Conveners
Chemistry and Material Science SIG Seminar: II
- Marile Landman (University of Pretoria)
Chemistry and Material Science SIG Seminar: II
- Cornie van Sittert (North-West University)
Chemistry and Material Science SIG Seminar: IV
- There are no conveners in this block
Chemistry and Material Science SIG Seminar: I
- Jeanet Conradie (University of the Free State)
Description
A dedicated Chemistry and Material Science SIG session consisting of keynotes, ordinary oral presentations, student oral presentations as well as flash poster presentations. The program will also include the annual SIG meeting.
Program:
09:00 Keynote: John Mack, Rhodes University, The use of Gaussian 09 to identify trends in the optical properties and electronic structures of porphyrin and BODIPY dyes
09:30 Talk: Marianne Conradie, UFS, Determination of the steric effect of a bulky R substituent on the reaction mechanism of [Rh(CH3COCRCOCH3)(CO)(PPh3)] + CH3I
09:50 Talk: Cliffton Masedi, UL, Computer Simulation and Phase Diagram Prediction of Li2S1-xSex Systems
10:10 Talk: Thishana Singh, DUT, Biosynthesis and computational analysis of amine-ended dual thiol ligand functionalized gold nanoparticles
10:30 Morning Tea Break
11:00 Student talk: Cameron Matthews, NMU, A theoretical study of electronic (QTAIM NBO) and geometric structures of a series of lanthanide trichloride LnCl3 complexes (Ln=La-Lu) with the N-donor ligand bis(2-pyridylmethyl)amine (DPA)
11:15 Student talk: Elkana Rugut, Wits, Thermoelectric properties of CdAl2O4 spinel
11:30 Student talk: Fisayo Olotu, UKZN, Delving through the wonders of green tea - Probing the dynamic selectivity of polyphenol Epigallocatechin gallate
11:45 Student talk: Francis Opoku, UJ, Tuning the electronic structures
12:00 Student poster flash presentation: Ramogohlo Diale, UL, Computational modelling of TiPd-Ir high temperature shape memory alloys
12:05 Student poster flash presentation: Sharlene-Asia Naicker, UKZN, Computational studies of the corrosion mechanisms in transformers
12:10 Student poster flash presentation: Surya Narayana Maddila, UKZN, Synthesis and spectral properties of 5-substituted 1H-tetrazole derivatives using with Mn/HAp catalyst and DFT calculations
12:15 Student poster flash presentation: Nkosinathi Malaza, Wits, Double-layer capacitance from ab initio simulations
12:20 Student poster flash presentation: Jonathan Gertzen, UCT, MAX Phases as an Electrocatalyst Support Material: A DFT Study
12:25 Discussion
12:30 Lunch Break
13:30 Talk: Nkululeko Damoyi, MUT, A DFT study of the ODH of n-hexane over isolated H3VO4 and H4V2O7
13:50 Student talk: Adebayo Adeniyi, UFS, The theoretical investigation of reduction potentials and and spectroscopic properties of nitrobenzene and keto-enol molecules
14:05 Student talk: Abdulgaffar, UP, Hybrid functional study of BiOi, BiCs, BiBsHi and BiOiOi Complexes in Silicon
14:20 Student talk: Joseph Simfukwe, UP, First Principles study of Zn/Cu doped hematite surfaces for Photoelectrochemical water splitting
14:35 Talk: Khalid Ahmed, UKZN, Understanding the influence of pH/pKa by theoretical and computational method for loading/release of Ibuprofen (To Be Confirmed)
14:55 Discussion
15:00 Afternoon Tea Break
15:30 SIG Meeting
Titanium metal and its alloys are widely applied as structural materials in aerospace, automobile and biomedicine due to their good ductility, light-weight ratio and biocompatibility. During investment casting of titanium components a thin layer is formed on the surface known as alpha case layer. Formation of this layer degraded the fatigue and ductility, that results in material...
Recently, the attention to sodium-ion batteries has been refocused on large-scale energy storage applications, due to sodium's low cost and infinite abundance. The current study focuses on the effects of high temperatures on nanoporous Na -TiO2 within the temperature ranges of 0 K -2000K. Molecular dynamics simulations studies were carried out using the DL_POLY 2.20 code on South Africa’s...
biochemical processes make the discovery of drugs and biomaterials possible. A research
framework common to genomics and proteomics is needed to conduct biomolecular
simulations that will connect biological data to the dynamic molecular mechanisms of
enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of
complex setups and a myriad of possible choices preventing...
Background: The use of small molecule antagonists in cancer immunotherapy represents a paradigm shift towards the achievement of novel treatment modalities with improved efficacies. This strategy was potentiated with the recent identification of novel inhibitors; BMS-1001 and BMS-1166, which specifically target PDL-1, induced dimerization and prevent association with PD-1, its naturally...
In the last few year members of the Chemistry and Materials Science SIG expressed the need for a forum to present their work. Especially for students working in HPC to be exposed to experts in the field of research. However, due to the diversity of the application in the field of HPC the only common denominator for all the researchers in this field is the use of the CHPC.
For this reason the...
Numerical methods are essential in many scientific applications for their ability to make discrete data
sets continuous. Interpolation is one commonly used method, which helps one to predict the value
of any point between two adjacent data points of a data set. Cubic spline interpolation is highly
regarded as the most useful method for its ability to interpolate between data points in a...
There are several computational techniques and experimental studied minerals sulfides [1-2]. Group of sulfides in nature and significant importance because they serve as a source of economic for many applications. It is also in a main various precious metals such as iron, cobalt, nickel and lead. We used parameterization technique to study iron sulfides, pyrite nanoparticles (NP’s) and...
The Molecular Dynamics calculations of the LiCl and Li-Cl-Ti systems were achieved by utilizing various codes of MD simulations at the CHPC.
The Thermodynamic properties and temperature dependence calculations of the structures were achieved by utilizing the DL_POLY code.
Application code: DL_POLY
Problem size: 216 – 1024 atoms
Core count: 48
Computational modelling methods were employed to investigate pyrite surfaces, and the effect of water molecule on the three typical thiol collectors (xanthate, dithiocarbomate and dithiophosphate) interactions at the pyrite surfaces. The calculated surface energies for {100}, {110}, {111} and {210} showed that {100} surface is most stable whereas {110} is the least stable. Morphologies of...
Abstract
Using a ligand-based pharmacophore screening workflow, two well-defined molecular drug targets were identified; these are epidermal growth factor receptor (EGFR) and estrogen receptor-α (ERα). These proteins have been imperative chemotherapeutic targets in current treatment regimens of breast cancer. Molecular docking studies were performed on the most active compounds for each...
Spinel LiMn2O4 is one of the most attractive material for the next generation of Li-ion batteries, due to the low cost of manganese and straightforward synthesis. In this paper, we have used the MedeA-Universal Cluster Expansion package which allows to set up, construct and automatically converge cluster expansion for LiMn2O4 spinel systems and generate the unique structures within the random...
Abstract
Background/Aim: Thrombosis occurs when blood clots and blocks a blood vessel thereby reducing blood flow, serving as the underlying mechanism of some globally prominent ‘lethal’ diseases such as myocardial infarction, ischemic stroke, and venous thromboembolism (VTE). Moreover, the critical roles of activated Hageman Factor XII (FXIIa) in the coagulation cascade have presented it as a...
The Denoising Autoencoder Self-Organizing Map (DASOM) is a combined machine learning
method of dimensionality reduction, feature extraction, and clustering[1]. Deep learning techniques
show significant promise in improving the results of various clustering unsupervised learning
algorithms, however unsupervised learning requires extremely large data sets in order to obtain
accurate results.
The...
Density functional theory study of copper zinc tin sulphide (Cu${}_2$ZnSnS${}_4$) doped with calcium and barium
T.M. Mlotshwa${}^1$, N.E. Maluta${}^1$, R.R. Maphanga${}^2$
${}^1$Department of physics, University of Venda, P/Bag X 5050, Thohoyandou, 0950, Limpopo province, South Africa
${}^2$Council for scientific and Industrial Research, P.O Box 395, Pretoria, 0001, Gauteng province,...
Metal-to-ligand charge transfer compounds, specifically the ruthenium bipyridyl complexes, are presently amongst the ideal photocatalytic compounds used, not just in the DSSC conversion of solar energy into usable electric current,[1] but also in photocatalytic reduction of both CO2 and H2O, towards the production of renewable H2 fuel and CO,[2] the latter being the main reagent in the...
Fischer carbenes have been explored mainly for their usefulness in the synthesis of organic and natural products in the past. These metal carbene complexes have been further investigated in metathesis catalytic processes and poor activity has been reported [1]. Very few catalytic studies on any other transformations using Fischer carbenes have been reported to date. The focus of our study was...
The adsorption heterocyclic collectors such MBT, MBO, MBI and their derivatives on pyrite mineral forms a basis in understanding the reactivity that may be applicable in a wide range of sulphide minerals. This study explored the structural and atomic charges directly related to the reactivity of MBT, MBO, MBI, n-Et-MBT, n-Et-MBO and n-Et-MBI onto pyrite (100) surface. We employed the CASTEP...
Sustainable, environmentally friendly energy is currently well sought after. Biomass is considered as one of the world’s major energy sources, as the break-down of biomass leads to the production of biofuel and “green” chemicals. The degradation of biomass is however, recalcitrant and not yet sustainable. Researching the activity and mechanisms of the bacterial enzymes that utilize and...
First principles studies of Zn/Cu doped {0001} and {012} surfaces of hematite for enhanced photoelectrochemical water splitting have been carried out. Doping was confined to planes in close proximity to the termination region, precisely from the top most layer to the third inner layer (plane P1, P2 and P3) of Fe atoms. The two surfaces and the three doped layers were found thermodynamically...
Free energy has always served as a necessary measure for understanding
chemical reactions, particularly knowing whether a reaction will occur
spontaneously, but it is also a useful quantity when considering equilibrium
systems, revealing qualities such as mean distances and preferred orientations.
However adequate sampling of full multidimensional free energy surfaces from
molecular dynamic...
A combination of global search techniques and density functional theory (DFT) methods were employed to determine the structural stabilities of β-MnO2 nanoclusters across the energy landscape. Nanostructuring offers the ability to improve material properties by adjusting the size to explore their novel collective optical, mechanical, magnetic and electronic properties. Several nanostructured...
The Chemical Abstracts Service reports that over 60 million compounds have been produced through synthetic chemistry over the past 20 years and the combined academic and commercial collections of small molecules worldwide are at an estimate of above 100 million. A point to note however is that these large numbers cannot ascertain efficacy, absence of side effects and toxicity, thus the need...
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and...
Bacterial resistance to antibiotics is of great concern in the development of new infectious therapeutics especially as there are two million deaths due to bacterial infection annually worldwide. There is therefore a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a...
**INTRODUCTION:The management of Alzheimer’s disease (AD) has posed a global burden; most especially in the developed countries of the world as millions of dollar is spent annually to alleviate the disease among old people. Recently it was noted that the progression of Alzheimer's disease involves a decrease in the activity level of mitochondrial ATP synthase in the brain cell which makes it...
Conventional p-n junction based silicon solar cells are costly for reasons such as production methods and high-priced materials. SnO2 due to its outstanding electrical properties it’s regarded as reassuring competitor for photovoltaic cells. Absorption of water and oxygen on SnO2 then becomes a primary understanding for several application of metal oxide including glass coating, ceramic...
BACKGROUND:
Stroke is the third leading cause of death worldwide, with 87% of cases being ischemic stroke. The
two primary therapeutic strategies to reduce post-ischemic brain damage are cellular and vascular
approaches. The vascular strategy aims to rapidly re-open obstructed blood vessels, while the
cellular approach aims to interfere with the signalling pathways that facilitate neuron...
Titanium and its alloys, with their high strength to weight ratio and high-temperature properties, are used extensively by the aerospace industry. They are typically utilized for airplane parts and in medical industries. Recently, demand for shape memory alloys, which can be used at high temperature has increased. The first principle approach was employed to investigate the effect of the third...
The ability of a drug molecule to selectively bind to and inhibit a biological target is an important attribute that account for high efficiency and reduced toxicity. More recently, drug selectivity has been highly considered in the discovery and developmental processes of antimicrobial compounds with broad spectrum activities. Although bacterial RNA polymerase (bRNAP) was reported as a...
Selective covalent inhibition of Hepatitis C virus (HCV) is a highly neglected domain in literature, intensified by the evident lack of efficient structure-based drug design protocols. Herein, we provide an atomistic insight into a novel selective approach to potentially inhibit HCV polymerase. Covalent molecular dynamic analyses revealed the inhibitory mechanism of compound 47 on the...
Covalent inhibition targeting non-catalytic residues is rapidly gaining attention in drug discovery. Protein tyrosine phosphatases 1B (PTP1B) is an attractive target for therapeutic interventions in cancer and other diseases. Two binding sites of PTP1B enzyme were identified, catalytic and allosteric. The catalytic site is deep and narrow which protects the active site amino acid residue...
Lithium-ion batteries have been broadly used in various portable electronic devices and the application targets are currently moving from small-sized mobile devices to large-scale electric vehicles and grid energy storage. As such, high-energy cathodes particularly Li2MnO3–LiMnO2 layered–layered materials are of significant interest due to their high specific...
The structural properties of graphene oxide (GO) were studied through the classical molecular dynamic simulations. The variation of energy and temperature for the NVT, NPT and NVE ensemble was explored, and in the process the entropy was computed to determine the degree of disorder in the system. The pair distribution functions were plotted for carbon-carbon atoms and the nearest neighbouring...
The use of the Gaussian 09 software package on the Lengau cluster to carry out DFT and TD-DFT calculations to identify structure-property relationships in the properties of porphyrin [1] and BODIPY [2] dyes will be described. An analysis of the DFT and TD-DFT calculations for these dyes can provide an insight into their electronic structures and hence guide the rational design of novel dyes...
Discovery of new compounds active against human cancers is vital for the ongoing battle against the disease. Structure-based drug design could be used to identify high quality leads. Even though current drugs provide significant therapeutic effects, tumor heterogeneity and resistance often render them ineffective. That is why we need highly potent inhibitors against reliable targets that can...
Deep learning techniques show significant promise in improving the results of unsupervised learning
algorithms such as the Self Organising Map (SOM) which allow for clustering and visualisation of
datasets. One such approach is the use of autoencoders[1] which aim to encode a dataset in a way
which provides an improved representation of the data. The Growing Hierarchical...
Blocking the oncogenic signaling of B-cell receptor (BCR) has been recently explored as a viable therapeutic approach in the treatment of Diffuse large B-cell lymphoma (DLBCL), an aggressive form of Non-Hodgkin Lymphoma. This involves the multi-targeting of certain members of the SRC kinase family; LYN, FYN and BLK, which propagate BCR signals to downstream effectors. In a recent study, the...
