Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels. Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments. We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems. / QC 20110530

The electronic spectra of sulfide minerals can be complex, and their features difficult to assign. Often, therefore, they are interpreted using electronic-structure models obtained from quantum-chemical calculations. The aim of this study is to provide such models for the minerals sphalerite, wurtzite, pyrite, marcasite, and chalcopyrite. All are important minerals within a mining context, either as a source for their component metals or as a gangue mineral. They are also semiconductors. Each is the structural archetype for a particular class of semiconductors, and so a knowledge of their electronic structures has wider applicability. / Thesis (PhDAppliedScience)--University of South Australia, 2006.

The electronic spectra of sulfide minerals can be complex, and their features difficult to assign. Often, therefore, they are interpreted using electronic-structure models obtained from quantum-chemical calculations. The aim of this study is to provide such models for the minerals sphalerite, wurtzite, pyrite, marcasite, and chalcopyrite. All are important minerals within a mining context, either as a source for their component metals or as a gangue mineral. They are also semiconductors. Each is the structural archetype for a particular class of semiconductors, and so a knowledge of their electronic structures has wider applicability. / Thesis (PhDAppliedScience)--University of South Australia, 2006.

Thesis (PhD)--University of South Australia, 2000

Thesis (Ph. D.)--University of Washington, 1990. / Vita. Includes bibliographical references (leaves [217]-225).

Thesis (Ph.D.)--University of Delaware, 2008. / Principal faculty advisor: Douglas J. Doren, Dept. of Physics & Astronomy. Includes bibliographical references.

No description available.

The adsorption isotherm and the equation of state for the two-dimensional gas are derived from the grand canonical ensemble. Then the quantum statistical equation'of state is developed and applied to the two-dimensional second virial coefficient, B⁽²⁾, and the second gas-surface virial coefficient, B[subscript]AS, We compare theoretically the (12,6) and (12,6,3) potential models for B⁽²⁾. Finally the adsorption data for CH₄, CD₄, H₂ and D₂ on graphite are analysed quantally for the two-dimensional second virial coefficient and the second gas-surface virial coefficient. / Science, Faculty of / Chemistry, Department of / Graduate

The dependence of the point properties at the nucleus, electron density (Qe(0) )and spin density (Qs(0) ), on the nuclear cusp is examined for lithium atomic configuration interaction (CI) wave functions. Several series of CI wave functions with 18 and fewer terms, are studied. Importance of the triplet core spin function to Qs(0) is substantiated. Necessary, but not sufficient, spin and electron integral cusp conditions are applied as linear constraints. For the functions studied, Qs(0) improves on applying the spin cusp constraint if the free variational spin cusp is greater than -Z, but becomes worse otherwise. The electron cusp constraint invariably overcorrects Qe(0). The effect of necessary off-diagonal weighting constraints is also examined. No obvious trends could be found. It is concluded that forcing CI functions with a small number of terms to satisfy necessary diagonal or off-diagonal integral cusp conditions has very limited usefulness. A good Qs(0) can be obtained without constraining by (l) including triplet core spin terms. (2) optimizing orbital exponents. Sufficient nuclear cusp constraints are developed for CI wave functions. The generalized cusp-satisfying CI function has multiconfigurational SCF form with the correct cusp for each orbital. Sample calculations with a small basis set are presented. These simple functions give extremely good Qs(0) expectation values but convergence of Qs(0) with respect to basis set size is yet to be tested. The most interesting discovery is the appearance of Dirac [symbol omitted]-like correction basis orbitals from energy minimization of the orbital exponents. A scheme is depicted classifying previous and present work on cusp constraints in terms of necessity and/or sufficiency. / Science, Faculty of / Chemistry, Department of / Graduate

<p>The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined.</p><p>The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.</p>