Adaptive finite element simulation of flow and transport applications on parallel computers

The field of molecular and atomic sensing has seen a vast growth over the last few decades. Yet many advances still remain to be made. This dissertation takes an in depth look at the two major aspects in a molecular sensing or signaling scaffold—namely the binding of a target followed by the transduction of an observable signal. Chapter 1 will deal with intermolecular binding forces in the form of a case study on electrophilic coordination to carbonyl compounds. Computational studies are performed to determine the optimal geometry of an electrophile interacting with a carbon acid to affect the greatest enhancement in the acidity at the α-carbon. We find that partial interaction through the π-system of the carbonyl and the resulting enolate affords the greatest acidity enhancement. Chapter 2 then switches to studies on the development of a novel signaling method for a molecular signaling assay. Two novel elements—transition metal catalytic signal amplification and peroxyoxalate chemiluminescence—are utilized to generate a signaling motif incorporating two new methodologies for signal generation. The first uses of catalytic signal amplification for the detection of small organic analytes and peroxyoxalate chemiluminescence for signal generation in a molecular recognition event are described. Finally, both elements are brought together in Chapter 3, which describes a mature ionophoric chemodosimeter with both highly sensitive binding and strong signal output. The use of a squaraine dye as a signaling unit for the detection of palladium(II) salts is described in which an aliphatic thiol acts as the theoretical “host” in a covalent displacement type assay. Palladium(II) and other transition metal detection is of importance both industrially and environmentally, and the assay described is sensitive to levels desired in both arenas.