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.

Interfaces between semiconductors and adsorbed molecules form a central area of research in surface science, occurring in many different contexts. One such application is the so-called Dye-Sensitized Solar Cell (DSSC) where the nanostructured dye-semiconductor interface is of special interest, as this is where the most important ultrafast electron transfer process takes place. In this thesis, structural and electronic aspects of these interfaces have been studied theoretically using quantum chemical computations applied to realistic dye-semiconductor systems. Periodic boundary conditions and large cluster models have been employed together with hybrid HF-DFT functionals in the modeling of nanostructured titanium dioxide. A study of the adsorption of a pyridine molecule via phosphonic and carboxylic acid anchor groups to an anatase (101) surface showed that the choice of anchor group affects the strength of the bindings as well as the electronic interaction at the dye-TiO2 interface. The calculated interfacial electronic coupling was found to be stronger for carboxylic acid than for phosphonic acid, while phosphonic acid binds significantly stronger than carboxylic acid to the TiO2 surface. Atomistic and electronic structure of realistic dye-semiconductor interfaces were reported for RuII-bis-terpyridine dyes on a large anatase TiO2 cluster and perylene dyes on a periodic rutile (110) TiO2 surface. The results show strong influence of anchor and inserted spacer groups on adsorption and electronic properties. Also in these cases, the phosphonic acid anchor group was found to bind the dyes significantly stronger to the surface than the carboxylic acid anchor, while the interfacial electronic coupling was stronger for the carboxylic anchor. The estimated electron injection times were twice as fast for the carboxylic anchor compared to the phosphonic anchor. Moreover, the electronic coupling was affected by the choice of spacer group, where unsaturated spacer groups were found to mediate electron transfer more efficiently than saturated ones.

Many-body perturbation theory and coupled-cluster theory, combined with carefully constructed basis sets, can be used to accurately compute the properties of small molecules. We applied a series of methods and basis sets aimed at reaching the ab initio limit to determine the barrier to planarity for ethylene cation. For potential energy surfaces corresponding to bond dissociation, a single Slater determinant is no longer an appropriate reference, and the single-reference hierarchy breaks down. We computed full configuration interaction benchmark data for calibrating new and existing quantum chemical methods for the accurate description of potential energy surfaces. We used the data to calibrate single-reference configuration interaction, perturbation theory, and coupled-cluster theory and multi-reference configuration interaction and perturbation theory, using various types of molecular orbitals, for breaking single and multiple bonds on ground-state and excited-state surfaces. We developed a determinant-based method which generalizes the formulation of many-body wave functions and energy expectation values. We used the method to calibrate single-reference and multi-reference configuration interaction and coupled-cluster theories, using different types of molecular orbitals, for the symmetric dissociation of water. We extended the determinant-based method to work with general configuration lists, enabling us to study, for the first time, arbitrarily truncated coupled-cluster wave functions. We used this new capability to study the importance of configurations in configuration interaction and coupled-cluster wave functions at different regions of a potential energy surface.

This thesis is dedicated to the theoretical study of the methyl cation CH3+ electronic states and, globally, falls within the study of the interstellar clouds molecular synthesis and the chemistry of the hydrocarbons which are present in high-energy plasmas such as in the experimental nuclear fusion reactor ITER. Among the different possible formation reactions, we chose two reactions involved in these fields: the ionization of the methyl radical CH3 ground state and the reactive collisions between simple carbonated or hydrocarbonated (C, CH+ and CH2+) and hydrogen species (H3+, H2 and H, respectively).<p><p>As this cation is characterized by 8 electrons and 4 nuclei, this allowed us to perform high-level ab initio calculations using the CASSCF/MRCI method with the Dunning aug-cc-p(C)VXZ basis sets. These calculations were completed by a study of different methodological effects such as the core-valence electronic correlation, the complete basis set extrapolation and the basis set superposition error.<p><p>We calculated equilibrium geometries (precision within 10^-5 angtröm and 10^-2° and their energies for the methyl radical and cation, studied the potential energy surfaces involved by the Jahn-Teller effect targeting the methyl cation E' states and achieved frequencies calculations. From these values were derived ionization potentials (IP) from the methyl radical ground state towards the methyl cation lowest-lying states (precision within 10^-2 eV). Vibrational corrections and nuclear relaxation effects were taken into account.<p><p>The calculated IPs and frequencies should facilitate the analysis of methyl radical threshold photoelectron spectra leading to the methyl cation lowest-lying states, recorded at the synchrotron facility Soleil by the Dr. Alcaraz group from the Université Paris-Sud.<p><p>Through reaction paths calculations using a quadratic steepest-descent method, we have proposed new reactional pathways enabling the connections between the different dissociation channels correlated to the cation lowest-lying triplet states. The absence of potential barriers in the energy profiles allows us to propose these reactions as sources, in interstellar clouds, of hydrocarbonated molecules whose stability increases with growing size according to the series C -> CH+ -> CH2+ -> CH3+.<p><p>The groups of Pr. Urbain from UCL and Dr. Savin from Columbia University studied the collisions in copropagating beams of C and H3+ leading to the formation of these hydrocarbonated species. The proposed reactional mechanisms are in good agreement with the experimental observations, what permits a better understanding of the chemistry behind these collisional processes of astrochemical interest. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

<p>Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. </p><p>The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.</p><p>The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-<i>Z,syn</i> configuration (in the inactive form of the protein) to C15-<i>E,anti</i> (in the active form). In this work, a reaction mechanism for this isomerization is proposed. </p><p>DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.</p><p>Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.</p>

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work. The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed. DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied. Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

<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>

<p>The serendipitous discovery of the potent cytotoxic properties of cisplatin brought about a revolution in the treatment of certain types of cancer, but almost fifty years later, there still remain unknown areas in the chemistry of cisplatin. There are questions regarding which form of the drug reaches its DNA target, or why certain DNA sequences are more preferred than others for reaction with cisplatin. The work presented here aims to address some of these problems, using quantum chemical calculations to complement and interpret available experimental data.</p><p>Cisplatin's activation reactions are explored by Density Functional Theory (DFT) on two model systems, one solely using a self-consistent reaction field (SCRF) for modeling bulk water, and one including an additional partial solvation shell of water molecules. It is concluded that adding explicit solvation provides a better picture than using SCRF solvation alone. The energy surface supports the view that the active form of cisplatin is the monoaquated form.</p><p>The activation reactions of the cisplatin-derived drug, JM118, are investigated using DFT and SCRF calculations using three solvation model systems. The results show a slower rate of hydrolysis for the first reaction, and a faster rate for the second, suggesting diaquated JM118 as the main DNA binding form of the drug.</p><p>Diaquated cisplatin's first and second reaction with guanine and adenine are studied using DFT and SCRF solvation. Cisplatin's propensity toward guanine in the first substitution is explained by larger stabilisation energy for the initially formed complex and by favoured kinetics. For the second substitution, higher stability in complexation with guanine over adenine is ascribed as the main factor favouring guanine over adenine substitution. This provides the first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) adducts, and the direction specificity of the 1,2-d(ApG) adducts.</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.

The serendipitous discovery of the potent cytotoxic properties of cisplatin brought about a revolution in the treatment of certain types of cancer, but almost fifty years later, there still remain unknown areas in the chemistry of cisplatin. There are questions regarding which form of the drug reaches its DNA target, or why certain DNA sequences are more preferred than others for reaction with cisplatin. The work presented here aims to address some of these problems, using quantum chemical calculations to complement and interpret available experimental data. Cisplatin's activation reactions are explored by Density Functional Theory (DFT) on two model systems, one solely using a self-consistent reaction field (SCRF) for modeling bulk water, and one including an additional partial solvation shell of water molecules. It is concluded that adding explicit solvation provides a better picture than using SCRF solvation alone. The energy surface supports the view that the active form of cisplatin is the monoaquated form. The activation reactions of the cisplatin-derived drug, JM118, are investigated using DFT and SCRF calculations using three solvation model systems. The results show a slower rate of hydrolysis for the first reaction, and a faster rate for the second, suggesting diaquated JM118 as the main DNA binding form of the drug. Diaquated cisplatin's first and second reaction with guanine and adenine are studied using DFT and SCRF solvation. Cisplatin's propensity toward guanine in the first substitution is explained by larger stabilisation energy for the initially formed complex and by favoured kinetics. For the second substitution, higher stability in complexation with guanine over adenine is ascribed as the main factor favouring guanine over adenine substitution. This provides the first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) adducts, and the direction specificity of the 1,2-d(ApG) adducts.