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Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques
Thesis (PhD)--University of Pretoria, 2020.
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University of Pretoria
2020
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| access_status_str | Open Access |
| author2 | Ouma, Cecil Naphtaly Moro |
| author_browse | Ouma, Cecil Naphtaly Moro |
| author_facet | Ouma, Cecil Naphtaly Moro |
| collection | Thesis |
| dc_rights_str_mv | © 2019 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD)--University of Pretoria, 2020. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/75547 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:25.198Z |
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| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2020 |
| publishDateRange | 2020 |
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| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/75547 Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques Ouma, Cecil Naphtaly Moro nyangiwenangamso9@gmail.com Nyangiwe, Nangamso Nathaniel UCTD Engineered nanoparticles Natural organic matter Ag (111) surface DFT DFT-D Engineering, built environment and information technology theses SDG-06 Engineering, built environment and information technology theses SDG-09 Engineering, built environment and information technology theses SDG-12 Engineering, built environment and information technology theses SDG-13 Engineering, built environment and information technology theses SDG-14 Thesis (PhD)--University of Pretoria, 2020. With increasing number of nanoproducts being commercialized globally; and consequent release of engineered nanoparticles (ENPs) into different environmental compartments with unknown impacts has raised concerns. Several experimental studies have attempted to elucidate the fate of ENPs in the aquatic systems especially following their interactions with natural organic matter (NOM). This consequently makes valuation of the fate and behavior of ENPs essential especially when it comes to the design of goods that are harmless and function as intended without causing unwanted special effects to biological lifeforms in the aquatic systems. Most of these studies used experiments which require considerable, effort and expensive equipment. Hence therefore there is an urgent need for the development of computational models to envisage the fate and behavior of ENPs in the aquatic systems and use these results to guide experimental investigations. Thus, in this thesis, we employ in silico techniques aimed at generating descriptors that can offer insights on fate and behavior of ENPs. We look for descriptors that will enhance our understanding of ENP-NOM interactions at fundamental level. Using density functional theory (DFT) calculations augmented with classical lattice dynamics (CLD), we have investigated several properties of the ENP-NOM systems. This was done using three case studies where different NOM’s were adsorbed on different nanoparticle shapes and surfaces. In the first case, descriptors associated with low molecular weight NOMs were investigated on silver nanoparticles in different shapes (spherical, cylindrical etc.) both gas phase and solvent phase. Findings of adsorption energies showed that molecular weight plays a crucial role because an increasing trend was observed relative to the molecular weight the NOM. Results revealed higher adsorption energies for ascorbic acid. NOM adsorption on tetrahedron-shaped Ag ENP (111) surface was also characterised with high adsorption energies. For Ag, the (111) face is characterised by high metal density (14 Ag/nm2) and low surface tension (Azcárate et al. 2013) and the close-packed (111) plane has the lowest energy crystal plane with maximum packing, and therefore, is most stable (Marzbanrad et al. 2015). For this reason, the (111) facet is widely studied (Hatchett and White 1996) because silver reactivity favours high atom density facets, (Ajayan and Marks 1988) and similarly, it was chosen as facet of investigation in this study. Global reactivity descriptors that can offer insights and enhance our understanding as well as account at a fundamental level the fate and behavior of ENPs in the aquatic systems such the dipole moment (μ), molecular surface area (MSA), absolute electronegativity (χ), and absolute hardness (η) were also performed using frontier molecular orbital theory. In the second case, the interactions of ENPs with high molecular weight NOMs (fulvic acid and humic acid) was considered in both gas and solvent phases. Both fulvic acid and humic acid are ambiguously found in the aquatic systems and hence their choice for this study. Similar to the first case, dispersion corrected density functional theory (DFT-D) techniques was used to generate descriptors. Results from this case study showed that the calculated adsorption energies for humic acid (HA), formic acid(FA) and cryptochrome (Cry) on Ag (111) surface were -1.21 (-0.80) eV, -1.66 (-0.81) eV, and -6.24 (-6.54) eV respectively in the gas (solvent) phase and the equilibrium distances between the surface and HA, FA and Cry molecules were 1.87 (2.18) Å, 2.31(2.31) Å and 1.91 (1.70) Å respectively in the gas (solvent) phase. In both gas and solvent phase Cry showed stronger adsorption which meant it had a stronger interaction with Ag (111) surface compared HA and FA. The results for adsorption energy, solvation energy, isosurface of charge deformation difference, total density of state and partial density of states indicated that indeed these chosen adsorbates do interact with the surface and were favorable on Ag (111) surface. The third case considered was the co-adsorption of Low Molecular Weight (LMW) NOMs mixtures on the surfaces of nAg (111), where n = 1, 2, 3, 4 implies 1 to 4 molecules are considered in a given co-adsorption case considered. This is because the NOMs exist as mixtures in aquatic systems. The approach and methodology for this investigation followed that which was applied in both the first and second cases. To the best of our knowledge, this is the first study where adsorption of an NOM mixture of formic acid, acetic acid and ascorbic on a nanoparticle surface had been done using DFT-D. This study provides understanding to clarify how a mixture of NOMs may have diverse set of implications on the fate of ENPs in aquatic systems using first-principles calculations; and may be a useful reference in designing experiments on the influence of different NOMs on the ENMs fate in aquatic systems. The results for this case study showed that the calculated adsorption energies suggest that the interaction of four molecules of formic acid (4FA), two molecules of acetic acid (2AA1) and two molecules of ascorbic acid (2AA2) with Ag (111) surface is the strongest with the most negative values (-6.54 and -3.84 eV) in both gas phase and Conductor-like screening model (COSMO) respectively which indicates that it is the most stable system. More importantly, the study found that water as a solvent does not play a crucial in enhancing the adsorption. This analysis serves as the first step toward gaining a more accurate understanding of specific interactions at the interface in gas phase and in aqueous media. National Research Foundation Department of Science and Technology Council for Scientific and Industrial Research mi2026 Chemical Engineering PhD Unrestricted SDG-06: Clean water and sanitation SDG-09: Industry, innovation and infrastructure SDG-12: Responsible consumption and production SDG-13: Climate action SDG-14: Life below water 2020-08-04T19:15:43Z 2020-08-04T19:15:43Z 2020-09-07 2020 Thesis http://hdl.handle.net/2263/31804 2020 http://hdl.handle.net/2263/75547 en © 2019 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf application/pdf University of Pretoria |
| spellingShingle | UCTD Engineered nanoparticles Natural organic matter Ag (111) surface DFT DFT-D Engineering, built environment and information technology theses SDG-06 Engineering, built environment and information technology theses SDG-09 Engineering, built environment and information technology theses SDG-12 Engineering, built environment and information technology theses SDG-13 Engineering, built environment and information technology theses SDG-14 Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title | Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title_full | Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title_fullStr | Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title_full_unstemmed | Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title_short | Modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| title_sort | modelling the interactions of engineered nanoparticles with natural organic matter using in silico techniques |
| topic | UCTD Engineered nanoparticles Natural organic matter Ag (111) surface DFT DFT-D Engineering, built environment and information technology theses SDG-06 Engineering, built environment and information technology theses SDG-09 Engineering, built environment and information technology theses SDG-12 Engineering, built environment and information technology theses SDG-13 Engineering, built environment and information technology theses SDG-14 |
| url | http://hdl.handle.net/2263/31804 http://hdl.handle.net/2263/75547 |