Browsing by Subject "Chemical physics"

Now showing 1 - 3 of 3
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    Computational methods for understanding RNA catalysis: a molecular approach
    (2014-09) Radak, Brian K.
    Molecular simulation is a powerful technology for providing a detailed picture of a wide range of chemical phenomena. The results of simulation studies are now increasingly used in supplementing experimental studies both as a predictive tool and as a lens through which to interpret results and generate new hypotheses. This dissertation describes several advancements in the development and application of molecular simulation methods to the study of RNA catalysis. Such reactions are representative of a broad class of chemistry associated with important biological functions including storage of genetic information, metabolism, and cell signaling and replication. Furthermore, the existence of naturally occuring RNA sequences that catalyze these reactions has significant implications for the origins of life and the potential design of new RNA based technologies. The work presented here offers new insights into these problems and contributes to a detailed, molecular understanding of the fundamental chemical principles that are in action.
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    Development of fragment-based quantum mechanical methods and combined quantum mechanical and molecular mechanical methods
    (2014-08) Wang, Yingjie
    This thesis is dedicated to develop fragment-based QM methods and QM/MM schemes: For the first part, the fragment-based explicit polarization (X-Pol) method has been extended in three aspects: I. the inclusion of exchange repulsion terms in the X-Pol model is examined by antisymmetrizing the X-Pol Hartree-product wave function; this yields X-Pol with full eXchange, called X-Pol-X; II. the original X-Pol method, where all fragments are treated using the same electronic structure theory, is extended to a multilevel representations, called multilevel X-Pol, in which different electronic structure methods are used to describe different fragments; III. a fragment-based variational many-body (VMB) expansion method is described to directly account for exchange repulsion, charge delocalization (charge transfer) and dispersion interactions in the X-Pol method. For the second part, a universal QM/MM scheme, the projected hybrid orbital (PHO) method, is proposed to handle the covalent boundary at QM/MM interface at ab initio level with arbitrary basis sets. As an extension to the generalized hybrid orbital (GHO) method in which hybrid orbitals are constructed using the valence orbitals on the boundary atom, the PHO method further represents the core and valence electrons with a secondary, minimal basis set by projecting the original (primary) basis set used in the QM system. The PHO method is then validated on several aspects: geometry optimization, charge population and proton-affinity calculation. Comparison with standard QM results shows that PHO is a robust and balanced QM/MM scheme that yields satisfactory structural, electronic, and energetic properties.
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    Electronic structure theory and multi-structural statistical thermodynamics for computational chemical kinetics.
    (2012-08) Papajak, Ewa
    This thesis involves the development and application of methods for accurate computational thermochemistry. It consists of two parts. The first part focuses on the accuracy of the electronic structure methods. In particular, various augmentation schemes for one-electron basis sets are presented and tested for density functional theory (DFT) calculations and for wave function theory (WFT) calculations. The relationship between diffuse basis functions and basis set superposition error is discussed. For WFT, we also compare the efficiency of conventional one-electron basis-sets to that of newly developed explicitly correlated methods. Various ways of approaching the complete basis set limit of WFT calculations are explained, and recommendations are made for the best ways of achieving balance between the basis set size, higher-order correlation, and relativistic corrections. Applications of this work include computation of barrier heights, reaction and bond energies, electron affinities, ionization potentials, and noncovalent interactions. The second part of this thesis focuses on the problem of incorporating multistructural effects and anharmonicity effects in the torsional modes into partition function calculations, especially by using a new multi-structural torsion (MS-T) method. Applications of the MS-T method include partition functions of molecules and radicals important for combustion research. These partition functions are used to obtain thermodynamic functions that are the most reliable results available to date for these molecules. The multi-structural approach is also applied to two kinetics problems: • the hydrogen abstraction from carbon-3 of 1-butanol by hydroperoxyl radical • the 1,5-hydrogen shift isomerization of the 1-butoxyl radical In both cases multi-structural effects play an important role in the final results.