The Born-Oppenheimer approximation is a mainstay in molecular physics and chemistry and can be considered a two step process. The first step is to solve the electronic problem with nuclei fixed in space while the second step is to then determine the nuclear dynamics on a given electronic potential energy surface. This first-step calculation of the wavefunction and electronic energies for fixed nuclei has been at the center of modern quantum chemistry for decades. While the majority of chemical processes can be investigated by considering these single electronic surface dynamics, there exist problems in which the dynamics are not constrained to a single electronic surface. One such problem that justifies going beyond the typical adiabatic approximation is the determination of energy levels in systems with strongly coupled electronic states. While some work has been done using diabatic or quasidiabatic Hamiltonians to describe such systems, the work has historically been of qualitative accuracy. Model Hamiltonians have been constructed using experimental data to help calibrate the model parameters aided by the use of lower level adiabatic calculations to help inform the model. It is only within the last few years that theorists have been able to attempt parameterization of such models using only ab initio methods. The goal of this work is to develop a computational framework for the parameterization of quantitatively accurate quasidiabatic Hamiltonians based purely on ab initio information and apply it to a notoriously difficult problem that has plagued the theoretical community for decades -- high accuracy treatment of the energy levels of the NO₃ radical. In this dissertation, high-level ab initio calculations that employ the equation-of-motion coupled-cluster method in the single, doubles and triples (EOMIP-CCSDT) have been used in conjunction with a quasidiabatic ab initio approximation to construct a vibronic Hamiltonian for the strongly coupled X²A'₂ and B²E' states of the NO₃ radical. A quartic vibronic coupling model potential of the form advocated by Köppel et al. has been used to determine the energy levels of this system to quantitative accuracy when compared to experimental data. In order to obtain sufficiently accurate potential energy surfaces necessary to parameterize a quantitatively accurate model Hamiltonian, thousands of large calculations had to be run that do not fit in memory on even the largest HPC systems. The resulting large, out-of-core solves do not map to traditional systems in a way to enable any reasonable parallelization. As a result, a new MPI-based utility has been developed to support out-of-core methods on distributed memory systems. This and other advances in scientific computing form the basis of the developed computational framework. / text

The fact that loosely bonded DNA bases could tolerate large structural fluctuations, form a dissipative environment for a charge traveling through the DNA. Nonlinear stochastic nature of structural fluctuations facilitates rich charge dynamics in DNA. We study the complex charge dynamics by solving a nonlinear, stochastic, coupled system of differential equations. Charge transfer between donor and acceptor in DNA occurs via different mechanisms depending on the distance between donor and acceptor. It changes from tunneling regime to a polaron assisted hopping regime depending on the donor-acceptor separation. Also we found that charge transport strongly depends on the feasibility of polaron formation. Hence it has complex dependence on temperature and charge-vibrations coupling strength. Mismatched base pairs, such as different conformations of the G・A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. I report here on our investigations, via the I –V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I –V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G・A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti)・A(syn) conformation of the G・A mispair. For inhomogeneous (generic) DNA molecules, the mispair result can be either suppression or an enhancement of the current, depending on the type of mispairs and actual DNA sequence.

The fact that loosely bonded DNA bases could tolerate large structural fluctuations, form a dissipative environment for a charge traveling through the DNA. Nonlinear stochastic nature of structural fluctuations facilitates rich charge dynamics in DNA. We study the complex charge dynamics by solving a nonlinear, stochastic, coupled system of differential equations. Charge transfer between donor and acceptor in DNA occurs via different mechanisms depending on the distance between donor and acceptor. It changes from tunneling regime to a polaron assisted hopping regime depending on the donor-acceptor separation. Also we found that charge transport strongly depends on the feasibility of polaron formation. Hence it has complex dependence on temperature and charge-vibrations coupling strength. Mismatched base pairs, such as different conformations of the G・A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. I report here on our investigations, via the I –V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I –V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G・A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti)・A(syn) conformation of the G・A mispair. For inhomogeneous (generic) DNA molecules, the mispair result can be either suppression or an enhancement of the current, depending on the type of mispairs and actual DNA sequence.

Les travaux présentés dans cette thèse peuvent être divisés en deux parties. Dans une première partie, nous avons étudié le processus de photoisomérisation dans plusieurs systèmes. Une analyse de structure électronique accompagnée d’un calcul préliminaire de dynamique semi-classique ont été appliqué à un modèle minimal du rétinal afin d’extraire les degrés de libertés les plus importants lors de l’isomérisation. Cela dans le but de construire des surfaces d’énergie potentielle diabatiques pour effectuer une étude de dynamique quantique. Une approche de type dynamique semi-classique a été appliquée à un modèle de moteur moléculaire dans le but d’étudier l’origine de l’uni-directionalité de sa rotation. Finalement, une étude de structure électronique d’un complexe de Rhénium contenant un ligand de type rétinal a été effectué pour étudier l’influence du métal sur la spectroscopie du ligand rétinal. Dans une deuxième partie nous nous sommes intéressés à l’étude des croisements intersystème dans un complexe de Rhénium. Afin de pouvoir apporter une explication à un comportement contrintuitif de ce complexe, nous avons développé un Hamiltonien modèle capable de tenir compte des couplages vibroniques interétats et spin-orbit. Cet Hamiltonien a été testé sur ce-dit système, et nous a permis, grâce à une étude de structure électronique de proposer un mécanisme de relaxation différent de celui proposé expérimentalement. / This thesis can be divided in two parts.In the first one, we have studied the photoisomerization process in several systems. An electronic structure analysis mixed with a preliminary semi-classical dynamics investigation has been applied to a minimal model of the retinal chromophore in order to select the most important degrees of freedom involved in the process. The goal of this is to build diabatic potential energy surfaces in order to conduct quantum dynamics simulations. A semi-classical approach has also been applied to a molecular motor model to study the origin of the unidirectionality of its rotary motion. Finally, an electronic structure of a rhenium complex with a retinal-like ligand has been performed to study the effect of the coordination to a metallic atom on the spectroscopy of the retinal ligand. In the second part, we have investigated the intersystem crossings in a rhenium complex. In order to bring an explanation to an experimentally observed conterintuitive behavior of this complex, we have developed a model Hamiltonian that includes both interstate vibronic coupling and spin-orbit coupling. This Hamiltonian has been tested on the said complex and, in complement to an electronic structure study, allowed us to formulate a decay mechanism different from the one proposed based on experiments.