This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed. In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered. The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations. At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.

In recent years, the potential benefits of high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking, since proteins are sophisticated structures with complicated interactions for which either molecule might reshape itself. Even the very limited flexibility model to be considered here, using ligand conformation ensembles, requires six dimensions of exploration - three translations and three rotations - per rigid conformation. The functions for evaluating pose suitability can also be complex to calculate. Consequently, the programs being written for these biochemical simulations are extremely resource-intensive. This work introduces a pure computer science approach to the field, developing techniques to improve the effectiveness of such tools. Their architecture is generalized to an abstract pattern of nested layers for discussion, covering scoring functions, search methods, and screening overall. Based on this, new stratagems for molecular docking software design are described, including lazy or partial evaluation, geometric analysis, and parallel processing implementation. In addition, a range of novel algorithms are presented for applications such as active site detection with linear complexity (PIES) and small molecule shape description (PASTRY) for pre-alignment of ligands. The various stratagems are assessed individually and in combination, using several modified versions of an existing docking program, to demonstrate their benefit to virtual screening in practical contexts. In particular, the importance of appropriate precision in calculations is highlighted.

<div><div><div><p>Pincer ligands are a cornerstone of modern transition metal catalysis. An increasing interest in bimetallic catalysis motivated us to develop binucleating variants of these mononucleating ligands. Expanded variants of the PDI and PyBOX ligands were targeted, leading to the development of the Naphthyridine Diimine (“NDI”) and Naphthyridine Bisoxazoline (“NapBOX”) ligands, respectively. Metalation of NDI with appropriate metal precursors yielded Fe2, Co2 and Ni2 complexes which exhibited unique stoichiometric and catalytic reactivity. Metalation of the NapBOX ligand with nickel carboxylate salts yielded Ni2 complexes which were capable of catalyzing an asymmetric intermolecular [4+1] cycloaddition reaction between 1,1-dichloroalkene-derived vinylidenes and 1,3-dienes. Each of these processes were studied experimentally and computationally in order to understand the fundamental reactivity of organic substrates across metal-metal bonds.</p></div></div></div>

This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed. In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered. The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations. At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.

<p> Radical species are essential in modern chemistry. In addition to fundamental chemistry, their unique chemical bonding and distinct physicochemical features serve critical functions in materials science in the form of organic electronics. Due to their high reactivity, radicals of the main group element are often transient. In recent years, remarkably stable radicals are often stabilized by π-delocalization, sterically demanding side groups, carbenes, and weakly coordinating anions. The impacts of modifications such as electron-donating, electron-withdrawing, and end-capping on the spin density distribution and thermodynamic and kinetic stability of archetypal radical-driven processes such as dimerization are not well understood. This dissertation aims to track the perturbation of spin density from EDG and EWG modifications, provide mechanistic insight into the radical-initiated reactions of conjugated radical cations, and establish correlations between molecular design and thermochemical properties and their resulting kinetic stability by computationally evaluating these characteristics against experimental data. The disclosed connections give useful new recommendations for the rational design of thermodynamically and kinetically stable novel materials.</p>

Advances in the knowledge of chemical structure of coal and development of high performance computational techniques led to more than hundred and thirty four proposed molecular level representations (models) of coal between 1942 and 2010. These models were virtually on the carboniferous coals from the northern hemisphere. There are only two molecular models based on the inertinite- and vitrinite-rich coals from the southern hemisphere. The current investigation is based on the chars derived from the Permian-aged coals in two major South African coalfields, Witbank #4 seam and Waterberg Upper Ecca. The two coals were upgraded to 85 and 93% inertinite- and vitrinite-rich concentrates, on visible mineral matter free basis. The coals were slow heated in inert atmosphere at 20 ℃ min-1 to 450, 700 and 1000 ℃ and held at that temperature for an hour. After the HCl-HF treatment technique at ambient temperatures, the characteristics of the coals and chars were examined with proximate, ultimate, helium density, porosity, surface area, petrographic, solid-state 13C NMR, XRD and HRTEM analytical techniques. The results largely showed that substantial transitions occurred at 700-1000 ℃, where the chars became physically different but chemically similar. Consequently, the chars at the highest temperature (1000 ℃) drew attention to the detailed study of the atomistic properties that may give rise to different reactivity behaviours with CO2 gas. The H/C atomic ratios for the inertinite- and vitrinite-rich chars were respectively 0.31 and 0.49 at 450 ℃ and 0.10 and 0.12 at 1000 ℃. The true density was respectively 1.48 and 1.38 g.cm-3 at 450 ℃ and 1.87 and 1.81 g.cm-3 at 1000 ℃. The char form results from the petrographic analysis technique indicated that the 700-1000 ℃ inertinite-rich chars have lower proportions of thick-walled isotropic coke derived from pure vitrinites (5-8%) compared with the vitrinite-rich chars (91-95%). This property leads to the creation of pores and increases of volume and surface area as the softening walls expand. It was found that the average crystallite diameter, La, and the mean length of the aromatic carbon fringes from the XRD and HRTEM techniques, respectively, were in good agreement and made a definite distinction between the 1000 ℃ inertinite- and vitrinite-rich chars. The crystallite diameter on peak (10) approximations, La(10), of 37.6Å for the 1000 ℃ inertinite-rich chars fell within the HRTEM’s range of minimummaximum length boundary of 11x11 aromatic fringes (27-45Å). The La (10) of 30.7Å for the vitrinite-rich chars fell nearly on the minimum-maximum length range of 7x7 aromatic fringes (17-28Å.) The HRTEM results showed that the 1000 ℃ inertinite-rich chars comprised a higher distribution of larger aromatic fringes (11x11 parallelogram catenations) compared with a higher distribution of smaller aromatic fringes (7x7 parallelogram catenations). The mechanism for the similarity between the 700-1000 ℃ inertinite- and vitrinite-rich chars was the greater transition occurring in the vitrinite-rich coal to match the more resistant inertinite-rich coal. This emphasised that the transitions in the properties of vitrinite-rich coals were more thermally accelerated than those of the inertinite-rich coals. The similarity between the inertinite- and vitrinite-rich chars was shown by the total maceral reflectance, proximate, ultimate, skeletal density and aromaticity results. Evidence for this was the carbon content by mass for the inertinite- and vitrinite-rich chars of respectively 90.5 and 85.3% at 450 ℃ and 95.9 and 94.1% at 1000 ℃. The aromaticity from the XRD technique was respectively 87 and 77% at 450 ℃ and 98 and 96% at 1000 ℃. A similar pattern was found in the hydrogen and oxygen contents, the atomic O/C ratios and the aromaticity from the NMR technique. The subsequent construction of large-scale molecular structures for the 1000 ℃ inertinite-rich chars comprised 106 molecules constructed from a total of 42929 atoms, while the vitrinite-rich char model was made up of 185 molecules consisting of a total of 44315 atoms. The difference between the number of molecules was due to the inertinite-rich char model comprising a higher distribution of larger molecules compared with the vitrinite-rich char model, in agreement with the XRD and HRTEM results. These char structures were used to examine the behaviour on the basis of gasification reactivity with CO2. The density functional theory (DFT) was used to evaluate the interactions between CO2 and the atomistic representations of coal char derived from the inertinite- and vitrinite rich South African coals. The construction of char models used the modal aromatic fringes (fringes of highest frequencies in size distributions) from the HRTEM, for the inertinite- and vitrinite-rich chars, respectively (11x11 and 7x7 parallelogram-shaped aromatic carbon rings). The structures were DFT geometrically optimized and used to measure reactivity with the Fukui function, f+(r) and to depict a representative reactive carbon edge for the simulations of coal gasification reaction mechanism with CO2 gas. The f+(r) reactivity indices of the reactive edge follows the sequence: zigzag C remote from the tip C (Czi = 0.266) > first armchair C (Cr1 = 0.087) > tip C (Ct = 0.075) > second armchair C (Cr2 = 0.029) > zigzag C proximate to the tip C (Cz = 0.027). The DFT simulated mean activation energy, ΔEb, for the gasification reaction mechanism (formation of second CO gas molecule) was 233 kJ mol-1. The reaction for the formation of second CO molecule is defines gasification in essence. The experimental activation energy determined with the TGA and random pore model to account essentially for the pore variation in addition to the gasification chemical reaction were found to be very similar: 191 ± 25 kJ mol-1 and 210 ± 8 kJ mol-1; and in good agreement with the atomistic results. The investigation gave promise towards the utility of molecular representations of coal char within the context of fundamental coal gasification reaction mechanism with CO2. / PhD (Chemical Engineering), North-West University, Potchefstroom Campus, 2015

Advances in the knowledge of chemical structure of coal and development of high performance computational techniques led to more than hundred and thirty four proposed molecular level representations (models) of coal between 1942 and 2010. These models were virtually on the carboniferous coals from the northern hemisphere. There are only two molecular models based on the inertinite- and vitrinite-rich coals from the southern hemisphere. The current investigation is based on the chars derived from the Permian-aged coals in two major South African coalfields, Witbank #4 seam and Waterberg Upper Ecca. The two coals were upgraded to 85 and 93% inertinite- and vitrinite-rich concentrates, on visible mineral matter free basis. The coals were slow heated in inert atmosphere at 20 ℃ min-1 to 450, 700 and 1000 ℃ and held at that temperature for an hour. After the HCl-HF treatment technique at ambient temperatures, the characteristics of the coals and chars were examined with proximate, ultimate, helium density, porosity, surface area, petrographic, solid-state 13C NMR, XRD and HRTEM analytical techniques. The results largely showed that substantial transitions occurred at 700-1000 ℃, where the chars became physically different but chemically similar. Consequently, the chars at the highest temperature (1000 ℃) drew attention to the detailed study of the atomistic properties that may give rise to different reactivity behaviours with CO2 gas. The H/C atomic ratios for the inertinite- and vitrinite-rich chars were respectively 0.31 and 0.49 at 450 ℃ and 0.10 and 0.12 at 1000 ℃. The true density was respectively 1.48 and 1.38 g.cm-3 at 450 ℃ and 1.87 and 1.81 g.cm-3 at 1000 ℃. The char form results from the petrographic analysis technique indicated that the 700-1000 ℃ inertinite-rich chars have lower proportions of thick-walled isotropic coke derived from pure vitrinites (5-8%) compared with the vitrinite-rich chars (91-95%). This property leads to the creation of pores and increases of volume and surface area as the softening walls expand. It was found that the average crystallite diameter, La, and the mean length of the aromatic carbon fringes from the XRD and HRTEM techniques, respectively, were in good agreement and made a definite distinction between the 1000 ℃ inertinite- and vitrinite-rich chars. The crystallite diameter on peak (10) approximations, La(10), of 37.6Å for the 1000 ℃ inertinite-rich chars fell within the HRTEM’s range of minimummaximum length boundary of 11x11 aromatic fringes (27-45Å). The La (10) of 30.7Å for the vitrinite-rich chars fell nearly on the minimum-maximum length range of 7x7 aromatic fringes (17-28Å.) The HRTEM results showed that the 1000 ℃ inertinite-rich chars comprised a higher distribution of larger aromatic fringes (11x11 parallelogram catenations) compared with a higher distribution of smaller aromatic fringes (7x7 parallelogram catenations). The mechanism for the similarity between the 700-1000 ℃ inertinite- and vitrinite-rich chars was the greater transition occurring in the vitrinite-rich coal to match the more resistant inertinite-rich coal. This emphasised that the transitions in the properties of vitrinite-rich coals were more thermally accelerated than those of the inertinite-rich coals. The similarity between the inertinite- and vitrinite-rich chars was shown by the total maceral reflectance, proximate, ultimate, skeletal density and aromaticity results. Evidence for this was the carbon content by mass for the inertinite- and vitrinite-rich chars of respectively 90.5 and 85.3% at 450 ℃ and 95.9 and 94.1% at 1000 ℃. The aromaticity from the XRD technique was respectively 87 and 77% at 450 ℃ and 98 and 96% at 1000 ℃. A similar pattern was found in the hydrogen and oxygen contents, the atomic O/C ratios and the aromaticity from the NMR technique. The subsequent construction of large-scale molecular structures for the 1000 ℃ inertinite-rich chars comprised 106 molecules constructed from a total of 42929 atoms, while the vitrinite-rich char model was made up of 185 molecules consisting of a total of 44315 atoms. The difference between the number of molecules was due to the inertinite-rich char model comprising a higher distribution of larger molecules compared with the vitrinite-rich char model, in agreement with the XRD and HRTEM results. These char structures were used to examine the behaviour on the basis of gasification reactivity with CO2. The density functional theory (DFT) was used to evaluate the interactions between CO2 and the atomistic representations of coal char derived from the inertinite- and vitrinite rich South African coals. The construction of char models used the modal aromatic fringes (fringes of highest frequencies in size distributions) from the HRTEM, for the inertinite- and vitrinite-rich chars, respectively (11x11 and 7x7 parallelogram-shaped aromatic carbon rings). The structures were DFT geometrically optimized and used to measure reactivity with the Fukui function, f+(r) and to depict a representative reactive carbon edge for the simulations of coal gasification reaction mechanism with CO2 gas. The f+(r) reactivity indices of the reactive edge follows the sequence: zigzag C remote from the tip C (Czi = 0.266) > first armchair C (Cr1 = 0.087) > tip C (Ct = 0.075) > second armchair C (Cr2 = 0.029) > zigzag C proximate to the tip C (Cz = 0.027). The DFT simulated mean activation energy, ΔEb, for the gasification reaction mechanism (formation of second CO gas molecule) was 233 kJ mol-1. The reaction for the formation of second CO molecule is defines gasification in essence. The experimental activation energy determined with the TGA and random pore model to account essentially for the pore variation in addition to the gasification chemical reaction were found to be very similar: 191 ± 25 kJ mol-1 and 210 ± 8 kJ mol-1; and in good agreement with the atomistic results. The investigation gave promise towards the utility of molecular representations of coal char within the context of fundamental coal gasification reaction mechanism with CO2. / PhD (Chemical Engineering), North-West University, Potchefstroom Campus, 2015

This thesis presents an experimental and theoretical study of the collision dynamics of OH(A²Σ⁺) with Kr and Xe. These two systems both exhibit a significant degree of electronically non-adiabatic behaviour, and a particular emphasis of the work presented here is to characterise the competition and interplay between electronic quenching on the one hand, and electronically adiabatic collisional processes on the other. Quenching takes place close to the bottom of the deepest potential well for both systems. In collisions that remain in the excited electronic state, this same region of the potential is also largely responsible for rotational energy transfer (RET) and the collisional depolarisation of angular momentum. Therefore, the direct competition between these processes suppresses the cross-sections for RET and collisional depolarisation from their expected value in the absence of quenching. To investigate this, experiments were carried out to measure cross-sections for the collisional transfer of electronic, vibrational and rotational energy in OH(A, v=0,1) + Kr and OH(A, v=0) + Xe. In addition, measurements were made of the j-j' correlation -- that is, the relationship between the angular momentum of the OH radical before and after a collision -- in collisions with Kr and Xe, using the experimental technique of Zeeman quantum beat spectroscopy. Collisions with both Kr and Xe tend to effectively depolarise the angular momentum of the OH radical, due to the very anisotropic character of the potential on which the process occurs. Electronic quenching, which plays an essential role in both systems, is more prevalent with xenon as the crossing to the ground state potential is located in a more accessible location. These experimental results were compared with single surface quasi-classical trajectory (QCT) calculations, where the overestimate of rotational energy transfer or collisional depolarisation helps to elucidate the degree to which the presence of quenching suppresses these processes. Surface hopping QCT was then used to account for non-adiabatic transitions in the theory, which led to an improvement in agreement with experiment. However, standard surface hopping QCT theory failed to account for the full extent of quenching in these two systems. A major focus of this work is therefore on the development of an extension to standard surface hopping QCT theory to incorporate rovibronic couplings. In non-linear configurations, the excited state of the OH + Kr, Xe systems has A' symmetry, while the ground state is split into symmetric (A') and antisymmetric (A'') components. For these symmetry reasons, coupling is restricted to the two states of the same symmetry, however a rotation of the correct (A'') symmetry can induce transitions to the A'' state too. Inclusion of all three electronic states, and the relevant couplings between them, is found to be crucial for a proper description of experimental reality.

This Thesis describes the synthesis and characterisation of new alkaline earth- and rare earth-transition metal complexes. Experimental and computational studies were performed to investigate the structure and bonding in these complexes. Their reactivity was also studied. Chapter 1 introduces metal-metal bonded complexes and current alkaline earth- and rare earth-transition metal bonded complexes. Chapter 2 describes experimental and computational studies of new alkaline earth- and lanthanide-Fe complexes possessing the [CpFe(CO)2]- anion. Chapter 3 presents experimental studies of the reduction of Fe3(CO)12 with Ca. Chapter 4 describes experimental and computational studies of new alkaline earth- and lanthanide-Co complexes containing the [Co(CO)3(PR3)]- anion. Chapter 5 presents full experimental procedures and characterising data for the new complexes reported. Appendix describes the attempted synthesis of [Ca{CpRu(CO)2}2(THF)x]y and study by DFT of [CaRp2(THF)3]2 CD Appendix contains .cif files for all new crystallographically characterised complexes described.

Inositol phosphates play a fundamental role in many intracellular processes. Of particular importance is the role of phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] in the protein kinase B (PKB/Akt) signalling pathway. PtdIns(3,4,5)P3 recruits PKB to the cell membrane through binding interactions with its pleckstrin homology (PH) domain. In several human cancers, this signalling pathway is upregulated, resulting in increased cell growth and proliferation. In order to investigate the therapeutic potential of the PtdIns(3,4,5)P3–PH domain binding interaction, it is necessary to develop inositol phosphate-based probes. This DPhil dissertation highlights the synthesis of a number of derivatives of the PtdIns(3,4,5)P3 head group – inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P4]. These derivatives incorporated phosphate isosteres at both the 3- and 5-positions of Ins(1,3,4,5)P4, through the utilisation of novel protection and deprotection strategies. In addition, this dissertation highlights the efficient synthesis of the natural product inositol 1,3-bisphosphate [Ins(1,3)P2] and our work towards the synthesis of inositol pyrophosphate derivatives.