ have been reported so far: H2 L(SO4)·3H2O (Clifford et al., 2012 ▸), H2 L·2(Cl)·2H2O (Hu et al., 2006 ▸) and H2 L(CoCl4) (Matthews et al., 2003 ▸). For HL +, three crystal structures have also been reported: HL(ClO4) (Sun et al., 2004 ▸), one co-crystal with trimesic acid and the corresponding carboxylate anion (Feng & Jiang, 2010 ▸), and one CoII complex (Wen et al., 2014 ▸). However, more structures based on the neutral bis-benzimidazole L have been deposited in the CSD, with 22 hits, but all are coordination compounds. In particular, it is surprising that the crystal structure of L has never been reported.
Regarding the conformation of the cation HL + or the neutral molecule L, all possibilities are represented, with central propane bridges found in trans–trans, trans–gauche and gauche–gauche conformations, although the trans–gauche conformation, observed for HL + in the present complex, is less common, being observed for only one example (Wang & An, 2016 ▸). With such flexibility, almost any relative position for the benzimidazole rings is possible. For the 28 hits retrieved from the CSD, the dihedral angles between benzimidazole rings span a range from 4 to 87°, and the distances between the centroids of the imidazole rings span the range from 3.33 to 5.29 Å.
5. Synthesis and crystallization
A solution of 1,3-bis(1H-benzo[d]imidazol-2-yl)propane (L, 12.4 mg, 0.045 mmol) and gallic acid (HGal, 7.6 mg, 0.045 mmol) in 10 mL of ethyl acetate was heated at boiling temperature until dissolution of the reactants. After filtration, the solution was left at room temperature for slow evaporation of the solvent, giving purple crystals suitable for single-crystal X-ray diffraction analysis.
6. Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸ where the solvent molecules are not considered in the given chemical formula and other crystal data. All H atoms bonded to heteroatoms were refined with free coordinates, in order to achieve an accurate hydrogen-bonding model. Other H atoms were placed in calculated positions. Atom C26 is placed on the twofold rotation axis in space group I2/a, and therefore, H atoms for this methylene group were modelled with two H atoms (H26A and H26B) with occupancies of 1/2, in such a way that H26B is the image of H26A through the symmetry axis and vice versa (command HFIX 23 in SHELXL; Sheldrick, 2015b ▸).
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | 2C17H17N4 +·2C7H5O5 −·C17H16N4 |
| M r | 1169.25 |
| Crystal system, space group | Monoclinic, I2/a |
| Temperature (K) | 295 |
| a, b, c (Å) | 16.82625 (15), 16.73298 (17), 26.7833 (3) |
| β (°) | 105.2162 (11) |
| V (Å3) | 7276.57 (14) |
| Z | 4 |
| Radiation type | Mo Kα |
| μ (mm−1) | 0.07 |
| Crystal size (mm) | 0.60 × 0.48 × 0.37 |
| Data collection | |
| Diffractometer | Xcalibur, Atlas, Gemini |
| Absorption correction | Gaussian (CrysAlis PRO; Rigaku OD, 2022 ▸) |
| T min, T max | 0.761, 1.000 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 188774, 11088, 8064 |
| R int | 0.064 |
| (sin θ/λ)max (Å−1) | 0.714 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.049, 0.149, 1.06 |
| No. of reflections | 11088 |
| No. of parameters | 414 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.30, −0.18 |
Supplementary Material
Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989023004279/wm5683sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023004279/wm5683Isup2.hkl
CCDC reference: 2263401
Additional supporting information: crystallographic information; 3D view; checkCIF report
supplementary crystallographic information
Crystal data
| 2C17H17N4+·2C7H5O5−·C17H16N4 | F(000) = 2456 |
| Mr = 1169.25 | Dx = 1.067 Mg m−3 |
| Monoclinic, I2/a | Mo Kα radiation, λ = 0.71073 Å |
| a = 16.82625 (15) Å | Cell parameters from 53060 reflections |
| b = 16.73298 (17) Å | θ = 1.5–33.7° |
| c = 26.7833 (3) Å | µ = 0.07 mm−1 |
| β = 105.2162 (11)° | T = 295 K |
| V = 7276.57 (14) Å3 | Block, purple |
| Z = 4 | 0.60 × 0.48 × 0.37 mm |
Data collection
| Xcalibur, Atlas, Gemini diffractometer | 11088 independent reflections |
| Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source | 8064 reflections with I > 2σ(I) |
| Graphite monochromator | Rint = 0.064 |
| Detector resolution: 10.5564 pixels mm-1 | θmax = 30.5°, θmin = 1.6° |
| ω scans | h = −24→24 |
| Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2022) | k = −23→23 |
| Tmin = 0.761, Tmax = 1.000 | l = −38→38 |
| 188774 measured reflections |
Refinement
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.049 | Hydrogen site location: mixed |
| wR(F2) = 0.149 | H atoms treated by a mixture of independent and constrained refinement |
| S = 1.06 | w = 1/[σ2(Fo2) + (0.0782P)2 + 1.8337P] where P = (Fo2 + 2Fc2)/3 |
| 11088 reflections | (Δ/σ)max = 0.001 |
| 414 parameters | Δρmax = 0.30 e Å−3 |
| 0 restraints | Δρmin = −0.18 e Å−3 |
| 0 constraints |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | Occ. (<1) | |
| N1 | 0.62719 (6) | 0.20714 (6) | 0.69126 (4) | 0.0409 (2) | |
| N2 | 0.70426 (6) | 0.31366 (7) | 0.68709 (4) | 0.0415 (2) | |
| H2 | 0.7153 (9) | 0.3686 (10) | 0.6889 (6) | 0.050* | |
| N3 | 0.29155 (6) | 0.28875 (6) | 0.65905 (4) | 0.0410 (2) | |
| H3 | 0.2821 (9) | 0.3375 (10) | 0.6465 (6) | 0.049* | |
| N4 | 0.35419 (6) | 0.17996 (6) | 0.69126 (5) | 0.0456 (3) | |
| H4 | 0.3956 (10) | 0.1491 (10) | 0.7050 (6) | 0.055* | |
| C1 | 0.63565 (6) | 0.28528 (7) | 0.69822 (4) | 0.0369 (2) | |
| C2 | 0.69506 (7) | 0.18377 (8) | 0.67405 (5) | 0.0417 (3) | |
| C3 | 0.71780 (10) | 0.10890 (10) | 0.66007 (7) | 0.0588 (4) | |
| H3A | 0.686161 | 0.063838 | 0.661591 | 0.071* | |
| C4 | 0.78909 (12) | 0.10380 (12) | 0.64384 (8) | 0.0715 (5) | |
| H4A | 0.805713 | 0.054293 | 0.634429 | 0.086* | |
| C5 | 0.83663 (11) | 0.17096 (12) | 0.64124 (7) | 0.0710 (5) | |
| H5 | 0.884062 | 0.165163 | 0.629939 | 0.085* | |
| C6 | 0.81553 (9) | 0.24544 (11) | 0.65486 (6) | 0.0586 (4) | |
| H6 | 0.847519 | 0.290187 | 0.653195 | 0.070* | |
| C7 | 0.74379 (7) | 0.25066 (8) | 0.67130 (5) | 0.0420 (3) | |
| C8 | 0.58072 (7) | 0.34195 (8) | 0.71577 (6) | 0.0454 (3) | |
| H8A | 0.570693 | 0.387335 | 0.692415 | 0.055* | |
| H8B | 0.609617 | 0.361623 | 0.749748 | 0.055* | |
| C9 | 0.49824 (7) | 0.30894 (8) | 0.71883 (5) | 0.0458 (3) | |
| H9A | 0.469890 | 0.349272 | 0.733691 | 0.055* | |
| H9B | 0.507561 | 0.263106 | 0.741808 | 0.055* | |
| C10 | 0.44301 (7) | 0.28374 (8) | 0.66621 (6) | 0.0454 (3) | |
| H10A | 0.432614 | 0.329527 | 0.643194 | 0.055* | |
| H10B | 0.471005 | 0.243466 | 0.651070 | 0.055* | |
| C11 | 0.36365 (7) | 0.25125 (7) | 0.67136 (5) | 0.0410 (3) | |
| C12 | 0.23293 (7) | 0.24029 (7) | 0.67147 (5) | 0.0403 (3) | |
| C13 | 0.14945 (8) | 0.25199 (9) | 0.66602 (6) | 0.0542 (4) | |
| H13 | 0.123234 | 0.299434 | 0.653072 | 0.065* | |
| C14 | 0.10775 (9) | 0.18973 (11) | 0.68079 (7) | 0.0650 (4) | |
| H14 | 0.051424 | 0.194600 | 0.677015 | 0.078* | |
| C15 | 0.14755 (9) | 0.11917 (10) | 0.70137 (7) | 0.0637 (4) | |
| H15 | 0.116961 | 0.078516 | 0.711040 | 0.076* | |
| C16 | 0.23059 (8) | 0.10804 (9) | 0.70774 (6) | 0.0536 (3) | |
| H16 | 0.257062 | 0.061314 | 0.721899 | 0.064* | |
| C17 | 0.27263 (7) | 0.17010 (8) | 0.69195 (5) | 0.0422 (3) | |
| N5 | 0.45349 (6) | 0.41770 (7) | 0.53870 (4) | 0.0448 (3) | |
| N6 | 0.41648 (6) | 0.41115 (7) | 0.45294 (4) | 0.0386 (2) | |
| H6A | 0.3833 (9) | 0.4196 (9) | 0.4214 (6) | 0.046* | |
| C18 | 0.39799 (6) | 0.43829 (7) | 0.49600 (4) | 0.0363 (2) | |
| C19 | 0.51184 (7) | 0.37344 (8) | 0.52212 (5) | 0.0427 (3) | |
| C20 | 0.58383 (9) | 0.33716 (11) | 0.55080 (6) | 0.0620 (4) | |
| H20 | 0.599317 | 0.339769 | 0.586743 | 0.074* | |
| C21 | 0.63136 (10) | 0.29722 (12) | 0.52407 (7) | 0.0707 (5) | |
| H21 | 0.679105 | 0.271436 | 0.542360 | 0.085* | |
| C22 | 0.60934 (9) | 0.29471 (11) | 0.47023 (7) | 0.0655 (4) | |
| H22 | 0.643155 | 0.267777 | 0.453395 | 0.079* | |
| C23 | 0.53885 (8) | 0.33102 (10) | 0.44121 (6) | 0.0533 (3) | |
| H23 | 0.524628 | 0.329751 | 0.405239 | 0.064* | |
| C24 | 0.48992 (6) | 0.36969 (8) | 0.46827 (5) | 0.0392 (3) | |
| C25 | 0.32225 (6) | 0.48543 (8) | 0.49463 (5) | 0.0398 (3) | |
| H25A | 0.306067 | 0.514498 | 0.462208 | 0.048* | |
| H25B | 0.334742 | 0.524315 | 0.522463 | 0.048* | |
| C26 | 0.250000 | 0.43372 (11) | 0.500000 | 0.0390 (3) | |
| H26A | 0.232262 | 0.399658 | 0.469816 | 0.047* | 0.5 |
| H26B | 0.267739 | 0.399662 | 0.530185 | 0.047* | 0.5 |
| C27 | 0.24259 (6) | 0.48453 (6) | 0.66505 (4) | 0.0286 (2) | |
| O1 | 0.22012 (4) | 0.42873 (5) | 0.63255 (3) | 0.03592 (18) | |
| O2 | 0.19661 (4) | 0.51802 (5) | 0.68876 (4) | 0.0406 (2) | |
| C28 | 0.33088 (5) | 0.51107 (6) | 0.67702 (4) | 0.0279 (2) | |
| C29 | 0.36507 (6) | 0.55315 (6) | 0.72219 (4) | 0.0301 (2) | |
| H29 | 0.332142 | 0.568311 | 0.743553 | 0.036* | |
| C30 | 0.44827 (6) | 0.57278 (6) | 0.73570 (4) | 0.0304 (2) | |
| O30 | 0.48495 (5) | 0.61169 (5) | 0.78071 (4) | 0.0434 (2) | |
| H30 | 0.4435 (11) | 0.6401 (11) | 0.7912 (6) | 0.065* | |
| C31 | 0.49785 (6) | 0.55062 (6) | 0.70354 (4) | 0.0305 (2) | |
| O31 | 0.57953 (4) | 0.56927 (6) | 0.71834 (4) | 0.0422 (2) | |
| H31 | 0.6076 (11) | 0.5401 (10) | 0.7008 (7) | 0.063* | |
| C32 | 0.46247 (6) | 0.51162 (7) | 0.65697 (4) | 0.0307 (2) | |
| O32 | 0.51369 (5) | 0.49489 (6) | 0.62700 (3) | 0.0442 (2) | |
| H32 | 0.4854 (11) | 0.4668 (11) | 0.5968 (7) | 0.066* | |
| C33 | 0.37932 (6) | 0.49074 (7) | 0.64409 (4) | 0.0307 (2) | |
| H33 | 0.356292 | 0.463270 | 0.613533 | 0.037* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| N1 | 0.0334 (5) | 0.0412 (5) | 0.0503 (6) | −0.0029 (4) | 0.0148 (4) | 0.0086 (4) |
| N2 | 0.0328 (5) | 0.0429 (5) | 0.0490 (6) | −0.0068 (4) | 0.0112 (4) | 0.0071 (4) |
| N3 | 0.0297 (4) | 0.0356 (5) | 0.0566 (6) | 0.0051 (4) | 0.0091 (4) | 0.0087 (4) |
| N4 | 0.0278 (4) | 0.0397 (5) | 0.0654 (7) | 0.0072 (4) | 0.0054 (4) | 0.0122 (5) |
| C1 | 0.0278 (5) | 0.0421 (6) | 0.0392 (6) | −0.0040 (4) | 0.0059 (4) | 0.0085 (5) |
| C2 | 0.0363 (6) | 0.0467 (6) | 0.0437 (6) | −0.0009 (5) | 0.0132 (5) | 0.0077 (5) |
| C3 | 0.0602 (9) | 0.0508 (8) | 0.0708 (10) | 0.0004 (7) | 0.0269 (8) | 0.0013 (7) |
| C4 | 0.0716 (11) | 0.0710 (11) | 0.0812 (12) | 0.0131 (9) | 0.0368 (9) | −0.0051 (9) |
| C5 | 0.0561 (9) | 0.0932 (13) | 0.0751 (11) | 0.0046 (9) | 0.0373 (8) | −0.0008 (10) |
| C6 | 0.0445 (7) | 0.0755 (10) | 0.0628 (9) | −0.0070 (7) | 0.0264 (7) | 0.0043 (8) |
| C7 | 0.0346 (5) | 0.0511 (7) | 0.0410 (6) | −0.0033 (5) | 0.0112 (5) | 0.0090 (5) |
| C8 | 0.0349 (6) | 0.0421 (6) | 0.0598 (8) | −0.0039 (5) | 0.0132 (5) | −0.0001 (6) |
| C9 | 0.0343 (6) | 0.0468 (7) | 0.0581 (8) | −0.0011 (5) | 0.0155 (5) | 0.0017 (6) |
| C10 | 0.0303 (5) | 0.0464 (7) | 0.0587 (8) | 0.0019 (5) | 0.0101 (5) | 0.0086 (6) |
| C11 | 0.0274 (5) | 0.0401 (6) | 0.0524 (7) | 0.0047 (4) | 0.0051 (5) | 0.0052 (5) |
| C12 | 0.0293 (5) | 0.0403 (6) | 0.0501 (7) | 0.0040 (4) | 0.0084 (5) | 0.0056 (5) |
| C13 | 0.0334 (6) | 0.0585 (8) | 0.0719 (9) | 0.0114 (6) | 0.0159 (6) | 0.0165 (7) |
| C14 | 0.0340 (6) | 0.0784 (11) | 0.0854 (11) | 0.0052 (6) | 0.0205 (7) | 0.0242 (9) |
| C15 | 0.0445 (7) | 0.0668 (10) | 0.0807 (11) | −0.0059 (7) | 0.0181 (7) | 0.0238 (8) |
| C16 | 0.0434 (7) | 0.0478 (7) | 0.0665 (9) | 0.0008 (6) | 0.0093 (6) | 0.0170 (6) |
| C17 | 0.0304 (5) | 0.0422 (6) | 0.0505 (7) | 0.0031 (4) | 0.0047 (5) | 0.0062 (5) |
| N5 | 0.0292 (4) | 0.0697 (7) | 0.0353 (5) | 0.0067 (4) | 0.0078 (4) | −0.0058 (5) |
| N6 | 0.0260 (4) | 0.0542 (6) | 0.0341 (5) | 0.0023 (4) | 0.0056 (4) | −0.0030 (4) |
| C18 | 0.0233 (4) | 0.0482 (6) | 0.0383 (6) | −0.0028 (4) | 0.0096 (4) | −0.0035 (5) |
| C19 | 0.0271 (5) | 0.0609 (8) | 0.0392 (6) | 0.0048 (5) | 0.0074 (4) | −0.0040 (5) |
| C20 | 0.0398 (7) | 0.0968 (12) | 0.0447 (7) | 0.0201 (7) | 0.0025 (6) | 0.0013 (8) |
| C21 | 0.0443 (7) | 0.0944 (13) | 0.0682 (10) | 0.0301 (8) | 0.0057 (7) | −0.0013 (9) |
| C22 | 0.0461 (7) | 0.0837 (11) | 0.0679 (10) | 0.0210 (7) | 0.0172 (7) | −0.0135 (8) |
| C23 | 0.0434 (7) | 0.0711 (9) | 0.0458 (7) | 0.0088 (6) | 0.0126 (5) | −0.0130 (6) |
| C24 | 0.0274 (5) | 0.0507 (7) | 0.0384 (6) | 0.0014 (4) | 0.0066 (4) | −0.0054 (5) |
| C25 | 0.0251 (5) | 0.0489 (7) | 0.0473 (7) | 0.0008 (4) | 0.0130 (4) | −0.0009 (5) |
| C26 | 0.0233 (6) | 0.0469 (9) | 0.0475 (9) | 0.000 | 0.0106 (6) | 0.000 |
| C27 | 0.0185 (4) | 0.0291 (5) | 0.0372 (5) | 0.0008 (3) | 0.0053 (4) | 0.0035 (4) |
| O1 | 0.0221 (3) | 0.0364 (4) | 0.0450 (4) | −0.0009 (3) | 0.0012 (3) | −0.0033 (3) |
| O2 | 0.0209 (3) | 0.0428 (4) | 0.0608 (5) | −0.0012 (3) | 0.0156 (3) | −0.0077 (4) |
| C28 | 0.0174 (4) | 0.0298 (5) | 0.0366 (5) | 0.0004 (3) | 0.0070 (3) | 0.0014 (4) |
| C29 | 0.0203 (4) | 0.0318 (5) | 0.0403 (5) | 0.0004 (3) | 0.0116 (4) | −0.0040 (4) |
| C30 | 0.0217 (4) | 0.0303 (5) | 0.0391 (5) | −0.0007 (3) | 0.0078 (4) | −0.0061 (4) |
| O30 | 0.0251 (4) | 0.0513 (5) | 0.0539 (5) | −0.0036 (3) | 0.0104 (3) | −0.0250 (4) |
| C31 | 0.0180 (4) | 0.0323 (5) | 0.0418 (6) | −0.0009 (3) | 0.0086 (4) | −0.0024 (4) |
| O31 | 0.0183 (3) | 0.0525 (5) | 0.0571 (5) | −0.0054 (3) | 0.0124 (3) | −0.0179 (4) |
| C32 | 0.0202 (4) | 0.0394 (5) | 0.0340 (5) | 0.0008 (4) | 0.0096 (4) | −0.0001 (4) |
| O32 | 0.0231 (3) | 0.0740 (6) | 0.0385 (4) | −0.0028 (4) | 0.0137 (3) | −0.0109 (4) |
| C33 | 0.0210 (4) | 0.0388 (5) | 0.0317 (5) | −0.0007 (4) | 0.0057 (4) | −0.0024 (4) |
Geometric parameters (Å, º)
| N1—C1 | 1.3230 (16) | C16—H16 | 0.9300 |
| N1—C2 | 1.3950 (15) | N5—C18 | 1.3184 (15) |
| N2—C1 | 1.3520 (14) | N5—C19 | 1.3922 (15) |
| N2—C7 | 1.3712 (17) | N6—C18 | 1.3496 (15) |
| N2—H2 | 0.936 (16) | N6—C24 | 1.3822 (14) |
| N3—C11 | 1.3282 (14) | N6—H6A | 0.893 (15) |
| N3—C12 | 1.3831 (15) | C18—C25 | 1.4910 (15) |
| N3—H3 | 0.880 (16) | C19—C20 | 1.3920 (18) |
| N4—C11 | 1.3330 (16) | C19—C24 | 1.3933 (17) |
| N4—C17 | 1.3872 (15) | C20—C21 | 1.378 (2) |
| N4—H4 | 0.867 (16) | C20—H20 | 0.9300 |
| C1—C8 | 1.4841 (18) | C21—C22 | 1.392 (2) |
| C2—C3 | 1.390 (2) | C21—H21 | 0.9300 |
| C2—C7 | 1.4007 (17) | C22—C23 | 1.377 (2) |
| C3—C4 | 1.382 (2) | C22—H22 | 0.9300 |
| C3—H3A | 0.9300 | C23—C24 | 1.3909 (17) |
| C4—C5 | 1.392 (3) | C23—H23 | 0.9300 |
| C4—H4A | 0.9300 | C25—C26 | 1.5293 (15) |
| C5—C6 | 1.371 (3) | C25—H25A | 0.9700 |
| C5—H5 | 0.9300 | C25—H25B | 0.9700 |
| C6—C7 | 1.3921 (18) | C26—H26A | 0.9700 |
| C6—H6 | 0.9300 | C26—H26B | 0.9700 |
| C8—C9 | 1.5158 (16) | C27—O2 | 1.2545 (12) |
| C8—H8A | 0.9700 | C27—O1 | 1.2648 (13) |
| C8—H8B | 0.9700 | C27—C28 | 1.5024 (13) |
| C9—C10 | 1.5298 (19) | C28—C29 | 1.3876 (14) |
| C9—H9A | 0.9700 | C28—C33 | 1.3910 (14) |
| C9—H9B | 0.9700 | C29—C30 | 1.3903 (13) |
| C10—C11 | 1.4814 (16) | C29—H29 | 0.9300 |
| C10—H10A | 0.9700 | C30—O30 | 1.3665 (13) |
| C10—H10B | 0.9700 | C30—C31 | 1.3973 (14) |
| C12—C13 | 1.3874 (16) | O30—H30 | 0.946 (18) |
| C12—C17 | 1.3909 (16) | C31—O31 | 1.3629 (11) |
| C13—C14 | 1.371 (2) | C31—C32 | 1.3953 (15) |
| C13—H13 | 0.9300 | O31—H31 | 0.894 (18) |
| C14—C15 | 1.397 (2) | C32—O32 | 1.3521 (12) |
| C14—H14 | 0.9300 | C32—C33 | 1.3946 (13) |
| C15—C16 | 1.375 (2) | O32—H32 | 0.948 (19) |
| C15—H15 | 0.9300 | C33—H33 | 0.9300 |
| C16—C17 | 1.3838 (18) | ||
| C1—N1—C2 | 104.86 (10) | C17—C16—H16 | 121.8 |
| C1—N2—C7 | 108.02 (10) | C16—C17—N4 | 132.87 (11) |
| C1—N2—H2 | 120.2 (9) | C16—C17—C12 | 121.54 (11) |
| C7—N2—H2 | 131.7 (9) | N4—C17—C12 | 105.59 (10) |
| C11—N3—C12 | 109.02 (10) | C18—N5—C19 | 105.11 (10) |
| C11—N3—H3 | 126.4 (10) | C18—N6—C24 | 107.69 (10) |
| C12—N3—H3 | 124.5 (10) | C18—N6—H6A | 121.8 (9) |
| C11—N4—C17 | 109.51 (10) | C24—N6—H6A | 130.4 (9) |
| C11—N4—H4 | 122.3 (11) | N5—C18—N6 | 112.55 (10) |
| C17—N4—H4 | 127.7 (11) | N5—C18—C25 | 124.47 (10) |
| N1—C1—N2 | 112.50 (11) | N6—C18—C25 | 122.98 (10) |
| N1—C1—C8 | 128.54 (10) | C20—C19—N5 | 129.82 (12) |
| N2—C1—C8 | 118.96 (11) | C20—C19—C24 | 120.47 (12) |
| C3—C2—N1 | 130.46 (12) | N5—C19—C24 | 109.69 (10) |
| C3—C2—C7 | 119.99 (12) | C21—C20—C19 | 117.68 (13) |
| N1—C2—C7 | 109.55 (11) | C21—C20—H20 | 121.2 |
| C4—C3—C2 | 117.62 (15) | C19—C20—H20 | 121.2 |
| C4—C3—H3A | 121.2 | C20—C21—C22 | 121.31 (14) |
| C2—C3—H3A | 121.2 | C20—C21—H21 | 119.3 |
| C3—C4—C5 | 121.58 (16) | C22—C21—H21 | 119.3 |
| C3—C4—H4A | 119.2 | C23—C22—C21 | 121.81 (14) |
| C5—C4—H4A | 119.2 | C23—C22—H22 | 119.1 |
| C6—C5—C4 | 121.89 (14) | C21—C22—H22 | 119.1 |
| C6—C5—H5 | 119.1 | C22—C23—C24 | 116.82 (13) |
| C4—C5—H5 | 119.1 | C22—C23—H23 | 121.6 |
| C5—C6—C7 | 116.60 (15) | C24—C23—H23 | 121.6 |
| C5—C6—H6 | 121.7 | N6—C24—C23 | 133.16 (11) |
| C7—C6—H6 | 121.7 | N6—C24—C19 | 104.94 (10) |
| N2—C7—C6 | 132.60 (13) | C23—C24—C19 | 121.89 (11) |
| N2—C7—C2 | 105.08 (10) | C18—C25—C26 | 113.19 (11) |
| C6—C7—C2 | 122.32 (13) | C18—C25—H25A | 108.9 |
| C1—C8—C9 | 116.07 (11) | C26—C25—H25A | 108.9 |
| C1—C8—H8A | 108.3 | C18—C25—H25B | 108.9 |
| C9—C8—H8A | 108.3 | C26—C25—H25B | 108.9 |
| C1—C8—H8B | 108.3 | H25A—C25—H25B | 107.8 |
| C9—C8—H8B | 108.3 | C25i—C26—C25 | 111.10 (14) |
| H8A—C8—H8B | 107.4 | C25i—C26—H26A | 109.4 |
| C8—C9—C10 | 113.20 (11) | C25—C26—H26A | 109.4 |
| C8—C9—H9A | 108.9 | C25i—C26—H26B | 109.4 |
| C10—C9—H9A | 108.9 | C25—C26—H26B | 109.4 |
| C8—C9—H9B | 108.9 | H26A—C26—H26B | 108.0 |
| C10—C9—H9B | 108.9 | O2—C27—O1 | 124.43 (9) |
| H9A—C9—H9B | 107.8 | O2—C27—C28 | 117.82 (9) |
| C11—C10—C9 | 111.09 (11) | O1—C27—C28 | 117.73 (9) |
| C11—C10—H10A | 109.4 | C29—C28—C33 | 119.94 (9) |
| C9—C10—H10A | 109.4 | C29—C28—C27 | 119.76 (9) |
| C11—C10—H10B | 109.4 | C33—C28—C27 | 120.24 (9) |
| C9—C10—H10B | 109.4 | C28—C29—C30 | 120.36 (9) |
| H10A—C10—H10B | 108.0 | C28—C29—H29 | 119.8 |
| N3—C11—N4 | 108.96 (10) | C30—C29—H29 | 119.8 |
| N3—C11—C10 | 126.19 (11) | O30—C30—C29 | 122.21 (9) |
| N4—C11—C10 | 124.80 (10) | O30—C30—C31 | 117.75 (8) |
| N3—C12—C13 | 131.16 (12) | C29—C30—C31 | 120.02 (9) |
| N3—C12—C17 | 106.91 (10) | C30—O30—H30 | 107.7 (11) |
| C13—C12—C17 | 121.92 (12) | O31—C31—C32 | 121.88 (9) |
| C14—C13—C12 | 116.31 (13) | O31—C31—C30 | 118.67 (9) |
| C14—C13—H13 | 121.8 | C32—C31—C30 | 119.44 (9) |
| C12—C13—H13 | 121.8 | C31—O31—H31 | 110.8 (11) |
| C13—C14—C15 | 121.82 (13) | O32—C32—C33 | 123.76 (10) |
| C13—C14—H14 | 119.1 | O32—C32—C31 | 116.02 (9) |
| C15—C14—H14 | 119.1 | C33—C32—C31 | 120.21 (9) |
| C16—C15—C14 | 121.98 (14) | C32—O32—H32 | 110.7 (11) |
| C16—C15—H15 | 119.0 | C28—C33—C32 | 119.91 (10) |
| C14—C15—H15 | 119.0 | C28—C33—H33 | 120.0 |
| C15—C16—C17 | 116.41 (13) | C32—C33—H33 | 120.0 |
| C15—C16—H16 | 121.8 | ||
| C2—N1—C1—N2 | −0.44 (14) | C13—C12—C17—N4 | 179.89 (13) |
| C2—N1—C1—C8 | 179.31 (12) | C19—N5—C18—N6 | −0.52 (15) |
| C7—N2—C1—N1 | 0.51 (14) | C19—N5—C18—C25 | 178.77 (11) |
| C7—N2—C1—C8 | −179.26 (11) | C24—N6—C18—N5 | −0.21 (14) |
| C1—N1—C2—C3 | −179.18 (15) | C24—N6—C18—C25 | −179.51 (11) |
| C1—N1—C2—C7 | 0.21 (14) | C18—N5—C19—C20 | 179.82 (16) |
| N1—C2—C3—C4 | 179.44 (15) | C18—N5—C19—C24 | 1.06 (15) |
| C7—C2—C3—C4 | 0.1 (2) | N5—C19—C20—C21 | −179.31 (16) |
| C2—C3—C4—C5 | −0.3 (3) | C24—C19—C20—C21 | −0.7 (2) |
| C3—C4—C5—C6 | 0.3 (3) | C19—C20—C21—C22 | 1.5 (3) |
| C4—C5—C6—C7 | −0.2 (3) | C20—C21—C22—C23 | −0.8 (3) |
| C1—N2—C7—C6 | 179.15 (14) | C21—C22—C23—C24 | −0.7 (3) |
| C1—N2—C7—C2 | −0.35 (13) | C18—N6—C24—C23 | −178.24 (15) |
| C5—C6—C7—N2 | −179.35 (15) | C18—N6—C24—C19 | 0.84 (14) |
| C5—C6—C7—C2 | 0.1 (2) | C22—C23—C24—N6 | −179.50 (15) |
| C3—C2—C7—N2 | 179.55 (13) | C22—C23—C24—C19 | 1.5 (2) |
| N1—C2—C7—N2 | 0.09 (14) | C20—C19—C24—N6 | 179.93 (14) |
| C3—C2—C7—C6 | 0.0 (2) | N5—C19—C24—N6 | −1.18 (15) |
| N1—C2—C7—C6 | −179.47 (12) | C20—C19—C24—C23 | −0.9 (2) |
| N1—C1—C8—C9 | −9.7 (2) | N5—C19—C24—C23 | 178.03 (13) |
| N2—C1—C8—C9 | 170.03 (11) | N5—C18—C25—C26 | −86.02 (14) |
| C1—C8—C9—C10 | −63.93 (16) | N6—C18—C25—C26 | 93.19 (13) |
| C8—C9—C10—C11 | 179.45 (11) | C18—C25—C26—C25i | 172.70 (12) |
| C12—N3—C11—N4 | 0.14 (15) | O2—C27—C28—C29 | 18.00 (15) |
| C12—N3—C11—C10 | −177.42 (13) | O1—C27—C28—C29 | −160.52 (10) |
| C17—N4—C11—N3 | 0.16 (16) | O2—C27—C28—C33 | −164.68 (10) |
| C17—N4—C11—C10 | 177.76 (13) | O1—C27—C28—C33 | 16.80 (15) |
| C9—C10—C11—N3 | 103.86 (15) | C33—C28—C29—C30 | −2.24 (16) |
| C9—C10—C11—N4 | −73.33 (17) | C27—C28—C29—C30 | 175.09 (9) |
| C11—N3—C12—C13 | −179.73 (15) | C28—C29—C30—O30 | −177.66 (10) |
| C11—N3—C12—C17 | −0.38 (15) | C28—C29—C30—C31 | 0.45 (16) |
| N3—C12—C13—C14 | 177.75 (15) | O30—C30—C31—O31 | −0.48 (16) |
| C17—C12—C13—C14 | −1.5 (2) | C29—C30—C31—O31 | −178.67 (10) |
| C12—C13—C14—C15 | 1.5 (3) | O30—C30—C31—C32 | −179.25 (10) |
| C13—C14—C15—C16 | −0.3 (3) | C29—C30—C31—C32 | 2.55 (16) |
| C14—C15—C16—C17 | −0.9 (3) | O31—C31—C32—O32 | −1.24 (16) |
| C15—C16—C17—N4 | −178.51 (16) | C30—C31—C32—O32 | 177.49 (10) |
| C15—C16—C17—C12 | 0.9 (2) | O31—C31—C32—C33 | 177.48 (10) |
| C11—N4—C17—C16 | 179.11 (16) | C30—C31—C32—C33 | −3.78 (16) |
| C11—N4—C17—C12 | −0.39 (15) | C29—C28—C33—C32 | 1.01 (16) |
| N3—C12—C17—C16 | −179.11 (13) | C27—C28—C33—C32 | −176.32 (9) |
| C13—C12—C17—C16 | 0.3 (2) | O32—C32—C33—C28 | −179.36 (10) |
| N3—C12—C17—N4 | 0.46 (15) | C31—C32—C33—C28 | 2.02 (16) |
Symmetry code: (i) −x+1/2, y, −z+1.
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···O2ii | 0.936 (16) | 1.924 (17) | 2.8204 (14) | 159.7 (13) |
| N3—H3···O1 | 0.880 (16) | 1.832 (16) | 2.6433 (13) | 152.4 (14) |
| N4—H4···O30iii | 0.867 (16) | 2.043 (16) | 2.8509 (12) | 154.6 (14) |
| N4—H4···O31iii | 0.867 (16) | 2.394 (16) | 3.0199 (14) | 129.5 (13) |
| N6—H6A···O1i | 0.893 (15) | 1.955 (16) | 2.8018 (12) | 157.9 (13) |
| O30—H30···N1iv | 0.946 (18) | 1.785 (18) | 2.7238 (12) | 171.3 (16) |
| O31—H31···O2ii | 0.894 (18) | 1.882 (18) | 2.7314 (11) | 157.8 (16) |
| O32—H32···N5 | 0.948 (19) | 1.717 (19) | 2.6515 (14) | 167.9 (16) |
| C8—H8A···O32 | 0.97 | 2.52 | 3.4736 (17) | 168 |
| C10—H10B···N1 | 0.97 | 2.64 | 3.2566 (16) | 122 |
Symmetry codes: (i) −x+1/2, y, −z+1; (ii) x+1/2, −y+1, z; (iii) −x+1, y−1/2, −z+3/2; (iv) −x+1, y+1/2, −z+3/2.
Funding Statement
Funding for this research was provided by: Consejo Nacional de Ciencia y Tecnología (scholarship No. 737995 to JCPR).
References
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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, global. DOI: 10.1107/S2056989023004279/wm5683sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023004279/wm5683Isup2.hkl
CCDC reference: 2263401
Additional supporting information: crystallographic information; 3D view; checkCIF report