Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Recent developments in the atmospheric treatment of low-grade nickel laterite ores at Anglo American plc has culminated in the conceptual iron-focused laterite (ARFe) process. In addition to the recovery of nickel and cobalt from laterite ore, this process uniquely aims to recover iron as a saleable by-product. The reduction of soluble iron(III) (Fe(III)) by sulfur dioxide gas (SO2) is central to the ARFe concept and represents a complex, multiphase system involving simultaneous gas-liquid mass transfer, thermodynamic speciation and chemical reaction. The chemistry of iron-containing systems is generally poorly understood and accurately predicting their behaviour is challenging, especially under aggressive hydrometallurgical conditions. The primary objective of this work is the development of an engineering model capable of describing the rate and extent of ferric reduction with SO2 under conditions typical of the ARFe process. Thermodynamic considerations provide a rigorous framework for the interpretation of chemical reactions, however little experimental data are openly available for the associated solution species in acidic iron sulfate systems. A key contribution of this work, and critical for the development of the overall model, is the direct measurement of speciation in iron sulfate solutions. Raman and UV-vis spectroscopy were utilised to make direct speciation measurements in the various subsystems of the Fe2(SO4)3-FeSO4-H2SO4-H2O system that were previously unavailable in the open literature. The FeSO+4 and Fe(SO4)– 2 species were explicitly identified and measurements were supported and rationalised by static computational quantum mechanical calculations and ultimately permit the calibration of a robust, ion-interaction solution model with the explicit recognition of the important solution species up to 1.6 mol/kg Fe2(SO4)3, 0.8 mol/kg H2SO4 over 25 – 90 C. Batch and continuous Fe(III) reduction kinetics were measured and the effects of initial Fe2(SO4)3 and H2SO4 concentrations, temperature and in-situ neutralisation quantified. The retardation effect of sulfuric acid was observed to be the most significant factor influencing the initial reaction rate and the achievable extent of reduction at fixed residence time, which varied between about 20 and 80 % after 180 minutes of reaction. A reaction mechanism that is limited by the slow ligand-to-metal electron transfer in the FeIIISO+3 solution species’ decomposition is proposed and spectroscopic measurements and computational quantum mechanical calculations are used to support this mechanism. A kinetic model, comprising a system of differential mass-balance equations, is incorporated into the thermodynamic framework. This reaction model permits the prediction of kinetic profiles over the full range of experimental conditions and can be incorporated into more elaborate simulation models of the ARFe circuit. The specific original contributions of this work are • The direct measurement of aqueous speciation in the Fe2(SO4)3-H2SO4-H2O system by Raman and UV-vis spectroscopy • The development of a modelling framework to characterise speciation, activity coefficients and solubility in the mixed Fe2(SO4)3-FeSO4-H2SO4-H2O system. • The measurement of Fe(III) reduction kinetics using SO2 in concentrated sulfate solutions as a function of initial composition and temperature. • The development of a solution reaction model of Fe(III) reduction with SO2 that accurately predicts the solution speciation and reaction rate with time as a function of composition and temperature. Lastly, the vast complexity of industrial systems will nearly always result in a lack of specific experimental data that are required for the development of phenomenological models. This work emphasises the crucial role that engineering studies hold in the generation of such data to derive maximum practical value for industrial process development and optimisation. / AFRIKAANSE OPSOMMING: Onlangse ontwikkelinge in die atmosferiese behandeling van lae-graad nikkel lateriet erts by Anglo American plc het gelei tot die konseptuele yster gefokus lateriet (ARFe) proses. Bykommend tot die herwinning van nikkel en kobalt uit laterite erts is hierdie proses uniek en daarop gemik om yster te herwin as ’n verkoopbare by-produk. Die vermindering van oplosbare yster(III) (Fe(III)) met swaeldioksied (SO2) is sentraal tot die ARFe konsep en verteenwoordig ’n komplekse, multifase stelsel wat gelyktydige gas-vloeistof massa-oordrag, termodinamiese spesiasie en chemiese reaksie behels. Die oplossingschemie van ysterstelsels word, oor die algemeen, swak verstaan en om hul gedrag akuraat te voorspel is ’n uitdaging, veral onder aggressiewe hidrometallurgiese kondisies. Die primêre doel van hierdie werk is die ontwikkeling van ’n ingenieursmodel wat die tempo en omvang van yster(III) vermindering met SO2 onder tipiese ARFe proses toestande beskryf. Termodinamiese oorwegings stel ’n streng raamwerk voor vir die interpretasie van chemiese reaksies, alhoewel daar egter min eksperimentele data openlik beskikbaar is vir die gepaardgaande oplossing spesies in suur yster(III) sulfaat stelsels. ’n Belangrike bydrae van hierdie werk, en van kritieke belang vir die ontwikkeling van die algehele model, is die direkte meting van spesiasie in yster(III) sulfaat oplossings. Raman en UV-vis spektroskopie is gebruik om direkte spesiasie metings te maak in die verskillende subsisteme van die Fe2(SO4)3-FeSO4-H2SO4-H2O stelsel wat voorheen nie in die oop literatuur beskikbaar was nie. Die FeSO+4 en Fe(SO4)– 2 spesies is ekplisiet geïdentifiseer, terwyl die metings ondersteun en gerasionaliseer is deur statiese kwantummeganiese berekeninge wat uiteindelik die kalibrasie van ’n robuuste, ioon-interaksie model tot gevolg hê wat ook die belangrike oplossingspesies duidelik beklemtoon tot en met 1.6 mol/kg Fe2(SO4)3, 0.8 mol/kg H2SO4 en tussen 25 – 90°C. Enkellading en kontinue yster(III) verminderingskinetika is gemeet en die gevolge van die aanvanklike Fe2(SO4)3 en H2SO4 konsentrasies, temperatuur en in-situ neutralisasie is gekwantifiseer. Die waargeneemde vertragingseffek van swaelsuur is die mees beduidende faktor wat die aanvanklike reaksietempo en die haalbare reaksie omvangsvermindering na ’n vaste residensietyd van 180 minute bepaal, wat wissel tussen ongeveer 20 en 80%. ’n Reaksiemeganisme word voorgestel wat beperk word deur die stadige ligand-totmetaal elektronoordrag in ontbinding van die Fe(III)SO+3 oplossing-spesies en wat verder deur spektroskopiese metings en kwantummeganiese berekenings ondersteun word. A kinetiese model, wat bestaan uit ’n stelsel van gedifferensieerde massa-balans vergelykings, is in die termodinamiese raamwerk geïnkorporeer. Hierdie reaksie-model laat die voorspelling van kinetiese profiele toe oor die volle omvang van die eksperimentele toestande en kan in meer uitgebreide simulasie modelle van die ARFe proces geinkorporeer word. Die spesifieke en oorspronklike bydraes van hierdie werk is • Die direkte meting van die spesiasie in die Fe2(SO4)3-H2SO4-H2O stelsel deur Raman en UV-vis spektroskopie • Die ontwikkeling van ’n modelraamwerk om spesiasie, aktiwiteitskoëffisiënte en oplosbaarheid in die gemengde Fe2(SO4)3-FeSO4-H2SO4-H2O stelsel te karakteriseer. • Die meting van yster(III) vermideringskinetieka deur SO2 in gekonsentreerde sulfate oplossings te gebruik as ’n funksie van die aanvanklike samestelling en temperatuur. • Die ontwikkeling van ’n oplossingsreaksie-model van yster(III) vermindering met SO2 wat die oplossing-spesiasie en reaksietempo met die tyd as ’n funksie van samestelling en temperatuur akkuraat voorspel. Laastens, die oorgrote kompleksiteit van industriële stelsels sal byna altyd lei tot ’n gebrek van spesifieke eksperimentele data wat nodig is vir die ontwikkeling van fenomenologiese modelle. Hierdie werk beklemtoon die belangrike rol wat ingenieursstudies speel in die generasie van data wat sodanig tot maksimum praktiese waarde vir industriële prosesontwikkeling en optimalisering lei.

Master of Science / Department of Biochemistry / Paul E. Smith / We are developing a force field (FF) for molecular dynamics (MD) simulations of peptides and small proteins that is grounded in the Kirkwood-Buff theory of solutions. Here we present the Kirkwood-Buff Force Field (KBFF) parameters for the aromatic amino acids, based upon simulations of binary mixtures of small molecules representative of these amino acids over their entire composition ranges (excluding Histidine). Many aromatics are not fully soluble in water, so they have instead been studied in solvents of methanol or toluene. The parameters were developed by studying the following binary solutions: Phenylalanine − benzene + methanol, toluene + methanol, and toluene + benzene; Tyrosine − toluene + phenol and toluene + p-Cresol; Tryptophan − pyrrole + methanol and indole + methanol; Histidine − pyrrole + methanol, pyridine + methanol, pyridine + water, histidine + water (at 0.25 molal), and histidine monohydrochloride + water (at 0.3 molal and 0.6 molal). Our simulations reproduce the Kirkwood-Buff integrals, which guarantees that the KBFF provides an adequate balance of solute-solvent, solute-solute, and solvent-solvent interactions. Additionally, we show that the KBFF does not sacrifice reproduction of other solution properties in order to achieve this improved description of intermolecular interactions. We present these results as validating evidence for the future use of the KBFF in simulations of peptides and small proteins.

Mathematical modelling of cellular osmotic responses to low temperatures is being increasingly used to overcome obstacles in the successful cryopreservation of cells and tissues. Current cryobiological models often contain simplifying assumptions regarding the solution behaviour of the complicated, multisolute intra- and extra-cellular solutions. In order to obtain more accurate predictions of cryobiological outcomes, equations derived from thermodynamic principles that more accurately describe the biological solution behaviour could be used to greatly advance the design of novel cryopreservation protocols. The general hypothesis of this thesis is that the application of the multisolute osmotic virial equation, with mixing rules derived from thermodynamic first principles, to solutions of interest in cryobiology will result in more accurate predictions of the multisolute solution behaviour, which will lead to improved cryobiological modelling and increased understanding of cellular responses to cryopreservation. Specifically, this thesis demonstrates that the osmotic virial coefficients, obtained from single-solute solution data, can be used in the multisolute osmotic virial equation to accurately predict the multisolute solution behaviour, without the need to fit multisolute solution data. The form of the multisolute osmotic virial equation proposed in this thesis was used to predict the solution behaviour of a range of multisolute solutions of interest in cryobiology. The equation commonly used in cryobiology to describe cellular osmotic equilibrium is based on ideal, dilute solution assumptions. In this thesis, a non-ideal osmotic equilibrium equation was derived and, combined with the multisolute osmotic virial equation, used to more accurately predict the osmotic equilibrium of human erythrocytes. The improved equations proposed in this thesis were combined with experimental measurements of the incidence of intracellular ice formation in order to further the understanding of the role of several important cryobiological parameters on the formation of intracellular ice. This thesis work has significantly contributed to the field of cryobiology by substantially improving the accuracy of two key equations used in the modelling of cellular osmotic responses to cryopreservation. The combination of accurate mathematical modelling and results from experiments will allow increased understanding of cellular responses to cryopreservation, leading to the design of novel cryopreservation protocols. / Chemical Engineering and Medical Sciences

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Orientador: Carlos Francisco Sampaio Bonafe / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T21:45:48Z (GMT). No. of bitstreams: 1 Bispo_JoseAiltonConceicao_D.pdf: 6481701 bytes, checksum: eac9f13bfaae7f2d8718ad2773ff3e57 (MD5) Previous issue date: 2006 / Resumo: Sistemas reacionais em fase líquida compreendem boa parte dos processos físicoquímicos que são estudados para fins de pesquisa e aplicação industrial. Estes estudos são conduzidos em geral de forma a se obter parâmetros de caracterização que tornem possível a padronização e otimização de processos, sejam eles de aplicação químico industrial ou biotecnológica. Em meio a esta necessidade de compreensão de diversos processos físicoquímicos, um ponto que chama a atenção de muitos grupos de pesquisa é a necessidade de aperfeiçoamento dos sistemas de caracterização e modelagem destes processos de forma a tornálos mais informativos e eficientes, tanto no que diz respeito à sua capacidade de caracterização quanto à sua capacidade de previsão. Neste contexto, a maior parte dos sistemas estudados têm como base a metodologia de caracterização desenvolvida por Gibbs-Duhem a aprtir do comportamento de gases ideais. Desvios no comportamento pressão volume são, nestes casos, corrigidos através do parâmetro definido como atividade. Assim, a estrutura de base desenvolvida por Gibbs-Duhem para gases ideais é mantida, deixando praticamente inalterada a relação que expressa a variação do potencial químico. No presente estudo observou-se que este tipo de abordagem e caracterização não produz resultados satisfatórios para o processo de dissociação por pressão de grandes agregados protéicos, e em alguns casos gerou dificuldades matemáticas que impediram a sua implementação em processos bastante comuns. A solução encontrada e o objetivo desta tese foram então o de conduzir uma nova abordagem para a caracterização destes sistemas que envolvem a dissociação por pressão de macromoléculas a partir de equações mais flexíveis para as mudanças de volume que as dos g ases ideais utilizadas por Gibbs-Duhen. O resultado desta nova abordagem foram relações com grande potencial de informação, de fácil aplicação e com uma alta capacidade de previsão / Abstract: The reaction processes involving macromolecules in liquid phase represent a significant part of the studies aiming industrial and technological applications.These studies are in general performed aiming access the parameters of characterization that allows the optimiz ation of chemical and biotechnological processes. In this view, the needing of understand distinct physicochemical processes represent a point that deserves the attention of many laboratories due to the needing of improvement modeling systems that furnish more efficient and precise information about the protein behavior under solution. Although the most of the studies performed aiming to reach this goal are based on the processes of characterization developed by Gibbs-Duhen, deviations on the pressure/volume furnished by the ideal gas equation are usually observed and corrected by means of the activity coefficient. Thus, the structural basis of the Gibbs-Duhem approach is maintained in despite of more complexes systems sho ws a nonlinearbehavior that produces in some cases significant deviations. In the present studie s we observed that the processes of pressure dissociation/denaturation of macromolecules leads to significant errors in respect to the experimental data. In this case the correction of these approach by means of the activity coefficient was not possible since the characterization equations became very complex. The goal of the present work was than to find a new description for these complex systems that allows to determine the properties of system and a precise thermodynamic modeling of these kind of processes / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / The Kirkwood-Buff (KB) theory of solutions, published in 1951, established a route from integrals over radial (pair) distribution functions (RDFs) in the grand canonical ensemble to a set of thermodynamic quantities in an equivalent closed ensemble. These “KB integrals” (KBIs) can also be expressed in terms of the particle-particle (i.e., concentration or density) fluctuations within grand canonical ensemble regions. Contributions by Ben-Naim in 1977 provided the means to obtain the KBIs if one already knew the set of thermodynamic quantities for the mixture of interest; that is, he provided the inversion procedure. Thus, KB theory provides a two-way bridge between local (microscopic) and global (bulk/thermodynamic) properties. Due to its lack of approximations, its wide ranging applicability, and the absence of a competitive theory for rigorously understanding liquid mixtures, it has been used to understand solution microheterogeneity, solute solubility, cosolvent effects on biomolecules, preferential solvation, etc. Here, after using KB theory to test the accuracy of pair potentials, we present and illustrate two extensions of the theory, resulting in a general Fluctuation Solution Theory (FST). First, we generalize KB theory to include two-way relationships between the grand canonical ensemble’s particle-energy and energy-energy fluctuations and additional thermodynamic quantities. This extension allows for non-isothermal conditions to be considered, unlike traditional KB theory. We illustrate these new relationships using analyses of experimental data and molecular dynamics (MD) simulations for pure liquids and binary mixtures. Furthermore, we use it to obtain conformation-specific infinitely dilute partial molar volumes and compressibilities for proteins (other properties will follow) from MD simulations and compare the method to a non-FST method for obtaining the same properties. The second extension of KB theory involves moving beyond doublet particle fluctuations to additionally consider triplet and quadruplet particle fluctuations, which are related to derivatives of the thermodynamic properties involved in regular KB theory. We present these higher order fluctuations obtained from experiment and simulation for pure liquids and binary mixtures. Using the newfound experimental third and fourth cumulants of the distribution of particles in solution, which can be extracted from bulk thermodynamic data using this extension, we also probe particle distributions’ non-Gaussian nature.