Browsing by Department "Department of Chemistry"
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- ItemOpen Access[1,2-Bis(diphenylphosphino)ethane]-diiodidoplatinum(II) dichloromethane disolvate(2007) Sivaramakrishna, Akella; Su, Hong; Moss, John RIn the title compound, [PtI2(C26H24P2)]·2CH2Cl2, the PtI2(dppe) [dppe = 1,2-bis(diphenylphosphino)ethane] molecules possess twofold rotation symmetry. The Pt coordination displays a square-planar arrangement, with the sum of the angles around the Pt atom being 360.01 (2)°. The Pt-I distance is 2.6484 (5) Å. In the crystal structure, intermolecular C-H...I contacts link the PtI2(dppe) molecules into rows along the c axis, with a C...I distance of 3.873 (5) Å.
- ItemOpen Access1,7-Dimethylpentacyclo[5.4.0.02,6.-03,10.05,9]undecane-8,11-dione(International Union of Crystallography, 2010) Chakka, Sai Kumar; Onajole, Oluseye K; Govender, Thavendran; Maguire, Glenn E M; Su, Hong; Kruger, Hendrik GThe structure of the title compound, C13H14O2, a pentacycloundecane cage derivative, exhibits unusual Csp3 —Csp3 singlebond lengths ranging from 1.505 (3) to 1.607 (2) A˚ and strained bond angles as small as 88.7 (1) and as large as 121.0 (2). In this meso compound, an internal non-crystallographic mirror plane exists, bisecting the molecule. In the crystal, weak C—HO hydrogen bonds link the molecules into an infinite spiral about a twofold screw axis along the [100] direction.
- ItemOpen Access2-Aminophenazine carboxylic acids(1962) Brock, David John Henry; Holliman, F G
- ItemOpen Access5-Iodo-1-Arylpyrazoles as Potential Benchmarks for Investigating the Tuning of the Halogen Bonding(2020-12-17) Dumitrescu, Denisa; Shova, Sergiu; Man, Isabela C; Caira, Mino R; Popa, Marcel Mirel; Dumitrascu, Florea5-Iodo-1-arylpyrazoles are interesting templates for investigating the halogen bond propensity in small molecules other than the already well-known halogenated molecules such as tetrafluorodiiodobenzene. Herein, we present six compounds with different substitution on the aryl ring attached at position 1 of the pyrazoles and investigate them in the solid state in order to elucidate the halogen bonding significance to the crystallographic landscape of such molecules. The substituents on the aryl ring are generally combinations of halogen atoms (Br, Cl) and various alkyl groups. Observed halogen bonding types spanned by these six 5-iodopyrazoles included a wide variety, namely, C–I· · · O, C–I· · · π, C–I· · · Br, C–I· · · N and C–Br· · · O interactions. By single crystal X-ray diffraction analysis combined with the descriptive Hirshfeld analysis, we discuss the role and influence of the halogen bonds among the intermolecular interactions.
- ItemOpen AccessA comparative study between the cubic spline and b-spline interpolation methods in free energy calculations(2020) Kaya, Hikmet Emre; Naidoo, Kevin JNumerical methods are essential in computational science, as analytic calculations for large datasets are impractical. Using numerical methods, one can approximate the problem to solve it with basic arithmetic operations. Interpolation is a commonly-used method, inter alia, constructing the value of new data points within an interval of known data points. Furthermore, polynomial interpolation with a sufficiently high degree can make the data set differentiable. One consequence of using high-degree polynomials is the oscillatory behaviour towards the endpoints, also known as Runge's Phenomenon. Spline interpolation overcomes this obstacle by connecting the data points in a piecewise fashion. However, its complex formulation requires nested iterations in higher dimensions, which is time-consuming. In addition, the calculations have to be repeated for computing each partial derivative at the data point, leading to further slowdown. The B-spline interpolation is an alternative representation of the cubic spline method, where a spline interpolation at a point could be expressed as the linear combination of piecewise basis functions. It was proposed that implementing this new formulation can accelerate many scientific computing operations involving interpolation. Nevertheless, there is a lack of detailed comparison to back up this hypothesis, especially when it comes to computing the partial derivatives. Among many scientific research fields, free energy calculations particularly stand out for their use of interpolation methods. Numerical interpolation was implemented in free energy methods for many purposes, from calculating intermediate energy states to deriving forces from free energy surfaces. The results of these calculations can provide insight into reaction mechanisms and their thermodynamic properties. The free energy methods include biased flat histogram methods, which are especially promising due to their ability to accurately construct free energy profiles at the rarely-visited regions of reaction spaces. Free Energies from Adaptive Reaction Coordinates (FEARCF) that was developed by Professor Kevin J. Naidoo has many advantages over the other flat histogram methods. iii Because of its treatment of the atoms in reactions, FEARCF makes it easier to apply interpolation methods. It implements cubic spline interpolation to derive biasing forces from the free energy surface, driving the reaction towards regions with higher energy. A major drawback of the method is the slowdown experienced in higher dimensions due to the complicated nature of the cubic spline routine. If the routine is replaced by a more straightforward B-spline interpolation, sampling and generating free energy surfaces can be accelerated. The dissertation aims to perform a comparative study between the cubic spline interpolation and B-spline interpolation methods. At first, data sets of analytic functions were used instead of numerical data to compare the accuracy and compute the percentage errors of both methods by taking the functions themselves as reference. These functions were used to evaluate the performances of the two methods at the endpoints, inflections points and regions with a steep gradient. Both interpolation methods generated identically approximated values with a percentage error below the threshold of 1%, although they both performed poorly at the endpoints and the points of inflection. Increasing the number of interpolation knots reduced the errors, however, it caused overfitting in the other regions. Although significant speed-up was not observed in the univariate interpolation, cubic spline suffered from a drastic slowdown in higher dimensions with up to 103 in 3D and 105 in 4D interpolations. The same results applied to the classical molecular dynamics simulations with FEARCF with a speed-up of up to 103 when B-spline interpolation was implemented. To conclude, the B-spline interpolation method can enhance the efficiency of the free energy calculations where cubic spline interpolation has been the currently-used method.
- ItemOpen Access
- ItemOpen AccessA computational study of acidic Ionic Liquids for cellobiose hydrolysis in ionic liquids(2019) Nel, Jessica Lisé; Venter, Gerhard AThe current environmental situation, with respect to global warming and the ever– approaching depletion of fossil fuel sources, places significance on the development of green fuel and platform chemical production methods. In this context, processes that utilise biomass sources as feedstock, are of great interest. Cellulose, which is the most abundant biopolymer in nature, is a renewable low–cost carbon resource derived from harvest residues and sources like wood and straw. Glucose generation from cellulose requires a saccharide conversion, whereby the β-(1,4)-glycosidic bond linkages in the cellobiose polymer repeating units are cleaved. Problems arise in the hydrolysis of cellulose as experimental and theoretical studies have shown cellulose to have very low solubility in water and most other general molecular solvents. This results in the use of harsh pretreatments at high temperatures and pressures to extract cellulose from lignocellulosic material and strong acids catalysts (pKa < −3.2). Room temperature ionic liquids (RTILs) provide potentially environmentally friendly alternative. It has been shown that ILs can dissolve cellulose under relatively benign conditions and can possibly be adapted into a one-pot-like process of hydrolysis using acid-functionalised IL catalysts. This dissertation investigated the effect of various ionic liquids on the thermodynamics of cellobiose acid hydrolysis, as both a catalyst and as a solvent, using computational means. An appropriate thermodynamic cycle protocol, a DLPNO-CCSD(T)/ccpVTZ//TPSS/def2-TZVP [M05-2X/6-31+G** (SMD)] proton exchange cycle, was established through benchmarking for the prediction of Brønsted acid-functionalised ionic liquid pKa values in ionic liquids. The sulfonyl-functionalised acidic IL was shown to be the most acidic IL resulting in a lower protonation free energy. Solvation in ionic liquids resulted in higher protonation and barrier height free energies relative to solvation in water. The current environmental situation, with respect to global warming and the ever– approaching depletion of fossil fuel sources, places significance on the development of green fuel and platform chemical production methods. In this context, processes that utilise biomass sources as feedstock, are of great interest. Cellulose, which is the most abundant biopolymer in nature, is a renewable low–cost carbon resource derived from harvest residues and sources like wood and straw. Glucose generation from cellulose requires a saccharide conversion, whereby the β-(1,4)-glycosidic bond linkages in the cellobiose polymer repeating units are cleaved. Problems arise in the hydrolysis of cellulose as experimental and theoretical studies have shown cellulose to have very low solubility in water and most other general molecular solvents. This results in the use of harsh pretreatments at high temperatures and pressures to extract cellulose from lignocellulosic material and strong acids catalysts (pKa < −3.2). Room temperature ionic liquids (RTILs) provide potentially environmentally friendly alternative. It has been shown that ILs can dissolve cellulose under relatively benign conditions and can possibly be adapted into a one-pot-like process of hydrolysis using acid-functionalised IL catalysts. This dissertation investigated the effect of various ionic liquids on the thermodynamics of cellobiose acid hydrolysis, as both a catalyst and as a solvent, using computational means. An appropriate thermodynamic cycle protocol, a DLPNO-CCSD(T)/ccpVTZ//TPSS/def2-TZVP [M05-2X/6-31+G** (SMD)] proton exchange cycle, was established through benchmarking for the prediction of Brønsted acid-functionalised ionic liquid pKa values in ionic liquids. The sulfonyl-functionalised acidic IL was shown to be the most acidic IL resulting in a lower protonation free energy. Solvation in ionic liquids resulted in higher protonation and barrier height free energies relative to solvation in water.
- ItemOpen AccessA computer simulation of the trace metal speciation in seawater(1994) Woolard, Christopher Dennis; Linder, P W
- ItemOpen AccessA contribution to the vibrational analysis of metal complexes with pyridine and related ligands(1984) Verhoeven, Paul Felix Maria
- ItemOpen AccessA general quantitative spectrographic method for the analysis of ores, and associated metallurgical products(1963) Carlton, Claire Julietta Elizabeth; Ahrens, L H
- ItemOpen AccessA metallomic, proteomic and lipidomic investigation of the malaria parasites digestive vacuole and insights into the mediators of haemozoin formation(2019) Mohunlal, Roxanne; Egan, Timothy JohnNovel and unambiguous mechanistic details of the biochemical processes that enable the most virulent form of the malaria pathogen, Plasmodium falciparum, to thrive within the human host are desperately required in order to find innovative strategies to counteract emerging parasite resistance that will inevitably render current malarial therapies obsolete. This study focused on exploring the Plasmodium falciparum metallome and investigated the mediators of haemozoin formation, an ingenious parasite-specific process critical to host immune evasion as well as parasite survival and one that is surprisingly rather contentious. In order to obtain a comprehensive view of metal distribution, the trace metal content in parasites isolated at varying time-points over the 48 h intraerythrocytic cycle were measured by ICP-MS. The trace metals detected; namely, iron, magnesium, zinc, manganese and copper, were compared to control uninfected erythrocytes. With the malaria parasite being a haematophagous organism, iron was detected as the most abundant trace metal and found to exhibit a significant increase up to 32 h into the life cycle after which the measured iron content remained relatively constant and lower than the control. This was attributed to the maximum amount of haemoglobin having been ingested at this mature trophozoite stage and the active conversion of free haem (Fe(III)PPIX) into biocrystalline haemozoin. All other trace metals exhibited 2 to 4-fold increases in metal ion content as the parasite matured and were detected in amounts higher than those found in the erythrocyte control, demonstrating uptake of these ions from the external medium. These increases coincided with specific cellular events such as cell division and enhanced parasite metabolism. Qualitative proteomic analysis of parasite material identified several metalloproteins but most significant, was the discovery of magnesium and copper transporters. Together, these findings suggest that transition metal import is essential to promote important cellular events and parasite growth and are indicative of unique parasite-specific metal transport pathways. The mediators of crystal formation were investigated by interrogating the haemozoin proteome and lipidome. Haemozoin was obtained from parasitised erythrocytes following a fractionation approach which culminated in their release from purified digestive vacuoles (DVs) following multiple freeze-thaw cycles. Isolated crystals were extensively washed with aqueous sodium acetate buffer (0.5 M, pH 5.2), detergent(4% SDS) and organic solvents (acetone/methanol) prior to base dissolution (0.1 M NaOH). Mass spectrometry was used to investigate the biomolecules occluded by haemozoin by analysing extensively washed and dissolved crystals. Haem detoxification protein (HDP), a protein currently postulated to be potent in mediating haemozoin formation in vivo, was detected in high relative abundance in the dissolved haemozoin fraction by semi-quantitative label-free proteomics. Expression and purification of recombinant soluble HDP was optimised and both soluble and refolded protein were further investigated. Characterisation by circular dichroism and fluorescence spectroscopy revealed that soluble HDP differed in conformation to its refolded counterpart. In aqueous solution (pH 7.4), UV-vis spectrophotometric titrations showed soluble and refolded HDP to bind Fe(III)PPIX in a 1:1 ratio with a Kd of 1.2 ± 0.5 µM and 0.35 ± 0.04 µM respectively. Crucially, activity studies under biomimetic conditions (pH 5.2, 37°C) demonstrated that this protein was not competent to promote β-haematin (synthetic haemozoin) formation without the incorporation of detergent. Mass spectrometry-based lipidomics identified and quantified over 400 lipids in dissolved haemozoin. Neutral lipids were found to be the dominant class comprising 90% cholesterol, 2% cholesterol esters and 0.6% acylglycerols. The detected lipids were used to prepare a model lipid blend which was found to efficiently promote β-haematin formation in yields greater than 90% in under 10 minutes and at concentrations as low as 18 µM. Crystals synthesised using the model lipid blend were found to exhibit similar morphological traits to haemozoin naturally produced by the parasite. Live-cell imaging by spinning disk confocal microscopy revealed that neutral lipid bodies localised externally from the DV or in close contact with the DV membrane but were not found in the immediate vicinity of haemozoin. β-Haematin was found to occlude labelled protein and lipid when synthesised in their presence. Furthermore, occluded biomolecules were not readily displaced from the crystal surface through simple washing with aqueous buffer (pH 5.2) but were only released upon base dissolution of crystals. Pre-formed β-haematin and haemozoin incubated with labelled biomolecules resulted in no further occlusion which demonstrated that these crystals occlude material in a manner non-exchangeable with the DV lumen, thus providing a window into the molecules present at the time and site of crystal formation. Overall, this multidisciplinary omics approach has revealed that the malaria parasite has a unique metallome which may provide promising new drug targets. Significantly, this study has unequivocally demonstrated that haemozoin occludes proteins and lipids in detectable amounts in a non-exchangeable manner with the external milieu but, crucially, lipids occluded by haemozoin are present at the time and site of formation within the DV and are potent mediators of haemozoin formation in the malaria parasite.
- ItemOpen AccessA single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods(2021) Abdulganiyyu, Ibrahim A; Jackson, Graham E; Marco, Heather GFlies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.
- ItemOpen AccessA study of mantle inclusions in the Koffiefontein Kimberlite pipe, South Africa(1980) CARDOSO_P; Gurney, John; Le Roex, AntonMantle derived rock and mineral fragments from the Koffiefontein Kimberlite Pipe have been studied in the form of xenoliths, megacrysts, concentrate minerals and inclusions in diamonds. Mantle derived xenoliths are unusuaLly scarce. The predominant xenoliths are pyroxenites. Peridotites are rare and eclogites are very rare. The pyroxenites have been assigned to five categories. In general, they show a clear metamorphic textural history with widespread evidence of exsolution, polygonisation and deformation. Some of these pyroxenites are interpreted to represent the crystallisation products of basaltic magma at depth. Some have been metasomatised. The pyroxene chemistries suggest that more than one pyroxenite body has been sampled. The peridotites are very similar to the common peridotites of N. Lesotho and are thought to represent depleted mantle. The Koffiefontein diamonds contain both eclogitic and peridotitic inclusions. The inclusions show evidence for lack of equilibration, and one appears to link tog~ther the two parageneses mentioned above. The presence of (MgFe)O as an inclusion is reported. The megacrysts studied consisted only of garnets, and a few pyroxenes. They are interpreted to have crystallised from a magma which cooled slowly and was relatively deficient in Tio2 to account for the scarcity of ilmenite. The heavy mineral concentrate contained garnet, orthopyroxene, opaque minerals and clinopyroxene in order of abundance. The opaque minerals were chromite and ilmenite. The chemical compositions of most of the concentrate grains do not match the mineral compositions found in xenolith s, or megacrysts. A small number of concentrate grains have compositions ma tched by the diamond inclusions. Attempts to a pply geothe r mobarometry to the pyroxenites and to the diamond inclusions gave conflicting results which areascribe d to lack of equilibration between co-existing mineral phases and/or within individual mineral grains. The Koffiefontein xenolith suite is unusual for the relative abundance of pyroxenite and the scarcity of peridotite. The concentrate is unusual for the relative abundance of orthopyroxene particularly and of chromi te.
- ItemOpen AccessA study of the factors affecting pigment production of Pseudomonas aeruginosa.(1957) Kreft, Gerhard
- ItemOpen AccessA survey of some South African plant gums with special reference to the chemistry of Watsonia corm polysaccharide(1965) Shaw, Derek Humphrey; Stephen, A M
- ItemOpen AccessA theoretical study of metal-organic frameworks(2018) Zwane, Reabetswe Robin; Venter, Gerhard; Oliver, Clive; Wilkinson, KarlAmong the options for carbon sequestration, the development of CO2 capture materials has gained momentum over the past two decades. The design and construction of chemical and physical absorbents for the capture of CO2 and clean energy storage are a crucial technology for a sustainable low-carbon future. Metal-organic frameworks (MOFs) provide a new vision for the adsorption of molecules on solid surfaces. The interest in MOFs is owed to their ultrahigh porosity, high surface areas and tuneable pore sizes and shapes. The main objective of this thesis was to adopt a rational predictive capacity used in MOF design to control properties such as framework porosity and flexibility on a molecular scale. The in-silico studies were carried out by using ab initio quantum mechanical approaches such as density functional theory and perturbation theory. In addition, semi-classical methods like the Grand Canonical Monte Carlo (GCMC) approach was also used. A structural motif called vicinal fluorination was adopted to study MOF linkers in isolation and in a framework. An extensive conformational study, in various solvents, was carried out to investigate the effect of vicinal fluorination on the isolated MOF linkers and therefore elucidate their conformational stability. The effect of fluorination on adsorption isotherms was also investigated. Moreover, various fluorination patterns were explored. Adsorption isotherms of a non-fluorinated copperbased MOF based on experimental work, and its various fluorinated analogues were predicted using the GCMC method. It was found that vicinal fluorination is not dominant in controlling conformations of some MOF linkers. Rather, an interplay of interactions, including solute and steric interactions, influence the conformational stability on rotational profiles. However, vicinal fluorination was shown to control the flexibility of the linkers used in MOFs as it controls the force constants around the minima of rotational profiles of isolated MOF linkers. The study also highlighted the importance of the solvent on the relative energies of the linker conformations – this has a potential impact on the synthesis of MOFs. With the help of computational methods and validation from experimental data, the structural and sorption properties of the framework, upon fluorination, were shown to have consequences on the adsorption properties of the MOF. Vicinally fluorinated frameworks were shown to have higher uptakes at a low temperature and low pressures.
- ItemOpen AccessAccelerator-based look-up table for coarse-grained molecular dynamics computations(2018) Gangopadhyay, Ananya; Naidoo, Kevin J.; Winberg, SimonMolecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologists to simulate and observe the physical properties of a system of particles or molecules. The method provides invaluable three-dimensional structural and transport property data for macromolecules that can be used in applications such as the study of protein folding and drug design. The most time-consuming and inefficient routines in MD packages, particularly for large systems, are the ones involving the computation of intermolecular energy and forces for each molecule. Many fully atomistic systems such as CHARMM and NAMD have been refined over the years to improve their efficiency. But, simulating complex long-time events such as protein folding remains out reach for atomistic simulations. The consensus view amongst computational chemists and biologists is that the development of a coarse-grained (CG) MD package will make the long timescales required for protein folding simulations possible. The shortcoming of this method remains an inability to produce accurate dynamics and results that are comparable with atomistic simulations. It is the objective of this dissertation to develop a coarse-grained method that is computationally faster than atomistic simulations, while being dynamically accurate enough to produce structural and transport property data comparable to results from the latter. Firstly, the accuracy of the Gay-Berne potential in modelling liquid benzene in comparison to fully atomistic simulations was investigated. Following this, the speed of a course-grained condensed phase benzene simulation employing a Gay-Berne potential was compared with that of a fully atomistic simulation. While coarse-graining algorithmically reduces the total number of particles in consideration, the execution time and efficiency scales poorly for large systems. Both fully-atomistic and coarse-grained developers have accelerated packages using high-performance parallel computing platforms such as multi-core CPU clusters, Field Programmable Gate Arrays (FPGAs) and Graphics Processing Units (GPUs). GPUs have especially gained popularity in recent years due to their massively parallel architecture on a single chip, making them a cheaper alternative to a CPU cluster. Their relatively shorter development time also gives them an advantage over FPGAs. NAMD is perhaps the most popular MD package that employs efficient use of a single GPU or a multi-GPU cluster to conduct simulations. The Scientific Computing Research Unit’s in-house generalised CG code, the Free Energy Force Induced (FEFI) coarse-grained MD package, was accelerated using a GPU to investigate the achievable speed-up in comparison to the CPU algorithm. To achieve this, a parallel version of the sequential force routine, i.e. the computation of the energy, force and torque per molecule, was developed and implemented on a GPU. The GPU-accelerated FEFI package was then used to simulate benzene, which is almost exclusively governed by van der Waal’s forces (i.e. dispersion effects), using the parameters for the Gay-Berne potential from a study by Golubkov and Ren in their work “Generalized coarse-grained model based on point multipole and Gay-Berne potentials”. The coarse-grained condensed phase structural properties, such as the radial and orientational distribution functions, proved to be inaccurate. Further, the transport properties such as diffusion were significantly more unsatisfactory compared to a CHARMM simulation. From this, a conclusion was reached that the Gay-Berne potential was not able to model the subtle effects of dispersion as observed in liquid benzene. In place of the analytic Gay-Berne potential, a more accurate approach would be to use a multidimensional free energy-based potential. Using the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method, a four-dimensional Free Energy Volume (FEV) for two interacting benzene molecules was computed for liquid benzene. The focal point of this dissertation was to use this FEV as the coarse-grained interaction potential in FEFI to conduct CG simulations of condensed phase liquid benzene. The FEV can act as a numerical potential or Look-Up Table (LUT) from which the interaction energy and four partial derivatives required to compute the forces and torques can be obtained via numerical methods at each step of the CG MD simulation. A significant component of this dissertation was the development and implementation of four-dimensional LUT routines to use the FEV for accurate condensed phase coarse-grained simulations. To compute the energy and partial derivatives between the grid points of the surface, an interpolation algorithm was required. A four-dimensional cubic B-spline interpolation was developed because of the method’s superior accuracy and resistance to oscillations compared with other polynomial interpolation methods. When The algorithm’s introduction into the FEFI CG MD package for CPUs exhausted the single-core CPU architecture with its large number of interpolations for each MD step. It was therefore impractical for the high throughput interpolation required for MD simulations. The 4D cubic B-spline algorithm and the LUT routine were then developed and implemented on a GPU. Following evaluation, the LUT was integrated into the FEFI MD simulation package. A FEFI CG simulation of liquid benzene was run using the 4D FEV for a benzene molecular pair as the numerical potential. The structural and transport properties outperformed the analytical Gay-Berne CG potential, more closely approximating the atomistic predicted properties. The work done in this dissertation demonstrates the feasibility of a coarse-grained simulation using a free energy volume as a numerical potential to accurately simulate dispersion effects, a key feature needed for protein folding.
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- ItemOpen AccessThe adsorption of Ni, Cu, Zn, Cd and Pb by δ-MnO₂ and its inclusion in an equilibrium model of metal partitioning in soils(1997) Pretorius, Patrius Julius; Linder, Peter WChemical equilibrium modelling provides a mechanistic tool for the prediction of metal partitioning in soils, which is important in predicting the fate and effects of metals in soil systems. In order to set up an equilibrium model of metal partitioning in soil systems, thermodynamic data for all processes influencing metal fate in soil systems are needed. In this work, the adsorption of the metals nickel, copper, zinc, cadmium and lead by δ-MnO₂ is investigated. This was done in order to provide thermodynamic data for an important adsorption phase in soils systems. Before this work, consistent adsorption data for only one adsorption phase, hydrous ferric oxide, were available. This precluded the inclusion of manganese dioxide in equilibrium models of metal fate in soil systems. Surface complexation properties of a synthetic manganese dioxide were investigated using glass electrode potentiometry. Experimental data were interpreted according to the surface complexation model in conjunction with the diffuse double layer model of the solid/solution interface. Adsorption constants were derived using the non-linear optimization program FITEQL. The surface complexation parameters determined in this fashion were validated against results obtained from the open literature. Following this, the surface complexation parameters were included in a chemical equilibrium model of soil systems. This model was used to predict the partitioning of nickel, copper, zinc, lead and cadmium in a number of soil samples collected in The Netherlands. Contrary to results presented by other workers, it was found that a non-homogeneous surface site model was needed to explain the potentiometric data obtained for proton and metal adsorption by manganese dioxide. Best fits of alkalimetric titration data were obtained with a two-site, three surface-species model of the δ-MnO₂ surface. Site concentrations of 2.231x10⁻³ mol.g⁻¹ and 7.656x10⁻⁴ mol.g⁻¹ were obtained. Corresponding equilibrium constants for the formation of the postulated surface species are -1.27 (=XO⁻), -5.99 (=YO⁻) and 3.52 (= YOH2₂⁺). This model was successful in a qualitative manner in describing adsorption results obtained from the open literature. The prediction of metal partitioning in soil systems showed that although the inclusion of manganese dioxide in the modelled to some improvement in the agreement between observed and predicted results, other factors are present which influence metal partitioning in soils. The discrepancy between observed and predicted results furthermore showed that the processes accounted for in the equilibrium model are incomplete.
- ItemOpen AccessThe adsorption of nitrogen and argon by evaporated films of sodium chloride(1969) Rodgers, Allen L; Linder, Peter WAn ultra-high vacuum apparatus has been designed and constructed. Pressures of the order of 1 x 10⁻⁸ torr have been attained routinely. The adsorption of nitrogen by Pyrex has been investigated and the results obtained have shown good agreement with those in the literature. Rigorously cleaned evaporated films of sodium chloride have been prepared and the adsorption of nitrogen and argon by them has been investigated. Isosteric heats and entropies of adsorption have been determined and theoretical entropies calculated. The appearance of a group of sites of uniform activity, hitherto unavailable owing to contamination of the surface, is postulated. The adsorption of nitrogen and argon has been found to be reasonably well represented by the immobile, localized model with indications of the adsorbed argon molecules occupying a different set of sites from the adsorbed nitrogen. Two novel methods for the preparation of evaporated films of alkali halides are suggested.