D.Phil. / Please refer to full text to view abstract

“Whiting” is a term used to describe a sharply defined patch of water that contains high levels of suspended, fine-grained calcium carbonate (CaCO3). These features are named for their bright (at times white) appearance when compared to surrounding waters, and have been found to occur globally, persisting for multiple consecutive days. Although whitings have been widely studied using chemical, biological, geological, and physical techniques, there has been little effort to document their spatio-temporal distributions in a systematic way, not to mention the lack of consensus on what generates whitings and allows them to persist for days to weeks at a time. In particular, although fishermen and aircraft pilots have reported whiting-like features off southwest Florida (e.g., a sighting off the Ten Thousand Islands was reported on October 29, 2013), there has been no targeted study on these features in this area. Therefore, the objective of this study is two fold: 1) to document the spatial-temporal distributions of whitings in southwest Florida (SWFL) coastal waters from 2003 through 2015 using satellite imagery to study how their occurrence is related to several environmental variables and 2) to conduct field and laboratory measurements to determine the particle composition and water characteristics in and outside the whiting features. To achieve objective one, a multi-year time series from 2003 through 2015 was developed over SWFL using Moderate Resolution Imaging Spectroradiometer (MODIS) observations. Customized processing was used in order to removed clouds and other artifacts and to delineate the surface whiting features. From this, statistics and distribution maps of whiting occurrence were generated. Annual mean whiting coverage peaked in 2011 (11 km2), when whiting reached a maximum daily visible coverage of 92 km2 on February 23. For the entire time series, the highest daily coverage observed was 126 km2 on December 6, 2008. Over all, whitings had higher spatial coverage during the spring and autumn, with 88% of all whiting coverage occurring within 40 km of the coastline. Images of average seasonal spatial distributions showed that over 90% of whitings located between 40 and 70 km of shore occurred specifically during the winter and autumn. A multivariate linear regression was performed, which found little to no correlation between annual whiting coverage and environmental factors such as sea surface temperature (SST), wind, and river discharge. This analysis was also applied to spatial distributions of whiting events within and outside of 20 km and 40 km from shore. The only statistically significant result was that of SST, as well as SST with river discharge and whiting events distributed more than 20 km from shore. In order to accomplish objective two, several field campaigns were conducted to collect in-situ data and water samples of pre-, post-, and occurring whiting event conditions to provide information on composition, driving forces, and variables that cannot be derived via satellites. Samples were collected for taxonomic identification, chemical analysis, bottom sediment grain size fractionation, in-situ remote sensing reflectance (Rrs), particle backscattering (bbp), chlorophyll-a concentration ([chl-a]), particulate absorption (ap), and gelbstoff (otherwise known as color dissolved organic matter, or CDOM) absorption (ag). Taxonomic identification of marine phytoplankton within whiting water revealed the presence of a dominant, small (<5 >μm), centric diatom species during a sampled whiting event. Through the use of scanning electron microscopy (SEM), these were identified as Thalassiosira sp. Amorphous to fully formed crystals of calcium carbonate were present, attached to cells of Thalassiosira sp., localized to the girdle bands. All other diatom species were devoid of similar growths. In comparing the waters within a whiting area to outside waters, no significant differences were found in ap, ag, nor [chl-a]. The carbonate parameters of whiting water differed from outside water, however due to low sample numbers these results are inconclusive. Average backscattering was twice as high within whiting waters compared to non-whiting water, and measured in-situ Rrs was higher at all wavelengths (400 – 700 nm) within whiting water, with a spectral shape similar to outside waters. Overall, this is the first time that SWFL whiting events have been characterized systematically using satellite imagery, field and laboratory as well as meteorological data to diagnose whiting causes and maintenance mechanisms. Although these results are inconclusive, they add new information to the existing literature on this phenomenon.

The Great Australian Bight (GAB) is an extensive W-E striking continental margin basin that drifted northwards during the Cenozoic following rifting and separation from Antarctica in the mid/late Cretaceous. Seafloor spreading accelerated in the mid-Eocene and was associated with local volcanism. The mid-Eocene succession of the GAB is conspicuously mounded and separates a dominantly siliciclastic succession below from a fully marine carbonate succession above. The mounded succession was penecontemporaneous with major changes in global climate, oceanographic conditions and tectonic re-organization in the region, and thus may hold important clues as to the palaeo-environmental changes associated with these changes. The mid Eocene has so far only been described locally or in passing, usually by studies focused on either the siliciclastics below or the carbonates above. It was therefore chosen as a major focus point for the research project reported herein. Exploration activity in the GAB has been limited despite the presence of a working petroleum system and large target structures, but industry interest has increased over the past few years leading to 3D seismic surveys being acquired in the GAB. The focus for exploration is the Cretaceous succession beneath the relatively thin Cenozoic cover, which however, is still important in terms of shallow hazards and as overburden to the anticipated productive sections. As is often the case, the new 3D seismic data shows many overburden features in great detail and thus affords new insights to be gained that improve our understanding of the post-rift evolution of the marginThis thesis expands upon and reinterprets a pre-existing sequence framework in the Cenozoic GAB based from ODP Leg 182 results. A vast database of 2D and 3D seismic surveys has been integrated with exploration wells and borehole data and several surfaces have been calibrated to borehole and well constraints, then mapped to the maximum lateral extent across the available dataset. Surface mapping provided new insight into sequence deposition and palaeoenvironmental settings. Structure maps and thickness maps highlight key depocentre locations and trends over the Cenozoic GAB as well as stacked mass debris aprons. The newly discovered sequences raise new questions regarding trigger mechanisms in a-seismic areas and feed into industry geohazard perception models. The base surface of the Cenozoic framework hosts a plethora of mounded features across shelf and basinal section. All mounds within the dataset have been mapped. A set a bryozoan reef mounds have been interpreted lying parallel to the margin as linear complexes over 500 km. They coincide with the underlying siliciclastic delta clinoform breakpoints and provide insight into the changing palaeoenvironment at the 43 Ma mark, cessation of siliciclastics and regional marine transgression. Further mound mapping aided by 3D attribute extractions along the base Cenozoic unconformity led to the interpretation of a series of enigmatic igneous-based mounded features. The discoveries have been included in a comparative study, comparing all mounded features (igneous or carbonate) and contrasting their individual characteristics of geometry, seismic facies, dimension in order to understand mound origin and emplacement. A new grouping of mounds in the GAB has been established, the origin and emplacement mechanisms of which contribute to the global knowledge base.

Botswana Ash (Pty) Ltd which is situated in Sua Pan, north east Bostwana, is one of Africa's largest suppliers of salt and soda ash. For a number of years, the company has been experiencing problems which have resulted in the final soda ash product being contaminated and discoloured. The problems experienced at Sua Pan have been reported also to occur in other salt works all over the world. It has been suggested that contamination in many salt works could be possibly be due to the microbial activity by halophilic algae and bacteria that grow in the solar ponds. This study was undertaken to investigate the nature of the contaminating organic compounds present in the brine, to identify the compounds, and to establish how these components vary during the various stages of the soda ash processing. For this study, two sets of brine samples were used; the first set was collected before the summer rains and the second set was collected after the summer rains. Solid bicarbonate and soda ash samples were also used. Extractions, desalting, UV and HPLC analysis and oxidative biotransformations using four enzymes, were used for developing profiles and characterizing the brine components. From these studies, we were able to confirm that the components of the brine are organic in nature. A thorough study of one of the compounds isolated,from solid bicarbonate and soda ash was conducted using UV, HPLC, IR, NMR, HPLC-MS, GC-MS and TLC. The results of these analyses, show that the. isolated compound was benzyl butyl phthalate which is generally regarded to be humic in nature. This compound was found to be present in all the brine samples collected after the summer rains including the well brine, suggesting this compound occurs naturally and is not formed during the processing.

Cette thèse vise à avancer dans la compréhension de la formation récemment découverte de carbonates amorphes intracellulaires par des cyanobactéries. Des synthèses abiotiques ont permis de produire des carbonates similaires aux inclusions intracellulaires en termes de morphologie, structure et composition chimique. Ceci a permis notamment de discuter les conditions chimiques présentes dans le milieu intracellulaire de ces bactéries, qui semblent incompatibles avec les connaissances actuelles de l’intérieur des cyanobactéries. Plusieurs souches de cyanobactéries formant ou non des carbonates intracellulaires ont été cultivées en laboratoire. Des études de chimie des solutions sur le milieu extracellulaire ont montré que la précipitation intracellulaire est un processus actif pour la cellule, c’est-à-dire nécessitant de l’énergie. De plus, les cyanobactéries formant des carbonates de calcium intracellulaires imposent de faibles concentrations en calcium dans leur milieu de vie. Le suivi de la formation de carbonates intracellulaires dans des milieux contrôlés a aussi permis de démontrer qu’une espèce formait spécifiquement des carbonates de baryum et de strontium grâce à une affinité pour le baryum supérieure à celle pour le strontium, elle-même supérieure à celle pour le calcium. Ceci ouvre des perspectives intéressantes pour la dépollution et questionne l’utilisation des rapports Sr/Ca comme proxy des paléo-environnements. / In this thesis we study the recently discovered formation of intracellular amorphous carbonates by cyanobacteria. Abiotic syntheses produced carbonates with a morphology, structure and composition similar as intracellular inclusions. The intracellular chemical conditions in the cyanobacteria can be discussed; they seem inconsistent with our current knowledge about cyanobacteria. Several cyanobacterial strains, forming intracellular carbonates or not, were cultured in the laboratory. Analyses of the chemical composition of extracellular solutions showed that intracellular precipitation is an active process, i.e., it needs energy. Also, cyanobacteria forming intracellular calcium carbonates imposed low concentrations in calcium in their living environment. Monitoring the formation of intracellular carbonates in controlled environments also demonstrated that one species formed carbonates of barium and strontium owing to an affinity for barium higher than for strontium and higher for strontium than calcium. This feature opens interesting perspectives on bioremediation and questions the use of Sr/Ca ratios as a proxy for paleo-environments.

The decline of tree islands in the freshwater-Everglades wetland because of hydrologic manipulation, has compromised valuable ecosystem services. Although the role of tree islands in maintaining freshwater quality stems largely from evapotranspiration processes, fundamental questions remain about the effects of different geologic materials on their hydrogeochemical functioning. To reduce this uncertainty, the lithological composition of a set of man-made tree islands was investigated coupled with long-term hydrologic and hydrochemical data. Key results indicate that limestone substrates and peat substrates with elevated proportions of sand, facilitated surface water-groundwater interactions and mineral dissolution. However, limestone-based islands were more effective in lowering the water table and concentrating solutes in response to evapotranspiration during low surface water stages. Additionally, the peat substrate of an island with low sand content favored the thermodynamic conditions for calcite accumulation in the phreatic zone, while phosphorus concentrations in the groundwater were associated with the breakdown of organic matter.

Deep well injection into non-potable saline aquifers of treated domestic wastewater has been used in Florida for decades as a safe and effective alternative to ocean outfall disposal. The objectives of this study were to determine the fate and transport of injected wastewater at two deep well injection sites in Miami Dade County, Florida, USA. Detection of ammonium in the Middle Confining units of the Floridan aquifer above the injection zone at both sites has been interpreted as evidence of upward migration of injected wastewater, posing a risk to underground sources of drinking water. Historical water quality data, including ammonia, chloride, temperature, and pH from existing monitoring wells at both sites from 1983 to 2008, major ions collected monthly from 2006 and 2008, and a synoptic sampling event for stable isotopes, tritium, and dissolved gases in 2008, were used to determine the source of ammonium in groundwater and possible migration pathways. Geochemical modeling was used to determine possible effects of injected wastewater on native water and aquifer matrix geochemistry. Injected wastewater was determined to be the source of elevated ammonium concentrations above ambient water levels, based on the results of major ion concentrations, tritium, dissolved noble gases and 15N isotopes analyses. Various possible fluid migration pathways were identified at the sites. Data for the south site suggest buoyancy-driven vertical pathways to overlying aquifers bypassing the confining units, with little mixing of injected wastewater with native water as it migrated upward. Once it is introduced into an aquifer, the injectate appeared to migrate advectively with the regional groundwater flow. Geochemical modeling indicated that CO2 -enriched injected wastewater allowed for carbonate dissolution along the vertical pathways, enhancing permeability along these flowpaths. At the north site, diffusive upward flow through the confining units or offsite vertical pathways were determined to be possible, however no evidence was detected for any on-site confining unit bypass pathway. No evidence was observed at either site of injected wastewater migration to the Upper Floridan aquifer, which is used as a municipal water supply and for aquifer storage and recovery.

The thesis entitled ‘Studies on the Chemistry of Carbonates and Carbamates’ comprises of seven chapters. Chapter 1 The reactivity of propargyloxycarbonyl (Poc) derivatives of amines and alcohols with various sulphur nucleophiles is addressed in this chapter. The chapter is divided into three different parts. Part 1: The difference in reactivity of propargyloxycarbonyl (Poc) derivatives of amines and alcohols with benzyltriethylammonium tetrathiomolybdate [(PhCH2NEt3)2MoS4, 1] is studied in detail and the results are discussed. It has been shown that amino alcohols can be protected as their diPoc derivatives using 2 equiv of propargyloxycarbonyl chloride (2). The selective deprotection of the O-Poc group using 1 equiv of 1 without affecting the N-Poc group is achieved (Scheme 1). Scheme 1 Part 2: The reactivity of propargyloxycarbonyl derivatives of various alcohols, phenols and primary and secondary amines with benzyltriethylammonium tetrathiomolybdate (1) is compared with the reactivity of these Poc derivatives with other sulphur nucleophiles such as sodium thiophenoxide, lithium sulphide, hydrogen sulphide and ammonium sulphide. The study reveals that tetrathiomolybdate (1) is the best sulphur nucleophile for the deprotection of Poc group. Poc derivatives of primary amines cyclized to the corresponding 4-methylene-2-oxazolidinones when treated with other sulphur nucleophiles (Scheme 2). Scheme 2 Part 3: The reaction between different propargyloxycarbonyl derivatives of alcohols and benzyltriethylammonium tetrathiomolybdate (1) is studied. It is found that propargyloxycarbonyl derivatives can be made more reactive towards tetrathiomolybdate by substituting the propargyl system with electron withdrawing substituents. Chapter 2 The application of propargyloxycarbonyl group for the protection of the side chain hydroxyl groups of serine, threonine and tyrosine is discussed. The O-Poc derivatives are shown to be stable to a variety of acidic and basic conditions and the applications of these derivatives in solution phase peptide synthesis is addressed. The easy and effective deprotection of the O-Poc group provides a new strategy for the synthesis of peptides bearing the hydroxy amino acid residues: serine, threonine and tyrosine. Scheme 3 Chapter 3 Development of a novel C2-symmetric protecting group for amines and amino acids is described in this chapter. But-2-ynyl-1,4-bisoxycarbonyl chloride (BbcCl, 3) is synthesized from 1,4-dihydroxybut-2-yne and used as a reagent for protecting amines as biscarbamates (Scheme 4). These biscarbamates (Bbc derivatives) are deblocked using benzyltriethylammonium tetrathiomolybdate (1) to get the amines back. Scheme 4 The orthogonal stability of the Bbc group with Boc, Cbz and Fmoc groups is established. It is also shown that Bbc group can be deblocked to the corresponding amines using resin-bound tetrathiomolybdate. The application of Bbc protected amino acids in solution phase peptide synthesis is demonstrated (Scheme 5). Scheme 5 Chapter 4 The simultaneous protection and activation of amino acids using various pentafluorophenyl carbonates is described in two parts. Part 1: A very efficient and high yielding method for the simultaneous protection of the amino group and activation of carboxylic acid group using propargyl pentafluorophenyl carbonate (PocOPfp, 4) is discussed. Treating amino acids with 2 equiv of 4 protects the amino group as a propargyl carbamate and activates the carboxylic acid group as a pentafluorophenyl ester (Scheme 6). Scheme 6 Part 2: The generality of the methodology developed for the simultaneous protection and activation of amino acids using PocOPfp (4) is studied with five different pentafluorophenyl carbonates viz. AlocOPfp, CbzOPfp, BocOPfp, EocOPfp and TrocOPfp. The studies reveal that the effectiveness of the methodology depends on the nature of the pentafluorophenyl carbonates and on the nature of the amino acids. Sterically bulky pentafluorophenyl carbonates such as BocOPfp reacted slowly with amino acids while electron deficient pentafluorophenyl carbonates such as TrocOPfp reacted faster and gave the N-protected active esters in very good yields. Amino acids bearing longer aliphatic side chains reacted better than the other amino acids. Chapter 5 The chapter describes results of the detailed studies on the base catalyzed cyclization of N-alkyl and N-aryl-O-propargyl carbamates to the corresponding 4-alkylidene-2-oxazolidinones. The effect of various bases and solvents on these cyclization reactions is studied systematically to design the most suitable conditions. The best results were obtained using catalytic amount of LiOH in DMF. The cyclization reactions of N-aryl-O-propargyl carbamates were faster than the cyclization of N-alkyl-O-propargyl carbamates. The effect of substitutions on the propargyl group in these reactions is studied by preparing various substituted propargyl carbamate derivatives from the corresponding amines and propargyl chloroformates (Scheme 7). Scheme 7 Chapter 6 An efficient procedure for the synthesis of dehydroalanine and dehydroamino butyric acid derivatives from the preformed carbonate derivatives of serine and threonine respectively, by treating with K2CO3 in DMF is discussed in this chapter. The reaction proceeds stereoselectively through a trans E2-elimination pathway to give only the Z-isomer of dehydroamino butyric acid derivatives from the carbonate derivatives of threonine. The methodology offers an easy access to dehydropeptides and proceeds without racemization of other stereogenic centers present in the peptide (Scheme 8). Scheme 8 Chapter 7 This chapter describes the use of propargyloxycarbonyl derivatives of lysine as an efficient tool for the synthesis of peptide conjugates using a click chemistry approach. The Cu(I) catalyzed cycloaddition reaction between azides and alkynes is employed in the synthesis of conjugates of lysine. Peptides bearing an Nε-Poc Lysine residue can be synthesized using traditional strategies and these peptides can be easily conjugated with azide derivatives of sugars and amino acids (Scheme 9). Scheme 9 The efficiency of the method is demonstrated by carrying out more than one click reaction in one pot using di and tri-propargyl derivatives of lysine. A dendritic core (6) is prepared from a tri-propargyl derivative (5) of lysine and an azide derived from leucine (Scheme 10). Scheme 10 The abbreviations used in the thesis are consistent with those reported in J. Org. Chem. 2007, 71, 23A. Less common abbreviations are defined, the first time they are mentioned in the thesis.

The nanostructure, physical properties and mechanical performance of C-S-H, 1.4 nm tobermorite, jennite, and ettringite were studied. C-S-H of variable stoichiometries was examined as a model system in comparison with that produced in the hydration of Portland cement. The current Master’s thesis is comprised of four research papers designed to improve the current understanding of the nanostructure and engineering properties of C-S-H systems and modified C-S-H systems. Many of the controversial issues in cement science were identified and were addressed in a comprehensive research study, which examined the key features of the C-S-H systems at the nano-structure level. In Chapter 4, each paper presented new evidence for a number of mechanical aspects of C-S-H materials. Numerous advanced analytical tools were used in order to verify the observations made in each section. The major achievements of the current work are mentioned briefly as follows: 1. It was determined that microindentation is a useful method for determining the creep behavior of C-S-H of various stoichiometries, 1.4 tobermorite, jennite, and ettringite. 2. Microindentation parameters i.e. creep modulus, indentation modulus and indentation hardness are porosity dependent. 3. Microindentation creep measurements on C-S-H (C/S = 0.80 and 1.20) demonstrated that creep modulus, indentation modulus, and indentation hardness are all dependent on mass-loss from the 11%RH condition. 4. Evidence was presented that the nanostructural role of interlayer water in C-S-H has a significant influence on the creep process.

Les sols qui ne rencontrent pas les normes d’ingénierie civile doivent êtres soumis à des améliorations géotechniques car les vibrations causées par les tremblements de terre ou par la surcharge sur des infrastructures en hauteur peuvent mener à la liquéfaction partielle ou totale des sols saturés en eau. Ceci peut donc entrainer des dommages importants aux structures construites sur ces sols. Certaines méthodes existent pour remédier à ce problème, mais elles demeurent couteuses et parfois toxiques car elles utilisent de l’acrylamide et des lignosulfates. La bio-précipitation in situ de calcite dans les sols représente une méthode alternative. Le tout se fait avec des bactéries qui démontrent une activité uréolytique. La présente étude s’est intéressée à l’activité uréolytique des souches Escherichia coli, Sporosarcina ureae, Bacillus pasteurii, Lysinibacillus sphaericus, Bacillus subtilis et Bacillus megaterium. Les résultats démontrent que l’urée est seulement dégradée par les souches S. ureae et S. pasteurii. L’incubation de S. ureae en présence de Ni2+ (0.1-1 ppm) et Fe2+ (1-10 ppm) a toutefois permis d’augmenter l’activité catalytique de la souche, ce qui démontre l’importance des éléments nutritifs lors de l’hydrolyse de l’urée. Afin de tester l’activité uréolytique des autres souches, nous avons introduit un système d’expression uréase dans la souche E. coli en substituant des amino-acides dans la structure primaire des protéines. Suite à cette modification, l’activité uréolytique de E. coli s’est améliorée et est devenue comparable à celle des souches S. ureae et S. pasteurii. L’injection de S. ureae et du mutant E. coli dans des sables non-consolidés a permis de cimenter de façon significative (p < 0.05) le matériel par rapport à des sables non inoculés, et ce après seulement 48 heures. Le transfert du système recombinant de E coli vers S. ureae est présentement en cours. Ces résultats prometteurs indiquent qu’il est possible de stimuler la précipitation in situ de calcite en utilisant des bactéries et de stabiliser les sols prônes à la liquéfaction. === Soils often do not satisfy functional requirements for civil engineering projects and as a result geotechnical improvements to soils are often made. Dynamic shaking during earthquakes or static overloading by overlying structures may still result in liquefaction in partially or fully water saturated soils. These have little bearing capacity for structures. Severe damages can result. Moreover, preventative soil grouting strategies are expensive, toxic, and permanent due to acrylamides, lignosulfonates, and otherwise harmful compounds present therein. Alternative methods of strength enhancement are advisable. Microbial induced calcite precipitation (MICP) was assessed in this investigation to consolidate loose, sandy soils. Ureolytic activty of Escherichia coli, Sporosarcina ureae, Bacillus pasteurii, Lysinibacillus sphaericus, Bacillus subtilis and Bacillus megaterium were assessed. Urea was readily degraded foremost by S. ureae and next by S. pasteurii with no significant (p <0.05) activity in other strains. Incubation of S. ureae with 0.1 - 1ppm Ni2+ and 1-10ppm Fe2+ was shown to improve catalytic activity, suggesting their importance as a dietary source for urea hydrolysis. A urease expression system was established in E. coli and particular amino acid substitutions in protein primary structure made. Enhanced ureolytic activity was observed in these E. coli mutants, comparable to native S. ureae activity. Application of wild type S. ureae and recombinant E. coli for MICP in a model sand showed significant (p < 0.05) improvements compared to controls after 48 hours. Transfer of the recombinant system in E. coli to S. ureae is currently underway. These results provide valuable insight affirming that a practical system for the application of MICP may be feasible in the field for the strength enhancement of native and construction-laid loose, sandy soils.