Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1-C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H-H interaction, rather than denoting the presence of "nonbonded steric repulsions", makes a stabilizing contribution of up to 10 kcal mol(-1) to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules-the physics of an open system-demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H-H interatomic surface is shown to account for the resulting stability. It is pointed out that H-H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

We show that the delocalization indices calculated within the framework of the quantum theory of atoms in molecules provide an excellent basis for the definition of a bond order in polycyclic aromatic hydrocarbons. We show that the two-electron information contained within the delocalization index can be estimated from the electron density at the bond critical point, a mapping that has no a priori reason to exist. The mapping between the bond order and the electron density at the bond critical point can be exploited to provide a fast estimate of bond orders from theoretical or experimental electron densities. Bond orders in these molecules are shown to be associated to other one-electron properties. We provide evidence to the strong coupling of the σ and π contributions to the electron density at the bond critical point, a nonseparability by virtue of which the electron density at the bond critical point reflects both contributions. Another remarkable finding is that the delocalization indices between bonded carbon atoms are also strongly negatively correlated to the electronic energy density at the bond critical point, the latter being another example of a two electron property. In this manner, bond order is associated to a stabilizing effect quantified by the electronic energy density at the bond critical point. Because aromaticity is rooted in electron delocalization within a ring system, the delocalization index is used to define an aromaticity index that measures alternation in the delocalization of electrons within a ring of a polycyclic aromatic hydrocarbon. The proposed aromaticity index represents a “local aromaticity measure”. We have analyzed in detail the effects of ring annealation on bond orders and on the aromatic character of a ring and explored its correlation with independent measures of aromaticity such as NICS and HOMA.

The recent synthesis of a crystalline compound containing Ti bonded to cyclopentadienyl and a substituted dienyl fragment prompted the question of whether Ti-C contacts that were found to be shorter than other such bonded contacts in the same molecule should be considered as short nonbonded contacts or "nonclassical metal-to-saturated-carbon atom interactions", fitting the description of agostic interactions. This question has a unique answer within the framework of the quantum theory of atoms in molecules (QTAIM). QTAIM uses the measurable electron density to assign a molecular structure and the physics of an open system to determine the nature of the bonded interactions. All of the classical bonding descriptors, when recast in terms of the topologies of the electron density and the pair density, are faithfully recovered when QTAIM is applied to the hydrocarbon framework of the Ti complex, thereby justifying its application to the analysis of the Ti-C interactions. No bond paths are found to link the Ti to the carbons exhibiting the "short contacts", and the topology of the density gives no indication of an incipient change in structure that would result in their formation.

The charge on an atom in a molecule is defined by the quantum theory of atoms in molecules (QTAIM) as the expectation value of the number operator, a Dirac observable. An atomic charge is measurable and it, together with its change, contributes to numerous measurable properties:  to all molecular moments, to molecular polarizability, to intensities of electronic, infrared, and Raman absorption intensities, and to the polarization of a dielectric. The properties resulting from an applied magnetic field parallel those induced by an electric field, with the induced atomic charge being replaced by the atomic current. The phenomena of polarization and magnetization, permanent or induced, have a common physical basis when described in terms of the physics of an open system, all expressions exhibiting a single underlying structure in terms of their atomic contributions. The paper points out that this physics and the appeal the experiment it affords are lost when one employs other definitions of an atomic charge.