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.

Chapter 1 gives background information on proteases and discusses the concept of protease inhibition as a therapeutic strategy for humans. It introduces the key concept that conformation defines biological activity. It also outlines how proteases almost universally bind their substrate/inhibitors in an extended β-strand conformation. The use of calpain as a prototype protease for the testing of β-strand mimics synthesised later in the thesis is also discussed. Chapter 2 describes how molecular modeling was used to rationalise the structure based activity relationships (SAR) of known calpain inhibitors. Molecular modeling was then used to successfully design a number of acyclic β-strand mimics. The synthesis and testing of eight such inhibitors is described. The most potent β-strand mimic prepared was 2.13. This was determined to have an IC₅₀ of 30 nM against calpain II. Chapter 3 outlines the history and application of ring closing metathesis (RCM) to the synthesis of cyclic compounds. The attempted synthesis of an eight membered cyclic nitrogen to nitrogen conformationally constrained dipeptide is described. The synthesis of a conformationally constrained β-amino acid calpain inhibitor (3.73) is also described. A novel calpain inhibitor motif was designed in Chapter 4. On the basis of this an in-silico combinatorial library of two hundred and eighty eight possible β-strand templates was prepared. Conformational analysis of this library was performed and from this a number of excellent β-strand templates were identified and selected for synthesis. The preparation of ten β-strand templates is described. New microwave irradiation methodology was developed to achieve this. vii The formation of a six-membered catalyst deactivating chelate is also proposed to explain why some dienes fail to undergo RCM. Two methods to circumvent the formation of such a chelate are outlined. The addition of Lewis acid chloro-dicyclohexyl borane to the RCM reaction mixture and chain length alteration are investigated. Chapter 5 describes the design of macrocyclic β-strand mimics using induced fit molecular modelling. The physicochemical properties of these were calculated in-silico. From this analysis a number of Tyr-XX-Gly based and Tyr-XX-Cys based macrocyclic calpain inhibitors were selected for synthesis. The preparation and testing of these are described. In the Tyr-XX-Gly macrocyclic system a number of variables were investigated and numerous SAR implications concluded. Aldehyde 5.14 was identified as the best electrophilic warhead macrocyclic calpain inhibitor with an IC₅₀ against calpain II of 27 nM. The best non-electrophilic warhead macrocycle (5.13) had an IC₅₀ against calpain II of 704 nM. Chapter 6 describes synthetic optimisation for the preparation of calpain inhibitors 2.13, 5.14 and 5.17. Multi-gram quantities of each were prepared. Aldehydes 2.13 and 5.14 were evaluated as anti-cataract agents using in-vivo cataract sheep model. Both of these β-strand mimics were demonstrated to retard cataract development. Macrocycle 5.14 was found to be the most effective, decreasing the rate of cataract development between forty four and forty nine per cent relative to control. Chapter 7 outlines the attempted development of RCM methodology for the chiral synthesis of α-α disubstituted amino acid lactams. In addition, methodology for the stereoselective incorporation of a C-N constrained β-amino acid carbocycle into a peptide or peptidomimetic is described.

We study correlated two-level quantum impurity models coupled to a metallic conduction band in the hope of gaining insight into the physics of nanoscale quantum dot systems. We focus on the possibility of formation of a spin-1 impurity local moment which, on coupling to the band, generates an underscreened (USC) singular Fermi liquid state. By employing physical arguments and the numerical renormalization group (NRG) technique, we analyse such systems in detail examining in particular both the thermodynamic and dynamic properties, including the differential conductance. The quantum phase transitions occurring between the USC phase and a more ordinary Fermi liquid (FL) phase are analysed in detail. They are generically found to be of Kosterlitz-Thouless type; exceptions occur along lines of high symmetry where first-order transitions are found. A `Friedel-Luttinger sum rule' is derived and, together with a generalization of Luttinger's theorem to the USC phase, is used to obtain general results for the $T=0$ zero-bias conductance --- it is expressed solely in terms of the number of electrons present on the impurity and applicable in both the USC and FL phases. Relatedly, dynamical signatures of the quantum phase transition show two broad classes of behaviour corresponding to the collapse of either a resonance or antiresonance in the single-particle density of states. Evidence of both of these behaviours is seen in experimental devices. We study also the effect of a local magnetic field on both single- and two-level quantum impurities. In the former case we attempt to resolve some points of contention that remain in the literature. Specifically we show that the position of the maximum in the spin resolved density of states (and related peaks in the differential conductance) is not linear in the applied field, showing a more complicated form than a simple `Zeeman splitting'. The analytic result for the low-field asymptote is recovered. For two-level impurities we illustrate the manner in which the USC state is destroyed: due to two cancelling effects an abrupt change in the zero-bias conductance does not occur as one might expect. Comparison with experiment is made in both cases and used to interpret experimental findings in a manner contrary to previous suggestions. We find that experiments are very rarely in the limit of strong impurity-host coupling. Further, features in the differential conductance as a function of bias voltage should not be simply interpreted in terms of isolated quantum dot states. The many-body nature of such systems is crucially important to their observed properties.

In this thesis a reduced dimensionality quantum scattering model is applied to the study of polyatomic reactions of type X + CH4 <--> XH + CH3. Two dimensional quantum scattering of the symmetric hydrogen exchange reaction CH3+CH4 <--> CH4+CH3 is performed on an 18-parameter double-Morse analytical function derived from ab initio calculations at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator mode motion is approximately treated via inclusion of curvilinear or rectilinear projected zero-point energies in the potential surface. The close-coupled equations are solved using R-matrix propagation. The state-to-state probabilities and integral and differential cross sections show the reaction to be primarily vibrationally adiabatic and backwards scattered. Quantum properties such as heavy-light-heavy oscillating reactivity and resonance features significantly influence the reaction dynamics. Deuterium substitution at the primary site is the dominant kinetic isotope effect. Thermal rate constants are in excellent agreement with experiment. The method is also applied to the study of electronically nonadiabatic transitions in the CH3 + HCl <--> CH4 + Cl(2PJ) reaction. Electrovibrational basis sets are used to construct the close-coupled equations, which are solved via Rmatrix propagation using a system of three potential energy surfaces coupled by spin-orbit interaction. Ground and excited electronic surfaces are developed using a 29-parameter double-Morse function with ab initio data at the CCSD(T)/ccpV( Q+d)Z-dk//MP2/cc-pV(T+d)Z-dk level of theory, and with basis set extrapolated data, both corrected via curvilinear projected spectator zero-point energies. Coupling surfaces are developed by fitting MCSCF/cc-pV(T+d)Z-dk ab initio spin orbit constants to 8-parameter functions. Scattering calculations are performed for the ground adiabatic and coupled surface models, and reaction probabilities, thermal rate constants and integral and differential cross sections are presented. Thermal rate constants on the basis set extrapolated surface are in excellent agreement with experiment. Characterisation of electronically nonadiabatic nonreactive and reactive transitions indicate the close correlation between vibrational excitation and nonadiabatic transition. A model for comparing the nonadiabatic cross section branching ratio to experiment is discussed.

The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner. This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region. To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system. Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity. / <p>The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.</p><p></p><p>QC 20170209</p>

Electrochemistry is the science of electron transfer. The subject is of great importance and appeal because detailed information can be obtained using relatively simple experimental techniques. In general, the raw data is sufficiently complicated to preclude direct interpretation, yet is readily rationalised using numerical procedures. Computational analysis is therefore central to electrochemistry and is the main topic of this thesis. Chapters 1 and 2 provide an introductory account to electrochemistry and numerical analysis respectively. Chapter 1 explains the origin of the potential difference and describes its relevance to the thermodynamic and kinetic properties of a redox process. Voltammetry is introduced as an experimental means of studying electrode dynamics. Chapter 2 explains the numerical methods used in later chapters. Chapter 3 presents a review of the use of nanoparticles in electrochemistry. Chapter 4 presents the simulation of a random array of spherical nanoparticles. Conclusions obtained theoretically are experimentally confirmed using the Cr³⁺/Cr²⁺ redox couple on a random array of silver nanoparticles. Chapter 5 presents an investigation into the concentration of supporting electrolyte required to make a voltammetric experiment quantitatively diffusional. This study looks at a wide range of experimental conditions. Chapter 6 presents an investigation into the deliberate addition of insufficient supporting electrolyte to an electrochemical experiment. It is shown that this technique can be used to fully study a stepwise two electron transfer. Conclusions obtained theoretically are experimentally confirmed using the reduction of anthracene in acetonitrile. Chapter 7 presents a new method for simulating voltammetry at disc shaped electrodes in the presence of insufficient supporting electrolyte. It is shown that, under certain conditions, the results obtained from this complicated simulation can be quantitatively obtained by means of a much simpler ‘hemispherical approximation’. Conclusions obtained theoretically are experimentally confirmed using the hexammineruthenium ([Ru(NH₃)₆]³⁺/[Ru(NH₃)₆]²⁺) and hexachloroiridate ([IrCl₆]²⁻/[IrCl₆]³⁻) redox couples. Chapter 8 presents an investigation into the voltammetry of stepwise two electron processes using ionic liquids as solvents. It is shown that these solvents can be used to fully study a stepwise two electron transfer. Conclusions obtained theoretically are experimentally confirmed using the oxidation of N,N-dimethyl-p-phenylenediamine in the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([C₄ mim][BF₄]). The work presented in this thesis has been published as 7 scientific papers.

The possibility of using methylamines instead of ammonia as a nitrogen precursor for the CVD of nitrides is studied using quantum chemical computations of reaction energies: reaction electronic energy (Δ𝑟𝐸𝑒𝑙𝑒𝑐) reaction enthalpy (Δ𝑟𝐻) and reaction free energy (Δ𝑟𝐺). The reaction energies were calculated for three types of reactions: Uni- and bimolecular decomposition to more reactive nitrogen species, adduct forming with trimethylgallium (TMG) and trimethylaluminum (TMA) followed by a release of methane or ethane and surface adsorption to gallium nitride for both the unreacted ammonia or methylamines or the decomposition products. The calculations for the reaction entropy and free energy were made at both STP and CVD conditions (300°C-1300°C and 50 mbar). The ab inito Gaussian 4 (G4) theory were used for the calculations of the decomposition and adduct reactions while the surface adsorptions were calculated using the Density Functional Theory method B3LYP. From the reactions energies it can be concluded that the decomposition was facilitated by the increasing number of methyl groups on the nitrogen. The adducts with mono- and dimethylamine were more favorable than ammonia and trimethylamine. 𝑁𝐻2 was found to be most readily to adsorb to 𝐺𝑎𝑁 while the undecomposed ammonia and methylamines was not willingly to adsorb.