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. 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.

This thesis presents time-dependent density functional theory studies on electronic and vibronically resolved linear and nonlinear optical absorption and dichroism spectra of organic molecules. Special attention has been paid to the influence of solvent environment and molecular vibrations on one-, two- and three-photon absorption and one- and two-photon circular dichroism. It is found that dielectric medium as described by polarizable continuum model can enhance remarkably three-photon absorption cross section of a highly conjugated fluorene derivative, for which the simplified two-state model is shown to be largely inadequate. Origin-invariant density functional calculations on one- and two-photon circular dichroisms of a chiral molecule confirm that the recently developed CAMB3LYP functional performs better than the popular B3LYP functional for Rydberg-states. The first experimental measurement of TPCD spectra is performed on an axial chiral system in tetrahydrofunan, where the double L-scan technique is applied. Theoretical calculations well reproduce the experimental profiles when both the electron correlation and the solvent effect are taken into account. Vibronically resolved one- and two-photon absorption spectra of charge-transfer molecules have been obtained using a Linear Coupling model, where the 'borrowing mechanism' for the so-called Herzberg-Teller contribution is analyzed in detail. It is shown that Herzberg-Teller contribution can introduce a change of sign to the chiral responses of a molecule without the involvement of different electronic states, which has important consequences for the assignment of absolute configurations of chiral molecules. Adiabatic harmonic Franck-Condon model is also applied to simulate vibronically resolved one- and two-photon circular dichroism spectra of the same chiral system, where the sign-inversion and the interference between Franck-Condon and Herzberg-Teller contributions are also observed. / QC 20100727

<p>When light exhibits particle properties, and when matter exhibits wave properties quantum mechanics is needed to describe physical phenomena. </p><p>A two-photon source produces nonmaximally entangled photon pairs when the source is small enough to diffract light. It is shown that diffraction degrades the entanglement. Quantum states produced in this way are used to probe the complementarity between path information and interference in Young's double slit experiment.</p><p>When two photons have a nonmaximally entangled polarization it is shown that the Pancharatnam phase is dependent on the entanglement in a nontrivial way. This could be used for implementing simple quantum logical circuits. </p><p>Magnetic traps are capable of holding cold neutral atoms. It is shown that magnetic traps and guides can be generated by thin wires etched on a surface using standard nanofabrication technology. These <i>atom chips</i> can hold and manipulate atoms located a few microns above the surface with very high accuracy. The potentials are very versatile and allows for highly complex designs, one such design implemented here is a beam splitter for neutral atoms. Interferometry with these confined de Broglie is also considered. These atom chips could be used for implementing quantum logical circuits.</p>

When light exhibits particle properties, and when matter exhibits wave properties quantum mechanics is needed to describe physical phenomena. A two-photon source produces nonmaximally entangled photon pairs when the source is small enough to diffract light. It is shown that diffraction degrades the entanglement. Quantum states produced in this way are used to probe the complementarity between path information and interference in Young's double slit experiment. When two photons have a nonmaximally entangled polarization it is shown that the Pancharatnam phase is dependent on the entanglement in a nontrivial way. This could be used for implementing simple quantum logical circuits. Magnetic traps are capable of holding cold neutral atoms. It is shown that magnetic traps and guides can be generated by thin wires etched on a surface using standard nanofabrication technology. These atom chips can hold and manipulate atoms located a few microns above the surface with very high accuracy. The potentials are very versatile and allows for highly complex designs, one such design implemented here is a beam splitter for neutral atoms. Interferometry with these confined de Broglie is also considered. These atom chips could be used for implementing quantum logical circuits.

This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

<p>Quantum dynamics is the study of time-dependent phenomena in fundamental processes of atomic and molecular systems. This thesis focuses on systems where nature reveals its quantum aspect; e.g. in vibrational resonance structures, in wave packet revivals and in matter wave interferometry. Grid based numerical methods for solving the time-dependent Schrödinger equation are implemented for simulating time resolved molecular vibrations and to compute photo-electron spectra, without the necessity of diagonalizing a large matrix to find eigenvalues and eigenvectors.</p><p>Pump-probe femtosecond laser spectroscopy on the sodium potassium molecule, showing a vibrational period of 450 fs, is theoretically simulated. We find agreement with experiment by inclusion of the finite length laser pulse and finite temperature effects.</p><p>Complicated resonance structures observed experimentally in photo-electron spectra of hydrogen- and deuterium chloride is analyzed by a numerical computation of the spectra. The dramatic difference in the two spectra arises from non-adiabatic interactions, i.e. the interplay between nuclear and electron dynamics. We suggest new potential curves for the 3²Σ⁺ and 4²Σ⁺ states in HCI⁺.</p><p>It is possible to guide slow atoms along magnetic potentials like light is guided in optical fibers. Quantum mechanics dictates that matter can show wave properties. A proposal for a multi mode matter wave interferometer on an atom chip is studied by solving the time-dependent Schrödinger equation in two dimensions. The results verifies a possible route for an experimental realization.</p><p>An improved representation for wave functions using a discrete set of coherent states is presented. We develop a practical method for computing the expansion coefficients in this non-orthogonal set. It is built on the concept of frames, and introduces an iterative method for computing a representation of the identity operator. The phase-space localization property of the coherent states gives adaptability and better sampling efficiency.</p>

Quantum dynamics is the study of time-dependent phenomena in fundamental processes of atomic and molecular systems. This thesis focuses on systems where nature reveals its quantum aspect; e.g. in vibrational resonance structures, in wave packet revivals and in matter wave interferometry. Grid based numerical methods for solving the time-dependent Schrödinger equation are implemented for simulating time resolved molecular vibrations and to compute photo-electron spectra, without the necessity of diagonalizing a large matrix to find eigenvalues and eigenvectors. Pump-probe femtosecond laser spectroscopy on the sodium potassium molecule, showing a vibrational period of 450 fs, is theoretically simulated. We find agreement with experiment by inclusion of the finite length laser pulse and finite temperature effects. Complicated resonance structures observed experimentally in photo-electron spectra of hydrogen- and deuterium chloride is analyzed by a numerical computation of the spectra. The dramatic difference in the two spectra arises from non-adiabatic interactions, i.e. the interplay between nuclear and electron dynamics. We suggest new potential curves for the 32Σ+ and 42Σ+ states in HCI+. It is possible to guide slow atoms along magnetic potentials like light is guided in optical fibers. Quantum mechanics dictates that matter can show wave properties. A proposal for a multi mode matter wave interferometer on an atom chip is studied by solving the time-dependent Schrödinger equation in two dimensions. The results verifies a possible route for an experimental realization. An improved representation for wave functions using a discrete set of coherent states is presented. We develop a practical method for computing the expansion coefficients in this non-orthogonal set. It is built on the concept of frames, and introduces an iterative method for computing a representation of the identity operator. The phase-space localization property of the coherent states gives adaptability and better sampling efficiency.

Quantum chemical calculations have been used to model dye-sensitized nanostructured titanium dioxide systems that can be used in solar cells for solar energy to electricity conversion. Structural, electronic and spectral properties of isolated dyes and both bare and dye-sensitized TiO2 have been calculated with density functional theory, providing detailed information about both the separate parts and the dye-TiO2 interface. The connection between the geometry, the ligand field splitting and the lifetime of the triplet metal-to-ligand charge transfer (MLCT) excited state has been explored for a series of ruthenium polypyridyl dyes. Moreover, the relative energetics of MLCT and metal centered triplet excited states have been studied for a number of such systems. It was found that small alterations of the polypyridyl ligands can result in significant changes in ligand field splitting and in the energetics of the triplet states. Attachment of the dyes to the TiO2 surface is achieved via anchor and spacer groups. The influence of such groups on various properties of the dye and their ability to act as mediators of photo-induced surface electron transfer has been studied. Delocalization of the lowest unoccupied dye orbital onto the spacer and/or anchor group indicates that certain unsaturated groups can mediate electron transfer. With a combination of methods that enables efficient computations and a scheme for construction of metal oxide clusters, chemical models for bare TiO2 nanocrystals in the 1-2 nm size range have been developed. The electronic structures show well-developed band structures with essentially no electronic band gap defect states. Atomistic models of the interface between TiO2 nanocrystals and Ru(II)-bis-terpyridine dyes, the so-called N3 dye as well as perylene dyes are reported. Electronic coupling strengths, which provide estimates for the electron injection times, are extracted from the interfacial electronic structure and the lowest electronic excitations are calculated.

<p>Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.</p><p>The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.</p><p>Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.</p>

<p>Oscillator strengths and transition energies are calculated for several mono-substitutes of benzene and naphthalene molecules. The substituents investigated are chlorine, bromine and iodine. Calculations for these molecules are presented, at the Hartree-Fock and DFT level of theory. The functional used in DFT is CAM-B3LYP.</p>