In the present thesis, the reaction mechanisms of several di-zinc hydrolases have been explored using quantum chemical modeling of the enzyme active sites. The studied enzymes are phosphotriesterase (PTE), aminopeptidase from Aeromonas proteolytica (AAP), glyoxalase II (GlxII), and alkaline phosphatase (AP). All of them contain a binuclear divalent zinc core in the active site. The density functional theory (DFT) method B3LYP functional was employed in the investigations. The potential energy surfaces (PESs) for various reaction pathways have been mapped and the involved transition states and intermediates have been characterized. The hydrolyses of different types of substrates were examined, including phosphate esters (PTE and AP) and the substrates containing carbonyl group (AAP and GlxII). The roles of zinc ions and individual active-site residues were analyzed and general features of di-zinc enzymes have been characterized. The bridging hydroxide stabilized by two zinc ions has been confirmed to be capable of the nucleophile in the hydrolysis reactions. PTE, AAP, and GlxII all employ the bridging hydroxide as the direct nucleophile. Furthermore, it is shown that either one of or both zinc ions provide the main catalytic power by stabilizing the negative charge developing during the reaction and thereby lowering the barriers. In the cases of GlxII and AP, one of zinc ions also contributes to the catalysis by stabilizing the leaving group. These features perfectly satisfy the two requisites for the hydrolysis, i.e. sufficient nucleophilicity and stabilization of charge. A competing mechanism, in which the bridging hydroxide acts as a base, was shown to have significantly higher barrier in the case of PTE. For phosphate hydrolysis reactions, it is important to characterize the nature of the transition states involved in the reactions. Associative mechanisms were observed for both PTE and AP. The former uses a step-wise associative pathway via a penta-coordinated intermediate, while the latter proceeds through a concerted associative path via penta-coordinated transition states. Finally, with PTE as a test case, systematic evaluation of the computational performance of the quantum chemical modeling approach has been performed. This assessment, coupled with other results of this thesis, provide an effective demonstration of the usefulness and powerfulness of quantum chemical active-site modeling in the exploration of enzyme reaction mechanisms and in the characterization of the transition states involved. / QC 20100715 / Quantum Chemical Modeling of Binuclear Zinc Enzymes

This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed. In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered. The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations. At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.

This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed. In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered. The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations. At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.