Abstract:

The computation of activation free energies for reactions in liquids and solids allows one to manipulate their chemistry and provide invaluable information when the experimental measurements become prohibitive.

The computation of activation free energies for the aqueous phase reactions are studied with density functional theory quantum mechanical methods in the first five chapters. Chapter 1 consists of the benchmarking of various quantum mechanical techniques for the calculation of accurate activation free energies for the transfer of methyl groups from sulfonium and ammonium salts to amines in water. The rate

constants of the enzymatic reactions in the absence of enzyme in water are used to calculate rate enhancements (kcat / kuncat ) and catalytic proficiencies (kcat /KM /kuncat ) of enzymes. Chapter 2 focuses on the calculation of the base catalyzed rates for the hydrolysis of cyclopropanecarboxylic acid esters. The aqueous phase decomposition of peroxynitrous acid (HOONO) is studied with Car-Parrinello Molecular Dynamics (CPMD) simulations in Chapter 3. Peroxynitrous acid is formed by the reaction of nitric oxide and superoxide. The formation of HOONO in living systems causes oxidative stress via the reactions of HOONO, or of HOONO decomposition products, with biomolecules. The decomposition of HOONO in water gives nitrate and a reactive oxidant. This oxidant has been argued to be hydroxyl radical, but reported yields of hydroxyl radical trapped products range from zero to 40% in different experiments. In Chapters 4 and 5, a novel mechanism for the hydrolysis of esters and amides in pure water are presented. According to density functional theory calculations, the hydrolysis of esters and amides may proceed via the prior formation of hydroxide and hydronium in water. In this mechanism, the hydroxide and hydronium ions are generated via water autoionization.

Solid state materials can provide beneficial hydrogen storage media for on-board applications due to their capabilities of safely confining large quantities of hydrogen in small volumes. Clarification of the mechanisms by which metal hydrides decompose to release/store hydrogen can aid in de novo design of new storage materials. In the solid state hydrogen storage materials, the release and uptake of hydrogen may require the transport of metal species. Chapter 6 considers the diffusion of hydrogen in aluminum. The mechanism of NaAlH4 decomposition was studied with CPMD simulations in Chapter 7. According to CPMD simulations, the activation energy for Al mass transport via AlH3 vacancies is the rate determining step and the computed activation energy is in excellent agreement with experimentally measured activation energies in Ti-catalyzed NaAlH4 . The generation of AlH3 vacancies on the NaAlH4 (001) surface was studied with density functional theory calculations in Chapter 8. In Chapter 9, the mechanism of vacancy promoted dehydrogenation LiNH2 plus LiH mixture is presented.