Applications of the Quantum Theory of Atoms in Molecules to Chemical and Biochemical Problems

Abstract

<p>The quantum theory of atoms in molecules (QT-AIM) is a generalization of quantum mechanics to open subsystems. The theory enables one to study the properties of atoms or functional groups within a molecule, recovering the empirical observation that they exhibit characteristic and additive contributions to every molecular property. This thesis applies theory to explain and predict experiment. In this work, atomic and group properties were shown to provide an excellent basis for the construction of quantitative statisical models which accurately predict the physicochemical properties of the amino acides and uncover regularities in the genetic code. The transferability and addivity of atomic properties were exploited to develop a method of assembling large molecules from buffered fragments, a method which reduces the computational effort and - as a result - brings large biological molecules within theoretical reach. The buffered fragments method was applied to obtain accurate properties of key opiod molecules. The additivity of atomic properties applies to any and all molecular properties including, for example, dielectric polarization. The dielectic polarization of a crystal was shown to be reducible to a sum of the polarization of its composing cells taken together with a sum of the dipoles arising from the charge transfer between neighbouring cells. The problem of aromaticity has been recast in terms of the pair densities in conjunction with QT-AIM, an approach that was shown to explain and predict several chemical and spectroscopic properties of polycyclic aromatic hydrocarbons. The criteria of bonding were revisited and applied to provide a clear-cut answer in a case where distance alone - as a criterion for bonding - provides ambiguous answers.</p> <p>The thread tying this work together is the philosophy of "reductionism" in the narrow sense that the whole (e.g. a molecule or a crystal) is nothing but the sum of its spatially bounded non-overlapping parts (atoms). By resorting to this philosophy one not only gains a deeper insight into the physical basis of chemistry but is capable of accurately predicting experiment as well.</p>