Browsing by Author "Venter, Gerhard A"

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    A computational study of acidic Ionic Liquids for cellobiose hydrolysis in ionic liquids
    (2019) Nel, Jessica Lisé; Venter, Gerhard A
    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. 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.
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    Aqueous phase catalysis using mono- and bimetallic transition metal complexes
    (2015) Matsinha, Leah Charlie; Smith, Gregory S; Mapolie, Selwyn F; Venter, Gerhard A
    The synthesis and characterization of monomeric and dimeric salicylaldimine water-soluble ligands is discussed. The salicylaldimine ligands (2.3-2.10) were synthesised via Schiff base condensation reactions of various amines with water-soluble sulfonated salicylaldehydes (2.1 and 2.2). The ligands were characterized using various analytical and spectroscopic techniques. Complexation reactions of these water-soluble ligands (2.3-2.10) with [Rh(COD)Cl]2 gave the corresponding water-soluble mononuclear (2.11-2.14) and binuclear (2.15-2.18) Rh(I) complexes. All the complexes were characterized using nuclear magnetic resonance spectroscopy, infrared spectroscopy, single crystal X-ray diffraction (for complex 2.14), mass spectrometry, elemental analysis and melting point determinations.
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    Development of a force field with condensed phase consistent charges for N,N' - dialkylimidazolium room temperature ionic liquids
    (2015) Mngadi, Vela; Venter, Gerhard A
    Most force field models for Room temperature ionic liquids cannot properly elucidate statics and dynamics. It is in this context that we set to assess the most efficient way to model RTILs while maintaining the integrity of the liquids statics and dynamics. The development approach begins with the investigation of the effects that the linear scaling of partial atomic charges on nonpolarisable force fields from a reference potential has on the structure and dynamics of the room temperature ionic liquids (RTILs) 1-butyl-3-methylimidazolium tetraflouroborate [C4MIM][BF4] and 1-butyl-3-methylimidazolium hexaflourophosphate [C4MIM][PF6]. The results show that the three-dimensional structure of the liquid is changed ever so slighter by the linear scaling of atomic charges. While dynamic properties such as viscosity and self-diffusion coefficients were majorly affected by charge scaling. Self-diffusion coefficients that span a range of four orders of magnitude between the original model and the scaled model where the ionic charge was ±0.6 e. Viscosity estimates calculated using the Green-Kubo and the Einstein relationships revealed that the linear scaling of atomic charges results in increased mobility of the simulated liquid. Implicit inclusion of polarisation effects was investigated, Here a new charge scheme development using Quantum mechanics/Molecular mechanics (QM/MM) methods in CHARMM 35 interfaced with GAMESS-UK was propose. The atomic charges were derived from liquid phase calculations using an iterative procedure. This was carried out for individual ions and cation-anion pairs, for the analysis of charge transfer, within the liquid environment. The results obtained gave predictions of density, liquid structure and self-diffusion coefficients that were in excellent agreement with experimental data available. This method is preferable over the commonly used charge scaling methodology which is deem as an unphysical approach for the simulation of [C4MIM][BF4] and [C4MIM][PF6]. A polarisable force field based on the Drude oscillator model is presented. The model proves to be most effective for the simulation of RTILs. The force field accurately reproduced experimental results for the physicochemical properties reviewed.
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    Experimental and time-dependent density functional theory characterization of the UV−Visible spectra of monomeric and μ‑Oxo dimeric ferriprotoporphyrin IX
    (American Chemical Society, 2012) Kuter, David; Venter, Gerhard A; Naidoo, Kevin J; Egan, Timothy J
    Speciation of ferriprotoporphyrin IX, Fe(III)PPIX, in aqueous solution is complex. Despite the use of its characteristic spectroscopic features for identification, the theoretical basis of the unique UV−visible absorbance spectrum of μ- [Fe(III)PPIX]2O has not been explored. To investigate this and to establish a structural and spectroscopic model for Fe(III)PPIX species, density functional theory (DFT) calculations were undertaken for H2O−Fe(III)PPIX and μ- [Fe(III)PPIX]2O. The models agreed with related Fe(III)porphyrin crystal structures and reproduced vibrational spectra well. The UV−visible absorbance spectra of H2O−Fe(III)PPIX and μ-[Fe(III)PPIX]2O were calculated using time-dependent DFT and reproduced major features of the experimental spectra of both. Transitions contributing to calculated excitations have been identified. The features of the electronic spectrum calculated for μ-[Fe(III)PPIX]2O were attributed to delocalization of electron density between the two porphyrin rings of the dimer, the weaker ligand field of the axial ligand, and antiferromagnetic coupling of the Fe(III) centers. Room temperature magnetic circular dichroism (MCD) spectra have been recorded and are shown to be useful in distinguishing between these two Fe(III)PPIX species. Bands underlying major spectroscopic features were identified through simultaneous deconvolution of UV−visible and MCD spectra. Computed UV−visible spectra were compared to deconvoluted spectra. Interpretation of the prominent bands of H2O−Fe(III)PPIX largely conforms to previous literature. Owing to the weak paramagnetism of μ-[Fe(III)PPIX]2O at room temperature and the larger number of underlying excitations, interpretation of its experimental UV−visible spectrum was necessarily tentative. Nonetheless, comparison with the calculated spectra of antiferromagnetically coupled and paramagnetic forms of the μ-oxo dimer of Fe(III)porphine suggested that the composition of the Soret band involves a mixture of π→π* and π→dπ charge transfer transitions. The Q-band and charge transfer bands appear to amalgamate into a mixed low energy envelope consisting of excitations with heavily admixed π→π* and charge transfer transitions.
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    Identification of natural product stereochemistry via calculation of ECD spectra
    (2018) Lolli, Riccardo; Venter, Gerhard A; Wilkinson, Karl A; Terenziani, Francesca
    Most commercially available antibiotics are obtained from natural products, secondary metabolites of bacteria or other living organisms. Due to the importance of this class of compounds in medicinal chemistry and growing drug resistance, efforts to discover, characterize and isolate new or improved antibiotics are continually increasing. The assignment of the absolute configuration (AC) adopted by these compounds is a crucial aspect of the characterization step and knowledge of the stereochemistry is an important factor in deciphering the interaction of these compounds with the organism and thus, the mechanism of action. In order to assign the AC, several techniques, such as X-ray diffraction and NMR experiments as well as the standard electronic spectroscopy experiments (UV-Vis, ECD, etc.) or less widespread vibrational and rotational spectroscopy experiments (VCD, ROA, etc.) can be used, often in combination. However, sophisticated synthetic strategies or difficult isolation of the natural compound often leads to a small amount of product available, making some of the previous techniques unpractical; in addition to the potential structural complexity of the molecule, this can make the experimental assignment of the AC problematic. For this reason, a computational approach, aimed at calculating observable properties of the products, generating spectra and assigning the AC through comparison between the calculated and the experimental spectra, has proven useful in many cases. Formicamycin is a natural product, isolated from a new member of Streptomyces bacteria, which has shown great activity against pathogenic drug-resistant bacteria and fungi, without developing antimicrobial resistance. This dissertation shows that the chiral axis of Formicamycin can be assigned as R, through the calculation of electronic circular dichroism (ECD) spectra and comparison to the experimentally determined spectrum in methanol. ECD spectroscopy is very sensitive to the chiral environment of chromophores and can be used to distinguish between different isomers. The computational procedure has been broadly defined in previous studies and involves three general steps: 1) generation of an ensemble of structures, 2) optimization of the structures and calculation of the rotational strengths of each and 3) generation of the Boltzmannweighted spectrum. Here, two different force fields (OPLS3 and MMFFs) were used for generating the ensemble of conformers, followed by PBE0 DFT calculations to determine the optimal geometry and finally, TDDFT calculations to compute the rotational strengths of each conformer. Furthermore, the spectra were calculated in four different solvents, using the implicit SMD method, in order to inform future studies about “variable solvent circular dichroism”. Different conformations of a molecule can be controlled by the choice of solvent and it is hypothesised that a change in solvent will result in a “fingerprint” shift in the ECD spectra that could permit assignment of the stereochemistry. The entire process was automated using a module written in Python.
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    The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning
    (American Society for Biochemistry and Molecular Biology, 2013) Weber, Brandon W; Kimani, Serah W; Varsani, Arvind; Cowan, Donald A; Hunter, Roger; Venter, Gerhard A; Gumbart, James C; Sewell, Trevor B
    All known nitrilase superfamily amidase and carbamoylase structures have an additional glutamate thatis hydrogen bonded to the catalytic lysine in addition to the Glu, Lys, Cys “catalytic triad.” In the amidase from Geobacillus pallidus, mutating this glutamate (Glu-142) to a leucine or aspartate renders the enzyme inactive. X-ray crystal structure determination shows that the structural integrity of the enzymeismaintained despite themutation with the catalytic cysteine (Cys-166), lysine (Lys-134), and glutamate (Glu- 59)in positions similar to those of the wild-type enzyme. In the case of the E142L mutant, a chloride ion is located in the position occupied by Glu-142 O 1 in the wild-type enzyme andinteracts with the active site lysine. In the case of the E142D mutant, this site is occupied by Asp-142 O1.In neither case is an atom located at the position of Glu-142 O 2 in the wild-type enzyme. The active site cysteine of the E142Lmutant was found to form aMichael adduct with acrylamide, which is a substrate of the wild-type enzyme, due to an interaction that places the double bond of the acrylamide rather than the amide carbonyl carbon adjacent to the active site cysteine. Our results demonstrate that in the wild-type active site a crucial role is played by the hydrogen bond between Glu-142 O 2 and the substrate amino groupin positioning the substrate with the correct stereoelectronic alignment to enable the nucleophilic attack on the carbonyl carbon by the catalytic cysteine.
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    Molecular dynamics simulations of the electrical conductivities of high temperature metallurgical slags
    (2018) Mongalo, Lehlohonolo; Venter, Gerhard A; Lopis, Anton S
    The structural properties and electrical conductivities of nine CaO-MgO-Al₂O₃-SiO₂ slags with compositions in the peralkaline region have been calculated using molecular dynamics simulations. Where applicable, results were compared to those estimated from composition data alone. The proportion of nonbridging oxygen (NBO) and bridging oxygen (BO) atoms were determined from simulation and shown to be in reasonable agreement with theoretical prediction, with the number of NBOs increasing as the number of network modifying cations increase. Bridging oxygen atoms were classified into Si-O-Si, Si-O-Al or Al-O-Al linkages and the results used to establish whether the Al avoidance principle is applicable. Consistent with experimental and simulation results reported elsewhere for aluminosilicates, a surprisingly large number of fivefold–coordinated Al atoms were found, even though the simulated compositions contain CaO and MgO far in excess of the tectosilicate join. The number of bridging oxygens coordinated to tetrahedral [SiO₄]⁴⁻ and [AlO₄]⁵⁻ units, namely the Qⁿ distribution, was determined. Although a good comparison to the theoretical average Q was found at low basicity, at higher basicity greater deviation was seen. Finally, electrical conductivities calculated using the Einstein relation, taking cross–correlations into account, were in excellent agreement with experimentally measured values, although Nernst–Einstein conductivities, estimated from self–diffusion coefficients alone, showed large deviations. In doing these calculations, it is implicitly assumed that the total electrical conductivity of the slags results from motion of the ions alone and that there is no electronic component to the conductivity. Results therefore show that molecular dynamics simulations are able to reliably predict conductivity, but values calculated indirectly, i.e. using the Nernst–Einstein relationship, should be used with care. At low basicity theoretical predictions of structural disorder, based on Zachariasen's Random Network Model, are in reasonable agreement with simulation, but this agreement worsens as the proportion of network modifying cations increases. Artificial neural network (ANN) models for predicting electrical conductivities of slags, based on structural properties, were also successfully developed. Two layer MLP feedforward ANN models, using the resilient back propagation algorithm for training, were used to predict conductivities. The input and output parameters were calculated using MD simulations and different combinations of input parameters, as well as number of hidden neurons, were used to find the best model. The best models were identified based on having low MSE errors, when applied on a test data set for which experimental results are known. Using a subset of structural parameters (average Q⁰, Q¹ distributions and the number of NBO atoms) yielded the best model with an MSE of 6.8. More general models using a greater set of structural parameters had MSEs in the range of 33.0 to 35.2. The artificial neural network models have demonstrated a reasonable agreement in predicting the MD calculated electrical conductivities of slags and hence, proved to be effective methods for the prediction of electrical conductivities of slags using structural properties as input parameters.
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    The nature of interactions in Alkylimidazolium based ionic liquids
    (2015) Sinxi, Monde; Venter, Gerhard A
    Ionic liquids are materials that have the ability to be designed for specific tasks. Their properties can be adjusted by changing the molecular constituents of the liquid or the intermolecular interactions between composite ions through functionalisation. Therefore, understanding the nature of the interactions between ions is important. In the thesis, we use density functional theory calculations to obtain conformers of 1-ethyl-3-methylimidazolium ([emim]+)paired with the anions [Cl]-, [Br]-, [MeCO2]-, [CF3CO2]-, [MeSO3]-, [CF3SO3]-, [BF4]- and [PF6]-. We analyse the structures of the pairs and then explore the nature of the electrostatic, dispersion and hydrogen bonding interactions. Electrostatic interactions were the most dominant interactions. The dispersion interaction energies were found to be of the same order as the estimated energy of the hydrogen bond. The non-covalent index (NCI) analysis was used to visualise the non-covalent interactions in real space as enclosed surfaces. The properties of the surfaces were used to characterise interaction types, namely van der Waals interactions and hydrogen bonds. Furthermore, we find that the density enclosed within the hydrogen bonding surfaces can be used to estimate the potential of the hydrogen bond. To our knowledge, a potential for hydrogen bonding from NCI has not been explored for ionic liquids. Finally, the average strength of the hydrogen bond was calculated from structures extracted from molecular dynamics simulations. They reveal that the hydrogen bond strength for [emim][MeCO2] is approximately two-thirds weaker in the condensed phase than in the gas phase. The effect of the polarising environment is also found to weaken the hydrogen bond slightly.
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    Using solvent binding and dielectric friction to interpret the hydration behavior of complex anions
    (American Chemical Society, 2011) Matthews, Richard P; Venter, Gerhard A; Naidoo, Kevin J
    We investigate the hydration structure and water/ion dynamics about complex anions using a revised platinum group metal chloro-anion force field. Nanosecond atomistic molecular dynamics simulations were performed for the platinum group metal chloro-anion complexes. This investigation makes the first attempt at describing diffusion trends of polyatomic complex anions with counterions such as these using both hydrodynamic and dielectric friction properties of the anion solution. The transition metal anion complex diffusion rates are shown to be correlated to their first solvent shell radial distribution function peaks, their mean water residence times, and their solvation volumes as calculated by Voronoi tessellation of the simulation cell. The general trend is for slower diffusion rates to result from larger hydration shell volumes. This diffusion rate trend calculated from Stokes’ law is best described using the solventberg approach with well-chosen effective solvated radii. However, to improve the diffusion constant estimates when they are compared with those calculated from computer simulations, the dielectric friction is required.