The aim of this work is to predict the influence of phonon modulations (Kozina et al. 2019 [1]) on the x-ray absorption near-edge fine structure of the Ti-L2,3-edge (Yamaguchi et al. 1982 [2], Thole et al. 1985 [3], De Groot 1990 [4]) in cubic SrTiO3. Employing Density Functional Theory in combination with Multiplet Ligand Field Theory (Haverkort et al. 2012 [5], Luder et al. 2017 [6]), previous experimental and theoretical data on the octahedrally symmetric structure are reproduced with good agreement. Phonon modulations with a maximum atomic displacement of 5% of the lattice parameter are shown to cause polarization-dependent changes in the x-ray absorption spectra just within reach of experimental resolution. This is suggested to reflect the strong susceptibility of the electronic structure to collective lattice excitations in SrTiO3.

Intermetallic compounds are solid phases containing two or more metallic elements, whose crystal structure differs from that of its constituents [1]. The largest group among these compounds with more than 1400 binary and ternary representatives are the so-called Laves phases. The classification of an intermetallic compound as a Laves phase is solely based on the atomic configuration and the component ratio in the crystal structure. With the ideal composition AB2, the Laves phases crystallize in three closely related structure types which are named after their representatives, MgCu2 (C15, cubic), MgZn2 (C14, hexagonal) and MgNi2 (C36, hexagonal). Laves phases are built by almost all metals of the periodic system of the elements. A significant feature of many of these is the formation of broad homogeneity ranges by mutual substitution of atoms in combination with composition or temperature dependent phase transformations between the different Laves phase polytypes. Laves phases have received considerable attention in recent years as potential structural and functional materials. They combine high melting points with considerable creep resistance, high strength and fracture toughness and good corrosion and oxidation resistance. Some Laves phases like NbFe2 [2] or TaFe2 [3] show intriguing magnetic and electronic properties which provide a deeper inside into phenomenons like quantum criticality. Especially transition-metal based Laves phases like NbCr2 [4] and ZrCr2 [5] are promising candidates for the development of new high-temperature structural materials. The major drawback of the Laves phases, however, is their low-temperature brittleness. Many experimental and theoretical investigations have shown, that the low-temperature ductility can be improved by controlling the crystal structure with the help of phase transformations, by mechanical twinning or the addition of third elements. The addition of ternary alloying elements can alter the physical and electronic properties of the Laves phases and plays an important role in the composition dependent stability of the different polytypes. Some ternary Laves phases show an interesting phenomenon called site occupation reversal. It describes a composition dependent behavior of the alloying elements which prefer to occupy different crystallographic sites at different concentrations. The understanding of the point defect structure/mechanism and the site occupation of the alloying elements is thus of critical importance for the proper description of phase stability. The basis for the broad application of any metallic material is the knowledge of the corresponding phase diagram. The experimental determination of phase diagrams however, is tedious, time consuming and expensive work and the huge abundance of Laves phase makes this an impractical task. Thus, the time it takes to discover new advanced materials and to move them from the laboratory to the commercial market place is fairly long today. A cheap and fast enhancement for the development of new materials is the calculation of phase diagrams and physical properties using techniques like CALPHAD (CALculation of PHAse Diagrams) and DFT (Density Functional Theory). Very recently the Office of Science and Technology Policy of the United States White House announced to provide a budget of $100 million to launch the Materials Genome Initiative [6, 7]. The aim of this initiative is to provide the infrastructure and training needed to discover, develop, manufacture, and deploy advanced materials in a more expeditious and economical way [8]. One of the project’s three supporting legs is the calculation and prediction of crystal structures and physical properties using advanced Computational tools. "An early benchmark will be the ability to incorporate improved predictive modeling algorithms of materials behavior into existing product design tools. For example, the crystal structure and physical properties of the materials [. . . ]." [8]. Their computational tools of choice are the same as used in this work to predict crystal structures and site occupation factors. Contents of this work is the investigation of the substitutional disorder in binary and ternary Laves phases. This includes the experimental determination of the composition dependent stability of the Laves phase polytypes and the distribution of the substitution atoms in the crystal lattice of the respective phases, i.e., the site occupation factors (s.o.f.). For this purpose, detailed experimental studies on the two systems Cr–Co–Nb and Fe–Ta–V were performed and the Laves phase polytypes, their homogeneity ranges, the lattice parameters and the site occupation factors were determined. The experimental results are compared with the results obtained from quantum mechanical calculations. DFT is used to determine the composition dependent enthalpies of formation which serve as a measure for the stability of the different Laves phase polytypes. Additionally, the applicability of various approximations and their influence on the results has been checked. This study is thus also supposed to develop and improve the tools necessary for the calculation of phase stability and homogeneity ranges in ternary phases. Chapter two in the first part of this work describes the crystal structures of the Laves phases in detail with focus on the polytype stability, the site occupation and the c/a-ratio of hexagonal C14 Laves phases. Subsequently, the phase diagrams of the investigated systems and the occurring Laves phases are discussed. Chapter three briefly describes the experimental and theoretical methods used in this work. The last section of part one gives a detailed explanation of how the phase stability, the lattice parameters and the site occupation factors are calculated. The second part "Results and discussion" contains the discussion of the experimental and theoretical results for the intensively investigated systems Co–Cr–Nb (chapter five) and Fe–Ta–V (chapter six). Several other ternary C14 Laves phases and their site occupation behavior are studied in chapter seven. The thesis is concluded with a summary in chapter eight. Several additional information is contained in the appendix.

This thesis has been focused around the Diels Alder reaction with the goal to design an enzyme catalyzed reaction pathway. To achieve this goal computer aided enzyme design was utilized. Common traditional methods of computational chemistry (B3LYP, MP2) do not do well when calculating reaction barriers or even reaction energies for the Diels Alder reaction. New calcu- lation methods were developed and tested. This was the focus of the first part of the thesis, by choosing a small system, extensive and heavy calculations could be done with CBS-QB3. Then by benchmarking faster methods of calculation (SCS-MP2, M06-2X) against the results, they could be graded by efficiency and cost. This was done anticipating that the same accuracy could be applied to larger systems where CBS-QB3 cannot be used. In the second part activating groups were investigated for both the diene and the dienophile, along with their effects on reaction rates. A qualitative analysis was done. This is important not only for the uncatalyzed reaction, but also interesting when searching for possible substrates for the enzyme reaction. In the last part the thesis presents a designed enzyme that catalyzes Diels Alder in silico using ∆5−3−Keto steroid isomerase. Using empirical calculations, the enzyme was scanned for catalytic activity. The catalytic effect was then showed with ab initio Quantum chemical calculations.

In the search for a sustainable and environmentally friendly energy source, artificial photosynthesis has been proposed  as a promising solution. Using water as a substrate, solar energy can be utilised to store energy in the chemical form of hydrogen fuel. In part of this global scientific effort, this thesis work focuses on enabling molecular dynamics simulations of a particular set of ruthenium centred  water oxidation catalysts. The new catalysts show great success because of a binuclear  reaction  pathway in aqueous solution which makes it very interesting to model and investigate. Utilising quantum  mechanical tools, a set of molecular mechanics force field parameters for Ru-involved bonds, angles, torsions, and partial charges was successfully obtained and examined. The work allows future large scale simulation of water  oxidation and oxygen evolution in order to gain understanding and improve artificial photosynthesis.

Thesis (M.Sc. (Physics)) -- University of Limpopo, 2021 / The ab initio density functional theory and molecular dynamics approach have been used to study the properties of Zr-based systems. In particular Zr-Nb, Zr-Nb-X (X = Co and Sn). We have calculated the structural, elastic, mechanical properties and temperature dependence particularly to determine their stabilities. These alloys are important for a wide range of technological applications, primarily in the nuclear and chemical industries due to their good irradiation stability, wear and corrosion resistance, high mechanical strength and superior neutron economy. The virtual crystal approximation was used to introduce small amounts of either Co or Sn contents on Zr-Nb system. The main idea is to advance high-temperature applications of Zr-Nb system through ternary alloying. Calculations were carried out using the ab initio DFT employing the plane-wave pseudopotential method as implemented within the CASTEP code. The influence of partial substitution for Nb concentration with either Co or Sn concentrations was investigated on the Zr-Nb-X systems of various concentrations. The resulting equilibrium lattice parameters, heats of formation, elastic properties, and the density of states were evaluated to mimic their structural, thermodynamic and mechanical stability trends. The lattice parameters of binary systems Zr99Nb1.0, Zr98.8Nb1.2, Zr98.1Nb1.9, Zr97.5Nb2.5, Zr97Nb3, Zr78Nb22, Zr78Nb22 and Zr50Nb50 gave better agreement with available experimental data to within 5 %, while those for ternary systems have shown a decrease with the introduction of the third element i.e. Co or Sn. The heats of formation were negative (stable) at smaller concentrations of ≤ 1 at. % Co. Moreover, the correlation of electronic stability using the DOS and the ∆Hf calculations has indicated that the systems are thermodynamically stable within ≤ 1 at. % Co for (Zr99Nb1-xCox, Zr98.8Nb1.2-xCox, Zr98.1Nb1.9Cox, Zr97.5Nb1.5-xCox, Zr97Nb3- xCox and Zr78Nb22-xCox) systems. It was found that the increase in Co concentration enhances the thermodynamic, elastic and mechanical stability of the systems and they are found to be stable at small concentrations of about 1 at. % Co. Furthermore, the temperature dependence was carried out using Dmol3 . In particular, the canonical ensemble (NVT) calculations were carried out at different temperatures and we observed their structural behaviour with regard to the binding energy and elastic properties at any given temperature up to 2400 K. We compare the temperature dependence of Zr, Zr50Nb50, Zr78Nb22, Zr78Nb21Co1, Zr78Nb20Co2, Zr78Nb19Co3, Zr50Nb49Sn1, Zr50Nb48Sn2 and Zr50Nb47Sn3 systems. In the case of binary system, the Zr78Nb22 was more promising, showing lower binding energy of - 6.87eV/atom. It was shown that ternary additions with small atomic percentages of Co and Sn have a significant impact on Zr-Nb alloy. Particularly, their elastic properties showed a possible enhancement on the strength and ductility at high temperature. This was observed for 1 at. % since it satisfied the requirements for ductility and strength as specified in literature. The Co and Sn addition on the Zr78Nb22 system is more promising for high-temperature applications, with Sn being more preferable. / National Research Foundation (NRF) and Titanium Centre of Competence (TiCoC)

Här undersöks en strategi som behandlar dendrittillväxt på en solid litiumanod i ett litiumbatteri. Med hjälp av täthetfunktionalsteori adsorberades fyra flytande kristaller på litiumytan vilket ledde till en gränsskiktsstabilisering. Denna stabilisering har i en tidigare rapport länkats till dendrittillväxt i en fasfältsmodell. Fasfältsmodellen replikerades ej i denna rapport utan det ses som ett eventuellt nästa steg. Molekylerna interagerade starkt med ytan och de beräknade adsorptionsenergierna hade stor inverkan på litiumytans gränsskiktsenergi. De flytande kristallernas fas simulerades också, vilken hade en beräknad kohesivenergi i samma storleksordning som flytande vatten. Denna energi var lägre än adsorptionsenergierna, vilket tyder på att det finns en drivkraft för molekylerna att interagera med ytan. Vidare så undersöktes redoxstabiliteten hos molekylerna, där det visade sig att två av molekylerna hade LUMO-energier under Ferminivån hos litium. Dessa molekyler är således inte stabila nära litiumytan, utan kommer eventuellt ta del i elektrokemiska reaktioner. Slutligen så undersöktes diffusionsbarriären hos adsorberade litiumatomer. Här jämfördes barriären mellan fall då molekyler var adsorberade och inte, och det visade sig att med adsorberade molekyler så är diffusionsbarriären högre. / A strategy to suppress the growth of dendrites on solid state lithium anodes was investigated. Using density functional theory, four liquid crystal molecules were adsorbed on a solid lithium surface leading to an interfacial stabilization. This stabilization has earlier been used as a descriptor in a phase-field model which investigated dendrite suppression. The replication of this phase-field model was out of the scope of this thesis and left as future work. The LC molecules interacted strongly with the surface, and the calculated adsorption energies had an considerable impact on the interfacial energies of the lithium surface. A liquid crystal phase was also simulated, with a cohesive energy of the same magnitude as liquid water. This energy was lower than the adsorption energies, indicating that there is a driving force for the LC molcules to adsorb to the surface. Furthermore, the redox stability of the molecules in the proximity of the lithium surface was investigated, where two of them had LUMO energies below the Fermi level of lithium. Those two molecules were thus not considered sufficiently stable to not take part in any electrochemical reactions with solid lithium. Finally, the surface diffusion barrier of adsorbed lithium atoms was investigated. The barrier with and without the liquid crystals adsorbed to the surface was compared, which showed that the diffusion barrier was even higher with the molecules adsorbed.

Most ab initio simulation packages based on Density Functional Theory (DFT) use the Superposition of Atomic Densities (SAD) as a starting point of the self-consistent fi eld (SCF) iteration. However, this trial charge density without modeling atomic iterations nonlinearly may lead to a relatively slow or even failed convergence. This thesis proposes a machine learning-based scheme to improve the initial guess. We train a 3-Dimensional Convolutional Neural Network (3D CNN) to map the SAD initial guess to the corresponding converged charge density with simple structures. We show that the 3D CNN-processed charge density reduces the number of required SCF iterations at different unit cell complexity levels.

We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.

Ab initio Hartree-Fock and density functional theory calculations were carried out to investigate the structures, energies, and vibrational spectra of indole and two of its hydrogen migration tautomers. The calculated results of indole are in good agreement with experiments. Rotational constants and infrared spectral features of 2H-indole and 3H-indole are predicted to assist future experimental identification of the two tautomers. Transition states of unimolecular isomerization among the three tautomers are also optimized and activation barriers of the isomerization reactions evaluated. The results indicate that unimolecular indole → 3H-indole proceeds via 2H-indole with an activation barrier of 51 kcal/mol.

The molecular structures and vibrational spectra of Dewar benzene, benzvalene, trimethylenecyclopropane, prismane and 3,4-dimethylenecyclobutene have been investigated by density functional theory using Becke's exchange with Lee-Yang-Parr's correlation functional and the 6-31G* basis set. Both the calculated structural parameters and vibrational frequencies are in good agreement with available experimental data. On the basis of the agreement between the calculated and experimental results, assignments of fundamental vibrational frequencies of Dewar benzene, benzvalene, and trimethylenecyclopropane were examined and some reassignments are proposed. The calculations also predict prominent IR and Raman spectral features of prismane and 3,4-dimethylenecyclobutene, which can assist experimental identification of these compounds and the assignment of observed spectral features when they are available.