Theoretical studies of intra- and intermolecular interactions.
Item
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Title
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Theoretical studies of intra- and intermolecular interactions.
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Identifier
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AAI3169937
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identifier
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3169937
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Creator
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Kobko, Nadezhda (Nadya).
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Contributor
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Adviser: J. J. Dannenberg
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Date
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2005
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Language
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English
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Publisher
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City University of New York.
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Subject
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Chemistry, Physical
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Abstract
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In the first part of my dissertation I present a theoretical study of hydrogen bonding cooperativity in different systems that model elements of the secondary structure of proteins and in the base pairs of normal DNA. In Chapter II I talk about an unusually high degree of cooperativity for hydrogen-bonding chains of formamide molecules similar to the H-bonding chains found in proteins. I empirically fit the energetic data obtained from the DFT calculations using parameters based upon the H-bonding chain length and the position of the H-bond in the chain. In Chapter III I discuss the stabilization trend in the row of polyglycine conformers. Chapter IV presents an analysis of the effects of H-bonding cooperativity on the infrared vibrational spectra of structures related to peptides. I compare vibrational frequencies and intensities of the coupled N-H, C=O stretches (amide I) and C-N stretch/CNH bend (amide II) for polyglycines in beta-strands and chains of H-bonded formamides at the DFT level. I show that coupling through hydrogen bonding in the chains of formamides is stronger than coupling through covalent bonding in the polyglycines. I also explore the effects of isotopic substitution of individual nuclei on the vibrational spectra of the systems studied. Finally, in Chapter V I compare H-bonding cooperativity in the two base pairs of normal DNA: the guanine-cytosine and adenine-thymine base pairs.;In the second part of my dissertation (Chapter VI) I discuss the effect of Basis Set Superposition Error (BSSE) upon ab initio and DFT calculations of organic transition states (TSs). I show that the CP-optimized (using counterpoise correction for BSSE) TSs obtained using small basis sets resemble the TSs obtained using the larger basis sets without the CP-correction in both energies, and geometries. The geometry of the concerted Diels-Alder TS for ethylene and butadiene becomes more compact upon CP-optimization, whereas the apparent TS for the 1,2-H-atom shift in ethyl radical is shown to be an artifact of BSSE (at least at the HF and DFT levels). The TS for the radical abstraction reaction is shown to move toward product upon CP-optimization.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
