Communication: Evidence of halogen bonds in clathrate cages

Interaction energy of Cl2 and Br2 with H2 O: Exchange, dispersion and density the crucial ingredients

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X₂ -H₂ O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl₂ and Br₂ inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl₂ @5¹² , -5.3 ± 0.3 kcal/mol; Cl₂ @5¹² 6² , -5.5 ± 0.1 kcal/mol; Br₂ @5¹² 6² , -7.6 ± 1.0 kcal/mol; Br₂ @5¹² 6³ , -10.6 ± 1.0 kcal/mol; Br₂ @5¹² 6⁴ , -10.9 ± 0.8 kcal/mol.

Supramolecular Organization in Confined Nanospaces

Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.

Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization

Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates

Clathrate hydrate phases of Cl₂ and Br₂ guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen–halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen–halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme–substrate compounds. The nature of the halogen–water interactions for the Cl₂ and Br₂ molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl₂ and Br₂ guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.