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Oxidations with endocyclic peroxides and their derivatives
No full textThis thesis describes two novel transformations (a method to synthesize alkylidene phthalides and a different approach toward the Baeyer-Villiger oxidation) and the development and mechanistic study of a metal-free oxidation of arenes.Chapter 1 introduces the concept of alkene oxyamination. Synthesis of a series of hydroxylamine derivatives of endocyclic peroxides was undertaken, which were then reacted with nitrogen, sulfur and carbon nucleophiles. This led to the discovery of a new reaction that provides access to alkylidene phthalides, a class of compounds which exhibit interesting biological activity.Chapter 2 describes the development of an alternative approach to the Baeyer-Villiger oxidation, through the reaction of hydrogen peroxide and a nitrile in the presence of a base.Chapter 3 describes direct methods for the formation of new aromatic C-O bonds, followed by the presentation of an organic peroxide mediated approach. Herein, an examination of the mechanism of the reaction of a malonoyl peroxide with an arene is studied through Hammett analysis, isotope labeling experiments, EPR studies, DFT calculations and reactivity patterns.Chapters 4 and 5 present the experimental procedures and analytical data relevant to the three reactions developed.Chapter 6 contains a bibliography.This thesis describes two novel transformations (a method to synthesize alkylidene phthalides and a different approach toward the Baeyer-Villiger oxidation) and the development and mechanistic study of a metal-free oxidation of arenes.Chapter 1 introduces the concept of alkene oxyamination. Synthesis of a series of hydroxylamine derivatives of endocyclic peroxides was undertaken, which were then reacted with nitrogen, sulfur and carbon nucleophiles. This led to the discovery of a new reaction that provides access to alkylidene phthalides, a class of compounds which exhibit interesting biological activity.Chapter 2 describes the development of an alternative approach to the Baeyer-Villiger oxidation, through the reaction of hydrogen peroxide and a nitrile in the presence of a base.Chapter 3 describes direct methods for the formation of new aromatic C-O bonds, followed by the presentation of an organic peroxide mediated approach. Herein, an examination of the mechanism of the reaction of a malonoyl peroxide with an arene is studied through Hammett analysis, isotope labeling experiments, EPR studies, DFT calculations and reactivity patterns.Chapters 4 and 5 present the experimental procedures and analytical data relevant to the three reactions developed.Chapter 6 contains a bibliography
Development of analytical methods for particulate-bound polycyclic aromatic hydrocarbons (PAHs) in Thailand
Get PDFThis study developed analytical methods to quantify particulate-bound polycyclic aromatic hydrocarbons (pPAHs). The methods were used to characterise PAHs in house dust and particulate matter (PM10) samples, respectively, in two case studies. Dust samples were collected from rural households in Malawi to represent indoor particles from biomass fuel combustion. PM10 samples were collected from three sites in the Bangkok Metropolitan Administration (BMA), Thailand to represent air pollutants in roadside, industrial and urban background environments. PAHs were quantified using a gas chromatograph-mass spectrometer (GC-MS). Comprehensive two-dimensional gas chromatograph coupled with time-of-flight mass spectrometer(GCxGC TOFMS) was used for the screening of unknown air pollutants in PM10. Low molecular weight 2-ring and 3-ring PAHs were more abundant in dust samples collected in Malawi, while high molecular weight 4-ring to 6-ring PAHs were more abundant in PM10 samples collected in Thailand. Spatial and temporal variations in PM10 and pPAH concentrations were examined between and within the three sampling sites in Thailand. Annual average benzo[a]pyrene (BaP) concentrations were 0.47 ± 0.39 ng m-3, 0.35 ± 0.27 ng m-3 and 0.24 ± 0.19 ng m-3 at the roadside, industrial and urban background sites, respectively. Cancer risks associated with pPAHs were estimated using BaP and BaP toxic equivalency (BaP-TEQ) concentrations. The highest incremental lifetime cancer risk was found in the residential adult group at 4.2 x 10-7 at the industrial site. Although the highest PM10 and total PAHs concentrations were found at the roadside site, the highest carcinogenic potential of total PAH (in terms of BaP toxic equivalency concentration) was found at the industrial site. Thus, the cancer risk estimation relies more on the composition of pPAHs than its concentration. Estimated lifetime lung cancer risks associated with pPAHs in all three sites were in the 'acceptable' range of less than 1 x 10-6 defined by the United States Environmental Protection Agency.This study developed analytical methods to quantify particulate-bound polycyclic aromatic hydrocarbons (pPAHs). The methods were used to characterise PAHs in house dust and particulate matter (PM10) samples, respectively, in two case studies. Dust samples were collected from rural households in Malawi to represent indoor particles from biomass fuel combustion. PM10 samples were collected from three sites in the Bangkok Metropolitan Administration (BMA), Thailand to represent air pollutants in roadside, industrial and urban background environments. PAHs were quantified using a gas chromatograph-mass spectrometer (GC-MS). Comprehensive two-dimensional gas chromatograph coupled with time-of-flight mass spectrometer(GCxGC TOFMS) was used for the screening of unknown air pollutants in PM10. Low molecular weight 2-ring and 3-ring PAHs were more abundant in dust samples collected in Malawi, while high molecular weight 4-ring to 6-ring PAHs were more abundant in PM10 samples collected in Thailand. Spatial and temporal variations in PM10 and pPAH concentrations were examined between and within the three sampling sites in Thailand. Annual average benzo[a]pyrene (BaP) concentrations were 0.47 ± 0.39 ng m-3, 0.35 ± 0.27 ng m-3 and 0.24 ± 0.19 ng m-3 at the roadside, industrial and urban background sites, respectively. Cancer risks associated with pPAHs were estimated using BaP and BaP toxic equivalency (BaP-TEQ) concentrations. The highest incremental lifetime cancer risk was found in the residential adult group at 4.2 x 10-7 at the industrial site. Although the highest PM10 and total PAHs concentrations were found at the roadside site, the highest carcinogenic potential of total PAH (in terms of BaP toxic equivalency concentration) was found at the industrial site. Thus, the cancer risk estimation relies more on the composition of pPAHs than its concentration. Estimated lifetime lung cancer risks associated with pPAHs in all three sites were in the 'acceptable' range of less than 1 x 10-6 defined by the United States Environmental Protection Agency
Online fashion shopping experiences : web atmospherics and consumer's emotions
Get PDFThis thesis was previously held under moratorium from 1st December 2016 until 1st December 2021.The notion of ‘experience’ marks a shift in consumer research from focusing on the rational consumer to focusing on emotions (Holbrook & Hirschman, 1982). This research studies consumer experiences in the specific context of online fashion shopping. It contributes to the field of atmospherics and consumption emotions and experiences, thus bridging a gap that has been highlighted in the literature (e.g. Turley & Milliman, 2000). This thesis aims to study the online fashion-shopping experience as the consumer lives and constructs it. The research conducted two studies that are underpinned by the philosophical stance of pragmatism. First, Kelly’s (1955) personal construct theory (PCT) is adopted to gain an in-depth understanding of consumers’ shopping experience using their own words and construction. The study conducted 25 repertory grid interviews, analysed first with Jankowicz’s (2005) method of initial eyeball and process analyses. Next, following Lemke, Clark, and Wilson (2011), qualitative construct coding was performed by multi-coders for inter-reliability checks. This study contributes to our understanding of the online fashion-shopping experience by (1) introducing the construction of the experience as emotional, perceptual, situational and behavioural, (2) highlighting how individuality in such experiences often changes the meaning of such constructs, and (3) arguing that situational constructs provide a context that shapes the whole experience. Second, screencast videography is introduced as a novel method that captures the shoppers’ live experiences. Critical incident analysis of ten videos allowed the experience journey to be mapped, highlighting the main critical incidents and the contexts (e.g. purposeful vs. purposeless browsing) that shape the experience. In addition to its methodological contribution, this study provides great insights into an otherwise unobservable phenomenon. Furthermore, it presents the ‘fashionscape’ as a concept tailored especially to understanding the online fashion-shopping environment in its visual, verbal, social and educational dimensions.The notion of ‘experience’ marks a shift in consumer research from focusing on the rational consumer to focusing on emotions (Holbrook & Hirschman, 1982). This research studies consumer experiences in the specific context of online fashion shopping. It contributes to the field of atmospherics and consumption emotions and experiences, thus bridging a gap that has been highlighted in the literature (e.g. Turley & Milliman, 2000). This thesis aims to study the online fashion-shopping experience as the consumer lives and constructs it. The research conducted two studies that are underpinned by the philosophical stance of pragmatism. First, Kelly’s (1955) personal construct theory (PCT) is adopted to gain an in-depth understanding of consumers’ shopping experience using their own words and construction. The study conducted 25 repertory grid interviews, analysed first with Jankowicz’s (2005) method of initial eyeball and process analyses. Next, following Lemke, Clark, and Wilson (2011), qualitative construct coding was performed by multi-coders for inter-reliability checks. This study contributes to our understanding of the online fashion-shopping experience by (1) introducing the construction of the experience as emotional, perceptual, situational and behavioural, (2) highlighting how individuality in such experiences often changes the meaning of such constructs, and (3) arguing that situational constructs provide a context that shapes the whole experience. Second, screencast videography is introduced as a novel method that captures the shoppers’ live experiences. Critical incident analysis of ten videos allowed the experience journey to be mapped, highlighting the main critical incidents and the contexts (e.g. purposeful vs. purposeless browsing) that shape the experience. In addition to its methodological contribution, this study provides great insights into an otherwise unobservable phenomenon. Furthermore, it presents the ‘fashionscape’ as a concept tailored especially to understanding the online fashion-shopping environment in its visual, verbal, social and educational dimensions
Small molecules based on novel electron-deficient acceptor units for organic electronic applications
Get PDFDemand for photovoltaic cells is ever-increasing due to the diminishing supply of oil-based fuels and the associated harmful environmental effects. Organic photovoltaic devices offer a light and flexible alternative to Si-based PVs. In addition to this, they can be processed using fabrication methods such as spin-coating and inkjet printing hence, such devices have potential to be produced cheaply on a large scale. Although they have been applied as donor materials with success, polymers often show end-group variation and are polydisperse so there can be batch-to-batch variation with respect to OPV performance. A solution to these problems is the use of small donor molecules which are monodisperse and have well-defined structures. However, the shorter conjugation of small molecules with respect to polymers requires measures to shorten the HOMO-LUMO gap. A common approach is the incorporation of electron-deficient acceptor units into the donor molecule, lowering the LUMO level and therefore the HOMO-LUMO gap.Chapter 1 reviews band theory, the development of organic semiconductors, including a summary of oligothiophene based materials and common electron-deficient acceptor units used, the principles behind OPV and OFET devices and how organic semiconductors can be optimised in order to produce the best working devices.The synthesis, physical properties and OPV performance of materials based on naphthyridine-2,6-dione acceptor unit are presented in chapter 2, focussing on the difference between compounds with Donor-Acceptor-Donor and Acceptor-Donor-Acceptor structures. Chapter 3 shows the novel naphthyridin-2-one moiety and the synthesis of materials containing the unit and how they have been used for different applications including ambipolar OFETs and both donor and acceptor materials for bulk heterojunction OPV devices.A study in improving the mobility of OFET devices is presented in chapter 4. Different inorganic nanoparticles were added to organic semiconductor solutions for and the effect of this simple process on the performance of the OFET devices is discussed.Chapter 5 introduces the thieno[3,2-b]thiophene-2,5-dione and novel furo[3,2-b]furan-2,5-dione acceptor units. The synthesis, optical and electrochemical properties, and OFET and OPV device optimisation of materials based on these moieties are presented and discussed.A summary of the work discussed is presented in chapter 6 whilst chapter 7 presents the experimental methods for electrochemistry, device work, and synthetic procedures for each compound presented in Chapters 2, 3, 4 and 5Demand for photovoltaic cells is ever-increasing due to the diminishing supply of oil-based fuels and the associated harmful environmental effects. Organic photovoltaic devices offer a light and flexible alternative to Si-based PVs. In addition to this, they can be processed using fabrication methods such as spin-coating and inkjet printing hence, such devices have potential to be produced cheaply on a large scale. Although they have been applied as donor materials with success, polymers often show end-group variation and are polydisperse so there can be batch-to-batch variation with respect to OPV performance. A solution to these problems is the use of small donor molecules which are monodisperse and have well-defined structures. However, the shorter conjugation of small molecules with respect to polymers requires measures to shorten the HOMO-LUMO gap. A common approach is the incorporation of electron-deficient acceptor units into the donor molecule, lowering the LUMO level and therefore the HOMO-LUMO gap.Chapter 1 reviews band theory, the development of organic semiconductors, including a summary of oligothiophene based materials and common electron-deficient acceptor units used, the principles behind OPV and OFET devices and how organic semiconductors can be optimised in order to produce the best working devices.The synthesis, physical properties and OPV performance of materials based on naphthyridine-2,6-dione acceptor unit are presented in chapter 2, focussing on the difference between compounds with Donor-Acceptor-Donor and Acceptor-Donor-Acceptor structures. Chapter 3 shows the novel naphthyridin-2-one moiety and the synthesis of materials containing the unit and how they have been used for different applications including ambipolar OFETs and both donor and acceptor materials for bulk heterojunction OPV devices.A study in improving the mobility of OFET devices is presented in chapter 4. Different inorganic nanoparticles were added to organic semiconductor solutions for and the effect of this simple process on the performance of the OFET devices is discussed.Chapter 5 introduces the thieno[3,2-b]thiophene-2,5-dione and novel furo[3,2-b]furan-2,5-dione acceptor units. The synthesis, optical and electrochemical properties, and OFET and OPV device optimisation of materials based on these moieties are presented and discussed.A summary of the work discussed is presented in chapter 6 whilst chapter 7 presents the experimental methods for electrochemistry, device work, and synthetic procedures for each compound presented in Chapters 2, 3, 4 and
Development of a superabsorber based haemofiltration technology for use in paediatric cardiac surgery
Get PDFPreviously held under moratorium from 30th November 2016 until 30th November 2021Cardiopulmonary bypass is known to cause great changes in a patient’s physiological fluidhomeostasis which frequently results in fluid accumulation in the interstitial space (edema). Theassociated inflammatory response can, in severe cases, result in systemic immune responsesyndrome, acute respiratory distress syndrome, and organ failure.Modified Ultrafiltration (MUF) involves pumping blood through a haemofilter post-bypass toremove excess plasma, and has been shown to successfully moderate haemodilution and theinflammatory response and improve clinical outcomes in paediatric patients for whom edema isa serious morbidity.In this research project, the current MUF technique is combined with a new superabsorberbased haemofiltration technology to develop a novel haemofiltration device.Design concepts were researched and the optimal device configuration was determined.Laboratory testing with bovine blood, computational modelling of blood flow and scanningelectron microscope imaging of the control membrane highlighted the importance of bothutilising flow disruption techniques to limit fouling, and controlling the swelling behaviour ofthe superabsorber material, in achieving rapid haemofiltration.The device is able to achieve passive, chemically driven haemofiltration at a fixed blood flowrate and is designed such that it requires minimal input from clinical staff to be suitable fordeployment in a clinical setting. The haemoconcentration time is close to current MUFprocedures but with further refinement of the system, equalling the MUF time for currentprocedures is certainly achievable.The blood haemoconcentrated by the device was of good quality with no significant change incell counts, cell morphology measures, or haemoglobin level measures after 60mins of MUFindicating little to no impact upon the blood constituents or haemolysis induced by the device.The device did not demonstrate selective removal of pro-inflammatory mediators but similarlythere was no increase in pro-inflammatory mediator concentrations observed. Furtherinvestigation of the inflammatory mediator impact is recommended.Cardiopulmonary bypass is known to cause great changes in a patient’s physiological fluidhomeostasis which frequently results in fluid accumulation in the interstitial space (edema). Theassociated inflammatory response can, in severe cases, result in systemic immune responsesyndrome, acute respiratory distress syndrome, and organ failure.Modified Ultrafiltration (MUF) involves pumping blood through a haemofilter post-bypass toremove excess plasma, and has been shown to successfully moderate haemodilution and theinflammatory response and improve clinical outcomes in paediatric patients for whom edema isa serious morbidity.In this research project, the current MUF technique is combined with a new superabsorberbased haemofiltration technology to develop a novel haemofiltration device.Design concepts were researched and the optimal device configuration was determined.Laboratory testing with bovine blood, computational modelling of blood flow and scanningelectron microscope imaging of the control membrane highlighted the importance of bothutilising flow disruption techniques to limit fouling, and controlling the swelling behaviour ofthe superabsorber material, in achieving rapid haemofiltration.The device is able to achieve passive, chemically driven haemofiltration at a fixed blood flowrate and is designed such that it requires minimal input from clinical staff to be suitable fordeployment in a clinical setting. The haemoconcentration time is close to current MUFprocedures but with further refinement of the system, equalling the MUF time for currentprocedures is certainly achievable.The blood haemoconcentrated by the device was of good quality with no significant change incell counts, cell morphology measures, or haemoglobin level measures after 60mins of MUFindicating little to no impact upon the blood constituents or haemolysis induced by the device.The device did not demonstrate selective removal of pro-inflammatory mediators but similarlythere was no increase in pro-inflammatory mediator concentrations observed. Furtherinvestigation of the inflammatory mediator impact is recommended
Discovering the biological and clinical implications of modulating glucocorticoid action using metabolomic profiling of human plasma samples
Get PDFPreviously held under moratorium from 22 December 2016 until 17 January 2022Background: Glucocorticoid deficiency and excess are difficult to identify because ofthe non-specificity of their clinical and biochemical features which are also poorlycorrelated with levels of circulating steroids. The lack of reliable biomarkers forglucocorticoid action makes it challenging to determine precise therapeutic needsof patients with GC-deficient or excessive conditions such as congenital adrenalhyperplasia and Cushing’s syndrome, respectively.Aim: To identify the main biomarkers indicative of changes in cortisol action inhealthy individuals and those with different metabolic diseases.Study design and methodology: Plasma samples were collected from threeseparate studies. The first study was a randomised double-blind crossover designinvolving 8 men with type 2 diabetes given either placebo or metyrapone +mifepristone (‘glucocorticoid blockade’) for 12 hours. In the second study, 20healthy men were given metyrapone with either low or high doses of insulin, plussuch a dose of hydrocortisone as to achieve low, medium or high plasma cortisollevels. Finally, plasma samples were also obtained from 119 patients with CAHreceiving standard clinical care. Liquid chromatography-mass spectrometry wasthen employed for the metabolomic profiling of all the plasma samples, andMzMatch software was used to identify the metabolites present. Multivariate andunivariate analyses were employed to determine the most reliable metabolites asbiomarkers for glucocorticoid action.Results: Branched chain amino acids, bile acids and their conjugates, and free fattyacids were the main metabolite groups that were significantly altered by at leasttwo of the three interventions. Compared to placebo, bile acids and theirconjugates were significantly (p < 0.05) elevated following glucocorticoid blockade,but subsequent insulin administration significantly lowered their levels. On theother hand, high glucocorticoid dose significantly (p < 0.05) increased the levels ofchenodeoxyglycocholate in patients with conginetal adrenal hyperplasia, but noeffects on bile acids were observed in similarly treated healthy men. Branched chainamino acids were significantly lowered in healthy men following high insulin dose,but were significantly (p < 0.05) increased upon high hydrocortisone infusion. HighBCAs levels were associated with high body mass index , and high systolic anddiastolic blood pressure in pateints with conginetal adrenal hyperplasia. In contrast,L-valine, was significantly elevated following glucocorticoid blockade in patientswith type 2 diabetes. A number of saturated and unsaturated fatty acids weresignificantly (p < 0.05) elevated following hydrocortisone infusion in healthy men,but insulin reduced their levels significantly (p < 0.05). High glucocorticoid dose inpatients with conginetal adrenal hyperplasia significantly increased C15:0, C16:0and C20:0 while C16:1 reduced. In contrast, use of insulin following glucocorticoidblockade in patients with type 2 diabetes significantly (p < 0.05) reduced levels ofC12:0, C18:0 and C18:3. Conclusion: These hypothesis-free metabolomics screening studies have identifiedmetabolites in plasma which are differentially sensitive to glucocorticoid deficiencyor excess and may be useful in clinical assessment of glucocorticoid therapy.Background: Glucocorticoid deficiency and excess are difficult to identify because ofthe non-specificity of their clinical and biochemical features which are also poorlycorrelated with levels of circulating steroids. The lack of reliable biomarkers forglucocorticoid action makes it challenging to determine precise therapeutic needsof patients with GC-deficient or excessive conditions such as congenital adrenalhyperplasia and Cushing’s syndrome, respectively.Aim: To identify the main biomarkers indicative of changes in cortisol action inhealthy individuals and those with different metabolic diseases.Study design and methodology: Plasma samples were collected from threeseparate studies. The first study was a randomised double-blind crossover designinvolving 8 men with type 2 diabetes given either placebo or metyrapone +mifepristone (‘glucocorticoid blockade’) for 12 hours. In the second study, 20healthy men were given metyrapone with either low or high doses of insulin, plussuch a dose of hydrocortisone as to achieve low, medium or high plasma cortisollevels. Finally, plasma samples were also obtained from 119 patients with CAHreceiving standard clinical care. Liquid chromatography-mass spectrometry wasthen employed for the metabolomic profiling of all the plasma samples, andMzMatch software was used to identify the metabolites present. Multivariate andunivariate analyses were employed to determine the most reliable metabolites asbiomarkers for glucocorticoid action.Results: Branched chain amino acids, bile acids and their conjugates, and free fattyacids were the main metabolite groups that were significantly altered by at leasttwo of the three interventions. Compared to placebo, bile acids and theirconjugates were significantly (p < 0.05) elevated following glucocorticoid blockade,but subsequent insulin administration significantly lowered their levels. On theother hand, high glucocorticoid dose significantly (p < 0.05) increased the levels ofchenodeoxyglycocholate in patients with conginetal adrenal hyperplasia, but noeffects on bile acids were observed in similarly treated healthy men. Branched chainamino acids were significantly lowered in healthy men following high insulin dose,but were significantly (p < 0.05) increased upon high hydrocortisone infusion. HighBCAs levels were associated with high body mass index , and high systolic anddiastolic blood pressure in pateints with conginetal adrenal hyperplasia. In contrast,L-valine, was significantly elevated following glucocorticoid blockade in patientswith type 2 diabetes. A number of saturated and unsaturated fatty acids weresignificantly (p < 0.05) elevated following hydrocortisone infusion in healthy men,but insulin reduced their levels significantly (p < 0.05). High glucocorticoid dose inpatients with conginetal adrenal hyperplasia significantly increased C15:0, C16:0and C20:0 while C16:1 reduced. In contrast, use of insulin following glucocorticoidblockade in patients with type 2 diabetes significantly (p < 0.05) reduced levels ofC12:0, C18:0 and C18:3. Conclusion: These hypothesis-free metabolomics screening studies have identifiedmetabolites in plasma which are differentially sensitive to glucocorticoid deficiencyor excess and may be useful in clinical assessment of glucocorticoid therapy
Probabilistic analysis of supply chains resilience based on their characteristics using dynamic Bayesian networks
Get PDFPreviously held under moratorium from 14 December 2016 until 19 January 2022There is an increasing interest in the resilience of supply chains given the growingawareness of their vulnerabilities to natural and man-made hazards. Contemporaryacademic literature considers, for example, so-called resilience enablers and strategies,such as improving the nature of collaboration and flexibility within the supply chain.Efforts to analyse resilience tend to view the supply chain as a complex system. Thepresent research adopts a distinctive approach to the analysis of supply resilience bybuilding formal models from the perspective of the responsible manager. DynamicBayesian Networks (DBNs) are selected as the modelling method since they are capableof representing the temporal evolution of uncertainties affecting supply. They alsosupport probabilistic analysis to estimate the impact of potentially hazardous eventsthrough time. In this way, the recovery rate of the supply chain under mitigation actionscenarios and an understanding of resilience can be obtained.The research is grounded in multiple case studies of manufacturing and retail supplychains, involving focal companies in the UK, Canada and Malaysia, respectively. Eachcase involves building models to estimate the resilience of the supply chain givenuncertainties about, for example, business continuity, lumpy spare parts demand andoperations of critical infrastructure. DBNs have been developed by using relevant datafrom historical empirical records and subjective judgement. Through the modellingpractice, It has been found that some SC characteristics (i.e. level of integration,structure, SC operating system) play a vital role in shaping and quantifying DBNs andreduce their elicitation burden. Similarly, It has been found that the static and dynamicdiscretization methods of continuous variables affect the DBNs building process.I also studied the effect of level of integration, visibility, structure and SC operatingsystem on the resilience level of SCs through the analysis of DBNs outputs. I found thatthe influence of the integration intensity on supply chain resilience can be revealedthrough understanding the dependency level of the focal firm on SC members resources. Ihave also noticed the relationship between the span of integration and the level ofvisibility to SC members. This visibility affects the capability of SC managers in the focalfirm to identify the SC hazards and their consequences and, therefore, improve the planning for adverse events. I also explained how some decision rules related to SCoperating system such as the inventory strategy could influence the intermediate ability ofSC to react to adverse events. By interpreting my case data in the light of the existingacademic literature, I can formulate some specific propositions.There is an increasing interest in the resilience of supply chains given the growingawareness of their vulnerabilities to natural and man-made hazards. Contemporaryacademic literature considers, for example, so-called resilience enablers and strategies,such as improving the nature of collaboration and flexibility within the supply chain.Efforts to analyse resilience tend to view the supply chain as a complex system. Thepresent research adopts a distinctive approach to the analysis of supply resilience bybuilding formal models from the perspective of the responsible manager. DynamicBayesian Networks (DBNs) are selected as the modelling method since they are capableof representing the temporal evolution of uncertainties affecting supply. They alsosupport probabilistic analysis to estimate the impact of potentially hazardous eventsthrough time. In this way, the recovery rate of the supply chain under mitigation actionscenarios and an understanding of resilience can be obtained.The research is grounded in multiple case studies of manufacturing and retail supplychains, involving focal companies in the UK, Canada and Malaysia, respectively. Eachcase involves building models to estimate the resilience of the supply chain givenuncertainties about, for example, business continuity, lumpy spare parts demand andoperations of critical infrastructure. DBNs have been developed by using relevant datafrom historical empirical records and subjective judgement. Through the modellingpractice, It has been found that some SC characteristics (i.e. level of integration,structure, SC operating system) play a vital role in shaping and quantifying DBNs andreduce their elicitation burden. Similarly, It has been found that the static and dynamicdiscretization methods of continuous variables affect the DBNs building process.I also studied the effect of level of integration, visibility, structure and SC operatingsystem on the resilience level of SCs through the analysis of DBNs outputs. I found thatthe influence of the integration intensity on supply chain resilience can be revealedthrough understanding the dependency level of the focal firm on SC members resources. Ihave also noticed the relationship between the span of integration and the level ofvisibility to SC members. This visibility affects the capability of SC managers in the focalfirm to identify the SC hazards and their consequences and, therefore, improve the planning for adverse events. I also explained how some decision rules related to SCoperating system such as the inventory strategy could influence the intermediate ability ofSC to react to adverse events. By interpreting my case data in the light of the existingacademic literature, I can formulate some specific propositions
An Exploration of Alkali Metal Ferrate Chemistry: Synthesis and Exploitation for N-Heterocyclic Carbene and Fluoroarene Functionalisation
Get PDFBuilding on previous developments on cooperative heterobimetallic reagents, this thesis aims to advance the understanding of the preparation and synthetic exploitation of alkali metal ferrates of Fe(II). Using bis(amide) Fe{N(SiMe3)2}2 as a precursor, here we report the syntheses and structures of a variety of sodium ferrates that have been prepared via direct co-complexation, where the single metal components NaN(SiMe3)2 and Fe{N(SiMe3)2}2 self-assemble in the presence of a range of Lewis donors with different electronic properties and denticities. Furthermore, in some cases the presence of these donors is not required and the isolation and structural elucidation of two novel unsolvated sodium ferrates has been accomplished which display unique polymeric arrangements in the solid state.;The ability of sodium ferrates to functionalise NHC ligands has also been assessed, finding that when unsaturated NHC IPr (IPr = 1,3-bis(diisopropylphenyl)-imidazol-2-ylidene) is treated sequentially with NaCH2SiMe3 and Fe{N(SiMe3)2}2, sodium ferrate (THF)3·Na[:C{[N(2,6-iPr2C6H3)]2CHCFe(HMDS)2}] (15) is formed, containing an anionic NHC which binds to Fe via its C4 position and to Na through its C2 site. Interestingly, this complex was found to be an excellent precursor for Fe-abnormal NHC complexes and when treated with MeOTf afforded [CH3C{[N(2,6-iPr2C6H3)]2CHCFe(HMDS)2}] (16). 1,4-dioxane solvate [dioxane·NaFe(HMDS)3] (17a) has been found to be an efficient chemoselective base to promote the direct ferration at room temperature of a wide range of fluoroaromatic molecules.;Structural elucidation of key organometallic intermediates has revealed the synergic bonding of the metals with Fe occupying the position previously filled by an H atom forming a strong Fe-C sigma bond, whereas the Na atom forms a dative bond with the F atom. These studies have revealed an important alkali metal effect, thus when the Na atom in 17a is replaced by Li or K, the ferration processes are inhibited. Remarkably, by using two molar equivalents of 17a, it is possible to di-ferrate tri-and tetrafluoro-substituted aromatics. These reactions take place at ambient temperature with excellent yields. Reaction of 1,3,5-trifluorobenzene with three molar equivalents of 17a, led to the isolation of [1,3-bis(FeHMDS)-2,4,6-tris(HMDS)-C6H] (38) resulting from the unprecedented two-fold C-H metallation/three-fold C-F activation of the substrate. Mechanistic studies suggest the reaction is partly driven by the formation of NaF. Magnetic studies using have revealed that this new compound displays single-molecule magnet behaviour.Building on previous developments on cooperative heterobimetallic reagents, this thesis aims to advance the understanding of the preparation and synthetic exploitation of alkali metal ferrates of Fe(II). Using bis(amide) Fe{N(SiMe3)2}2 as a precursor, here we report the syntheses and structures of a variety of sodium ferrates that have been prepared via direct co-complexation, where the single metal components NaN(SiMe3)2 and Fe{N(SiMe3)2}2 self-assemble in the presence of a range of Lewis donors with different electronic properties and denticities. Furthermore, in some cases the presence of these donors is not required and the isolation and structural elucidation of two novel unsolvated sodium ferrates has been accomplished which display unique polymeric arrangements in the solid state.;The ability of sodium ferrates to functionalise NHC ligands has also been assessed, finding that when unsaturated NHC IPr (IPr = 1,3-bis(diisopropylphenyl)-imidazol-2-ylidene) is treated sequentially with NaCH2SiMe3 and Fe{N(SiMe3)2}2, sodium ferrate (THF)3·Na[:C{[N(2,6-iPr2C6H3)]2CHCFe(HMDS)2}] (15) is formed, containing an anionic NHC which binds to Fe via its C4 position and to Na through its C2 site. Interestingly, this complex was found to be an excellent precursor for Fe-abnormal NHC complexes and when treated with MeOTf afforded [CH3C{[N(2,6-iPr2C6H3)]2CHCFe(HMDS)2}] (16). 1,4-dioxane solvate [dioxane·NaFe(HMDS)3] (17a) has been found to be an efficient chemoselective base to promote the direct ferration at room temperature of a wide range of fluoroaromatic molecules.;Structural elucidation of key organometallic intermediates has revealed the synergic bonding of the metals with Fe occupying the position previously filled by an H atom forming a strong Fe-C sigma bond, whereas the Na atom forms a dative bond with the F atom. These studies have revealed an important alkali metal effect, thus when the Na atom in 17a is replaced by Li or K, the ferration processes are inhibited. Remarkably, by using two molar equivalents of 17a, it is possible to di-ferrate tri-and tetrafluoro-substituted aromatics. These reactions take place at ambient temperature with excellent yields. Reaction of 1,3,5-trifluorobenzene with three molar equivalents of 17a, led to the isolation of [1,3-bis(FeHMDS)-2,4,6-tris(HMDS)-C6H] (38) resulting from the unprecedented two-fold C-H metallation/three-fold C-F activation of the substrate. Mechanistic studies suggest the reaction is partly driven by the formation of NaF. Magnetic studies using have revealed that this new compound displays single-molecule magnet behaviour
Development of site-specific RNA labeling strategies to probe alternative RNA splicing
Get PDFThe objective of this project was to develop a method for the labeling of RNA at specific locations using non-natural base pairs. This thesis details the efforts made towards this objective through the development of a modular synthetic platform for an expanded genetic alphabet and its evaluation using transcriptional assays.Chapter 1 introduces the structure and function of RNA, followed by a description of RNA processing events with emphasis placed on alternative RNA splicing and how aberrations in splicing can lead to disease. The concept of RNA labeling follows and examples from the literature are presented along with challenges associated with these techniques to elucidate key mechanistic splicing concepts. The concept of orthogonal base pairs is then introduced along with representative examples from the literature. The application of this concept in RNA labeling is then presented along with key examples from the literature. The limitations of these methods are highlighted followed by the specific aims behind this project.Chapter 2 presents the efforts made towards the development of a modular synthetic route for the synthesis of C-ribonucleosides, with a Heck reaction as the key step. Specifically, its application in the synthesis of the Z ribonucleoside developed by the Benner group is investigated. The chapter starts with re-introducing the Z/P pair developed by the Benner group and highlighting the reasons that placed it as our chosen base pair for RNA labeling. The synthesis of C-deoxyribonucleosides utilizing the Heck reaction is presented, followed by the challenges associated with C-ribonucleoside synthesis.The syntheses of the alkene and halide coupling partners of the proposed Heck reaction are firstly presented.Investigations on the Heck reaction are then presented, followed by investigations on the transformation of nitro group in Z to moieties suitable for further derivatization. The key outcome of this work is that a synthetic route involving the Heck reaction for the synthesis of C-ribonucleosidesis not feasible. This is due to long reaction times required to drive the Heck reaction to completion and difficulties encountered with elucidation of its stereselectivity. Furthermore, PCR experiments conducted by our collaborators within the Eperon group at the University of Leicester revealed significant misincorporation of Z opposite G. Consequently, a change in strategy towards the use of nucleotides developed by the Hirao group was made.Chapter 3 describes the development of a robust synthetic route for the synthesis of a library of C6-functionalized 2-aminopurines as potential candidates for an expanded genetic alphabet in RNA. The s/Pa pair developed by the Hirao group is re-introduced.The installation of an alkyne functionality on the guanosine scaffold via a Sonogashira reaction is described,followed by investigations of [3+2] cycloaddition reactions between the alkyne and azides or aldehyde oximes. Finally, the development of a novel Suzuki-Miyaura protocol for the direct installation of heterocyclic substituents on the guanosine scaffold is also reported.Key outcomes of this chapter are the following. A robust method was developed for the expedient synthesis of C6-functionalized s analogues. This method enabled access to various classes of analogues in three or six steps,including triazoles, isoxazoles, thiophenes and pyrazoles. Attempts to install an azide moiety to the guanosine were partly successful, but the strategy was abanonded due to reaction reproducibility issues. In addition, a C-H activation strategy was not successful on installing an oxazole moiety Chapter 4 details the efforts towards the synthesis of nucleoside triphosphates based on the s analogues described in Chapter 3. This chapter will begin with the presentation of the most common strategies for the synthesis of nucleoside triphosphates. Initial attempts to synthesize triphosphates by global deprotection of nucleosides synthesized in Chapter 3 are next described. Attempts to install a silyl ether group in the 5'-OH are presented, followed by the installation of acetates on the 2'/3' hydroxyls and attempts to protect the exocyclic amine on guanosine as the phenoxyacetamide. The installation of a pyrazole moiety via Suzuki-Miyauraprotocol using the corresponding boronic acid pinacol ester described in Chapter 3 is presented. The installation of an alkyne moiety is also described and the synthesis of an isoxazole analogue using this alkyne precursor will follow. The chapter will end with the presentation of the synthesis of pyrazole and isoxazole triphosphate analogues. The key outcome of this chapter is that employing different protecting groups on the 5' and the 2'/3' hydroxyls enabled the synthesis of pure triphosphates. Chapter 5 presents the evaluation of the nucleotide triphosphates synthesized in Chapter 4 regarding their transcriptional efficiency. Key outcome of this work are that high concentrations (>0.5 mM mM) are needed in order to observe significant incorporation of the analogues, compared to s, which needs 0.1 mM for efficient incorporation. At high concentration, the isoxazole moiety exhibits better incorporation efficiency compared to the pyrazole analogue. Furthermore, the addition of 0.5 mM of MnCl2 resulted in increased incorporation efficiency of the pyrazole analogue, while s and the isoxazole exhibited reduced efficiency under these conditions.The objective of this project was to develop a method for the labeling of RNA at specific locations using non-natural base pairs. This thesis details the efforts made towards this objective through the development of a modular synthetic platform for an expanded genetic alphabet and its evaluation using transcriptional assays.Chapter 1 introduces the structure and function of RNA, followed by a description of RNA processing events with emphasis placed on alternative RNA splicing and how aberrations in splicing can lead to disease. The concept of RNA labeling follows and examples from the literature are presented along with challenges associated with these techniques to elucidate key mechanistic splicing concepts. The concept of orthogonal base pairs is then introduced along with representative examples from the literature. The application of this concept in RNA labeling is then presented along with key examples from the literature. The limitations of these methods are highlighted followed by the specific aims behind this project.Chapter 2 presents the efforts made towards the development of a modular synthetic route for the synthesis of C-ribonucleosides, with a Heck reaction as the key step. Specifically, its application in the synthesis of the Z ribonucleoside developed by the Benner group is investigated. The chapter starts with re-introducing the Z/P pair developed by the Benner group and highlighting the reasons that placed it as our chosen base pair for RNA labeling. The synthesis of C-deoxyribonucleosides utilizing the Heck reaction is presented, followed by the challenges associated with C-ribonucleoside synthesis.The syntheses of the alkene and halide coupling partners of the proposed Heck reaction are firstly presented.Investigations on the Heck reaction are then presented, followed by investigations on the transformation of nitro group in Z to moieties suitable for further derivatization. The key outcome of this work is that a synthetic route involving the Heck reaction for the synthesis of C-ribonucleosidesis not feasible. This is due to long reaction times required to drive the Heck reaction to completion and difficulties encountered with elucidation of its stereselectivity. Furthermore, PCR experiments conducted by our collaborators within the Eperon group at the University of Leicester revealed significant misincorporation of Z opposite G. Consequently, a change in strategy towards the use of nucleotides developed by the Hirao group was made.Chapter 3 describes the development of a robust synthetic route for the synthesis of a library of C6-functionalized 2-aminopurines as potential candidates for an expanded genetic alphabet in RNA. The s/Pa pair developed by the Hirao group is re-introduced.The installation of an alkyne functionality on the guanosine scaffold via a Sonogashira reaction is described,followed by investigations of [3+2] cycloaddition reactions between the alkyne and azides or aldehyde oximes. Finally, the development of a novel Suzuki-Miyaura protocol for the direct installation of heterocyclic substituents on the guanosine scaffold is also reported.Key outcomes of this chapter are the following. A robust method was developed for the expedient synthesis of C6-functionalized s analogues. This method enabled access to various classes of analogues in three or six steps,including triazoles, isoxazoles, thiophenes and pyrazoles. Attempts to install an azide moiety to the guanosine were partly successful, but the strategy was abanonded due to reaction reproducibility issues. In addition, a C-H activation strategy was not successful on installing an oxazole moiety Chapter 4 details the efforts towards the synthesis of nucleoside triphosphates based on the s analogues described in Chapter 3. This chapter will begin with the presentation of the most common strategies for the synthesis of nucleoside triphosphates. Initial attempts to synthesize triphosphates by global deprotection of nucleosides synthesized in Chapter 3 are next described. Attempts to install a silyl ether group in the 5'-OH are presented, followed by the installation of acetates on the 2'/3' hydroxyls and attempts to protect the exocyclic amine on guanosine as the phenoxyacetamide. The installation of a pyrazole moiety via Suzuki-Miyauraprotocol using the corresponding boronic acid pinacol ester described in Chapter 3 is presented. The installation of an alkyne moiety is also described and the synthesis of an isoxazole analogue using this alkyne precursor will follow. The chapter will end with the presentation of the synthesis of pyrazole and isoxazole triphosphate analogues. The key outcome of this chapter is that employing different protecting groups on the 5' and the 2'/3' hydroxyls enabled the synthesis of pure triphosphates. Chapter 5 presents the evaluation of the nucleotide triphosphates synthesized in Chapter 4 regarding their transcriptional efficiency. Key outcome of this work are that high concentrations (>0.5 mM mM) are needed in order to observe significant incorporation of the analogues, compared to s, which needs 0.1 mM for efficient incorporation. At high concentration, the isoxazole moiety exhibits better incorporation efficiency compared to the pyrazole analogue. Furthermore, the addition of 0.5 mM of MnCl2 resulted in increased incorporation efficiency of the pyrazole analogue, while s and the isoxazole exhibited reduced efficiency under these conditions
Investigating the role of neutrophils in Leishmania mexicana infection
No full textNeutrophil NETs have been a keen area of research in the few years since they were initially described. As well as apoptosis and necrosis, it was discovered that neutrophils also undergo a process known as NETosis by which DNA, histones and granule proteins are expelled from within the cell to form traps capable of killing fungi and bacteria. Here, we investigated the role of neutrophil NETs in response to infection with Leishmania mexicana. Using murine bone marrow derived neutrophils and dendritic cells, we used immunofluorescent staining of known NET markers and were able to identify that neutrophil NETs were capable of the capture of L. mexicana promastigotes following stimulation of neutrophils with PMA. Using flowcytometry and FITC-conjugated anti-H3cit antibodies, we were able todevelop a novel, cost effective and high throughout method of quantifyingNET release, which allowed us to determine that L. mexicana promastigotesdid not induce a significant increase in NET release by neutrophils. Using flow cytometry to determine parasite uptake, we were also able to determine that phagocytosis by dendritic cells was significantly downregulated in the presence of PMA-activated neutrophil NETs, suggesting that NETs may play a role in the activation of dendritic cells. Further investigation into the activation of dendritic cells using flow cytometry, however, showed that there was significant decrease of activation which may be due to parasite manipulation of dendritic cell activation. We were also able to determine that L. mexicana promastigotes were capable of downregulating glucose uptake in neutrophils potentially due to the metabolic activity of the parasite itself in growing and carrying out replication. Together, these findings suggest an involvement of neutrophil NETs in the immune response to infection with Leishmania mexicana, with more research necessary to determine the precise role in which they play.Neutrophil NETs have been a keen area of research in the few years since they were initially described. As well as apoptosis and necrosis, it was discovered that neutrophils also undergo a process known as NETosis by which DNA, histones and granule proteins are expelled from within the cell to form traps capable of killing fungi and bacteria. Here, we investigated the role of neutrophil NETs in response to infection with Leishmania mexicana. Using murine bone marrow derived neutrophils and dendritic cells, we used immunofluorescent staining of known NET markers and were able to identify that neutrophil NETs were capable of the capture of L. mexicana promastigotes following stimulation of neutrophils with PMA. Using flowcytometry and FITC-conjugated anti-H3cit antibodies, we were able todevelop a novel, cost effective and high throughout method of quantifyingNET release, which allowed us to determine that L. mexicana promastigotesdid not induce a significant increase in NET release by neutrophils. Using flow cytometry to determine parasite uptake, we were also able to determine that phagocytosis by dendritic cells was significantly downregulated in the presence of PMA-activated neutrophil NETs, suggesting that NETs may play a role in the activation of dendritic cells. Further investigation into the activation of dendritic cells using flow cytometry, however, showed that there was significant decrease of activation which may be due to parasite manipulation of dendritic cell activation. We were also able to determine that L. mexicana promastigotes were capable of downregulating glucose uptake in neutrophils potentially due to the metabolic activity of the parasite itself in growing and carrying out replication. Together, these findings suggest an involvement of neutrophil NETs in the immune response to infection with Leishmania mexicana, with more research necessary to determine the precise role in which they play
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