Determination of the Side-Reaction Coefficient of Desferrioxamine B in Trace-Metal-Free Seawater

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Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.

The Photooxidation of Domoic Acid

Domoic acid (DA) is a naturally occurring cyanotoxin, which upon ingestion, is responsible for amnesic shellfish poisoning (ASP) in both humans and animals. Produced by the marine diatom, Pseudonitzschia, DA is accumulated by a number of marine organisms including shellfish, clams and mussels which upon consumption can lead to headaches, nausea and seizures. Possessing a variety of functional groups the structure of DA contains three carboxyl groups, a pyrrole ring and a potent conjugated diene region allowing for binding to glutamate receptors in the dorsal hippocampus of the brain causing the described detrimental effects. Although limitations have been placed regarding the amount of DA that may be contained in seafood no limitations have been placed on the amount present in drinking water. Natural degradation of the toxin may occur through reactive oxygen species such as the hydroxyl radical and singlet oxygen at the conjugated diene region. In this work the photooxidation of DA via singlet oxygen has been studied using sorbic acid as a model compound. The three major reaction pathways observed during the photooxdiation process for both acids include 2 + 4 cycloaddition to produce endoperoxides , 2 + 2 reaction to afford aldehydes and ketones or an ene reaction to generate hydroperoxides. Under similar reaction conditions for SA and DA, the endoperoxide has been seen to be the major product for photoxidation of SA while the hydroperoxide has been seen to be the dominant product during photooxidation of DA.

Niobic acid nanoparticle catalysts for the aqueous phase transformation of glucose and fructose to 5-hydroxymethylfurfural

A family of bulk and SBA-15 supported peroxo niobic acid sols were prepared by peptisation of niobic acid precipitates with H2O2 as heterogeneous catalysts for aqueous phase glucose and fructose conversion to 5-hydroxymethylfurfural (5-HMF). Niobic acid nanoparticles possess a high density of Brønsted and Lewis acid sites, conferring good activity towards glucose and fructose conversion, albeit with modest 5-HMF yields under mild reaction conditions (100 °C). Thermally-induced niobia crystallisation suppresses solid acidity and activity. Nanoparticulate niobic acid dispersed over SBA-15 exhibits pure Brønsted acidity and an enhanced Turnover Frequency for fructose dehydration.

Acetic acid ketonization over Fe3O4/SiO2 for pyrolysis bio-oil upgrading

A family of silica supported, magnetite nanoparticle catalysts was synthesized and investigated for continuous flow acetic acid ketonization as a model pyrolysis bio-oil upgrading reaction. Physicochemical properties of Fe3O4/SiO2 catalysts were characterized by HRTEM, XAS, XPS, DRIFTS, TGA and porosimetry. Acid site densities were inversely proportional to Fe3O4 particle size, although acid strength and Lewis character were size invariant, and correlated with the specific activity for vapor phase acetic ketonization to acetone. A constant activation energy (~110 kJ.mol-1), turnover frequency (~13 h-1) and selectivity to acetone of 60 % were observed for ketonization across the catalyst series, implicating Fe3O4 as the principal active component of Red Mud waste.

Study of the Electrochemical, Physical and Morphological Characteristics of Anode Catalysts for Perfluorosulfonic Acid (PFSA) Membrane Water Electrolysers

A number of supported and un-supported Oxygen Evolution Reaction (OER) iridium based electrocatalysts for Polymer Electrolyte Membrane Water Electrolysis (PEMWE) were synthesized using a polyol method. The electrocatalysts and the supports were characterized using a wide range of physical and electrochemical characterization methods. The effect of morphological characteristics of the OER electrocatalyst and the support on the OER activity was studied. The results of this thesis contribute to the existing research to reduce the cost of PEMWE by enhancing the utilization of precious metal for OER electrocatalysis. Iridium electrocatalysts supported on antimony tin oxide (Ir/ATO) were synthesized using the polyol method with two different heating techniques: conventional and microwave-irradiation. It was shown that the physical morphology and electrochemical properties of Ir/ATO synthesized with the two heating methods were comparable. However, the microwave irradiation method was extremely faster than the conventional heating method. Additionally, the effect of heat treatment (calcination temperature) on the morphology and OER activity of Ir/ATO synthesized electrocatalyst with the conventional polyol method. It was found that the iridium electrocatalyst synthesized with the polyol method, consisted of 1-5 nm particles, possessed an amorphous structure, and contained iridium with an average oxidation state of less than +4. Calcining the catalyst at temperatures more than 400 ºC and less than 700ºC: 1) increased the size of the iridium particles to 30 nm, 2) changed the structure of iridium particles from amorphous to crystalline, 3) increased the iridium oxidation state to +4 (IrO2), 4) reduced the electrochemically active surface area by approximately 50%, and 5) reduced the OER activity by approximately 25%; however, it had no significant effect on the physical and chemical morphology of the ATO support. Moreover, potential support metal carbides and oxides including: Tantalum Carbide (TaC), Niobium Oxide (Nb2O5), Niobium Carbide (NbC), Titanium Carbide (TiC), Tungsten Carbide (WC) and Antimony-doped Tin Oxide (ATO, Sb2O5-SnO2), were characterized, and used as support for the iridium OER electrocatalysts. TaC was found to be a promising support, and increasing its surface area by 4% improved the OER performance of the final supported catalyst by approximately 50%.

Physicochemical complexity in complex chemical systems

Self-replication and compartmentalization are two central properties thought to be essential for minimal life, and understanding how such processes interact in the emergence of complex reaction networks is crucial to exploring the development of complexity in chemistry and biology. Autocatalysis can emerge from multiple different mechanisms such as formation of an initiator, template self-replication and physical autocatalysis (where micelles formed from the reaction product solubilize the reactants, leading to higher local concentrations and therefore higher rates). Amphiphiles are also used in artificial life studies to create protocell models such as micelles, vesicles and oil-in-water droplets, and can increase reaction rates by encapsulation of reactants. So far, no template self-replicator exists which is capable of compartmentalization, or transferring this molecular scale phenomenon to micro or macro-scale assemblies. Here a system is demonstrated where an amphiphilic imine catalyses its own formation by joining a non-polar alkyl tail group with a polar carboxylic acid head group to form a template, which was shown to form reverse micelles by Dynamic Light Scattering (DLS). The kinetics of this system were investigated by 1H NMR spectroscopy, showing clearly that a template self-replication mechanism operates, though there was no evidence that the reverse micelles participated in physical autocatalysis. Active oil droplets, composed from a mixture of insoluble organic compounds in an aqueous sub-phase, can undergo processes such as division, self-propulsion and chemotaxis, and are studied as models for minimal cells, or protocells. Although in most cases the Marangoni effect is responsible for the forces on the droplet, the behaviour of the droplet depends heavily on the exact composition. Though theoretical models are able to calculate the forces on a droplet, to model a mixture of oils on an aqueous surface where compounds from the oil phase are dissolving and diffusing through the aqueous phase is beyond current computational capability. The behaviour of a droplet in an aqueous phase can only be discovered through experiment, though it is determined by the droplet's composition. By using an evolutionary algorithm and a liquid handling robot to conduct droplet experiments and decide which compositions to test next, entirely autonomously, the composition of the droplet becomes a chemical genome capable of evolution. The selection is carried out according to a fitness function, which ranks the formulation based on how well it conforms to the chosen fitness criteria (e.g. movement or division). Over successive generations, significant increases in fitness are achieved, and this increase is higher with more components (i.e. greater complexity). Other chemical processes such as chemiluminescence and gelation were investigated in active oil droplets, demonstrating the possibility of controlling chemical reactions by selective droplet fusion. Potential future applications for this might include combinatorial chemistry, or additional fitness goals for the genetic algorithm. Combining the self-replication and the droplet protocells research, it was demonstrated that the presence of the amphiphilic replicator lowers the interfacial tension between droplets of a reaction mixture in organic solution and the alkaline aqueous phase, causing them to divide. Periodic sampling by a liquid handling robot revealed that the extent of droplet fission increased as the reaction progressed, producing more individual protocells with increased self-replication. This demonstrates coupling of the molecular scale phenomenon of template self-replication to a macroscale physicochemical effect.

Synthetic studies towards the total synthesis of hexacyclinic acid

In the first chapter of this thesis, published works found in the literature about hexacyclinic acid and FR182877 are reported and commented. A quick summary of the previous work done in the Prunet group is also described. In the second and third chapter, a more detailed account of the work undertaken during this PhD was given. Firstly, syntheses of two ABC tricycles incorporating tert-butyl and (trimethylsilyl)ethyl esters were undertaken. These syntheses include two key steps previously developed in the group, a diastereoselective Michael addition and a Snider cyclisation. Multiple conditions for the hydrolysis of the esters were attempted but none of them gave the desired product. The main part of this work is focused on the synthesis of a CDEF model and in particular about the development of the key step, the formation of a nine-membered ring. Several DEF fragments were synthesised in short synthetic sequences and as single isomers. Six different synthetic pathways were developed in total and a novel method, a Michael/elimination reaction, was found to be a very efficient way to close the desired medium-size ring. From the nine-membered ring, regioselective reduction and palladiumcatalysed allylic substitution led to the formation of the CDF tricycle. Final steps of the synthesis were fruitless and led only to decomposition. A synthesis of a chiral C-ring was also developed during this PhD. II Finally, another project was undertaken, not related to hexacyclinic acid. Methodology developed in the group for the diastereoselective formation of trisubstituted alkenes employing a temporary silicon-tethered ring-closing metathesis was extended to homoallylic alcohols. The first steps of the method were similar to the previous methodology but the end-game had to be modified in favour of an oxidation/reduction sequence to successfully obtain the desired products with the correct geometry. In the fourth chapter, procedures and analytical data for the synthesised compounds previously described are reported.

Upgrading Bio-Platform Molecules in the Gas-Phase: From Levulinic Acid to Bio-Chemicals

Levulinic acid (LA) is a polyfunctional molecule obtained from biomass. Because of its structure, the United States Department of energy classified LA as one of the top 12 building block chemicals. Typically, it is valorized through chemical reduction to γ-valerolactone (GVL). It is usually done with H2 in batch systems with high H2 pressures and noble metal catalysts, making it expensive and less applicable. Therefore, alternative approaches such as catalytic transfer hydrogenation (CTH) through the Meerwein–Ponndorf–Verley (MPV) reaction over heterogeneous catalysts have been studied. This uses organic molecules (alcohols) which act as a hydride transfer agent (H-donor), to reduce molecules containing carbonyl groups. Given the stability of the intermediate, reports have shown the batch liquid-phase CTH of levulinate esters with secondary alcohols, and remarkable results (GVL yield) have been obtained over ZrO2, given the need of a Lewis acid (LASites) and base pair for CTH. However, there were no reports of the continuous gas-phase CTH of levulinate esters. Therefore, high surface area ZrO2 was tested for gas-phase CTH of methyl levulinate (ML) using ethanol, methanol and isopropanol as H-donors. Under optimized conditions with ethanol (250 ℃), the reaction is selective towards GVL (yield 70%). However, heavy carbonaceous materials over the catalyst surface progressively blocked LASites changing the chemoselectivity. The in situ regeneration of the catalyst permitted a partial recovery of the LASites and an almost total recovery of the initial catalytic behavior, proving the deactivation reversible. Tests with methanol were not promising (ML conversion 35%, GVL yield 4%). As expected, using isopropanol provided complete conversion and a GVL yield of 80%. The reaction was also tested using bioethanol derived from agricultural waste. In addition, a preliminary study was performed for the hydrogenolysis of polyols to produce bioethanol, were Pd-Fe catalyst promoted the ethanol selective (37%) hydrogenolysis of glycerol.

Lewis acid catalysed direct glycosylation of N-acetyl-D-glucosamine

Incorporation of the relevant monosaccharide N-Acetyl-D-glucosamine (GlcNAc) into synthetic oligosaccharides by chemical glycosylation is still a very challenging object of studies, since direct reactions are low yielding. This issue is generally ascribed to its low solubility in common solvents and to the formation of a poorly reactive oxazoline intermediate, which is typically bypassed by introducing extra synthetic steps to avoid the presence of the NHAc moiety during glycosylation. Recently, a new direct Lewis acids-catalysed GlcNAc-ylation protocol has been disclosed, with acylated donors appearing to hold potential for high yielding glycosylation reactions. This master project focused indeed on a novel synthesis of promising 1-acyl GlcNAc donors, in order to test them in direct Lewis acid catalysed glycosylation without the need of N-protecting groups. Screening of various Lewis acids and reaction conditions with these acylated donors has been carried out, in presence of reactive primary alcohols as well as more challenging carbohydrate acceptor alcohols. These experiments demonstrated that the fine tuning of the leaving group combined with a suitable metal triflate could lead to a successful reaction outcome in the direct glycosylation. Successful methodology of this kind would provide rapid access to naturally occurring N-glycan motifs, such as the highly relevant human milk oligosaccharides (HMOs).

Catalysts study of adipic acid synthesis from 1,6-hexanediol

Sustainable chemicals currently have a very limited market share due to current low production but biomass is expected to become one of the major renewable energy and fine chemicals sources in the coming years. Bearing in mind the compromise of all nations to climatic change remediation, the industries will need to use efficient catalysts and green processes to meet the requirements of emissions and efficiency. This project is expected to develop new catalysts to convert 1,6-hexanediol to adipic acid through a green approach based on the “nano-catalysis” and “green chemistry” concepts. Supported Au and Pd nanoparticles were used to study one-pot reaction of HDO oxidation to AA using O2 as a final oxidant and H2O as a solvent. Catalytic results showed that under low pressure O2 atmosphere and low temperature (< 120°C) AuNPs supported on basic-supports are more active than acid and amphoteric oxides. The effect of basic oxide (MgO) addition to MgF2 was studied. The study showed that doping of MgF2 with MgO increased significantly the activity of the catalyst. The best results were obtained with the Au/0.4MgF2-0.6MgO sample, which gave the selectivity to AA of 33% at HDO conversion of 62%.

Investigation of gold-based catalysts for liquid phase oxidation of glucose to glucaric acid

Glucaric acid (GA) is one of the building block chemicals derived from sugar biomass with higher added value. Nowadays, GA is produced by oxidation of glucose (Glu) with either stoichiometric oxidants (HNO3), or by means of electrochemical or biochemical synthesis. However, these processes show drawbacks from either the environmental or economic viewpoint. For this reason, gold nanoparticles (Au NPs) supported on activated carbon (AC) have been studied as catalysts for the oxidation of Glu, using O2 as oxidant in the presence of a base. Using sol immobilization technique, Au NPs have been supported on AC following different experimental procedures. UV-Vis spectroscopy, XRD, TEM and TG analysis were utilized in the characterization of the catalysts. The operational conditions were optimized obtaining 24% of yield of GA, 37% to GO and 27% to byproducts in 1 h, 1000 rpm, 10 bar of O2 and Glu:Au:NaOH molar ratio of 1000:1:3000. Under such conditions, catalysts show relatively high Glu conversion (≥82%) with different GA yields. GO+GA yield is around 58-61%. Therefore, the oxidation reaction was performed at 15 min where Au/AC PVA0 reached the highest yield of GA (16%) and Au/AC PVA2.4 gave the lowest (8%). It is evident that the presence of PVA influences to a higher degree the reaction rate than the Au NPs size. Hence, the effect of different heat treatments where applied for the removal of PVA: washing with water at 60℃ or heat treatment (120-250℃) with Air/H2. Washing treatment and heat treatment at 120℃ with Air/H2 may have resulted in the mildest treatments for the removal of PVA. Finally, two different supports have been used in order to study the effect of metal-support interaction in the immobilization of Au NPs: ZrO2 and AC. Au/AC catalyst demonstrated a higher conversion of GO to GA at short reaction times (15.1% yield GA) compared to Au/ZrO2 (2.4% yield GA).

Computational study on the asymmetric aminocatalysed Michael addition reaction of cyclohexanone to trans–β–nitrostyrene

Asymmetric organocatalysed reactions are one of the most fascinating synthetic strategies which one can adopt in order to induct a desired chirality into a reaction product. From all the possible practical applications of small organic molecules in catalytic reaction, amine–based catalysis has attracted a lot of attention during the past two decades. The high interest in asymmetric aminocatalytic pathways is to account to the huge variety of carbonyl compounds that can be functionalized by many different reactions of their corresponding chiral–enamine or –iminium ion as activated nucleophile and electrophile, respectively. Starting from the employment of L–Proline, many useful substrates have been proposed in order to further enhance the catalytic performances of these reaction in terms of enantiomeric excess values, yield, conversion of the substrate and turnover number. In particular, in the last decade the use of chiral and quasi–enantiomeric primary amine species has got a lot of attention in the field. Contemporaneously, many studies have been carried out in order to highlight the mechanism through which these kinds of substrates induct chirality into the desired products. In this scenario, computational chemistry has played a crucial role due to the possibility of simulating and studying any kind of reaction and the transition state structures involved. In the present work the transition state geometries of primary amine–catalysed Michael addition reaction of cyclohexanone to trans–β–nitrostyrene with different organic acid cocatalysts has been studied through different computational techniques such as density functional theory based quantum mechanics calculation and force–field directed molecular simulations.

Computational Investigation of the Molecular Mechanisms Regulating Nucleic Acid Processing Metalloenzymes

Polymerases and nucleases are enzymes processing DNA and RNA. They are involved in crucial processes for cell life by performing the extension and the cleavage of nucleic acid chains during genome replication and maintenance. Additionally, both enzymes are often associated to several diseases, including cancer. In order to catalyze the reaction, most of them operate via the two-metal-ion mechanism. For this, despite showing relevant differences in structure, function and catalytic properties, they share common catalytic elements, which comprise the two catalytic ions and their first-shell acidic residues. Notably, recent studies of different metalloenzymes revealed the recurrent presence of additional elements surrounding the active site, thus suggesting an extended two-metal-ion-centered architecture. However, whether these elements have a catalytic function and what is their role is still unclear. In this work, using state-of-the-art computational techniques, second- and third-shell elements are showed to act in metallonucleases favoring the substrate positioning and leaving group release. In particular, in hExo1 a transient third metal ion is recruited and positioned near the two-metal-ion site by a structurally conserved acidic residue to assist the leaving group departure. Similarly, in hFEN1 second- and third-shell Arg/Lys residues operate the phosphate steering mechanism through (i) substrate recruitment, (ii) precise cleavage localization, and (iii) leaving group release. Importantly, structural comparisons of hExo1, hFEN1 and other metallonucleases suggest that similar catalytic mechanisms may be shared by other enzymes. Overall, the results obtained provide an extended vision on parallel strategies adopted by metalloenzymes, which employ divalent metal ion or positively charged residues to ensure efficient and specific catalysis. Furthermore, these outcomes may have implications for de novo enzyme engineering and/or drug design to modulate nucleic acid processing.

Multi-functional electrocatalysts for CO2 reduction reaction: towards the modulation of selectivity

The electrocatalytic reduction of CO2 (CO2RR) is a captivating strategy for the conversion of CO2 into fuels, to realize a carbon neutral circular economy. In the recent years, research has focused on the development of new materials and technology capable of capturing and converting CO2 into useful products. The main problem of CO2RR is given by its poor selectivity, which can lead to the formation of numerous reaction products, to the detriment of efficiencies. For this reason, the design of new electrocatalysts that selectively and efficiently reduce CO2 is a fundamental step for the future exploitation of this technology. Here we present a new class of electrocatalysts, designed with a modular approach, namely, deriving from the combination of different building blocks in a single nanostructure. With this approach it is possible to obtain materials with an innovative design and new functionalities, where the interconnections between the various components are essential to obtain a highly selective and efficient reduction of CO2, thus opening up new possibilities in the design of optimized electrocatalytic materials. By combining the unique physic-chemical properties of carbon nanostructures (CNS) with nanocrystalline metal oxides (MO), we were able to modulate the selectivity of CO2RR, with the production of formic acid and syngas at low overpotentials. The CNS have not only the task of stabilizing the MO nanoparticles, but the creation of an optimal interface between two nanostructures is able to improve the catalytic activity of the active phase of the material. While the presence of oxygen atoms in the MO creates defects that accelerate the reaction kinetics and stabilize certain reaction intermediates, selecting the reaction pathway. Finally, a part was dedicated to the study of the experimental parameters influencing the CO2RR, with the aim of improving the experimental setup in order to obtain commercial catalytic performances.