The quantum theory of atoms in molecules as an interpretative tool in chemistry

The Theory of Atoms in Molecules (AIM) developed by Bader is a wonderful extension of quantum mechanics to chemistry. It gives a quantum definition for atoms (open systems) in molecules, showing that they are bounded by zero-flux surfaces in the gradient vector field of the electron density. This remarkable result supports an important hypothesis in chemistry, which is the basis of chemistry as an experimental science: molecules are formed by the union (chemical bond) of atoms. Therefore, AIM serves to gain insight into many areas of chemistry including the characterization of the valence shells of atoms in molecular systems and the characterization of weak interactions in molecular systems. The results presented in this thesis demonstrate the use of AIM as an interpretative tool in inorganic and organic chemistry.; The valence shell of the fluorine atom in its compounds has not been fully characterized from a theoretical point of view. A detailed characterization of the valence shell charge concentration (VSCC) of fluorine through AIM is reported to provide a simple explanation for several intriguing facts in the chemistry of fluorine. Furthermore, a new empirical approach for the evaluation of fluorine-fluorine spin-spin coupling constants (J FF) in aromatic compounds is proposed as well as a complete AIM characterization of these aromatic systems.; Weak interactions make great contributions and play determinant roles in the stability and energetics of important molecular systems such as polyaromatic systems and inclusion complexes of cyclodextrins. A characterization of the weak interactions in terms of AIM parameters provides insight into the chemistry of these types of molecular systems. Several weak interactions in several difluorinated polyaromatic compounds and in the inclusion complex of p-chlorophenol inside alpha-cyclodextrin are reported and characterized.; The concept of resonance is especially useful for systems containing delocalized electrons and has been used to explain many phenomena in chemistry. A detailed study by means of AIM of the resonance effect exhibited in systems where a halogen is adjacent to a carbon-carbon double bond is carried out. Moreover, a comparable study of the respective saturated halo hydrocarbons and hydrocarbons, as well as the related unsaturated hydrocarbons is also carried out. Several observations that are consistent with the presence of the halogen resonance effect in compounds where the halogen is bonded to a carbon-carbon double bond are reported.; The thermolysis of many beta-hydroxyl compounds has been studied experimentally and theoretically. A mechanism involving a six-membered cyclic transition state where the hydrogen of the hydroxyl group interacts with the oxygen of the carbonyl group has been proposed previously. The proposed mechanism is studied for a series of beta-hydroxyl aldehydes. Rate constants and activation energies are reported as well as a study of the influence of tunneling on the reaction rates. The electron density at the ring critical points, population analyses by atoms in molecules (AIM) and natural bond orbital (NBO) methods, as well as atomic energy analyses, are used to gain insight into this interesting mechanism and into the effects of substituents.