| Literature DB >> 30002892 |
Hammouda Chebbi1,2, Samia Mezrigui1, Meriam Ben Jomaa1, Mohamed Faouzi Zid1.
Abstract
The title salt, C8H20N22+·2NO3-, was obtained by a reaction between 1,3-cyclohexa-nebis(methyl-amine) and nitric acid. The cyclo-hexane ring of the organic cation is in a chair conformation with the methyl-ammonium substituents in the equatorial positions and the two terminal ammonium groups in a trans conformation. In the crystal, mixed cation-anion layers lying parallel to the (010) plane are formed through N-H⋯O hydrogen-bonding inter-actions; these layers are formed by infinite undulating chains running parallel to the [001] direction. The overall inter-molecular inter-actions involved in the structure were qu-anti-fied and fully described by Hirshfeld surface analysis. In addition, energy-framework calculations were used to analyse and visualize the three-dimensional topology of the crystal packing. The electrostatic energy framework is dominant over the dispersion energy framework.Entities:
Keywords: Hirshfeld surface; crystal structure; energy framework; fingerprint plots; organic dinitrate; oxoanion salt
Year: 2018 PMID: 30002892 PMCID: PMC6038639 DOI: 10.1107/S2056989018008381
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The asymmetric unit of (I), showing the atom-labeling scheme, displacement ellipsoids at the 30% probability level and the two configurations, cis and trans, of (CHMA)2+.
Figure 2The EDX spectrum of (I), showing the presence of C, N, and O.
Figure 3Structure of (I) viewed along the [001] direction, showing the infinite layers parallel to the ac plane. The N—H⋯O hydrogen bonds are shown as orange dashed lines.
Figure 4Unit-cell contents for (I) shown in projection down the a axis, showing the infinite undulating chains. The orange dotted lines indicate N—H⋯O hydrogen bonds.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N1—H1 | 0.87 (4) | 2.22 (4) | 3.084 (6) | 169 (4) |
| N1—H1 | 0.87 (4) | 2.36 (4) | 3.013 (5) | 132 (3) |
| N1—H1 | 0.95 (4) | 2.59 (4) | 3.187 (6) | 121 (3) |
| N1—H1 | 0.95 (4) | 1.87 (4) | 2.818 (5) | 172 (3) |
| N1—H1 | 0.87 (5) | 2.12 (5) | 2.939 (6) | 157 (4) |
| N2—H2 | 0.77 (4) | 2.48 (4) | 3.142 (6) | 145 (4) |
| N2—H2 | 0.77 (4) | 2.19 (4) | 2.899 (6) | 153 (4) |
| N2—H2 | 0.99 (4) | 2.46 (4) | 3.178 (6) | 130 (3) |
| N2—H2 | 0.99 (4) | 1.88 (4) | 2.858 (5) | 173 (4) |
| N2—H2 | 0.96 (6) | 2.05 (6) | 2.967 (5) | 159 (5) |
| N2—H2 | 0.96 (6) | 2.23 (6) | 3.016 (6) | 139 (4) |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .
Figure 5A view showing the (3) motif built by N—H⋯O hydrogen bonds in the undulating chain. C and H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.
Figure 6A view of the supramolecular layer in the ac plane of (I), showing the formation of the (3), R 3(12) and R 4(14) motifs. C and H atoms not involved in hydrogen bonds (orange dashed lines) have been omitted for clarity.
Figure 7Hirshfeld surface around the constituents of (I) coloured according to d norm. The surface is shown as transparent to allow visualization of the orientation and conformation of the functional groups.
Figure 8Two-dimensional fingerprint plots for (I) showing contributions from different contacts: (a) H⋯O/O⋯H, (b) H⋯H, (c) H⋯N/N⋯H and (d) O⋯O.
Figure 9Void plot for (I).
Interaction energies
N refers to the number of molecules with an R molecular centroid-to-centroid distance (Å). Energies are in kJ mol−1.
|
| Symop |
|
|
|
|
|
|
|---|---|---|---|---|---|---|---|
| 2 | − | 8.51 | −63.9 | −50.6 | −6.3 | 5.4 | −107.1 |
| 1 | − | 9.69 | 32.1 | −42.9 | −4.6 | 1.8 | −0.7 |
| 2 |
| 8.86 | 0.0 | −53.8 | 0.0 | 0.0 | −39.8 |
| 2 |
| 5.33 | −23.1 | −75.4 | −20.1 | 14.1 | −89.0 |
| 1 |
| 5.60 | −21.5 | −50.6 | −6.3 | 2.1 | −64.4 |
| 1 |
| 5.77 | 11.3 | −14.6 | −0.5 | 0.0 | 0.7 |
| 1 |
| 5.33 | −44.5 | −18.9 | −0.8 | 0.0 | −61.8 |
| 1 | − | 7.97 | −128.4 | −53.8 | −4.3 | 0.2 | −179.2 |
| 1 | − | 6.43 | −9.8 | −18.9 | −0.8 | 0.0 | −25.0 |
Scale factors used to determine E tot: k ele = 1.057, k pol = 0.740, k dis = 0.871, k rep = 0.618 (Mackenzie et al., 2017 ▸).
Figure 10Energy framework diagram for separate electrostatic (left, red) and dispersion (middle, green) components of (I) and the total interaction energy (right, blue). The energy factor scale is 60 and the cut-off is 5.00 kJ mol−1.
Experimental details
| Crystal data | |
| Chemical formula | C8H20N2 2+·2NO3 − |
|
| 268.28 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 293 |
|
| 10.475 (4), 16.884 (4), 15.514 (2) |
|
| 2743.8 (13) |
|
| 8 |
| Radiation type | Mo |
| μ (mm−1) | 0.11 |
| Crystal size (mm) | 0.52 × 0.40 × 0.15 |
| Data collection | |
| Diffractometer | Enraf–Nonius CAD-4 |
| Absorption correction | ψ scan (North |
|
| 0.946, 1.000 |
| No. of measured, independent and observed [ | 3798, 2980, 991 |
|
| 0.036 |
| (sin θ/λ)max (Å−1) | 0.638 |
| Refinement | |
|
| 0.062, 0.173, 0.98 |
| No. of reflections | 2980 |
| No. of parameters | 187 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.17, −0.13 |
Computer programs: CAD-4 EXPRESS (Duisenberg, 1992 ▸; Macíček & Yordanov, 1992 ▸), XCAD4 (Harms & Wocadlo, 1995 ▸), SHELXS97 (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸), DIAMOND (Brandenburg, 2006 ▸), Mercury (Macrae et al., 2006 ▸), WinGX (Farrugia, 2012 ▸) and publCIF (Westrip, 2010 ▸).
| C8H20N22+·2NO3− | |
| Mo | |
| Orthorhombic, | Cell parameters from 25 reflections |
| θ = 11–15° | |
| µ = 0.11 mm−1 | |
| Plate, colorless | |
| 0.52 × 0.40 × 0.15 mm | |
| Enraf–Nonius CAD-4 diffractometer | 991 reflections with |
| Radiation source: fine-focus sealed tube | |
| Graphite monochromator | θmax = 27.0°, θmin = 2.4° |
| ω/2θ scans | |
| Absorption correction: ψ scan (North | |
| 3798 measured reflections | 2 standard reflections every 120 reflections |
| 2980 independent reflections | intensity decay: 1% |
| Refinement on | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 2980 reflections | Δρmax = 0.17 e Å−3 |
| 187 parameters | Δρmin = −0.13 e Å−3 |
| 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. |
| 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 > 2sigma(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. |
| N1 | 0.5381 (5) | 0.0463 (2) | 0.6598 (3) | 0.0659 (10) | |
| H1A | 0.601 (4) | 0.058 (2) | 0.694 (3) | 0.081 (16)* | |
| H1B | 0.550 (3) | 0.080 (2) | 0.611 (2) | 0.085 (13)* | |
| H1C | 0.471 (4) | 0.059 (3) | 0.690 (3) | 0.096 (19)* | |
| N2 | 0.4634 (5) | −0.1776 (3) | 1.0032 (3) | 0.0674 (10) | |
| H2D | 0.534 (4) | −0.178 (3) | 1.016 (3) | 0.081 (19)* | |
| H2E | 0.431 (4) | −0.155 (2) | 1.057 (3) | 0.098 (15)* | |
| H2F | 0.426 (5) | −0.230 (3) | 1.002 (3) | 0.16 (2)* | |
| C1 | 0.5681 (4) | −0.0935 (2) | 0.7032 (2) | 0.0606 (10) | |
| H1 | 0.6549 | −0.0819 | 0.7232 | 0.073* | |
| C2 | 0.4800 (4) | −0.0856 (2) | 0.7804 (2) | 0.0652 (11) | |
| H2A | 0.4832 | −0.0316 | 0.8016 | 0.078* | |
| H2B | 0.3930 | −0.0965 | 0.7626 | 0.078* | |
| C3 | 0.5166 (4) | −0.1416 (2) | 0.8520 (2) | 0.0601 (10) | |
| H3 | 0.6037 | −0.1279 | 0.8695 | 0.072* | |
| C4 | 0.5197 (4) | −0.2269 (2) | 0.8201 (2) | 0.0652 (11) | |
| H4A | 0.5512 | −0.2610 | 0.8657 | 0.078* | |
| H4B | 0.4338 | −0.2437 | 0.8058 | 0.078* | |
| C5 | 0.6040 (4) | −0.2355 (2) | 0.7419 (2) | 0.0784 (12) | |
| H5A | 0.6920 | −0.2259 | 0.7583 | 0.094* | |
| H5B | 0.5979 | −0.2893 | 0.7204 | 0.094* | |
| C6 | 0.5673 (4) | −0.1791 (2) | 0.6718 (2) | 0.0741 (12) | |
| H6A | 0.4826 | −0.1923 | 0.6510 | 0.089* | |
| H6B | 0.6264 | −0.1845 | 0.6241 | 0.089* | |
| C7 | 0.5393 (4) | −0.0372 (2) | 0.6311 (2) | 0.0701 (11) | |
| H7A | 0.6030 | −0.0436 | 0.5862 | 0.084* | |
| H7B | 0.4568 | −0.0503 | 0.6066 | 0.084* | |
| C8 | 0.4321 (4) | −0.1278 (2) | 0.9289 (2) | 0.0710 (11) | |
| H8A | 0.4386 | −0.0727 | 0.9458 | 0.085* | |
| H8B | 0.3442 | −0.1377 | 0.9123 | 0.085* | |
| N3 | 0.2781 (4) | −0.09045 (18) | 0.1598 (2) | 0.0718 (9) | |
| O1 | 0.2195 (3) | −0.10116 (18) | 0.0922 (2) | 0.1032 (11) | |
| O2 | 0.2248 (3) | −0.06216 (17) | 0.22373 (18) | 0.0826 (9) | |
| O3 | 0.3922 (3) | −0.1097 (2) | 0.16492 (19) | 0.1031 (11) | |
| N4 | 0.7872 (4) | −0.1535 (2) | 0.0224 (2) | 0.0685 (9) | |
| O4 | 0.7259 (3) | −0.09475 (18) | 0.0414 (3) | 0.1171 (12) | |
| O5 | 0.9065 (3) | −0.15214 (15) | 0.02450 (17) | 0.0747 (8) | |
| O6 | 0.7335 (3) | −0.21487 (18) | 0.0004 (2) | 0.1000 (11) |
| N1 | 0.070 (3) | 0.063 (3) | 0.065 (2) | −0.009 (2) | 0.001 (3) | 0.010 (2) |
| N2 | 0.071 (3) | 0.078 (3) | 0.054 (2) | 0.000 (2) | 0.001 (2) | 0.0046 (19) |
| C1 | 0.064 (3) | 0.059 (2) | 0.058 (2) | −0.004 (2) | 0.004 (2) | −0.001 (2) |
| C2 | 0.073 (3) | 0.056 (2) | 0.066 (2) | 0.009 (2) | 0.005 (2) | 0.0013 (19) |
| C3 | 0.062 (2) | 0.058 (2) | 0.060 (2) | 0.005 (2) | 0.000 (2) | 0.009 (2) |
| C4 | 0.072 (3) | 0.054 (2) | 0.069 (2) | 0.003 (2) | 0.000 (2) | 0.0053 (19) |
| C5 | 0.098 (3) | 0.058 (2) | 0.080 (3) | 0.013 (2) | 0.011 (3) | −0.001 (2) |
| C6 | 0.091 (3) | 0.062 (2) | 0.070 (3) | 0.003 (2) | 0.016 (2) | 0.000 (2) |
| C7 | 0.084 (3) | 0.063 (3) | 0.063 (2) | 0.000 (2) | 0.007 (2) | 0.000 (2) |
| C8 | 0.076 (3) | 0.071 (2) | 0.066 (2) | 0.012 (2) | 0.007 (2) | 0.007 (2) |
| N3 | 0.074 (3) | 0.068 (2) | 0.074 (3) | 0.001 (2) | 0.005 (2) | −0.0120 (19) |
| O1 | 0.092 (2) | 0.140 (3) | 0.078 (2) | 0.009 (2) | −0.0104 (19) | −0.0334 (19) |
| O2 | 0.081 (2) | 0.0903 (19) | 0.0764 (18) | 0.0065 (17) | 0.0102 (17) | −0.0262 (16) |
| O3 | 0.074 (2) | 0.140 (3) | 0.096 (2) | 0.028 (2) | −0.0052 (19) | −0.033 (2) |
| N4 | 0.070 (3) | 0.075 (2) | 0.060 (2) | −0.003 (2) | −0.016 (2) | 0.0003 (19) |
| O4 | 0.091 (2) | 0.095 (2) | 0.165 (3) | 0.024 (2) | −0.026 (2) | −0.042 (2) |
| O5 | 0.071 (2) | 0.082 (2) | 0.0709 (18) | −0.0077 (16) | −0.0064 (16) | −0.0090 (14) |
| O6 | 0.084 (2) | 0.0728 (17) | 0.143 (3) | −0.0103 (17) | −0.033 (2) | −0.0060 (18) |
| N1—C7 | 1.479 (5) | C4—C5 | 1.507 (5) |
| N1—H1A | 0.87 (4) | C4—H4A | 0.9700 |
| N1—H1B | 0.95 (4) | C4—H4B | 0.9700 |
| N1—H1C | 0.87 (5) | C5—C6 | 1.496 (5) |
| N2—C8 | 1.464 (5) | C5—H5A | 0.9700 |
| N2—H2D | 0.77 (4) | C5—H5B | 0.9700 |
| N2—H2E | 0.99 (4) | C6—H6A | 0.9700 |
| N2—H2F | 0.96 (6) | C6—H6B | 0.9700 |
| C1—C7 | 1.499 (5) | C7—H7A | 0.9700 |
| C1—C2 | 1.518 (5) | C7—H7B | 0.9700 |
| C1—C6 | 1.524 (5) | C8—H8A | 0.9700 |
| C1—H1 | 0.9800 | C8—H8B | 0.9700 |
| C2—C3 | 1.508 (4) | N3—O1 | 1.229 (4) |
| C2—H2A | 0.9700 | N3—O2 | 1.234 (4) |
| C2—H2B | 0.9700 | N3—O3 | 1.241 (4) |
| C3—C8 | 1.503 (5) | N4—O4 | 1.218 (4) |
| C3—C4 | 1.523 (5) | N4—O6 | 1.227 (4) |
| C3—H3 | 0.9800 | N4—O5 | 1.250 (4) |
| C7—N1—H1A | 113 (3) | C5—C4—H4B | 109.3 |
| C7—N1—H1B | 109 (2) | C3—C4—H4B | 109.3 |
| H1A—N1—H1B | 104 (3) | H4A—C4—H4B | 108.0 |
| C7—N1—H1C | 114 (3) | C6—C5—C4 | 111.9 (3) |
| H1A—N1—H1C | 103 (4) | C6—C5—H5A | 109.2 |
| H1B—N1—H1C | 113 (4) | C4—C5—H5A | 109.2 |
| C8—N2—H2D | 115 (3) | C6—C5—H5B | 109.2 |
| C8—N2—H2E | 112 (2) | C4—C5—H5B | 109.2 |
| H2D—N2—H2E | 96 (4) | H5A—C5—H5B | 107.9 |
| C8—N2—H2F | 114 (3) | C5—C6—C1 | 111.7 (3) |
| H2D—N2—H2F | 113 (5) | C5—C6—H6A | 109.3 |
| H2E—N2—H2F | 104 (4) | C1—C6—H6A | 109.3 |
| C7—C1—C2 | 114.3 (3) | C5—C6—H6B | 109.3 |
| C7—C1—C6 | 111.2 (3) | C1—C6—H6B | 109.3 |
| C2—C1—C6 | 109.4 (3) | H6A—C6—H6B | 107.9 |
| C7—C1—H1 | 107.2 | N1—C7—C1 | 112.4 (3) |
| C2—C1—H1 | 107.2 | N1—C7—H7A | 109.1 |
| C6—C1—H1 | 107.2 | C1—C7—H7A | 109.1 |
| C3—C2—C1 | 111.9 (3) | N1—C7—H7B | 109.1 |
| C3—C2—H2A | 109.2 | C1—C7—H7B | 109.1 |
| C1—C2—H2A | 109.2 | H7A—C7—H7B | 107.9 |
| C3—C2—H2B | 109.2 | N2—C8—C3 | 113.8 (3) |
| C1—C2—H2B | 109.2 | N2—C8—H8A | 108.8 |
| H2A—C2—H2B | 107.9 | C3—C8—H8A | 108.8 |
| C8—C3—C2 | 109.8 (3) | N2—C8—H8B | 108.8 |
| C8—C3—C4 | 114.6 (3) | C3—C8—H8B | 108.8 |
| C2—C3—C4 | 111.0 (3) | H8A—C8—H8B | 107.7 |
| C8—C3—H3 | 107.0 | O1—N3—O2 | 121.1 (4) |
| C2—C3—H3 | 107.0 | O1—N3—O3 | 119.8 (4) |
| C4—C3—H3 | 107.0 | O2—N3—O3 | 119.1 (4) |
| C5—C4—C3 | 111.5 (3) | O4—N4—O6 | 120.9 (4) |
| C5—C4—H4A | 109.3 | O4—N4—O5 | 120.3 (4) |
| C3—C4—H4A | 109.3 | O6—N4—O5 | 118.8 (4) |
| H··· | ||||
| N1—H1 | 0.87 (4) | 2.22 (4) | 3.084 (6) | 169 (4) |
| N1—H1 | 0.87 (4) | 2.36 (4) | 3.013 (5) | 132 (3) |
| N1—H1 | 0.95 (4) | 2.59 (4) | 3.187 (6) | 121 (3) |
| N1—H1 | 0.95 (4) | 1.87 (4) | 2.818 (5) | 172 (3) |
| N1—H1 | 0.87 (5) | 2.12 (5) | 2.939 (6) | 157 (4) |
| N2—H2 | 0.77 (4) | 2.48 (4) | 3.142 (6) | 145 (4) |
| N2—H2 | 0.77 (4) | 2.19 (4) | 2.899 (6) | 153 (4) |
| N2—H2 | 0.99 (4) | 2.46 (4) | 3.178 (6) | 130 (3) |
| N2—H2 | 0.99 (4) | 1.88 (4) | 2.858 (5) | 173 (4) |
| N2—H2 | 0.96 (6) | 2.05 (6) | 2.967 (5) | 159 (5) |
| N2—H2 | 0.96 (6) | 2.23 (6) | 3.016 (6) | 139 (4) |