Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study
The nature of acids in an aqueous environment is fundamental to many aspects of chemistry and biology. The defining feature of an acid is its ability to transfer a proton to water or to any accepting base, but this seemingly simple process can be complex and highly dependent on the solvation involving different reaction intermediate species. This thesis describes computational studies based on first principles molecular dynamics simulations aimed at obtaining molecular-level descriptions of diverse proton transfer process involving acids and bases in liquid water.  For that, we have investigated a variety of systems including aqueous hydrofluoric acid, aqueous trifluoroacetic acid and a model system comprising of a phenol and a carboxyate molecule bridged by a water molecule in aqueous solution.    Two different intermediate stages of proton transfer from an acid were identified which are found to be stabilized by distinct local H-bond solvation pattern. Their spectroscopic signatures were characterized using infrared spectroscopy computed from first principles molecular dynamics simulations which incorporate nuclear quantum effects explicitly.  This study also identified three elementary reaction pathways that are responsible for proton translocation from acid to the base and their characteristic time scales. Conclusions drawn from this study are discussed in molecular detail, highlighting experimental comparisons.
Ab initio Molecular Dynamics Ab initio Centroid Molecular Dynamics Proton Transfer Proton Transfer Intermediates Acid Dissociation Acid dissociation Intermediates Wavelet Trasform Infrared Spectroscopy