Browsing by Author "Venter, Gerhard"

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    Open Access
    A theoretical study of metal-organic frameworks
    (2018) Zwane, Reabetswe Robin; Venter, Gerhard; Oliver, Clive; Wilkinson, Karl
    Among 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.
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    Open Access
    Computer simulations of a chromatographic column used in the separation of platinum group metal chlorinated complexes
    (2012) Michael, Nengwekhulu Thizwilondi; Naidoo, Kevin J; Venter, Gerhard
    The PGMs, which are comprised of Ru, Pt, Rh, Ir, Os and Pd, are highly regarded as technologically important precious metals. They have a wide range of applications and are used predominantly as catalysts. These metals are found collectively in nature and hence have similar chemical properties. This makes their separation from contaminants and each other a cumbersome process that requires the most technologically sophisticated refinery processes in metallurgical extraction. An efficient method in which these metal complexes are separated is based on gel chromatography. This uses a concentrated aqueous acidic medium, predominantly hydrochloric acid, and their separation is achieved through differentiation of their different elution orders. However, the similarity in their chemistry makes their separation via current experimental methods difficult.
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    Open Access
    Development and application of the CL&Pol polarisable force field for ionic liquid-based electrolytes
    (2025) Wilson, Tayla Lee; Venter, Gerhard
    Ionic liquids (ILs) are a fascinating class of molecular systems due to diverse and promising applications, including the potential use as electrolyte systems, replacing traditional volatile organic electrolytes. The appeal of ILs for such applications lies in the favourable properties, such as high diffusivity, thermal and electrochemical stability, and low volatility. Molecular dynamics (MD) simulation is a powerful tool for studying the physical properties of liquids; however, whereas traditional solvents are typically well described using classical, fixed-charge force fields (FFs), explicit inclusion of polarisation is essential for accurate description of IL dynamics. Consequently, the development and application of polarisable FFs for ILs is a necessary focus within IL research. The first aim of this work was therefore to extensively validate the recently developed Drude-based CL&Pol FF for six pure ILs and five alkali-earth containing IL-electrolytes. Reproducibility and precision are not often addressed when MD simulation is used to calculate thermophysical properties, yet without quantification of uncertainty, the value of a validation study is questionable. Hence, statistically meaningful uncertainties were reported for all properties as a 95 % confidence interval of the mean over replicate simulations. The simulation protocol was further validated by using well-known theoretical relationships (e.g., the Stokes Einstein and Nernst-Einstein equations) to confirm the internal consistency of key calculated transport properties. The accuracy of calculated properties of pure ILs varied, with average errors as low as 1 % for density to 35 % for viscosity, and 50 % for conductivity. Most properties could be calculated with uncertainties of ~20 %, while calculated conductivities had uncertainties of ~50 %. The second aim of this work involved the further development of the van der Waals component of the intermolecular interaction. The CL&Pol Lennard-Jones (LJ) parameters are carried over from its fixed-charge predecessor, CL&P. The parameters are then adjusted with prescribed scaling of the LJ well-depth (ε) to remove the induction contribution, making it transferable to the Drude FF featuring explicit polarisation. While scaling of ε produces reasonably accurate ii transport properties, the resulting induction-free LJ potentials for interactions involving the alkali metals do not reproduce the ab initio exchange-dispersion potentials, producing theoretically unsatisfactory van der Waals interactions. Furthermore, the existing OPLS ε parameters for the alkali metals do not correlate with the strength of the ab initio dispersion interactions, warranting reconsideration of these parameters. Thus, this work presents a stable and robust protocol for obtaining van der Waals potential parameters compatible with a Drude FF without the need of scaling, based on first-principles resolution of the dispersion and exchange components of the potential using Symmetry-Adapted Perturbation Theory (SAPT). However, while overall interaction energies can be accurately obtained with small basis sets, this is due to error cancellation in the components. Consequently, the f2+SAPT0 complete basis set (CBS) methodology was developed using the extended AHB21x5 dataset of anion-neutral dimers. This method uses basis set extrapolation and scaling of SAPT0 components to provide dispersion and exchange components with an average deviation of ~10 % from higher order SAPT2+/CBS equivalents. Finally, investigation into various potentials showed that Halgren's buffered LJ potential provides a description of the van der Waals interactions more consistent with the equivalent f2+SAPT0/CBS components, particularly at short range, than is offered by the CL&Pol scaled LJ potential.
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    The development of hybrid quantum classical computational methods for carbohydrate and hypervalent phosphoric systems
    (2014) Govender, Krishna Kuben; Naidoo, Kevin J; Venter, Gerhard
    Ab initio, density functional theory, and semi-empirical methods serve as major computational tools for quantum mechanical calculations of medium to large molecular systems. Semi-empirical methods are most effectively used in a hybrid quantum mechanics/molecular mechanics (QM/MM) dynamics framework. However, semi-empirical methods have been designed to provide accurate results for organic molecules, but often fail to treat hypervalent species accurately due to their use of an sp basis. Recently, significant breakthroughs have been made with the incorporation of d-orbitals into the semi-empirical framework, thereby allowing for accurate modeling of both hypervalent and transition metal systems. Here I consider two methods that adopt this new methodology, namely AM1/d-PhoT and AM1*. Our major focus is the simulation of chemical biological and more specifically chemical glycobiological problems of biochemical interest. When I tested the ability of both AM1/d-PhoT and AM1* to reproduce key metrics in chemical glycobiology (i.e., sugar ring pucker, phosphate participation in transferase reactions) these methods, in combination with the published parameters, performed very poorly. Using the AM1/d-PhoT and AM1* Hamiltonians I set out to re-parameterize these methods aiming to produce holistic biochemical QM/MM toolsets able to simulate fundamental problems of binding and enzyme reactivity in chemical glycobiology. We called these methods AM1/d-CB1 and AM1*-CB1. In the development of these parameter sets I focused specifically on proton transfer, carbohydrate ring puckering, bond polarization, amino acid interactions, and phosphate interactions (facets important to chemical glycobiology). Both AM1/d-CB1 and AM1*-CB1 make use of a variable property optimization parameter approach for the glycan molecular class and its chemical environment. The accuracy of these methods is evaluated for carbohydrates, amino acids and phosphates present in catalytic domains of glycoenzymes, and the are shown to be more accurate for key performance indices (puckering, etc.) and on average across all simulation derived properties (QM/MM polarization, protein performance, etc.) than all other NDDO semiempirical methods currently being used. A major objective of the newly developed AM1/d-CB1 and AM1*-CB1 is to provide a platform to accurately model reactions central to chemical glycobiology using hybrid QM/MM molecular dynamics (MD) simulations. AM1/d-CB1 is applied to a well-known reaction involving purine nucleoside phosphorylase (PNP) and results lead me to conclude that the method shows promise for modelling glycobiological QM/MM systems.
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    Investigating the Interaction of Chitin in Organic Electrolyte Solutions Using Molecular Dynamics
    (2019) Carroll, Lenard Leslie; Venter, Gerhard; Jardine, Anwar
    The dissolution, hydrolysis and fermentation of biopolymers afford biofuels, an alternative source of energy. Unfortunately, biopolymers have hydrogen bonding networks that are difficult to disrupt and dispersion forces to overcome, all of which make it insoluble in most common organic solvents and water under moderate conditions. Much work has been devoted to improving the dissolution of biopolymers, via alternative solvents or by developing new ground-breaking processes. One alternative solvent that has become quite popular in biomass dissolution studies are ionic liquids (ILs). Ionic liquids are attractive solvents due to its broad range of uses and advantageous properties. ILs have been promising in its use in separation, extraction, catalysis, lubricants, fuel cells, batteries and liquid crystal research. ILs also have low vapour pressure, which implies low toxicity with respect to their clean-up. While many ILs are produced under environmentally unfriendly conditions, more studies are being done on finding ways to synthesise these species using the 12 design principles of Green Chemistry. While a plethora of studies has been done on the experimental dissolution of cellulose in ionic liquids, similar studies have been minimal for chitin. As such, a computational investigation on the dissolution of chitin in ionic liquids and organic electrolyte solutions (OESs) is presented here. OESs consists of an ionic liquid and an additional aprotic organic molecular solvent, known henceforth as a co-solvent. These mixtures are considered as some ILs have high viscosities, which decreases its ability to effectively dissolve biopolymers, but by adding co-solvents to the IL, the mixture’s viscosity decreases, potentially improving on the solubility of the biopolymer. Computationally, the dissolution of chitin was modelled through molecular dynamics simulations as implemented in the AMBER MD code, by studying the separation of two 4-methyl-β-D-Nacetylglucosamine-(1→4’)-1’-methyl-β-D-N’-acetylglucosamine ((GlcNAc)2Me2) molecules (chosen as the model for chitin) in various solvent systems using potential of mean force calculations. The ionic liquids of choice were 1-butyl-3-methylimidazolium acetate ([C4C1im][CH3COO]) and 1-butyl3-methylimidazolium methyl sulfate ([C4C1im][CH3SO4]), two ILs that have experimental physical properties available, a requirement for MD simulation validation. The co-solvents chosen were dimethyl carbonate, propylene carbonate and γ-valerolactone, three structurally similar bio-based solvents. The solvation of a (GlcNAc)2Me2 monomer was also studied in this project via radial distribution functions, interaction energies and hydrogen bond analyses, as to support the results produced from the separation study. Additionally, the experimental swelling of chitin was investigated as to compare it to the interaction energy results, acting as further validation of the computational results. The computational results suggest that the (GlcNAc)2Me2 monomer will interact more favourably with pure [C4C1im][CH3COO], followed by the 8:2 [C4C1im][CH3COO]:co-solvent OESs, the 2:8 [C4C1im][CH3COO]:co-solvent OESs and then the pure co-solvents. The solvation study agrees with this trend. The PMF results also show that a (GlcNAc)2Me2 dimer will separate spontaneously in all the solvent systems, with the least amount of thermodynamic work required (to separate) in pure [C4C1im][CH3COO], and the most in pure dimethyl carbonate.
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    Mixed-ligand diruthenium complexes: theoretical modelling and interpretation of electronic absorption spectra
    (2025) Mutomb, Jean-Luc; Ngubane, Siyabonga; Venter, Gerhard
    The speciation and improved solubility of Ru₂(μ-O₂CCH₃)₃(μ-2-Fap)X complexes, where 2-Fap is 2-(2-fluoroanilino)pyridinate, and X represents Cl, Br or I, are influenced by the axial ligand (X) lability and solvent coordination at the axial site. These complexes have Ru(II) and Ru(III) metal centers that can be written as Ru₂⁵⁺. Researchers have observed distinctive spectroscopic and electrochemical characteristics of these Ru₂⁵⁺ complexes but lack an established theoretical framework to fully understand specific characteristic traits, such as a shoulder band in the visible range of the ultraviolet-visible (UV-Vis) spectrum in aqueous solutions, the absence thereof in solutions containing excess chloride ions, as well as the solvatochromic shifts of the UV-Vis bands in aqueous and non-aqueous solvents. This study therefore investigates the characteristics of Ru₂(μ-O₂CCH₃)₃(μ-2-Fap)X complexes using time-dependent density functional theory (TD-DFT) calculations that utilize the PBE/LANL2DZ level of theory and an Integral Equation Formalism Polarizable Continuum (IEF-PCM) solvent model using water, DCM and DMSO. Calculation of natural transition orbitals (NTOs) and spectrum deconvolution methods have aided in characterizing the electronic transitions of the prominent UV band at 250-350 nm as a combination of δ(Ru₂) → π*(Np,C), π(Cl) → π*(Cp,Np) and π(Cl) → π*(Cₐ) transitions, where the subscript “a” and “p” represents the aniline and pyridine moieties, respectively. On the other hand, the weak band at the 400-450 nm visible region is ascribed to the π (Cₐ,Nₐ)/δ*(Ru₂) → π*(Cp,Np) transition, whereas the broad band at 450-750 nm has been characterized as a combination of π(Cl,Ru₂) → δ*(Ru₂), δ(Ru₂) → δ*(Ru₂), π(Cl,Ru₂) → π*(Ru₂), π(F,Cₐ-Cₐ) → π*(Ru₂), π(Cl) → π*(Ru₂) and π(Cl,F,Cₐ-Cₐ) → π*(Ru₂) transitions. The near-infrared (NIR) region is characterized by a weak band at 900-1000 nm, which mainly consists of a δ(Ru₂) → δ*(Ru₂) transition. The equilibria, involving the cationic, neutral and anionic species in solution and corresponding spectroscopic changes are interpreted for Ru₂(μ-O₂CCH₃)₃(μ-2-Fap)X, along with the solvatochromic shift.
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    Molecular mechanism of action of tyrocidine antimicrobial peptides using NMR spectroscopy and computational techniques
    (2012) Munyuki, Gadzikano; Jackson, Graham Ellis; Venter, Gerhard
    The need to come up with new and novel antibiotics that utilize unique mechanisms, to which bacteria cannot generate resistance, was the main motivation of this study. Tyrocidine peptides are non-selective antibiotics that have such properties. However, very limited information is available about their mechanism of action. The aim of this study was to determine the mechanism of action of tyrocidine peptides, tyrocidine A, tyrocidine B and tyrocidine C.
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    Water dynamics about selected monosaccharides in solution
    (2014) Mokoena, Allistair Frans; Naidoo, Kevin J; Venter, Gerhard
    The solubility of molecules in water is governed, amongst other things, by the inherent properties of the solute molecules and water molecules. Water molecules are able to simultaneously form hydrogen bonds as donors and acceptors and thus have unique properties as solvent molecules. These properties influence how water interacts with solute molecules. The mechanism of hydrogen bond exchange plays a role in the hydration of solute molecules. A key to understanding some of the biological processes lies in understanding how solutes interact with water. In this thesis, the hydration of monosaccharides has been studied using computational methods. The hydration structure is elucidated by pair distribution functions and spatial distribution functions. Hydrogen bond exchange dynamics were investigated on the basis of the molecular jump mechanism. Evaluation of the hydrogen bond exchange dynamics reveals two possible pathways. The first pathway corresponds to the molecular jump mechanism reported in literature. The second pathway is described. This pathway provides details on the water-hydroxyl interactions taking place around the monosaccharides. It is shown that the presence of a primary alcohol on pyranose based molecules induces a configuration that allows favourable interactions between water molecules and hydroxyl groups on the sugar molecules. A region of high water density is formed between the primary alcohol, ring oxygen and the hydroxyl on the anomeric carbon. This is due to rotations by water molecules from one hydroxyl, to the adjacent hydroxyl on the sugar molecule. It is not only the presence of the primary alcohol that plays a role in the hydration of the monosaccharides. The relative position of the hydroxyl on the anomeric carbon is shown to create a topology conducive of hydroxyl to hydroxyl hydrogen bond exchanges. The hydration of monosaccharides is rationalised by these effects.