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Zugl.: Frankfurt (Main), University, Diss., 2008.

Iron containing metalloenzymes are an extremely important class of biocatalysts conserved throughout evolution because of their vital role in the biochemistry of life. Here we discuss a specific class of these enzymes that use molecular oxygen binding to enable there activity. We also attempt to describe synthetic analogues whose chemistry is based on that seen in those natural systems. This dissertation will highlight how computational research can illuminate specific aspects of the reaction mechanisms that these systems catalyse, which in many cases are unable to be understood purely experimentally. We report on two combined QM/MM and density functional theory (DFT) projects, which describe the AlkB demethylation enzyme and the SyrB2 halogenase; both highlight the strengths and weaknesses of each method. Our DFT work on an i-propyl-bis(imino)pyridine, an equatorial tridentate ligand, developed by one of the papers’ co-authors (Badiei, Siegler et al. 2011) exampifies superoxo chemistry based on the dioxygenases. Our other projects focus on monooxygenase catalysed chemistry one based on the biomimic [FeIV(O)(TPA)Cl]+ reports on a halogenase mimic that shows exciting chemoselectivity in halogenation vs. hydroxylation. I also report on publications examining two other biomimetic ligands. A imido-bridged diiron-oxo phtalocyanine complex capable of hydroxylating methane and a nonheme iron system which gives us a good deal of insight into the effects of secondary coordination sphere chemistry [FeII(N4Py2Ph)(NCCH3)](BF4)2. My computational studies have given insight into the chemical properties of metal-oxo oxidants and their reactivity patterns with substrate and have been utilized to explain experimentally observed data.

In this study, the novel, reaction energy profile-fragment attributed molecular system energy change (REP-FAMSEC) was applied in studying mechanisms of chemical reactions. The applicability of the REP-FAMSEC protocol was tested for the mechanism of proline catalysed aldol reaction whereby several possible mechanisms have been debated for the past four decades. The approach quantifies and explains energy changes for each successive step along with the reaction profile. It mainly uses interaction energies between meaningful polyatomic fragments of a molecular system and generates energy contribution made by each fragment of a molecule. The fragments or atoms driving or opposing a change can easily be discovered and the reason for their (un)reactivity can be established. The relative stability and catalytic behaviour of (S) proline conformers including the zwitterion were fully explained at an atomic and molecular level. Though the zwitterion becomes the most dominant conformer in dimethyl sulfoxide (DMSO) solvent, it is not the active catalyst in proline catalysis. It forms very weak interactions with the ketone donor and will not form the active enamine catalyst. The study shows that the first step of the catalytic reaction which was coined as the C–N bond formation using classical techniques, cannot be explained using the interaction of the N–,C+ atom pair but rather by the interaction of O-atom of acetone and the acidic H-atom of proline. Hence the first step is best described as the C–N bond formation/1st H-transfer. Based on this initial interaction the lowest energy conformer of proline is eliminated as a catalyst. When the REP is explored in the presence of an explicit solvent molecule of DMSO, FAMSEC shows that molecules of proline conformers (lowest 1a and higher energy 1b), acetone 2, and DMSO 3 are involved in strong intermolecular interactions when they form 3-molecular complexes (3-MCs). The interactions formed by the molecule of DMSO weaken interactions between 1a and 2 while strengthening those between 1b and 2, thereby eliminating 1a as an inactive catalyst. The zwitterion which becomes the most dominant in DMSO is converted to conformer 1a through a low energy barrier intramolecular proton transfer. When formed conformer 1a undergoes a puckering of the pyrrolidine ring resulting in its conversion to the catalytically active conformer 1b. The presence of a molecule of acetone, DMSO, or a combination of the two molecules facilitates the structural change of proline from conformer 1a to 1b. This shows that there is no need to adhere to a specific sequence of reagent addition in proline catalysis. During the formation of the active enamine catalyst from an initial imine, it was found that the molecule of the eliminated water acts as a medium for proton transfer relay while interaction involving the solvent molecule of DMSO is essential for decreasing the energy barrier and stabilising the resulting enamine catalyst. / Thesis (PhD)--University of Pretoria, 2020. / Chemistry / PhD / Unrestricted

Since the development of the correlation consistent composite approach (ccCA) in 2006, ccCA has been shown to be applicable across the periodic table, producing, on average, energetic properties (e.g., ionization potentials, electron affinities, enthalpies of formation, bond dissociation energies) within 1 kcal/mol for main group compounds. This dissertation utilizes ccCA in the investigation of several chemical systems including nitrogen-containing compounds, sulfur-containing compounds, and carbon dioxide complexes. The prediction and calculation of energetic properties (e.g., enthalpies of formation and interaction energies) of the chemical systems investigated within this dissertation has led to suggestions of novel insensitive highly energetic nitrogen-containing compounds, defined reaction mechanisms for sulfur compounds allowing for increased accuracy compared to experimental enthalpies of formation, and a quantitative structure activity relationship for altering the affinity of CO2 with substituted amine compounds. Additionally, a study is presented on the convergence of correlation energy and optimal domain criteria for local Møller–Plesset theory (LMP2).

<p> Partition Density Functional Theory (P-DFT) is a quantum chemistry method in which the system is fragmented into non-interacting components, and the energy is given by functionals of the fragment densities. The method is unique in the sense that it corrects for density functional approximation errors and sheds light on the individual structure of fragments within a molecule. In this work, we discuss the fundamental aspects of the theory as well as its challenges, and we introduce two software packages that were written to advance the understanding and applicability of the theory. The first, n2v focuses on the numerical procedure to obtain a potential that generates a given density, and the second, pyCADMium performs very accurate P-DFT calculations in diatomic molecules. Both packages are fully open-source and thus can be used and repurposed with any intention. We hope that these advances can be used to develop everyday embedding calculations. </p>

Quantum revolution has a great potential to impose massive impact on information technology. Point defects in solid-state materials such as NV center in diamond have been demonstrated to be promising qubit candidates. Defect levels in band gaps are analogous to molecular orbitals, serving as an excellent platform for quantum applications. Atomically thin two-dimensional materials are under the spotlight in recent years, as the sheet-like geometry brings advantages for operations of quantum defects. That includes the realization of patterned qubit fabrication, operation at room temperature, and improvement of coherence time through a highly-efficient isotope purification process. Although using point defects in 2D materials is a promising route toward quantum applications, searching for viable defects satisfying the criteria of magneto-optical properties for quantum applications is challenging. Thanks to the continued development of density functional theory, sophisticated multi-electron systems can be accurately simulated on the atomistic level to evaluate multiple ground-state properties, including total energy, magnetic polarization, and atomic orbitals. In addition to that, implementing constrained DFT renders the insight of excited-state properties. Benefited from the application of data-science tools in material science, we are now capable of performing data-driven analysis based on high-throughput computational techniques, including data mining/storage and automatic discovery workflow. Adopting the above tools and physical-principle-enabled symmetry analysis, we are able to identify a large set of quantum defects in a vast material space. We show that antisite defects in 2D transition metal dichalcogenides (TMDs) can provide a general platform for controllable solid-state spin qubit systems. Using high-throughput atomistic simulations that are enabled by a symmetry-based hypothesis, we identify several neutral antisite defects in TMDs that create defect levels deep in the bulk band gaps and host a paramagnetic triplet ground state. Our in-depth analysis reveals the presence of optical transitions and triplet-singlet intersystem crossing processes for fingerprinting these defect qubits. Finally, as an illustrative example, we discuss the initialization and readout principles of an antisite qubit in WS2, which is expected to be stable against interlayer interactions in a multilayer structure for qubit isolation and protection in future qubit-based devices. Motivated by the insight gained from the study of antisite defect qubits in TMDs, we significantly expanded the searching domain to all the binary 2D materials. As mentioned above, searching for defects with triplet ground states is one of the most crucial steps to identify more quantum defects that support multiple quantum functionalities. We design a comprehensive workflow for screening promising quantum defects based on the site-symmetry-based hypothesis. The discovery efforts reveal that the symmetry-enabled discovery workflow of quantum defects significantly increases the probability of finding triplet defects. To identify multiple functionalities for these quantum defects, including qubits and quantum emitters, the magneto-optical properties of triplet defects are comprehensively calculated. We demonstrate that 45 antisite defects in the various hosts, including post-transition metal monochalcogenides (PTMCs) and transition metal dichalcogenides (TMDs) are promising quantum defects. Most importantly, we propose that 16 antisites (both anion and cation based) in PTMCs can serve as the most promising quantum defect platform based on 2D materials, due to their well-defined defect levels, optimal magneto-optical properties, and the availability of host materials. This set of data-driven discovery efforts opens a new pathway for creating scalable, room-temperature spin qubits in 2D materials, including TMDs, PTMCs, and beyond. The comprehensive defect data created in this work, combined with experimental verification and demonstration in the future, will eventually lead to the fertilization of a 2D defect design platform that facilitates the design of point defects in 2D material families for multiple quantum functionalities, including quantum emitters, quantum sensor, transductor, and more. / Physics

Atmospheric aerosols are made up of suspended liquids and solids in the atmosphere. These aerosols play a very important role in the solar energy exchange in Earth’s atmosphere as well have dramatic impact on human health. Different aerosols have different effects on the atmosphere depending on the physical properties of the aerosols. The purpose of this research project is to understand how the structure of molecular chromophores impacts the solar absorption properties of aerosols. We propose a series of laboratory studies to investigate the outcomes from solar absorption of brown carbon chromophores: 1-phenylpyrrole, 2-phenyl-1-H-pyrrole, 2-phenylimadazole, as well as water complexes. Ultimately, we aim to reveal molecular-level insights into solar absorption processes of aerosols. Many forms of experimental analysis were performed on the compounds of interest. UV-Vis spectroscopy and fluorescence spectroscopy were used to provide useful information for further analysis such as the region in which the compound fluoresces and the compounds affinity to water for water complex analysis. These compounds were further analyzed using resonant two-photon ionization (R2PI) spectroscopy and computational methods to determine structural characteristics of the compounds with and without water complexes.

Kohn-Sham density functional theory is a widely-used method to predict the ground-state total energies and densities of interacting correlated electrons in atoms, molecules, clusters, solids, and liquids. In principle, exact results for these properties can be found by solving self-consistent one-electron Schrödinger equations based upon density functionals for the energy. In practice, the density functional for the exchange-correlation contribution to the energy must be approximated for the sake of computational efficiency. More accurate but still computationally efficient approximations are being developed by the satisfaction of exact constraints. These include the SCAN (strongly constrained and appropriately normed) semi-local density functional. We used the pressure induced structural phase transition of solids to validate SCAN. To predict an accurate critical pressure, a method must account for a small energy difference between close-lying phases which have very different electronic structures. We computed the critical pressure for the structural phase transition of 25 group IV, III-V, and II-VI compounds using the local density approximation (LDA), Perdew-Burke-Ernzerhof (PBE), and SCAN. LDA systematically underestimates the critical pressures as reported in a previous study. PBE which often improves upon LDA performances yields under- or overestimated pressures in many cases. SCAN, on the other hand, predicts accurate critical pressures with an accuracy comparable to the computationally expensive methods like the quantum Monte Carlo (QMC), random phase approximation (RPA), and the hybrid functional HSE06, in the cases where pressures with these methods are reported. The impressive success of the approximate density functionals, however, comes at a price. There is an incomplete cancellation of the hartree and approximate exchange energies for one-electron densities, giving rise to a spurious interaction of an electron with itself. This is called the self-interaction error (SIE). Perdew-Zunger self-interaction correction (PZ SIC) makes an approximate density functional SIE free for all one-electron density. The transition states, which involve stretched bonds, are poorly described by the semilocal density functionals. Thus LDA, PBE, and SCAN predict too low barrier height for a chemical reaction. We tested the Perdew-Zunger self-interaction correction (PZ SIC) for the barrier heights of the representative test set BH6. We found that the barrier heights are greatly improved when we go from LDA to PBE to SCAN. We also tested the PZ SIC for the atomization energies of the molecular test set AE6. SCAN predicts very accurate atomization energies, whereas SCAN-SIC severely worsens the atomization energies. We attribute such worsening to the noded localized orbitals, over which the PZ energy is minimized. The nodality of the orbital density is a consequence of the orthogonality criterion for overlapping real orbitals, and this nodality increases when free atoms bind to form a molecule. This explains why the error in the atomization energies is reduced when the PZ energy is minimized using complex orbitals, which yield nodeless orbital densities. The complex orbitals, however, do not completely eliminate the error. The remaining error is attributed to the fact that PZ SIC loses the exactness of LDA, PBE, or SCAN for densities that vary slowly over space, calling for a generalization of the PZ theory. / Physics

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