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We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn–Teller distortion ranges from 0.78 to 6.14 kcal mol−1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F−. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F− in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of −3.50 and −3.45 eV at CAM-B3LYP/6-311+G(d) and −3.61 and −3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis. [ABSTRACT FROM AUTHOR]

Abstract Heteroarenes such as (aza and oxa)borines are increasingly important as synthetic targets and reagents. We map the intramolecular cyclization of saturated heterocyclic chains through dative bonding. A related set of planar unsaturated aza-, oxa-, and fluora- rings that feature dative σ bonding enhanced by π delocalization are identified. The systems have, in general, the formulae A′(CH 2) m D′ and A′(CH) m D′, where m = 3 and 4, and A′ and D′ are acceptor and donor sites, respectively. In each case, the ring isomers, achievable via A′←D' internal coordination (in the manner of Kekulé's ouroboros), are more stable than chains. Unsaturated aromatic rings examined herein include a oxadiborine with a hypervalent oxygen center and a dioxadiborine. They are isoelectronic with an azaborine, which was synthesized more recently, and benzene. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

A remarkable transition in the chemical bonding in (HgF2) n clusters as a function of n is identified and characterized. HgF2 is a fascinating material. Certain significant consequences of relativistic effects on the structure of the HgF2 molecule, dimer, and trimer disappear in the extended solid. Relativistic effects in Hg ensure that HgX2 molecules (X≡F, Cl, Br, and I) are linear, rigid, and form weakly bound dimers and trimers held together by weak electrostatic and van der Waals-type forces (unlike ZnX2 and CdX2 systems in which the intermonomer contacts are strong polar covalent bonds). For HgF2, the location and nature of an apparent transition from weak interactions in the smallest (HgF2) n clusters to ionic bonding in the (fluorite) HgF2 extended solid has remained a mystery. Computational evidence obtained at the M06-2X, B97D3, and MP2 levels of theory and reported herein indicate that polar covalent bonding in (HgF2) n begins as early as n=5. For n=2 through to n=13, the transition or switch from weak (primarily dipole-dipole-type) intermonomer interactions to a preference for polar covalent bonding occurs within the range 5< n≤9. Thermodynamic evidence for this transition is provided. Our results demonstrate a significant risk associated with crystal structure prediction from the ground up (i.e., based on bonding patterns in small clusters). The path from monomers through to extended solids may be punctuated at one or several points (as n increases) with transitions in structure and bonding that are not anticipated or betrayed by the bonding in small clusters. [ABSTRACT FROM AUTHOR]

Wefind for distinct classes of halogen bonded complexes (MF3X···Y) that the ab initio BSSE-correctedbinding energies (ΔE) andenthalpies (ΔH) are predictedby functions of the form y = A/rn+ C. Here X is a halogen atom, Y is a base, ris the X···Y separation, and A, n, and Care constants. The actualvalue of n(5.5 < n< 7.0for ΔE) for each class isdetermined evidently by the availability of the lone pairs on thebase and is insensitive to M such that all of the complexes of a givenbase fall on the same curve for yversus r. Remarkably, several bases show the same behavior in somecases such that just three curves account for 55 MF3I···Ycomplexes of 11 bases, where M = C, Si, Ge, Sn, and Pb. Two additionalbases, THF and NF3, which form especially strong and weakcomplexes, respectively, are in classes by themselves. Anomalous modesof halogen bonding are identified; in particular, furan forms sigma-holecomplexes via carbons 2 and 3 (through the π system) in thering in preference to the oxygen site. These results are in line withexperimental observations for furan–dihalogen complexes, andseveral other small MF3I···Y pairs are proposedin this work for experimental interrogation. Instead of halogen bonding,CF4tends to form weak sigma-hole bonds to bases via thepolarized central carbon atom, and new examples of such pro-dativeinteractions to carbon in CF4are identified in this work.We find that GeF3I and SnF3I form I···Yhalogen bonds of comparable energies to those formed by the smallerand better studied CF3I. PbF3I forms the strongesthalogen bond regardless of the identity of the base; SiF3I consistently forms the weakest link. [ABSTRACT FROM AUTHOR]

How short can a C−C single bond get? The bonding in a set of molecules that are related structurally to previously synthesized or theoretically examined systems with short C−C bonds is investigated. According to calculations, a single C−C bond could be compressed to 1.313 Å! To the best of our knowledge, this is the shortest single C−C bond reported to date. This shortening is a consequence of a change in the C−C−C bond angle, θ, to minimize strain in the cages and an effort to offset the tension in the surrounding bridges. [ABSTRACT FROM AUTHOR]

Halogen bonding (R—X⋯Y) is a qualitative analogue of hydrogen bonding that may prove useful in the rational design of artificial proteins and nucleotides. We explore halogen-bonded DNA base pairs containing modified guanine, cytosine, adenine and thymine nucleosides. The structures and stabilities of the halogenated systems are compared to the normal hydrogen bonded base pairs. In most cases, energetically stable, coplanar structures are identified. In the most favorable cases, halogenated base pair stabilities are within 2 kcal mol-1 of the hydrogen bonded analogues. Among the halogens X = Cl, Br, and I, bromine is best suited for inclusion in these biological systems because it possesses the best combination of polarizability and steric suitability. We find that the most stable structures result from a single substitution of a hydrogen bond for a halogen bond in dA:dT and dG:dC base pairs, which allows 1 or 2 hydrogen bonds, respectively, to complement the halogen bond. [ABSTRACT FROM AUTHOR]