Atomistic modelling has widely been applied for studying structures and properties of materials. There are various methods to perform atomistic modelling. This master thesis presents a combined density functional theory (DFT) and cluster expansion (CE) study of Gd2O3 and Gd2O3-CeO2 interface (GCI) relevant for solid oxide fuel cells (SOFCs).    The energy differences (ΔE) of Va-O exchanges in C-type Gd2O3 and at GCI are calculated using both DFT and CE methods. We also calculated the migration energy (Emig) of Va jumps in Gd2O3 and at GCI by DFT. The comparison between the CE and DFT results demonstrates that the CE method provides a relatively accurate estimation of ΔE while it requires less computational resources. Furthermore, the CE method is used to study the Va migration in the vicinity of the Gd2O3-CeO2 interface. The potential energy landscapes of different types of paths are studied. / Atomistisk modellering har i stor utsträckning använts för att studera strukturer och  egenskaper  hos  material.  Det  finns  många  olika  metoder  för  att  utföra atomistisk   modellering.   Detta   masterprojekt   presenterar   en   kombinerad density functional theory (DFT) och   cluster expansion (CE) studie av Gd2O3- och Gd2O3-CeO2 gränssnittet (GCI), relevant för fastoxidbränsleceller (SOFC). Energiskillnaderna (ΔE) för Va-O-utbytet i C-typ Gd2O3 och vid GCI beräknas med   användning   av   både   DFT-   och   CE-metoder.   Vi   beräknade   också migrationsenergin   (Emig)   av   Va-hopp   i   Gd2O3   och   vid   GCI   med   DFT. Jämförelsen  mellan  CE  och  DFT-resultaten  visar  att  CE-metoden  ger  en relativt    noggrann    uppskattning    av ΔE    samt    att    den    kräver    mindre beräkningsresurser.   Vidare   används   CE-metoden   för   att   studera   Va- migrering  i   närheten   av   Gd2O3-CeO2-gränssnittet.   Det   potentiella   energilandskapet  för olika vägar studeras.

The growing interest of renewable fuel and energy sources has steadily increased over time due to climate changes. Research is being made around the world to find solutions for the different problems; one possible solution is to produce hydrogen gas to help phase out the usage of fossil fuels. So far, the technology for the hydrogen gas production is expensive for various reasons, one of the challenges is to minimize the energy usage for the production. Hydrogen could be used in fuel cells which can be used to fuel an electric car. In a fuel cell, hydrogen and oxygen gas are mixed to produce electrical energy as the main product, but it also forms thermal energy and water. Hydrogen gas can be produced from the reversed reaction; by electrolysis of water. This reaction requires energy and one way to minimize the energy usage for this is by using acatalyst. The goal with this master thesis was to see how the reaction rate of the oxygen evolution reaction can be affected by different single atom catalyst systems. The main structure for this catalyst in this thesis is aporphyrin molecule where different transition metals were tried as the active site. Different modifications on the structure were also made by exchanging some of the structures atoms and by adding different ligands.The purpose of this is to see how these modifications change the activity of the catalyst. The catalysts were optimized and calculated in a computational chemistry program called Gaussian 16. The calculations was made by using the DFT functional PBE0 and the basis sets Def2svp and Def2tzvpp. The results show that different modifications do affect the activity of the catalyst. The biggest variations in activity are from placing ligands under the active site while exchanging hydrogens to other substituents on the outer radial position can fine tune the results. The best active sites for this system came by using iridium, rhodium and cobalt which are all elements in group 9 of the periodic table. The lowest overpotential of 0.513 V was given by an iridium based system with four hydrogens exchanged by fluorides. / Runt om i världen finns ett ökat intresse för förnyelsebara energi och bränslekällor för att tackla klimat förändringarna. Stor del av forskningen som görs idag har i syfte att hitta nya lösningar för att minska klimatpåverkan i olika områden. Ett av forskningsområderna är hitta vägar till en miljövänligare vätgasproduktion där vätgasen skulle kunna användas i bränsleceller. Dessa celler kan sättas i elbilar och på så sätt fasa ut användingen av fossila bränslen. En av utmaningarna för vätgasproduktionen är att den idag är kostsam och kräver mycket energi. Forskare försöker hitta olika katalysatorer som kan minska energiåtgången som krävs vid elektrolys av vatten där syrgas och vätgas produceras. Målet med det här examensarbetet är att se hur en single atom catalyst kan påverka reaktionskinitiken för den syrgasbildande reaktionen vid elektrolys av vatten. Huvudstrukturen för katalysatorn som beräkningarna är gjorda på är en porphyrinmolekyl där olika övergångsmetaller kommer testas som det aktiva sätet i katalysatorn. Olika ligander kommer även tillsättas systemet samt utbyte av några väteatomer till olika substituenter i porfyrinstrukturen. Katalysatorn optimerades i det kvantkemiska beräkningsprogrammet Gaussian 16 med funktionalen PBE0 med basset Def2svp och Def2tzvpp. Resultaten visade att olika modifikationer på systemet hade en påverkan på katalysatorns aktivitet. Den största påverkan hade de olika liganderna som placerades under det aktiva sätet jämfört med de olika substituenterna. De bästa metallerna för katalysatorn var iridium, rhodium och kobolt vilket alla ligger i grupp nio i det periodiska systemet. Den lägsta överpotentialen på 0.513 V gavs av iridium systemet med fyra utbyta väten till fluor.

The goal of computational research in the fields of engineering, physics, chemistry or as a matter of fact in any field, is to study the properties of systems from the various principles available. In computational engineering, particularly in nano-scale simulations involving low-energy physics or chemistry, the goal is to model such structures and understand their properties from first principles or better known as \textit{Ab Initio} calculations. Geometry optimization is the basic component used in modeling molecules. The calculations involved are used to find the coordinates or the positions of the atoms of the molecule where it has the minimum energy and is hence stable. Efficient calculation of the forces acting on the atoms is the most important factor to be able to study the stable geometry of a molecule. In this thesis, the approach used begins with efficient electronic structure calculations using all electron calculations which paves the way for efficient force calculations. Kohn-Sham equations Density functional theory (DFT) are used to find the electron wave functions as accurately as possible using a finite element basis that introduces minimum errors in calculations. FEAST, a highly efficient density matrix based eigenvalue solver, is used to obtain accurate eigenvalues. Derivation of forces is done using the Hellmann-Feynman theorem. To find the minimum energy configuration of the system, Newton's iterative method is used that converges to the desired coordinates where the energy at the global minimum is found. The theory behind energy minimization and the calculations involved will be elaborated in this thesis and a method to move the atom in the existing framework will be discussed.

Many zeolites are deployed in various industrial processes owing to their robust catalytic performance and hydrothermal stability. Reactions in zeolites are catalyzed via framework aluminum. The Si/Al ratio is a metric that describes the relative aluminum content in zeolites. However, several researchers noted that the proximity of aluminum in the framework could impact the catalyst output [1–3]. In this work, the influence of paired acid sites is examined in ZSM-22. The 1-dimensional nature of ZSM-22 allows for direct assessment of aluminum proximity without the influence of channel intersection. Theoretical investigations via static density functional theory (DFT) optimization calculations on isolated and paired BAS in ZSM-22 revealed a potential increase in deprotonation potential energy (DPE), indicating a weaker acid with closer aluminum sites. One specific paired model, however, suggested stronger acid behavior, likely due to unfavorable proton-proton interactions influenced by proximity and orientation. Additionally, ammonia adsorption calculations inferred improved adsorption by isolated models, possibly due to unfavorable ammonium-proton interactions in the paired models. Reaction state calculations of ethylene and propylene oligomerization suggested enhanced stabilization of reactant molecules in paired sites. The synthesis of ZSM-22 showed sensitivity to precursor ratios and conditions, but pure samples were successfully achieved through iterative optimization. Catalytic testing of ethylene oligomerization with these samples, classified by their Si/Al ratios and unique fractions of paired acid sites, showed a correlation between higher fractions of paired BAS and increased catalytic activity and selectivity. Samples with higher fractions of paired BAS displayed a higher activity and selectivity for heavier hydrocarbons, explained by the enhanced adsorption capacity of paired BAS for larger reactant molecules, prompting further oligomerization and enhanced catalytic activity. Our findings demonstrate the impact of BAS proximity in dictating the activity and selectivity in ZSM-22 and provide valuable insights for designing more efficient industrial zeolite-based catalysts.

Thesis (Ph.D. (Physics)) -- University of Limpopo, 2017 / Density functional theory (DFT) study is employed in order to investigate the surfaces of, β-MnO2, β-TiO2 and β-VO2 (β-MO2) which act as catalysts in Li/Na-air batteries. Adsorption and co-adsorption of metal (Li/Na) and oxygen on (110) β-MO2 surface is investigated, which is important in the discharging and charging of Li/Na– air batteries. Due of the size of the supercell, and assuming that oxygen atoms occupy bulk-like positions around the surface metal atoms, only five values of (gamma) Γ are possible if constraint to a maximum of 1 monolayer (ML) of adatoms or vacancies: Γ= 0 surface is the stoichiometric surface, Γ= 1, 2 are the partially and totally oxidised surfaces, and Γ=-1, -2 are the partially and totally reduced surfaces. The manganyl, titanyl and vanadyl terminated surface is not the only surface that can be formed with Γ= +2. Oxygen can be adsorbed also as peroxo species (O2)2-, with less electron transfer from the surface vanadium atoms to the adatoms than in the case of manganyl and titanyl formation. The redox properties of the (110) surfaces are investigated by calculating the relative surface free energies of the non-stoichiometric compositions as a function of oxygen chemical potential. Increasing the temperature and lowering the pressure (i.e. more reducing conditions) we find the stoichiometric surface reduces first partially and then entirely at higher temperatures. The lithium orientation between two bridging oxygen and in-plane oxygen (bbi) orientation is much more stable for the three metal oxides, thus lithium generally prefers to adsorb where it will be triply coordinated to two bridging oxygens and one in-plane oxygen atom. However, sodium prefers to orientate itself on the bridging oxygen on the surface, but a triple coordination on sodium is also favourable. Oxygen adsorption on Li/MO2 was simulated and it was found that in all ii the metal oxides (MnO2, TiO2 and VO2) the most stable orientation is the dissociated composition where there is an oxygen atom on the “bulk-like” positions on top of each of the M cations. The surface lithium peroxide for MO2 simulated produces clusters with oxygen - oxygen bond lengths that are comparable to the calculated bulk and monomer discharge products reported in literature. Adsorption of oxygen on Na/MO2 was investigated and it was observed that the catalysts used encourage formation of the discharge product reported in literature, i.e. NaO2. The surface NaO2 appears to have comparable bond lengths to the calculated bulk and monomer NaO2. / National Research Foundation, South African Research Chair Initiative of the Department of Science Technology and Department of Energy storage Programme

Covalent SP3-hybridization defects in single-walled carbon nanotubes (CNTs) have been prevalent in recent experimental and theoretical studies for their interesting photophysical properties. These systems are able to act as excellent sources of single, infrared photons, even at room temperature, making them marketable for applications to sensing, telecommunications, and quantum information. This work was motivated by recent experimental studies on controllable defect placement and concentration as well as investigating carrier multiplication (CM) using DFT-based many-body perturbation theory (MBPT) methods to describe excitonic relaxation processes. We find that pristine CNTs do not yield appreciable MEG at the minimum threshold of twice the optical gap 2Eg, but covalent functionalization allows for improved MEG at the threshold. Finally, we see that defect-defect interactions within CNT systems can be modeled simply as HJ-aggregates in an effective Hamiltonian model, which is shown to be valid for certain, highly-redshifted defect configurations at low defect-defect separation lengths.

Complementing electronic components with molecular analogs is a promising alternative to further miniaturization of conventional silicon electronic devices in the quest to achieve functional molecular nanoscale circuit elements. To this end, molecular units have been widely investigated to evaluate their suitability for future nanoelectronic circuit applications. Previous work has typically either focused on tightly packed layers of dithiol molecule-encapsulated gold nanoparticles or small oligomeric structures comprised of nanoparticles linked by a few dithiol molecules. In this thesis, we study the electrical and electronic properties of metal-molecular networks having an intermediate number of dithiol molecules both theoretically and experimentally. Electronic transport through self-assembled networks with tunable thiol molecule: gold nanoparticle ratios (ranging from 1:1 to 50:1) is studied using two-terminal electrical characterization techniques. The tunability of the electrical properties (e.g., resistance, current etc.) of the molecular networks on modifying the thiol molecule: gold nanoparticle ratios and/or type of molecule used was observed. Specifically, the current in the molecular networks studied typically decreased with increasing molecule: AuNP. For example, in gold-benzenedithiol molecular networks with approximately the same length-to-width ratios, current at low bias, 0.3 V, was found to decrease from the μA range in 1:1 ratio samples to the nA range in 50:1 samples. Additionally, many gold-benzenedithiol molecular networks which had linear I-V characteristics at low biases displayed nonlinearities in their I-Vs at higher biases. In such cases, the nonlinearities in the I-Vs at higher biases became more pronounced with increasing molecule: AuNP ratio. For example, in a control sample, consisting of only gold nanoparticles, linear I-V behaviour was observed, while the 50:1 gold-benzenedithiol molecular network displayed NDR with a measured peak-to-valley ratio of approximately 1.52. A linear resistor circuit model provided accurate approximations of the low bias I-V behaviour of the molecular networks. Experimental studies were complemented with first principles density functional theory-based simulations of the molecular networks. Linear chains and branched networks of interconnected benzenedithiol molecules and Au6 clusters were the systems of interest in this study. Calculated current-voltage characteristics of the metal-molecular networks exhibited nonlinearities and rectification with negative differential resistance (NDR) peaks that became more pronounced with increasing chain length of the linear chains. Peak-to-valley current NDR ratios as large as ~ 500 and rectification ratios of ~ 10 (0.25 V) were shown for linear and branched circuit elements, respectively, illustrating how charge transport through molecular-scale devices could be controlled with precision by modifying the structure and geometry of molecule-nanoparticle networks. Observed nonlinearities (e.g., NDR, hysteresis, and rectification) in the I-Vs of the self-assembled metal-molecular networks studied highlight their potential for application as circuit elements in future nanoelectronic devices and circuits, including memory, logic, switching and sensing. Additionally, the device level physical randomness and imperfections induced during fabrication of the metal-molecular networks, as well as the variability of the resistance of the networks on modifying the molecule: gold nanoparticle ratios can be applied for generating random binary sequences. / Graduate

The mechanism of RAPRENOx reactions - RAPid REduction of Nitrogen Oxides using Isocyanic acid - proposed by Robert A. Perry1 in an attempt to help control the emission of nitrogen oxides pollutant into the atmosphere, has been re-investigated theoretically. The study of reaction mechanisms was carried out using Chemist software2. All mathematically possible elementary steps have been evaluated and the chemically reasonable ones have been considered to propose new sets of reaction mechanisms. Density Functional Theory (B3LYP/6-31 G**) calculations using Gaussian 983 were made in order to study the relative energies of all species and to predict the energy barrier of each elementary step. As a consequence of our study, there are two more sets of reaction mechanisms (in addition to Perry’s mechanism), that could be possible for the propagation step of RAPRENOx process.

Melatonin (N-acetyl-5-methoxytryptamin, MLT) is a naturally occurring antioxidant which has shown some potential for use as a spin trap. Spin traps react with short lived hydroxyl radicals (HO·) to produce more stable products called spin adducts which may be characterized by electron paramagnetic resonance spectroscopy. However, the relative stability of hydroxyl spin adducts of melatonin derivatives (MLTD) compared to 2-hydroxymelatonin (HO-MLT) has not been examined computationally. Computational studies have been done on four selected MLTD; methylmelatonin (Me-MLT), chloromelatonin (Cl-MLT), cyanomelatonin (CN-MLT), and nitromelatonin (NO2-MLT). Geometry of the structures were optimized at the HF/6-31G(d), cc-pVXZ, (X=D and T) and DFT/B3LYP/6-31G(d), cc-pVDZ and cc-pVTZ levels of theory and extrapolated to the complete basis set limit using cc-pVXZ (X=D, T) basis sets. The lowest relative energy was found to be a mix of results for 2-OH-MLT-Me at HF and 2-OH-MLT-NO2 at DFT.

Topological materials have discovered ultrahigh magnetoresistance, chiral anomalies, the inherent anomalous Hall effect, and unique Fermi arc surface states. Topological materials now include insulators, metals, and semimetals. Weyl semimetals (WSM) are topological materials that show linear dispersion with crossings in their band structure which creates the pair of Weyl nodes of opposite chirality. WSMs have topological Fermi arc surface states connecting opposing chirality Weyl nodes. Spin-orbit coupling can result in the band opening in Dirac nodal rings, and creating the pair of Weyl nodes either by breaking the time-reversal or spatial inversion symmetry (but not both) 1-3. The chirality of a Weyl node is set by the Berry flux through a closed surface in reciprocal space around it. The purpose of this thesis was to characterize and investigate the thermodynamic stability of WSM. To accomplish these goals, quantum mechanical modeling at the level of density functional theory (DFT) was used. WloopPHI, a Python module, integrates the characterization of WSMs into WIEN2k, a full-potential all-electron density functional theory package. It calculates the chirality of the Weyl node (monopole charge) with an enhanced Wilson loop method and Berry phase approach. First, TaAs, a well-characterized Weyl semimetal, validates the code theoretically. We then used the approach to characterize the newly discovered WSM YRh6Ge4, and we found a set of Weyl points into it. Further, we study the stability of the kagome-based materials A3Sn2S2, where A is Co, Rh, or Ru, in the context of the ternary phase diagrams and competing binary compounds using DFT. We demonstrated that Co3Sn2S2 and Rh3Sn2S2 are stable compounds by examining the convex hull and ternary phase diagrams. It is feasible to synthesize Co3Sn2S2 by a chemical reaction between SnS, CoSn and Co9S8. Moreover, Rh3Sn2S2 can be produced by SnS, RhSn and Rh3S4. On the other hand, we found that Ru3Sn2S2 is a thermodynamically unstable material with respect to RuS2, Ru3S7 and Ru. Our work provides some insights for confirming materials using the DFT approach. 1. S. M. Young et al. Dirac Semimetal in Three Dimensions. Physical Review Letters108(14) (2012), 140405. 2. J. Liu and D. Vanderbilt. Weyl semimetals from noncentrosymmetric topological insulators. Physical Review B 90(15) (2014), 155316. 3. H. Weng et al. Weyl Semimetal Phase in Noncentrosymmetric Transition-Metal Monophosphides. Physical Review X 5(1) (2015), 011029. / Thesis / Master of Applied Science (MASc)