Ph.D. Theses
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Browsing Ph.D. Theses by Subject "Chemical reactions."
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Item Modeling the selectivity in pericyclic reactions(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Ölçüm, Nihan Çelebi.; Aviyente, Viktorya.Pericyclic reactions are very powerful and widely utilized transformations to obtain complex molecules. The selective versions have received remarkable interest and have found extensive use in synthetic organic chemistry to access complex biologically active targets. In this work, the mechanistic details of some highly useful pericyclic reactions have been explored and the origins of the selectivity have been investigated. The first reaction of interest was the Diels−Alder reactions of -keto- , -unsaturated phosphonates with cyclopentadiene and 1,3-cyclohexadiene. The reaction constitutes an easy and straightforward method for the synthesis of dihydropyran derivatives, which are efficient substrates in the preparation of chiral building blocks. Second, diastereoselective cycloadditions of different chiral anthracene templates with maleic anhydride were explored. This reaction serves as the key element in determining the final stereochemistry of the product in the preparation of complex biologically active molecules such as butenolides, , -unsaturared lactams and related compounds in their enantiomerically pure forms. Finally, [3,3]- and [1,3]-sigmatropic rearrangements of allylic acetimidates have been studied. These reactions yield -amino acid and allyl amine derivatives that are important building blocks found in many bioactive molecules. In this work, bis-pericyclic, pseudopericyclic and stepwise pathways were shown to play a substantial role in determining the experimental observables such as the product distributions and the selectivity of the reaction, beside the widely accepted concerted pericyclic mechanism. The effect of catalysts on the mechanism and the selectivity have been studied and discussed in detail. The fundamental interactions in the key transition states have been analyzed and the factors affecting the stereoselectivity of the reaction have been elucidated. Comparative studies on highly selective and non selective variants have allowed us to identify the elements responsible for controlling the selectivity of the reactions of interest. This work brings a new perspective to the mechanism of pericyclic reactions and provides a deeper insight into the factors that determine the selectivity. However, the scope of the pericyclic reactions is very large and highly useful examples are not limited to the ones discussed in this dissertation. Future work will undoubtedly uncover many other important aspects of selective pericyclic reactions. Several suggestions for prospective studies have been outlined in the final chapter.Item Modeling the selectivity, catalytic and binding effects in organic reactions and protein environment(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.) Dedeoğlu, Burcu.; Aviyente, Viktorya.; Özen, Alimet Sema.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.