Electronic structure simulations of DNA base recognition and vibrational property analysis of polyanionic hydrides

This thesis presents electronic structure simulations of electron transport across DNA base-pairs for base recognition and analysis of vibrational properties for polyanionic hydrides.;The work on DNA base recognition is motivated by a recent experiment to sequence DNA by measuring tunnel conductance when a single stranded DNA molecule passes through a nanopore. An electric circuit is completed when a DNA base and the phosphate backbone form hydrogen bonds with the reader nucleobase and a guanidinium ion, respectively, tethered to either side of metal electrodes. The tunnel conductance has been obtained across DNA base-pairs, across nucleoside-base pairs, and for a complete circuit containing deoxycytidine-monophosphate (dCMP) by computing the complex bandstructure, Fermi level alignment, and current-voltage curve. The results indicate that a complete dCMP circuit has a very low conductance (on the order of fS) while the base-pair has a moderate conductance (on the order of tens of nS). An alternate base readout scheme, which uses a shorter tunneling path, is explored.;Electron transport through other organic single molecules is also examined. Examples include the effects of torsion angle between rings, oxidation states, and stretching on the electron transport properties of polyaniline molecules and the effects of molecule-metal contact geometries in alkanedithiol molecules.;Additionally, an analysis of vibrational properties is presented to understand the bonding of hydrogen in aluminum and gallium hydrides by computing phonon dispersion curve. Both Al-H and Ga-H stretching mode frequencies are found to be low compared to other hydrides. The weak Al(Ga)-H bond is balanced by Sr(Ba)-H interactions.;Finally, the electronic and the vibrational property changes are examined when superconducting MAlSi (M = Ca, Sr, Ba) absorbs hydrogen and forms semiconducting hydrides MAlSiH with hydrogen attached to Al exclusively. While only a minor rearrangement of the metal atoms occurs due to the hydrogenation, formation of Al-H bond causes a removal of partially occupied antibonding band responsible for metallic behavior and a stiffening of soft phonon mode pivotal for the superconducting properties of MAlSi. On the other hand, the Al-Si bond represented by Al-Si in-plane vibration is equally strong in the metals and semiconducting hydrides.