Halogen and Hydrogen Bond Motifs in Ionic Cocrystals Derived from 3-Halopyridinium Halogenides and Perfluorinated Iodobenzenes

The Geometry and Nature of C─I···O─N Interactions in Perfluoroiodobenzene-Pyridine N-oxide Halogen-Bonded Complexes

The N─Oxide oxygen in the 111 C─I···⁻O─N+ halogen bond (XB) complexes, formed by five perfluoroiodobenzene XB donors and 32 pyridine N-oxides (PyNO) XB acceptors, exhibits three XB modes: bidentate, tridentate, and monodentate. Their C─I···O XB angles range from 148° to 180°, reflecting the iodine σ-hole's structure-guiding influence. The I···⁻O─N+ angles range from 87° to 152°. On the contrary, the I···⁻O─N+ angles have a narrower range from 107° to 125° in stronger monodentate N─I···⁻O─N+ XBs of N-iodoimides and PyNOs. The C─I···⁻O─N+ systems exhibit a larger variation in I···⁻O─N+ angles due to weaker XB donor perfluoroiodoaromatics forming weak I···O XBs, which allows wider access to electron-rich N-O group regions. Density Functional Theory analysis shows that I···O interactions are attractive even when the I···⁻O─N+ angle is ≈80°. Correlation analysis of structural parameters showed that weak I···O XBs in perfluoroiodobenzene-PyNO complexes affect the C─I bond via n(O)→σ*(C─I) donation less than the N─I bond via n(O)→σ*(N─I) donation in very strong I···O XBs of N-iodoimide-PyNO complexes. This implies that PyNOs' oxygen self-tunes its XB acceptor property, dependent on the XB donor σ-hole strength affecting the bonding denticity, geometry, and interaction energies.

Molecular Insights into Water-Chloride and Water-Water Interactions in the Supramolecular Architecture of Aconine Hydrochloride Dihydrate

Despite the previous preparation of aconine hydrochloride monohydrate (AHM), accurate determination of the crystal's composition was hindered by severely disordered water molecules within the crystal. In this study, we successfully prepared a new dihydrate form of the aconine hydrochloride [C25H42NO9+Cl-·2(H2O), aconine hydrochloride dihydrate (AHD)] and accurately refined all water molecules within the AHD crystal. Our objective is to elucidate both water-chloride and water-water interactions in the AHD crystal. The crystal structure of AHD was determined at 136 K using X-ray diffraction and a multipolar atom model was constructed by transferring charge-density parameters to explore the topological features of key short contacts. By comparing the crystal structures of dihydrate and monohydrate forms, we have observed that both AHD and AHM exhibit identical aconine cations, except for variations in the number of water molecules present. In the AHD crystal, chloride anions and water molecules serve as pivotal connecting hubs to establish three-dimensional hydrogen bonding networks and one-dimensional hydrogen bonding chain; both water-chloride and water-water interactions assemble supramolecular architectures. The crystal packing of AHD exhibits a complete reversal in the stacking order compared to AHM, thereby emphasizing distinct disparities between them. Hirshfeld surface analysis reveals that H···Cl- and H···O contacts play a significant role in constructing the hydrogen bonding network and chain within these supramolecular architectures. Furthermore, topological analysis and electrostatic interaction energy confirm that both water-chloride and water-water interactions stabilize supramolecular architectures through electrostatic attraction facilitated by H···Cl- and H···O contacts. Importantly, these findings are strongly supported by the existing literature evidence. Consequently, navigating these water-chloride and water-water interactions is imperative for ensuring storage and safe processing of this pharmaceutical compound.

Thermodynamics and Spectroscopy of Halogen- and Hydrogen-Bonded Complexes of Haloforms with Aromatic and Aliphatic Amines

Similarities and differences of halogen and hydrogen bonding were explored via UV–Vis and ¹H NMR measurements, X-ray crystallography and computational analysis of the associations of CHX₃ (X=I, Br, Cl) with aromatic (tetramethyl-p-phenylenediamine) and aliphatic (4-diazabicyclo[2,2,2]octane) amines. When the polarization of haloforms was taken into account, the strengths of these complexes followed the same correlation with the electrostatic potentials on the surfaces of the interacting atoms. However, their spectral properties were quite distinct. While the halogen-bonded complexes showed new intense absorption bands in the UV–Vis spectra, the absorptions of their hydrogen-bonded analogues were close to the superposition of the absorption of reactants. Additionally, halogen bonding led to a shift in the NMR signal of haloform protons to lower ppm values compared with the individual haloforms, whereas hydrogen bonding of CHX₃ with aliphatic amines resulted in a shift in the opposite direction. The effects of hydrogen bonding with aromatic amines on the NMR spectra of haloforms were ambivalent. Titration of all CHX₃ with these nucleophiles produced consistent shifts in their protons’ signals to lower ppm values, whereas calculations of these pairs produced multiple hydrogen-bonded minima with similar structures and energies, but opposite directions of the NMR signals’ shifts. Experimental and computational data were used for the evaluation of formation constants of some halogen- and hydrogen-bonded complexes between haloforms and amines co-existing in solutions.

Bifurcated Halogen Bond-Driven Supramolecular Double Helices from 1,2-Dihalotetrafluorobenzene and 2,2′-Bi(1,8-naphthyridine)

The unique enantiomeric pairs of double helices have been found in the structure of the cocrystal between 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine). The formation of the supramolecular double helices is driven by the strong bifurcated iodine bonds which can force the herringbone packing arrangement of the molecules 2,2′-bi(1,8-naphthyridine) into a face-to-face π···π stacking pattern. In contrast, the cocrystal between 1,2-dibromotetrafluorobenzene (or 1,2-dichlorotetrafluorobenzene) and 2,2′-bi(1,8-naphthyridine) was not obtained under the same conditions. The interaction energies of the bifurcated halogen bonds and π···π stacking interactions were computed with the reliable dispersion-corrected density functional theory. The computational results show that the bifurcated iodine bond is much stronger than the bifurcated bromine bond and bifurcated chlorine bond, and it is the much stronger bifurcated iodine bond that makes the cocrystal of 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine) much easier to be synthesized.

Evaluation of Halogenopyridinium Cations as Halogen Bond Donors

We have performed a database survey and a structural and computational study of the potential and the limitations of halogenopyridinium cations as halogen bond donors. The database survey demonstrated that adding a positive charge on a halogenopyridine ring increases the probability that the halogen atom will participate in a halogen bond, although for chloropyridines it remains below 60%. Crystal structures of both protonated and N-methylated monohalogenated pyridinium cations revealed that the iodo- and bromopyridinium cations always form halogen-bonding contacts with the iodide anions shorter than the sum of the vdW radii, while chloropyridinium cations mostly participate in longer contacts or fail to form halogen bonds. Although a DFT study of the electrostatic potential has shown that both protonation and N-methylation of halogenopyridines leads to a considerable increase in the ESP of the halogen σ-hole, it is generally not the most positive site on the cation, allowing for alternate binding sites.