The effect of an alkyl chain and β-diketonato-metal moiety on the photochromic behaviour of azobenzene compounds as materials for solar thermal fuels
- Authors: Bokhe, Witness Londi
- Date: 2024-10-11
- Subjects: Photochemistry , Isomerization , Solar thermal energy , Solar thermal fuel , Liquid crystals , Optical materials
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/464510 , vital:76517
- Description: Scientists have been studying the development of renewable energy technologies in detail to create a sustainable energy supply. Among many new advanced material classes being researched recently are photo functional and photo responsive materials. These classes include azobenzene derivatives which are characterized by azo linkage (N=N) sandwiched by two phenyl rings. The trans-to-cis isomerization of azobenzene is a highly efficient and reversible process, making it an ideal candidate for solar thermal energy storage. This research investigates the impact of alkyl chain modifications and the incorporation of a β-diketonato-copper(II) complex on azobenzene derivatives, aiming to optimize their performance as efficient components in solar thermal fuel cells (STFs). The study focuses on a comprehensive analysis of these materials' ability to capture, convert, store, and release solar energy for enhanced sustainability in renewable energy applications. Experimental methodologies include synthesis of azobenzene derivatives with varying alkyl chain length, n (where n =8 & 10) and coordination of these compounds with a β-diketonato-copper(II) complex. Standard analytical techniques such as Nuclear Magnetic Resonance (1H and 13C NMR), Fourier Transform Infrared Spectroscopy (FTIR) and Ultraviolet/visible spectroscopy (UV/vis) were employed for chemical analysis of the synthesized material. Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), and Polarised Optical Microscope (POM) were used to study the thermal properties and morphology. The photostationery states were determined using NMR spectroscopy and the kinetic parameters of the cis-to-trans relaxation process determined by a UV spectroscopy study. The cis-to-trans isomerisation had a longer half-life than the trans-to-cis isomerisation. The band gap of the isomers is within the range of semiconducting inorganic materials. DSC and POM thermograms showed that the compounds are liquid crystalline. Finally, the study reports that the synthesised azobenzene derivatives show potential as material for solar thermal fuel cells because of their photo-isomerization ability. Furthermore, the synthesised compounds contribute to the advancement of sustainable and efficient solar energy utilization technologies, addressing the growing demand for clean energy solutions in the face of global environmental challenges. Because solar energy may be stored and used without causing direct emissions or pollution, they are considered clean energy. If solar thermal fuels fulfil sustainability standards, they may qualify as green energy. This entails minimising adverse effects on the environment, using non-toxic chemicals and procedures. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Bokhe, Witness Londi
- Date: 2024-10-11
- Subjects: Photochemistry , Isomerization , Solar thermal energy , Solar thermal fuel , Liquid crystals , Optical materials
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/464510 , vital:76517
- Description: Scientists have been studying the development of renewable energy technologies in detail to create a sustainable energy supply. Among many new advanced material classes being researched recently are photo functional and photo responsive materials. These classes include azobenzene derivatives which are characterized by azo linkage (N=N) sandwiched by two phenyl rings. The trans-to-cis isomerization of azobenzene is a highly efficient and reversible process, making it an ideal candidate for solar thermal energy storage. This research investigates the impact of alkyl chain modifications and the incorporation of a β-diketonato-copper(II) complex on azobenzene derivatives, aiming to optimize their performance as efficient components in solar thermal fuel cells (STFs). The study focuses on a comprehensive analysis of these materials' ability to capture, convert, store, and release solar energy for enhanced sustainability in renewable energy applications. Experimental methodologies include synthesis of azobenzene derivatives with varying alkyl chain length, n (where n =8 & 10) and coordination of these compounds with a β-diketonato-copper(II) complex. Standard analytical techniques such as Nuclear Magnetic Resonance (1H and 13C NMR), Fourier Transform Infrared Spectroscopy (FTIR) and Ultraviolet/visible spectroscopy (UV/vis) were employed for chemical analysis of the synthesized material. Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), and Polarised Optical Microscope (POM) were used to study the thermal properties and morphology. The photostationery states were determined using NMR spectroscopy and the kinetic parameters of the cis-to-trans relaxation process determined by a UV spectroscopy study. The cis-to-trans isomerisation had a longer half-life than the trans-to-cis isomerisation. The band gap of the isomers is within the range of semiconducting inorganic materials. DSC and POM thermograms showed that the compounds are liquid crystalline. Finally, the study reports that the synthesised azobenzene derivatives show potential as material for solar thermal fuel cells because of their photo-isomerization ability. Furthermore, the synthesised compounds contribute to the advancement of sustainable and efficient solar energy utilization technologies, addressing the growing demand for clean energy solutions in the face of global environmental challenges. Because solar energy may be stored and used without causing direct emissions or pollution, they are considered clean energy. If solar thermal fuels fulfil sustainability standards, they may qualify as green energy. This entails minimising adverse effects on the environment, using non-toxic chemicals and procedures. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-10-11
Application of computational methods in elucidating the isomerization step in the biosynthesis of coumarins
- Authors: Tshiwawa, Tendamudzimu
- Date: 2019
- Subjects: Coumarins , Isomerization , Biosynthesis , Organic compounds -- Synthesis , Cinnamic acid
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/67646 , vital:29124
- Description: The identity of the enzyme(s) responsible for the biosynthetic transformation of cinnamic acid derivatives to important, naturally occurring coumarins has yet to be established. This study constitutes a high-level theoretical analysis of the possibility that a recently reported molecular mechanism of the synthesis of coumarins from Baylis-Hillman adducts, may provide a viable model for three critical phases in the biosynthetic pathway Particular attention has been given to the first of these phases: i) E→Z isomerisation of the cinnamic acid precursor; ii) Cyclisation (lactonisation) to the hemi-acetal intermediate; and ii) Dehydration to afford the coumarin derivative. In order to accomplish this analysis, an enzyme capable, theoretically, of effecting this E→Z isomerisation required identification, and its potential involvement in the transformation mechanism explored. Combined Molecular Mechanics and high-level Quantum Mechanical/DFT calculations were used to access complementary models of appropriate complexes and relevant processes within the enzyme active sites of a range of eleven Chalcone Isomerase (CHI) enzyme candidates, the structures of which were downloaded from the Protein Data Bank. Detailed B3LYP/6-31+G(d,p) calculations have provided pictures of the relative populations of conformations within the ensemble of conformations available at normal temperatures. Conformations of several protonation states of cinnamic acid derivatives have been studied in this way, and the results obtained showed that coupled protonation and deprotonation of (E)-o-coumaric acid provides a viable approach to achieve the E→Z isomerization. In silico docking of the B3LYP/6-31+G(d,p) optimized (E)-o-coumaric acid derivatives in the active sites of each of the candidate CHI enzymes (CHI) revealed that (E)-o-coumaric acid fits well within the active sites of Medicago Sativa CHI crystallographic structures with 1FM8 showing best potential for not only accommodating (E)-o-coumaric acid , but also providing appropriate protein active site residues to effect the simultaneous protonation and deprotonation of the substrate , two residues being optimally placed to facilitate these critical processes. Further exploration of the chemical properties and qualities of selected CHI enzymes, undertaken using High Throughput Virtual Screening (HTVS), confirmed 1FM8 as a viable choice for further studies of the enzyme-catalysed E→Z isomerization of (E)-o-coumaric acid. A molecular dynamics study, performed to further evaluate the evolution of (E)-o-coumaric acid in the CHI active site over time, showed that the ligand in the 1FM8 active site is not only stable, but also that the desired protein-ligand interactions persist throughout the simulation period to facilitate the E→Z isomerization. An integrated molecular orbital and molecular mechanics (ONIOM) study of the 1FM8-(E)-o-coumaric acid complex, involving the direct protonation and deprotonation of the ligand by protein residues; has provided a plausible mechanism for the E → Z isomerization of (E)-o-coumaric acid within the 1FM8 active site; a transition state complex (with an activation energy of ca. 50 kCal.mol-1) has been located and its connection with both the (E)- and (Z)-o-coumaric acid isomer has been confirmed by Intrinsic Reaction Coordinate (IRC) calculations. More realistic models of the 1FM8-(E)-o-coumaric acid complex, with the inclusion of water solvent molecules, have been obtained at both the QM/MM and adaptive QM/MM levels which simulate the dynamic active site at the QM level. The results indicate that the simultaneous protonation and deprotonation of (E)-o-coumaric acid within the CHI enzyme is a water-mediated process – a conclusion consistent with similar reported processes. Visual inspection of the 1FM8-(Z)-o-coumaric acid complex reveals both the necessary orientation of the phenolic and carboxylic acid moieties of the (Z)-o-coumaric acid and the presence of appropriate, proximal active site residues with the potential to permit catalysis of the subsequent lactonisation and dehydration steps required to generate coumarin.
- Full Text:
- Date Issued: 2019
- Authors: Tshiwawa, Tendamudzimu
- Date: 2019
- Subjects: Coumarins , Isomerization , Biosynthesis , Organic compounds -- Synthesis , Cinnamic acid
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/67646 , vital:29124
- Description: The identity of the enzyme(s) responsible for the biosynthetic transformation of cinnamic acid derivatives to important, naturally occurring coumarins has yet to be established. This study constitutes a high-level theoretical analysis of the possibility that a recently reported molecular mechanism of the synthesis of coumarins from Baylis-Hillman adducts, may provide a viable model for three critical phases in the biosynthetic pathway Particular attention has been given to the first of these phases: i) E→Z isomerisation of the cinnamic acid precursor; ii) Cyclisation (lactonisation) to the hemi-acetal intermediate; and ii) Dehydration to afford the coumarin derivative. In order to accomplish this analysis, an enzyme capable, theoretically, of effecting this E→Z isomerisation required identification, and its potential involvement in the transformation mechanism explored. Combined Molecular Mechanics and high-level Quantum Mechanical/DFT calculations were used to access complementary models of appropriate complexes and relevant processes within the enzyme active sites of a range of eleven Chalcone Isomerase (CHI) enzyme candidates, the structures of which were downloaded from the Protein Data Bank. Detailed B3LYP/6-31+G(d,p) calculations have provided pictures of the relative populations of conformations within the ensemble of conformations available at normal temperatures. Conformations of several protonation states of cinnamic acid derivatives have been studied in this way, and the results obtained showed that coupled protonation and deprotonation of (E)-o-coumaric acid provides a viable approach to achieve the E→Z isomerization. In silico docking of the B3LYP/6-31+G(d,p) optimized (E)-o-coumaric acid derivatives in the active sites of each of the candidate CHI enzymes (CHI) revealed that (E)-o-coumaric acid fits well within the active sites of Medicago Sativa CHI crystallographic structures with 1FM8 showing best potential for not only accommodating (E)-o-coumaric acid , but also providing appropriate protein active site residues to effect the simultaneous protonation and deprotonation of the substrate , two residues being optimally placed to facilitate these critical processes. Further exploration of the chemical properties and qualities of selected CHI enzymes, undertaken using High Throughput Virtual Screening (HTVS), confirmed 1FM8 as a viable choice for further studies of the enzyme-catalysed E→Z isomerization of (E)-o-coumaric acid. A molecular dynamics study, performed to further evaluate the evolution of (E)-o-coumaric acid in the CHI active site over time, showed that the ligand in the 1FM8 active site is not only stable, but also that the desired protein-ligand interactions persist throughout the simulation period to facilitate the E→Z isomerization. An integrated molecular orbital and molecular mechanics (ONIOM) study of the 1FM8-(E)-o-coumaric acid complex, involving the direct protonation and deprotonation of the ligand by protein residues; has provided a plausible mechanism for the E → Z isomerization of (E)-o-coumaric acid within the 1FM8 active site; a transition state complex (with an activation energy of ca. 50 kCal.mol-1) has been located and its connection with both the (E)- and (Z)-o-coumaric acid isomer has been confirmed by Intrinsic Reaction Coordinate (IRC) calculations. More realistic models of the 1FM8-(E)-o-coumaric acid complex, with the inclusion of water solvent molecules, have been obtained at both the QM/MM and adaptive QM/MM levels which simulate the dynamic active site at the QM level. The results indicate that the simultaneous protonation and deprotonation of (E)-o-coumaric acid within the CHI enzyme is a water-mediated process – a conclusion consistent with similar reported processes. Visual inspection of the 1FM8-(Z)-o-coumaric acid complex reveals both the necessary orientation of the phenolic and carboxylic acid moieties of the (Z)-o-coumaric acid and the presence of appropriate, proximal active site residues with the potential to permit catalysis of the subsequent lactonisation and dehydration steps required to generate coumarin.
- Full Text:
- Date Issued: 2019
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