Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Abstract

Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π . . . π stacking and many other kinds of non-covalent atom-atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449-469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (E es ) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to E es . To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (E EML ) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between E EML and E es . However, strong relation between E EML and the charge penetration component of E es is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom-atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

The supramolecular behavior and molecular recognition of adeninium cations on anionic hydrogen selenite/diselenite frameworks: A structural and theoretical analysis

“…It can be concluded that charge transfer occurs from anions to adeninium cations. This observation is in accordance with the study of protonated nucleobases in their chloride salt crystals which found that the cations are not fully ionized [17,60]. This charge transfer is more pronouced when the configuration is more stable and confirmed by results of calculations under periodic boundary conditions.…”

“…9). An energetic analysis of protonated nucleobases/chloride crystal structures [17,60] showed that the organic cations can form metastable base pairs which are stabilized by the surrounding anions. Furthermore, hexamers play an important role in stabilizing the crystal packing, in which each hexamer contribute to bridge three successive ribbons layers via hydrogen bond interactions (Fig.…”

Attracting Opposites: Promiscuous Ion−π Binding in the Nucleobases

“…As such, the definition of charge penetration utilized herein is not quantitatively different from that used throughout the literature, and simply provides an alternative vantage point for conceptually exploring the nontrivial (and often counterintuitive) electrostatics in ion−π systems. Here, we would point out that our treatment of charge penetration effects in ion−π nucleobase complexes is also similar to the recent work of Dominiak and co-workers, 89 who employed the PIXEL method 90,91 to study the ion−ion interactions in ionic crystals of nucleobase chlorides, as well as Novotnýet al, 67 who investigated the role of charge penetration effects in a select set of off-axis anion−π complexes.…”

Phase Transition of Hypoxanthinium Nitrate Monohydrate

“…In our opinion, this is a more accurate, and more appropriate in the context of electrostatic interactions, selection criterion than the sum of van der Waals radii. 53 There are bigger differences between different temperatures (more than 0.5 Å) than between different methods (less than 0.25 Å). The distances between molecules placed in the same layer are practically unchangingin Figure 8 and Figures S4− S9, there are single dots without any "smear" symbolizing this.…”