We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A− arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A− and the σ* orbital of D–X.

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324–343. doi: 10.1002/wcms.1221

Halogen bonds, the formally noncovalent interactions where the halogen acts as a Lewis acid, have brought several controversies to the theoretical world regarding its nature and components, e.g., charge transfer (CT), electrostatics, dispersion, and polarization. The debate on whether all characteristics are accounted for by electrostatics is examined, highlighting the importance of the CT and repulsive interactions. A number of strongly halogen‐bonded complexes are as covalent as metal–ligand coordination bonds. Different levels of computational methods are reviewed with the objective of finding the best accuracy/cost ratios. The unusual electronic anisotropy of the halogen donor and its interaction with a Lewis base demand specific calculation schemes. From the wave‐function theory methods, only the ones with empirical corrections (spin‐component‐scaled MP2 or CCSD, and MP2.5) are suitable when CCSD(T) is unattainable. Density functional theory functionals with a high amount of exact exchange are fast and reliable methods for halogen bonds, but double hybrids are more robust if other types of interactions are involved. Molecular mechanics methods can be useful, but only when specific corrections are added to compensate for the inability of such methods to describe CT. The most common method introduces a virtual site with a partial positive charge to account for the quantum chemical effect of the halogen bond. This methodology has been successfully applied to study protein–ligand interactions for drug design. WIREs Comput Mol Sci 2014, 4:523–540. doi: 10.1002/wcms.1189 This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics Theoretical and Physical Chemistry > Thermochemistry

The oxidation of organic phenylselenides by H O is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental ( H and Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.

We have investigated the molecular geometries of a series of dicoordinated d10-transition-metal complexes ML2 (M=Co−, Rh−, Ir−, Ni, Pd, Pt, Cu+, Ag+, Au+; L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand–metal–ligand (L–M–L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L–M–L angle using quantitative Kohn–Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L–M–L structures is π backdonation. In situations of strong π backdonation, smaller angles increase the overlap of the ligand’s acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor π backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent.