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Date of Award

1-2001

Degree Type

Thesis

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

Supervisor

Professor R.F.W. Bader

Abstract

The theory of Atoms In Molecules (AIM) generalizes quantum mechanics by deriving the physics of an atom in a molecule. This is accomplished by associating an atom with a quantum mechanical open system , a region of real space capable of exchanging electrons and properties with the rest of the molecule. AIM recovers the basic cornerstone of chemistry: that atoms and functional groups possess characteristic and additive properties. When the properties of an atom or functional group are found to be transferable, the theory makes possible the synthesis of macro-molecules from the corresponding pieces. Many molecules of biological importance are composed of repeating structural units that appear to be highly transferable. These repeating units, when defined by AIM, are found to account for and recover this transferable behavior. As a consequence, theory can be used to construct a biological macromolecule from repeating units previously defined in simpler systems. The properties of amino acid residues, the building blocks of proteins, are determined in this thesis by sandwiching each residue between two simpler amino acids to form a three-residue protein. The form and properties of the residues determined in this manner are found to be highly transferable. Thus, this thesis reports the tabulation of a library of amino acid residues that can then be linked together to form any desired protein or portion thereof. Such a synthesis makes possible the theoretical prediction of the properties of large molecules and does so using modest computing resources. The resulting availability of the electron density distribution, among other properties of the protein, enables one to apply in a quantitative manner the models and tools, such as the electrostatic field and the van der Waals shape, presently employed in the investigation of problems in molecular recognition and docking. Perhaps more importantly, it makes possible new approaches to the study of these problems.

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