In this thesis, we use rst principles density functional theory (DFT) to study the energetics, structural and electronic properties of hydrogenated and lithiated bilayer graphene material systems. The newly developed four variants of the non-local van der Waals (vdW) exchange-correlation functionals (vdW-DF, vdW-DF2, vdW-DF C09x and vdW-DF2 C09x) are employed to explore all the possible con gurations of hydrogen adsorption at 50% and 100% coverage on a 1 1 unit cell. The results obtained are also compared with the GGA PBE functional. For 50% hydrogen coverage, 16 unique con gurations are identi ed in the unrelaxed state. Formation energy analysis reveals six possible energetically favourable con gurations with three low-energy competing con gurations. It is found that the properties of hydrogenated bilayer graphene greatly depend on the hydrogen con guration. For instance, the formation of a hydrogen dimer within the layers decouples the structure, whereas the dimer formation outside surfaces does not have a signi cant in uence on the van der Waals forces; thus the bilayers remain coupled. In this coupled con guration, the vdW-DF C09x functional predicts the lowest formation energy and shortest interlayer separation, whereas the GGA PBE functional gives the highest formation energy and largest interlayer distance. The reasons behind the variation of these functionals are discussed. Two of the three low-energy competing con gurations exhibit semimetallic behaviour, whereas the remaining con guration is a wide band gap material. The wide band gap structure is found to undergo a hydrogen-induced spontaneous phase transformation from hexagonal to tetrahedral (diamond-like) geometry. We conclude that this wide band gap con guration represents a viable template for synthesizing nanodiamonds from graphene by hydrogenation. At 100% coverage, ten unique hydrogen con gurations are identi ed from a 1 1 unit cell. All exchange-correlation functionals predict nine of the structures to have negative formation energies. From these nine structures, three low-energy competing structures are noted and found to be wide band gap semiconductors, whereas the other con gurations exhibit either a semimetallic or metallic character. Although a 1 1 unit-cell is able to present a clear picture for the interaction between hydrogen and graphene, our results reveal that it limits the occurrence of other interesting physics. The cell size was increased to 2 1, to identify other low-energy con gurations that are not possible in a 1 1 cell. The identi ed con gurations have shown physically interesting hydrogen arrangements such as chair-like, zigzag-like and boat-like con gurations. Furthermore, our results reveal that hydrogenation reduces the elastic properties of the pristine structures. We further perform a systematic investigation of the e ects of lithium (Li) on AA and AB stacking sequences of bilayer graphene. Two Li atoms are considered to examine the e ects of the Li-Li interaction on bilayer graphene, and a total of 12 unique con gurations for AB and 9 for AA stackings are identi ed. The vdW-DF consistently predicts the highest formation energies, whereas vdW-DF2 C09x gives the lowest. Unlike in the case of the pristine structures, it is noted that for lithiated bilayer graphene, GGA PBE gives comparable results to the other functionals. One of the Li intercalated con gurations undergoes a spontaneous translation from the AB to AA stacking, and is found to be the most energetically stable con guration. We therefore conclude that Li favours the AA stacking, and that con guration represents a feasible template for experimentally synthesizing and characterizing a Li-based anode material. We noticed that all identi ed Li con gurations exhibit metallic behaviour. Lastly, we found that the intercalated Li dimer weakly interacts with the graphene layers, whereas the intercalated isolated Li atom exhibits strong interaction. / Thesis (PhD)--University of Pretoria, 2014. / gm2014 / Physics / unrestricted

Les précurseurs de ligands base de Schiff électro-donneurs et électro-accepteurs R-ONOH₂ sont préparés par réaction de monocondensation entre les β-dicétones appropriées et respectivement le 1,2- et le 1,2-4-nitro-aminophénol. Ils existent exclusivement sous leurs formes tautomériques céto-énamine en solution et à l'état solide. Dans les complexes correspondants de NiII et de CuII, le métal adopte une géométrie plan carré et est coordiné par les atomes d'azote et d'oxygène du ligand dianionique tridentate et par l'azote du coligand pyridine. L'hyperpolarisabilité quadratique, déterminée par la technique DHL est très élevée. La substitution de la pyridine par la 4,4'-bipyridine conduit systématiquement aux complexes dimériques correspondants. Un composé similaire comportant l'espaceur bis(4-pyridyle)acétylène est formé après réaction de couplage croisé de Sonogashira. Cette même réaction de couplage croisé entre les blocs de construction électrodonneurs et électro-accepteur permettent de préparer le système «push-pull» D-π-A désiré. Les réponses ONL du second ordre des complexes contenant le ligand électro-actif methylène-pyrane peuvent être modulées par bi- (R = An) et tétra- (R = Fc) oxydation réversible avec formation/rupture d'une liaison C-C, constituant ainsi un nouvel exemple de commutateur ONL-2 réversible. / Electron donating and electron withdrawing ligand precursors R-ONOH₂ were prepared by monocondensation reaction of the appropriate β-diketones and 1,2- and 1,2-4-nitro-aminophenol, respectively. They do exclusively exist as their enaminone tautomeric form both in solid-state and in solution phase. In their corresponding Schiff base complexes of NiII and CuII, the central metal is tetracoordinated in a square-planar environment. The coordination sphere is formed by the nitrogen and oxygen atoms of the dianionic tridentate ligand and the fourth coordination site is occupied by the nitrogen atom of the pyridine co-ligand. The derivative exhibited a high quadratic hyperpolarizability (β1.91) determined by the HLS technique. Substitution of 4,4’-bipyridine for pyridine invariably leads to the formation of the respective dimers [(R-ONO)MII(4,4’-bipy)MII(ONO-R)]. A similar compound having the bis(4-pyridyle)acetylene as spacer was formed upon cross-coupling Sonogashira reaction with ethynylpyridine chlorhydrate. The same cross-coupling reaction carried out between the electron releasing and electron withdrawing building blocks, respectively, allowed the preparation of the expected «push-pull» D-π-A system. The second-order NLO responses of compounds bearing a redox active methylenepyran ligand can be modulated upon reversible bi- (R = An) and tetra- (R = Fc) oxydation involving C-C bond formation/breaking reactions, thus forming a new class of NLO molecular switches.

In this thesis, we deal with the application of transmission terahertz spectroscopy as an analysis tool for the study of molecular solids, in particular organic crystals of pharmaceutical interest. Most of the work has been performed using two computational packages aimed at the interpretation of the spectra, one based on molecular forcefields (DMACRYS), the other on solid state density functional theory (CASTEP). We compare low temperature determinations of several molecular organic crystals to calculated spectra, and attempt to assign calculated modes of vibrations to absorption peaks, based on the similarity in frequency between the measured and calculated peaks. One of the main aims of this work is to establish the limits of our forcefield approach, which is based on the approximation that the intramolecular degrees of freedom can be neglected. We analyse the normal modes of vibration calculated with CASTEP, evaluating the amount of rigid molecule rotational and translational contribution to each eigenvector as a function of frequency, in order to validate our forcefield approach. We also compare the two sets of eigenvectors from the DMACRYS and CASTEP calculations to assess the similarity between the two approaches. We perform the same eigenvectors analysis on several hydrate systems in order to understand the role of water in the lattice dynamics of crystalline hydrates. We attempt a classification of the eigenvectors based on the strength of the forces involved in the molecular vibrations and based on the amount of the water contribution to each normal mode. A set of isostructural crystals is analysed in order to understand the effect that small variations (in the molecular formula and in the unit cell arrangement) have on the measured and calculated absorption spectra of a crystal. Finally, we discuss the use and development of computational methods that allow us to have a more realistic description of the molecular electrostatic in DMACRYS.

Cette thèse porte sur la détermination et la modélisation, par la méthode PAW/GIPAW (Gauge Including Projector Augmented Waves), de paramètres RMN de fluorures inorganiques. Dans la première partie, une corrélation entre valeurs expérimentales de déplacements chimiques isotropes (diso) de 19F et de constantes d'écran isotropes (iso) de F calculées de fluorures binaires, dont les attributions sont triviales, est établie. Elle permet de prédire les spectres RMN de 19F avec une bonne précision. Les paramètres quadripolaires de ces fluorures sont aussi déterminés et calculés. Dans la seconde partie, la linéarité entre valeurs expérimentales de diso de 19F et valeurs calculées de iso de 19F permet une attribution non ambigüe des raies RMN de 19F de NbF5 et TaF5. Par contre, pour trois des quatre composés MF4 étudiés (b-ZrF4, HfF4, CeF4, ThF4), caractérisés par des gammes de valeurs de diso de 19F plus petites, les corrélations médiocres entre valeurs de diso et de siso de 19F ne le permettent pas. Enfin, NaAsF6 et KPF6 qui présentent des valeurs élevées de couplage 1J 19F-X et des transitions de phase à des températures proches de l'ambiante sont étudiés par DTA ou DSC et diffraction des rayons X sur poudre et RMN du solide multinucléaire à température variable. Les structures de a- et b-NaAsF6 sont déterminées. KPF6 adopte une structure de haute symétrie désordonnée à température ambiante mais les tentatives de détermination des positions atomiques des deux premières phases basse température sont restées vaines. Ce travail souligne les potentialités et quelques limites de cette méthode ainsi que l'attention qui doit être prêtée aux effets des optimisations. / This thesis focuses on the determination and the modeling, by the PAW/GIPAW (Gauge Including Projector Augmented Waves) method, of NMR parameters in inorganic fluorides. In the first part, a correlation between experimental 19F isotropic chemical shift (diso) and calculated 19F isotropic shieldings (siso) of binary fluorides with obvious assignments is established that allows to predict 19F NMR spectra with a good accuracy. The quadrupolar parameters of these fluorides are also determined and calculated. In the second part, a complete and unambiguous assignment of the 19F NMR lines of NbF5 and TaF5 is obtained, ensured by the linearity between experimental 19F diso values and calculated 19F siso values. On the other hand, for the studied MF4 (b-ZrF4, HfF4, CeF4, ThF4) compounds, characterized by smaller 19F diso ranges, except for ThF4, the poor correlations between experimental 19F diso and calculated 19F siso values prevent us to propose an assignment of the 19F NMR lines. In the last part, NaAsF6 and KPF6, exhibiting large 19F-X 1J-coupling and phase transitions at temperatures close to room temperature (RT) are investigated by DTA or DSC and variable temperature X-ray powder diffraction and multinuclear solid-state NMR. The structures of a- and b-NaAsF6 are determined. KPF6 adopts a disordered high symmetry structure at RT. Unfortunately, attempts to determine the atomic positions of the two first low temperature phases remain unsuccessful. This work highlights the potentialities and some limitations of this method as well as the care that must be taken when dealing with optimized structures.

Relativistic effects are extremely important for heavy atoms and heavy atom containing molecules. Therefore, a relativistic treatment is needed when calculating molecular properties of these species. The fully- relativistic Dirac treatment involves electronic and positronic wavefunctions and a very large basis set is required. This leads to calculations that are too costly and time-consuming for larger molecules. The Zeroth-Order Regular Approximation (ZORA) is an approximation to the Dirac approach, which only deals with the electronic wavefunction. However, unfortunately this method is plagued by the gauge-dependence problem. The gauge-independent ZORA (ZORA-GI) and strictly atomic ZORA approaches provide solutions to this problem.In this work, the ZORA-GI and strictly atomic ZORA codes have been successfully implemented into the Gaussian 09 program. They have been used to calculate the bond lengths, harmonic vibrational frequencies and dissociation energies of the I2, Au2 and Pt2 diatomic molecules. The results show good agreement with experiment and previous theoretical studies. The non-relativistic, ZORA-GI, strictly atomic ZORA and pseudopotential approximations have been used to investigate the electronic structure of the actinide monoxides, AnO, and actinide monoxide cations, AnO+ (An = Th – Cm). It was found that the ground state configurations were dependent on the relativistic approximation chosen. The bond lengths, harmonic vibrational frequencies and dissociation energies were also calculated, with the ZORA methods generally outperforming the pseudopotential approximation. The first theoretical g-tensor study of the organouranium(V) complexes [U(C7H7)2]-, [U(η8-C8H8)(NEt2)(THF)]+, [U(η5-C5H5)(NMe2)3(THF)]+, [U(η8-C8H8)(NEt2)3], [U(η5-C5H5)2(NEt2)2]+ and [U(η8-C8H8)(η5-C5H5)(NEt2)2] has been carried out. It was demonstrated that the choice of density functional affects the way in which the g-tensor axes are assigned. The ground state spin density and SOMO are also sensitive to the choice of density functional. It is these factors that determine the value of the g-tensor.

Light-matter interactions lead to a variety of interesting phenomena, for example photosynthesis which is a process fundamental to life on earth. There exists many different spectroscopic methods to measure light-matter interactions, for example UV/Vis spectroscopy, that can provide information about electronically excited states. However, numerical methods and theory are important to model and gain understanding of these experiments. Quantum chemistry provides that understanding, giving the possibility to numerically calculate molecular properties like excitation energies. The aim of this thesis was to implement a reduced-space algorithm in Dalton, to solve an eigenvalue equation obtained by response theory, for the calculation of excitation energies of molecular systems. There already was a similar algorithm in Dalton, that was able to perform these calculations. However, in a different module of Dalton used mainly for complex response theory, an algorithm to obtain eigenvalues was missing. The new implementation was similar to the existing one, except for the division of the reduced space into even and odd parts used in the complex response module. The thesis starts with a quick introduction of light-matter interactions and proceeds with a description of many-body theory, including numerical methods used in that field. In the end of the theoretical part, the eigenvalue equation, used to calculate excitation energies, is derived. In the following section, the reduced-space algorithm is described. In the end of the thesis, numerical results obtained with the algorithm are presented, including a small basis set and method study. The comparison with the existing implementation of the similar algorithm verified the successful implementation of the algorithm presented in this thesis.

Various gold complexes were computationally investigated, to probe their photophysical, geometric, and bonding properties. The geometry of AuI complexes (ground state singlet) is very sensitive to the electronic nature of the ligands: σ-donors gave a two-coordinate, linear shape; however, σ-acceptors yielded a three-coordinate, trigonal planar geometry. Doublet AuIIL3 complexes distort to T-shape, and are thus ground state models of the corresponding triplet AuIL3. The disproportionation of AuIIL3 to AuIL3 and AuIIIL3 is endothermic for all ligands investigated, however, σ-donors are better experimental targets for AuII complexes. For dimeric AuI complexes, only one gold center in the optimized triplet exciton displays a Jahn-Teller distortion, and the Au---Au distance is reduced versus the ground state distance (i.e., two reasons for large Stokes' shifts).

One of the main goals of computational methods is to identify reasonable geometries for target materials. Organometallic complexes have been investigated in this dissertation research, entailing a significant challenge based on transition metal diversity and the associated complexity of the ligands. A large variety of theoretical methods have been employed to determine ground state geometries of organometallic species. An impressive number of transition metals entailing diverse isomers (e.g., geometric, spin, structural and coordination), different coordination numbers, oxidation states and various numbers of electrons in d orbitals have been studied. Moreover, ligands that are single, double or triple bonded to the transition metal, exhibiting diverse electronic and steric effects, have been investigated. In this research, a novel de novo scheme for structural prediction of transition metal complexes was developed, tested and shown to be successful.

Les travaux présentés dans ce manuscrit portent sur la synthèse et l’étude des propriétés spectroscopiques de systèmes multichromophoriques à base de Bodipy, fluorophore choisi pour ses propriétés émissives remarquables (&#61541-&#61472-et élevés, ) et pour son aptitude à donner et accepter les électrons. Notre objectif est de contrôler sa luminescence par association à un ou plusieurs chromophores de nature variée et répondant à des stimuli déterminés. L’exposé est divisé en quatre chapitres, dont le premier rappelle les méthodes de synthèse et de fonctionnalisation du noyau et détaille leur influence sur les propriétés de fluorescence. Le second chapitre présente le contrôle des propriétés d’émission intrinsèques par extension de conjugaison, au moyen d’une nouvelle réaction de type Knœvenagel. Les résultats spectroscopiques y sont notamment étudiés par modélisation quantique (DFT). Ensuite, nous démontrons qu’il est possible de contrôler la fluorescence par désagrégation de fluorophores greffés, en milieu aqueux par ajout de surfactant et par chélation d’anions. Le troisième chapitre est consacré à la modulation de la fluorescence par changement de l’état « rédox » du partenaire (électrofluorochromisme). A cet effet, deux chromophores ont été employés : la s-tétrazine et le ferrocène. Enfin, nous terminons notre étude par un quatrième chapitre qui aborde la photomodulation des propriétés émissives du Bodipy par couplage à diverses entités photochromes : les azobenzènes, les aniles et les photochromes à cyclisation péricyclique. Nous y détaillons les difficultés synthétiques rencontrées au cours de notre étude. / This work deals with the synthesis and the study of multichromophoric systems, based on Bodipy which is known for its oustanding emission properties (high &#61541- and values, ) and for both, its donating and withdrawing electronic characteristics. Our goal is to couple the fluorophore to other(s) chromophore(s) sensitive to a specific stimulus, to modulate the Bodipy’s emission. The first part, a bibliographic report, focuses on the various ways to functionalize the Bodipy core and discusses their influence on its spectroscopic properties. The second section aims at describing, first, the emission shift by extension of the core conjugation via a new Knœvenagel type reaction. DFT calculations will support experimental facts. It also focuses on external modulation factors such as disaggregation of Bodipy in aqueous media and anion chelation. The third chapter is fully devoted to the possibility of controlling the fluorescence properties by modification of the counter-chromophore “redox” state (so called electrofluorochromism). To that, two chromophores are used: the s-tetrazine and the ferrocene. Final section gathers the preliminary results of coupling reaction of photochromic species with Bodipy, in order to photocommutate its photophysics properties. Synthetic issues are largely discussed so as to highlight some general synthetic pathways that one needs to follow to succeed.

Recent advances in computational technology and algorithms have made it feasible to accurately model the electronic structures of solids by means of density functional theory. The development of hybrid functionals have improved the accuracy of band gap calculations and made it possible to make qualitative predictions regarding the charge transition energy levels of defects in semiconductors. The Sb-V defect (also known as the E-center) in germanium is a well-known defect, which have been the subject of many experimental and some theoretical studies. It has been found to have interesting annealing properties and the aim of this study is to investigate the electronic properties of the Sb-V defect theoretically. The vacancy defect in germanium (VGe), the antimony substitutional (SbGe) defect in germanium and the defect complex (Sb-V) arising from the combination of these two defects is explored in great detail and how they interact in proximity to one another is presented here. In addition, this work can be seen as a test for the effectiveness of the technique to model defects in semiconductors correctly. The E-center defect was investigated using the HSE06 hybrid functional as implemented in the VASP code. A positive binding energy of 1.5 eV, 1.02 eV and 0.88 eV was found for the first, second and third nearest neighbor configurations respectively, between the Sb and the vacancy was predicted. No metastability was detected and the nearest-neighbor configuration had the lowest energy for all charge states. Four transition levels in the band gap were predicted, with energy level relative to the valence band maximum, lying at 0.52 eV (-2/-1), 0.40 eV (-1/0), 0.44 eV (0/+1) and 0.02 eV (+1/+2). The two mid-gap levels (-1/0) and (0/+1) had negative-U ordering with U= -0.04 eV. iv These findings were consistent with the current experimental model of the Sb-V complex in germanium whereby no metastability has been observed experimentally. The energy level of the (-2/-1) corresponded well with the experimental DLTS level in n-type material at 0.37 eV, though the correspondence for the other levels was not as good. Experimentally, no negative-U behavior was observed, but the predicted negative-U behavior was rather small and no deliberate experiments have been performed to investigate the presence of negative-U behavior in the Sb-V complex. / Dissertation (MSc)--University of Pretoria, 2016. / National Research Foundation (NRF) / Physics / MSc / Unrestricted