Research Articles (Chemistry)
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Browsing Research Articles (Chemistry) by Author "Conradie, Jeanet"
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Item Open Access Data to understand the nature of non-covalent interactions in the thiophene clusters(Elsevier, 2021) Malloum, Alhadji; Conradie, JeanetWe have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we have also provided the optimized Cartesian coordinates of all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to locate local and global minima structures of molecular clusters. The located geometries have been optimized at the MP2/aug-cc-pVDZ level of theory using Gaussian 16 suite of programs. To understand the nature of non-covalent interactions, we have performed a quantum theory of atoms in molecules (QTAIM) analysis on all the structures of the thiophene dimer. Furthermore, the QTAIM analysis has been performed also on the most stable structure of the thiophene trimer and tetramer. We have used the AIMAll program to perform the QTAIM analysis. The data reported in this paper contains the critical points, the bonds paths and their related properties, for each investigated structures. Besides, the data contains the optimized Cartesian coordinates of all the investigated structures of the thiophene clusters. This can be use for any further investigations involving thiophene clusters. For further information and analysis, the reader is referred to the original related research article (Malloum and Conradie, 2022).Item Open Access Density functional theory calculated data of the iodomethane oxidative addition to oligothiophene-containing rhodium complexes – importance of dispersion correction(Elsevier, 2021) Mateyise, Nandisiwe Ghandi Sibongile; Conradie, Jeanet; Conradie, Marrigje M.Electronic and free energy data of density functional theory calculated optimized geometries of the reactants, transition state of the oxidative addition reaction and different reaction products of the [Rh(RCOCHCOCF 3 )(CO)(PPh 3 )] + CH 3 I reactions (R = C 4 H 3 S, C 4 H 3 S-C 4 H 2 S and C 4 H 3 S-C 4 H 2 S-C 4 H 2 S) are presented to illustrate the influence of the amount of thiophene groups, the implicit solvent and dispersion correction on the calculated energies. All calculations were done with the B3LYP functional, in gas as well as in solvent phase, with and without dispersion correction. The data can save computational chemists time when choosing an appropriate method to calculate reaction energies of oxidative addition reactions. Detailed knowledge of energies involved in the oxidative addition reaction of methyl iodide to rhodium complexes have an important implication in catalysis, for example the Monsanto process where methanol is converted to acetic acid catalysed by a rhodium complex. For more insight in the reported data, see the related research article “Synthesis, characterization, electrochemistry, DFT and kinetic study of the oligothiophene-containing complex [Rh((C 4 H 3 S- C 4 H 2 S)COCHCOCF 3 )(CO)(PPh 3 )]”, published in Polyhedron.Item Open Access Dimethylsulfoxide (DMSO) clusters dataset: DFT relative energies, non-covalent interactions, and cartesian coordinates(Elsevier, 2022) Malloum, Alhadji; Conradie, JeanetTheoretical understanding of dimethylsulfoxide (DMSO) liquid depends on the understanding of the DMSO clusters. In this work, we provide the structures and the energetics of the DMSO clusters. The structures have been generated using ABCluster and further optimized at the MP2/aug-cc-pVDZ level of theory. The final structures have been optimized at two different levels of theory: PW6B95D3/aug-cc-pVDZ and ωB97XD/aug-cc-pVDZ. The Cartesian coordinates of the structures optimized at the MP2/aug-cc-pVDZ level of theory are also reported. The relative energies of the structures can be used to locate the most favorable structures of the DMSO clusters. The Cartesian coordinates of the structures can be used for further investigations on DMSO clusters. In addition, we report the data related to the quantum theory of atoms in molecule (QTAIM) analysis of the investigated clusters. The QTAIM data reported in this work can be used to understand and determine the nature of non-covalent interactions in DMSO clusters. For further reading and discussion on the data reported here, please report to the original manuscript Malloum and Conradie (2022).Item Open Access Free energy and enthalpy data of neutral and protonated clusters in the solvent phase(Elsevier, 2021) Malloum, Alhadji; Conradie, JeanetStructures of neutral and protonated acetonitrile in the sol- vent phase are important to describe proton behavior and to calculate thermodynamic quantities related to the solva- tion of ions or molecules in acetonitrile. In this work, we provide data related to the calculation of the solvation free energy and enthalpy of the proton in acetonitrile. We have thoroughly explored the potential energy surfaces (PESs) of neutral and protonated acetonitrile clusters from dimer to heptamer in the solvent phase at both MN15/6–31 ++ G (d,p) and MP2/aug-cc-pVDZ levels of theory. We report the struc- tures and relative stability of neutral and protonated acetoni- trile clusters in the solvent phase at the MN15/6–31 ++ G (d,p) level of theory. In addition, enthalpies and free energies of neutral and protonated acetonitrile are also reported at the MP2/aug-cc-pVDZ and MP2/CBS levels of theory. Further- more, Cartesian coordinates of the clusters in the solvent phase as optimized at the MP2/aug-cc-pVDZ level of theory are provided as supplementary file. The data provided in this work will be useful for further investigations that would in- volve neutral and protonated acetonitrile clusters. The free energies and enthalpies of the investigated clusters in the solvent phase have been used to compute the solvation free energy and enthalpy of the proton in acetonitrile. For more insights on the solvation free energy and enthalpy of the pro- ton in acetonitrile, see the related main research paper.Item Open Access Isotherm, kinetic, thermodynamics and reusability data on the adsorption of antidepressant onto silver nanoparticle-loaded biowaste(Elsevier Inc., 2021) Akpomie, Kovo G.; Conradie, JeanetThere has been an increase in the use of antidepressant drugs owing to significant economic challenges across the globe. Consequently, the increase in production of such drugs has impacted pharmaceutical pollution of industrial wastew- aters discharged into the environment. Hence, there is a need to develop efficient adsorbents for antidepressant wastewa- ter treatment. The impregnation of silver nanoparticles on biowaste was found to be highly effective in the treatment of oil-polluted water but has not been utilized in the adsorp- tion of drugs. Herein, the dataset associated with the adsorp- tion of antidepressants onto Ananas Comosus Peel (AP) and Silver nanoparticle-loaded Ananas Comosus peel (AgAP) was reported. Batch adsorption methodology was used to study the effect of antidepressant concentration (10–50 mg/L), son- ication time (10–120 min), temperature (300–320 K) and adsorbent dosage (0.10–0.18 g). The concentration of an- tidepressant (Nortriptyline) in solution before and after ad- sorption was determined by the UV-Spectrophotometer at a maximum wavelength of 239 nm. The isotherm dataset was obtained from the Langmuir, Freundlich, Temkin and Dubinin-Raduskevich models, while kinetic data was eval- uated by the pseudo-first order-pseudo-second-order, film diffusion and intraparticle diffusion rate equations. The data on the thermodynamics and adsorbent reusability were also provided. The dataset showed an adsorption capacity of 3.27 mg/g and 4.74 mg/g for AP and AgAP, respectively. The dataset is important to material and environmental scientists and revealed the efficiency of AP and AgAP in the treatment of antidepressant wastewater.Item Open Access Kinetic study of the oxidative addition reaction between methyl iodide and [Rh(imino-β-diketonato)(CO)(PPh)3] complexes, utilizing UV–vis, IR spectrophotometry, NMR spectroscopy and DFT calculations(MDPI, 2022) Ferreira, Hendrik; Conradie, Marrigje Marianne; Conradie, JeanetThe oxidative addition of methyl iodide to [Rh(β-diketonato)(CO)(PPh)3] complexes, as modal catalysts of the first step during the Monsanto process, are well-studied. The β-diketonato ligand is a bidentate (BID) ligand that bonds, through two O donor atoms (O,O-BID ligand), to rhodium. Imino-β-diketones are similar to β-diketones, though the donor atoms are N and O, referred to as an N,O-BID ligand. In this study, the oxidative addition of methyl iodide to [Rh(imino-β-diketonato)(CO)(PPh)3] complexes, as observed on UV–Vis spectrophotometry, IR spectrophotometry and NMR spectrometry, are presented. Experimentally, one isomer of [Rh(CH3COCHCNPhCH3)(CO)(PPh3)] and two isomers of [Rh(CH3COCHCNHCH3)(CO)(PPh3)] are observed—in agreement with density functional theory (DFT) calculations. Experimentally the [Rh(CH3COCHCNPhCH3)(CO)(PPh3)] + CH3I reaction proceeds through one reaction step, with a rhodium(III)-alkyl as the final reaction product. However, the [Rh(CH3COCHCNHCH3)(CO)(PPh3)] + CH3I reaction proceeds through two reaction steps, with a rhodium(III)-acyl as the final reaction product. DFT calculations of all the possible reaction products and transition states agree with experimental findings. Due to the smaller electronegativity of N, compared to O, the oxidative addition reaction rate of CH3I to the two [Rh(imino-β-diketonato)(CO)(PPh)3] complexes of this study was 7–11 times faster than the oxidative addition reaction rate of CH3I to [Rh(CH3COCHCOCH3)(CO)(PPh3)].Item Open Access Polypyridyl copper complexes as dye sensitizer and redox mediator for dye-sensitized solar cells(Elsevier, 2021) Conradie, JeanetDevelopments on the application of polypyridyl-based copper complexes in dye-sensitized solar cells (DSSCs) are briefly discussed in this mini review. Copper complexes in solar cells are special in that they can be used either as dye sensitizer and/or as redox mediator (redox couple) in dye-sensitized solar cells (DSSCs). Both the abundance and low cost of copper motivates research on the use of copper complexes, as cheaper and non-toxic alternative to the mostly used iodide/triiodide (I- /I3- ) electrolyte redox couple, and the expensive and rare rutheniumbased dyes of good performance, which currently are best known.Item Open Access QTAIM analysis dataset for non-covalent interactions in furan clusters(Elsevier, 2021) Malloum, Alhadji; Conradie, JeanetFuran clusters are very important to understand the dynam- ics and properties of the furan solvent. They can be used combined with quantum cluster equilibrium theory to theo- retically determine the thermodynamics properties of the fu- ran solvent. To understand the structures of the furan clus- ters, one needs to understand the non-covalent interactions that hold the furan molecules together. In this paper, we have provided the data necessary to understand the non-covalent interactions in furan clusters. Firstly, the structures of the furan clusters have been generated using classical molecu- lar dynamics as implemented in the ABCluster code. Sec- ondly, the generated structures have been fully optimized at the MP2/aug-cc-pVDZ level of theory. The optimized Carte- sian coordinates of all the investigated structures are re- ported in this work to enable further investigations of the furan clusters. These Cartesian coordinates will save compu- tational time for all further investigations involving the fu- ran clusters. Thirdly, to understand the nature of the non- covalent interactions in furan clusters, we have performed a quantum theory of atoms in molecule (QTAIM) analysis using AIMAll program. Using QTAIM, we have provided the critical points, bond paths and their related properties for all the in- vestigated structures. These data can be used to identify and classify the non-covalent interactions in furan clusters.Item Open Access Redox data of tris(polypyridine)manganese(II) complexes(MDPI, 2022) Mtshali, Zinhle; Von Eschwege, Karel G.; Conradie, JeanetVery little cyclic voltammetry data for tris(polypyridine)manganese(II) complexes, [MnII(N^N)3]2+, where N^N is bipyridine (bpy), phenanthroline (phen) or substituted bpy or phen ligands, respectively; are available in the literature. Cyclic voltammograms were found for tris(4,7-diphenyl-1,10-phenanthroline)manganese(II) perchlorate only. In addition to our recently published related research article, the data presented here provides cyclic voltammograms and corresponding voltage-current data obtained during electrochemical oxidation and the reduction of four [MnII(N^N)3]2+ complexes, using different scan rates and analyte concentrations. The results show increased concentration and scan rates resulting in higher Mn(II/III) peak oxidation potentials and increased peak current-voltage separations of the irreversible Mn(II/III) redox event. The average peak oxidation and peak reduction potentials of the Mn(II/III) redox events stayed constant within 0.01 V. Similarly, the average of the peak oxidation and reduction potentials of the ligand-based reduction events of [MnII(N^N)3]2+ were constant within 0.01 V.Item Open Access Review of DFT-simulated and experimental electrochemistry properties of the polypyridyl Row-1 Mn, Fe & Co, and Group-8 Fe, Ru and Os MLCT complexes(Elsevier, 2022) Von Eschwege, Karel G.; Conradie, JeanetRuthenium had up to date been pivotal in electro- and photocatalytic applications involving reduction of CO2 and H2O, and dye-sensitized solar cells. Commercial applications would seek use of earth-abundant metals instead. Towards this goal, it is key to review the synthesis, electrochemical and spectroscopical properties of associated metal-to-ligand charge transfer complexes of row-4 (Mn, Fe & Co) and column-8 (Fe, Ru & Os). The present report is limited to data obtained under exactly similar conditions, providing scientifically valid correlations. Only tris-coordinated bipyridyl and phenanthroline complex derivatives are considered, being representative of catalysts and dyes traditionally used in the above-mentioned fields. The accuracy of theoretical DFT techniques to simulate complex properties is highlighted.Item Open Access Synthesis, electrochemistry, and density functional theory of osmium(II) containing different 2,2′:6′,2″-terpyridines(MDPI, 2024) Mateyise, Nandisiwe G. S.; Conradie, Marrigje M.; Conradie, JeanetIn coordination chemistry, 2,2′:6′,2″-terpyridine is a versatile and extensively studied tridentate ligand. Terpyridine forms stable complexes with a variety of metal ions through coordination sites provided by the three nitrogen atoms in its pyridine rings. This paper presents an electrochemical study on various bis(terpyridine)osmium(II) complexes, addressing the absence of a systematic investigation into their redox behavior. Additionally, a computational chemistry analysis was conducted on these complexes, as well as on eight previously studied osmium(II)-bipyridine and -phenanthroline complexes, to expand both the experimental and theoretical understanding. The experimental redox potentials, Hammett constants, and DFT-calculated energies show linear correlations due to the electron-donating or electron-withdrawing nature of the substituents, as described by the Hammett constants. These substituent effects cause shifts to lower or higher redox potentials, respectively.Item Open Access Trans–cis kinetic study of azobenzene-4,4′-dicarboxylic acid and aluminium and zirconium based azobenzene-4,4′-dicarboxylate MOFs(MDPI, 2022) Mogale, Refilwe; Conradie, Jeanet; Langner, Ernst H. G.Metal organic frameworks (MOFs) are porous hybrid crystalline materials that consist of organic linkers coordinated to metal centres. The trans–cis isomerisation kinetics of the azobenzene-4,4′-dicarboxylic acid (AZB(COOH)2) precursor, as well as the Al3+ (Al-AZB)- and Zr4+ (Zr-AZB)-based MOFs with azobenzene-4,4′-dicarboxylate linkers, are presented. The photo-isomerization in the MOFs originates from singly bound azobenzene moieties on the surface of the MOF. The type of solvent used had a slight effect on the rate of isomerization and half-life, while the band gap energies were not significantly affected by the solvents. Photo-responsive MOFs can be classified as smart materials with possible applications in sensing, drug delivery, magnetism, and molecular recognition. In this study, the MOFs were applied in the dye adsorption of congo red (CR) in contaminated water. For both MOFs, the UV-irradiated cis isomer exhibited a slightly higher CR uptake than the ambient-light exposed trans isomer. Al-AZB displayed a dye adsorption capacity of over 95% for both the UV-irradiated and ambient light samples. The ambient light exposed Zr-AZB, and the UV irradiated Zr-AZB had 39.1% and 44.6% dye removal, respectively.Item Open Access Unexpected XPS binding energy observations further highlighted by DFT calculations of ruthenocene-containing [Irᴵᴵᴵ(ppy)₂(RCOCHCORc)] Complexes: Cytotoxicity and Crystal Structure of [Ir(ppy)₂(FcCOCHCORc)](MDPI, 2024) Buitendach, Blenerhassitt E.; Erasmus, Elizabeth; Fourie, Eleanor; Malan, Frederick P.; Conradie, Jeanet; Niemantsverdriet, J. W. (Hans); Swarts, Jannie C.The series of iridium(III) complexes, [Ir(ppy)₂(RCOCHCOR′)], with R = CH₃ and R′ = CH₃ (1), Rc (2), and Fc (3), as well as R = Rc and R′ = Rc (4) or Fc (5), and R = R′ = Fc (6), ppy = 2-phenylpyridinyl, Fc = Feᴵᴵ(η⁵–C₅H₄)(η⁵–C₅H₅), and Rc = Ruᴵᴵ(η⁵–C₅H₄)(η⁵–C₅H₅), has been investigated by singlecrystal X-ray crystallography and X-ray photoelectron spectroscopy (XPS) supplemented by DFT calculations. Here, in the range of 3.74 ≤ ΣχR ≤ 4.68, for Ir 4f, Ru 3d and 3p and N 1s orbitals, binding energies unexpectedly decreased with increasing ΣχR (ΣχR = the sum of Gordy group electronegativities of the R groups on β-diketonato ligands = a measure of electron density on atoms), while in Fe 2p orbitals, XPS binding energy, as expected, increased with increasing ΣχR. Which trend direction prevails is a function of main quantum level, n = 1, 2, 3. . ., sub-quantum level (s, p, d, and f), initial state energies, and final state relaxation energies, and it may differ from compound series to compound series. Relations between DFT-calculated orbital energies and ΣχR followed opposite trend directions than binding energy/ΣχR trends. X-ray-induced decomposition of compounds was observed. The results confirmed good communication between molecular fragments. Lower binding energies of both the Ir 4f₇/₂ and N 1s photoelectron lines are associated with shorter Ir-N bond lengths. Cytotoxic tests showed that 1 (IC₅₀ = 25.1 μM) and 3 (IC₅₀ = 37.8 μM) are less cytotoxic against HeLa cells than cisplatin (IC₅₀ = 1.1 μM), but more cytotoxic than the free β-diketone FcCOCH₂COCH₃(IC₅₀ = 66.6 μM).