Modeling the selectivity, catalytic and binding effects in organic reactions and protein environment

Abstract

In this dissertation, quantum chemical tools, in particular density functional methods are used to address problems related with the selectivity, catalytic and binding effects in different fields of chemistry, such as materials science, organic chemistry and biochemistry. The selectivity of photoluminescent polymers towards analytes in the explosive detection field has been investigated by modelling the complexes between the polymers and analytes. The simulated optoelectronic properties of the polymers and their complexes with the analytes highlighted the detection mechanism based on fluorescence quenching. The mechanism and selectivity in the asymmetric desymmetrization of meso-cyclic anhydrides induced by cinchona alkaloids have been investigated and base catalysis mechanism has been shown to operate in these reactions. The origins of stereoselectivity have been attributed to the spatial arrangement of the cinchona alkaloid catalyst in the transition state of asymmetric desymmetrization reaction related with the oxyanion stabilization. The inverse electron demand Diels-Alder reaction of phthalazine and siloxy alkyne activated by Ag(I)-bipyridine catalysis have been modeled and the barriers are compared with the uncatalyzed cycloaddition reaction to highlight the catalytic effect of Ag(I)-bipyridine. It has been shown that the primary role of Ag(I)-bipyridine catalyst in an inverse electron demand Diels-Alder reaction is to facilitate the overlap between HOMO of the dienophile and LUMO of the diene by reducing the energy gap. The iron binding-release mechanisms have been investigated in the cluster models of transferrin, iron binding protein. Possible routes for iron release are evaluated on the basis of the thermodynamic stabilities of the models.