Browsing by Author "Lopis, Anton S"

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    CCDC 2102346: Experimental Crystal Structure Determination
    (2021-12)
    This item contains the crystal structural determination on CSD associated with a journal article titled 'Iron(III) and copper(II) complexes derived from the flavonoids morin and quercetin: Chelation, crystal structure and DFT studies', accessible via https://doi.org/10.1016/j.molstruc.2022.132591
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    Scalability of DL_POLY on High Performance Computing Platform
    (2017-12) Mabakane, Mabule S; Moeketsi, Daniel M; Lopis, Anton S
    This paper presents a case study on the scalability of several versions of the molecular dynamics code (DL_POLY) performed on South Africa‘s Centre for High Performance Computing e1350 IBM Linux cluster, Sun system and Lengau supercomputers. Within this study different problem sizes were designed and the same chosen systems were employed in order to test the performance of DL_POLY using weak and strong scalability. It was found that the speed-up results for the small systems were better than large systems on both Ethernet and Infiniband network. However, simulations of large systems in DL_POLY performed well using Infiniband network on Lengau cluster as compared to e1350 and Sun supercomputer.
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    Synthesis, comprehensive characterization, crystallographic and density functional theory (DFT) studies of tridentate amic acid compounds
    (2025) Matinise, N; Ineza, C; Oladipo, SD; Begum, NM; Badeji, AA; Lopis, Anton S; Luckay, RC
    Amic acids constitute a class of organic acids which have both carboxylic as well as amide functional groups within their structure and their synthesis has gained significant interest due to their applications in medicine and hydrometallurgical industries. In this study, a series of novel tridentate amic acid-based ligands were synthesized via a bimolecular nucleophilic substitution (SN2) reaction between 2‑chloro‑N,N-dioctylacetamide and glycine derivatives to afford (2-(dioctylamino)-2-oxoethyl)glycine (L1), N-(2-(dioctylamino)-2-oxoethyl)-N-methylglycine (L2), N-(2-(dioctylamino)-2-oxoethyl)-N-ethylglycine (L3), N-(2-(dioctylamino)-2-oxoethyl)-N-isobutylglycine (L4) and (2-(dihexylamino)-2-oxoethyl) methylglycine (L5). Structural modifications were introduced by varying the alkyl substituents on the central amine nitrogen to investigate their influence on coordination behaviour. Ligands L1 – L5 were characterized using various spectroscopic techniques such as FT-IR ATR, NMR (1H and 13C), together with mass spectrometry to confirm their successful synthesis. The diagnostic peak for the methylene protons in the region of (3.8–4.0) ppm in the 1H NMR spectra corroborates the formation of a new bond between the amino acid moiety and the amide carbonyl carbon across all compounds. To further validate the coordination properties of these ligands, copper(II) complexes of two representative ligands (L2 and L5) were obtained and structurally characterized using single-crystal X-ray diffraction. The crystal structures of copper(II) complexes of L2 and L5 which adopt the general molecular formula of Cu(L2)2 and Cu(L5)2 also affirm the successful synthesis of the tridentate amic acids. These are the first reported crystal structures of copper complexes involving tridentate amic acid extractants. The complexes adopt a distorted octahedral geometry with the Cu²⁺ ion coordinated by two ligands in a tridentate fashion—through carboxylic, amide, and amine donor atoms—resulting in four five-membered chelate rings per complex Notably, the observed bite angles were smaller than 90°, indicating a constrained coordination environment and supporting a distorted geometry. To complement the experimental findings, Density Functional Theory (DFT) calculations at B3LYP (Becke-Lee-Yang-Parr) method with the LANL2DZ and 6–31 G (d, p) basis set were performed to model the electronic and structural properties of the ligands and their Cu(II) complexes. The calculations not only corroborated the crystallographic bond lengths and angles but also highlighted the role of alkyl substituent sterics and electronics in modulating complex stability. The results showed that electron-donating alkyl chains affect the bond metrics at the amine nitrogen, which in turn influences the metal-binding cavity and stability of the resulting complex. Overall, this work provides the first comprehensive correlation between synthetic, spectroscopic, crystallographic, and theoretical data for this class of ligands. It establishes a foundation for tailoring amic acid ligands with improved selectivity and efficiency for base metal ion separation.
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    The use of amino acids in gold leaching; the FTIR and DFT approach
    (2024-09) Tapfuma, A; Akdogan, G; Luckay, RC; Lopis, Anton S
    The drive towards environmentally benign gold mining, often referred to as ‘green mining’, has gained momentum as a response to the escalating environmental concerns linked to cyanide usage in gold processing. Recently, amino acids have emerged as promising gold-leaching lixiviants, offering advantages over the conventional cyanide methods. However, the bulk of research has predominantly focused on glycine, the first member of the alpha-amino acid group, leaving other amino acids unresearched. In a novel approach, this study shifts the focus to the use of alanine in gold leaching and associated gold-alanine complexation at both experimental and computational levels, coupled with dissolution work. Experimental analyses through Fourier Transform Infrared Spectroscopy (FTIR) showed that alanine, in either its neutral or deprotonated state, effectively bonds with gold through donor electrons from nitrogen (N) and oxygen (O) at the amine and carboxylic end, respectively. In addition, the complexes of deprotonated alanine, compared to neutral (zwitterion) alanine, exhibited higher characteristic peak shifts during complexation. Furthermore, quantum computational calculations revealed that deprotonated alanine formed the most stable gold complex compared to the neutral amino acid, characterized by the N-Au-N bonding. The complexation of gold and deprotonated alanine exhibits the larger complexation energy compared to the neutral form, as revealed by the computational analyses. The third part of the study involved the dissolution of gold using both the deprotonated and neutral molecules, and the results showed that gold dissolution was more pronounced using the deprotonated molecule. This study showed that the gold dissolution is connected to the complexation as shown by FTIR and DFT, and this can be seen in high gold dissolution corresponding to a high peak shift at deprotonation pH and high complexation energy for the gold with the deprotonated alanine compared to the neutral alanine. Lastly, the study suggests that deprotonated alanine can be a possible lixiviant to leach gold from secondary gold sources such as tailings.
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    ZEJQOY : bis(N'-[2,2-dimethyl-1-(oxo)propyl]-N-methyl-N-phenylcarbamimidothioato)-platinum(ii) Title of Journal (Source) ​​The Cambridge Crystallographic Data Centre (CCDC)
    (2022-06)
    The dataset (Experimental Crystal Structure Determination) is linked to the following study: Three new platinum(II) complexes derived from asymmetrically di-substituted pivaloylthiourea ligands (L1–3) are synthesized and characterized by 1H, and 195Pt{1H} NMR. The ligands and PtL1–3 complexes display configurational E,Z isomerism evinced by distinct sets of 1H, 195Pt{1H} NMR resonances observed in dichloromethane‑d2. Single-crystal X-ray diffraction studies reveal a bidentate cis-PtL1–3 coordination mode, in which two sulfur and oxygen donor atoms bind to Pt(II) forming a six-membered chelate. In addition, the EE isomers were preferentially isolated in acetonitrile for cis-PtL1 and cis-PtL2, while ZZ was obtained for cis-PtL3 with N-phenyl substituent. The relative energies of the cis-ZZ-Pt-L1–3, cis-EZ-Pt-L1–3, cis-EE-Pt-L1–3 configurational isomers are obtained by DFT analysis at the M06-2X/def2-SVP level of theory using an implicit acetonitrile solvent. Moreover, the structural studies indicate a potential intra-electron transfer from dz2 (HOMO) to dx2-y2 (LUMO), with a reduced electron affinity at the LUMO level for the cis-ZZ/ZE/EE-Pt-L1–3 structures. The antioxidant capacity of the L1–3 ligands and cis-PtL1–3 were evaluated using the ORAC, DPPH radical scavenging and FRAP methods. The free L1–3 ligands showed higher antioxidant activities in comparison to their coordinated cis-PtL1–3 complexes.