Excursions of the electron density over the potential energy landscape in the absence and presence of external perturbations

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Chemical change is often discussed in global terms, the enthalpy of a reaction being a typical example. In chemistry, one is also often interested in local change. A reaction involving the side chain of an amino acid in a gigantic polypeptide cannot, for example, be expected to affect remote regions of this macromolecule. This local character can be discussed at the level of individual chemical bonds or atoms within a molecule with the help of the theory of atoms in molecules (AIM). This theory analyzes the 3D topography of the electron density from which the topology characterizing this density is deduced. The electron density can be computed from theoretical calculations but can also be observed in X-ray diffraction experiments. Very recently, and due to considerable improvements in experimental techniques and in computer speeds, experimentalists and theoreticians began to study systems as they evolve along the reaction coordinate. This type of study is much more computationally demanding since instead of a handful of isolated critical points on the potential energy landscape, one now has to deal with the entire landscape typically sampled at tens or hundreds of points. The evolution of atomic and bond properties as the system evolves from reactants to products through the transition state is the subject of this proposal, an emerging and exciting line of research. This research will shed light on reactivity, kinetics, and thermodynamics of key biochemical processes and reactions, e.g.: (1) "Atomic Contributions to the Activation Energy of the Hydrolysis of ATP", aiming at understanding how chemical potential energy is stored in and released from ATP and the mode by which Mg2+ catalyzes the reactions of this molecule, reactions that are indispensible in sustaining life. (2) "The Mechanism of the Peptide Bond Formation in the Ribosome", aiming at elucidating the mechanism of formation of the peptide bond inside the active site of the ribosome. (3) "Field Effects on Löwdin Mechanism of Spontaneous Mutation", aiming at understanding the mechanism(s) by which external fields influence the rate of genetic mutations brought about by the proton hopping within DNA base pairs prior to transcription or replication of the genetic material.