Theoretical study of chloroperoxidase catalyzed chlorination of beta-cyclopentanedione and role of water in the chlorination mechanism

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate β-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Occurrence and transformation of organomercury in the Florida Everglades

In this study, a new method was developed based on aqueous phenylation, purge-and-trap preconcentration, gas chromatography (GC) separation, and detection by atomic fluorescence spectrometry (AFS) or inductively coupled plasma mass spectrometry (ICPMS). This technique is suitable for simultaneous determination of trace or ultratrace levels of CH3Hg+ and CH3CH2Hg+ in environmental samples. Method detection limits were 0.03 ng/L for both CH3Hg+ and CH3CH2Hg+ when AFS was used as the detector and 0.02 and 0.01 ng/L for CH3Hg+ and CH 3CH2Hg+ with ICPMS, respectively. The new method has the additional benefits of being free from interference by Cl - and dissolved organic matter. Using the method developed, both CH3Hg+ and CH3CH2Hg+ were detected in a number of soil and sediment samples collected from the Florida Everglades. The identity of CH3CH2Hg+ was verified by purge-and-trap-GC/MS analysis. The possibility of analytical artifact was excluded by using stable isotope tracer technique in combination with ICPMS detection. CH3CH 2Hg+ in the soil samples analyzed was at ng/g level, similar to that of CH3Hg+. The prevalence of CH 3CH2Hg+ in the soil of the Florida Everglades suggests that ethylation plays an important role in the geochemistry of Hg in this wetland. Soil incubation and sawgrass culture experiments using stable isotope tracers revealed that CH3Hg+ was mainly produced by microbial activities under anaerobic conditions, agreeing well with the general understanding of methylation mechanisms of Hg in the environment. Ethylation of Hg was not confirmed in these experiments, indicating that ethylation of Hg most probably follows different mechanisms in comparison to methylation. Further experiments revealed that trace levels of ethyllead species were able to transfer ethyl group to Hg in both deionized water and freshwater matrixes, producing CH3CH2Hg+. This might partially account for the occurrence of CH3CH2Hg+ in the relatively pristine environment of the Florida Everglades.

Periphyton as an indicator of restoration in the Everglades

Periphyton communities dominate primary production in much of the Florida Everglades wetland and therefore contribute to soil production, ecosystem metabolism and secondary production as well as the composition of dependent communities. Decades of research in the Everglades have supported research findings from other wetland types that cumulatively show that periphyton communities respond very rapidly to alterations in the two dominant drivers of wetland structure and function—hydrology and water quality. Hydrology controls periphyton productivity and composition by regulating moisture availability, substrate types available for colonization and supply of nutrients. Nutrients, particularly the limiting nutrient in this system, phosphorus (P), control levels of production and community composition. Because periphyton communities are well-established to be related to hydrology and water quality, an indicator was developed based on three periphyton attributes: abundance, quality (i.e., nutrient content) and community composition. This assessment tool offers a qualitative assessment of ecosystem response to potential changes in management activities at a time scale appropriate for active management. An example is provided of how the indicator can be used to assess the current water quality and hydrological conditions from high-density spatial surveys. Detected patterns of deterioration align with expectations derived from model predictions and known sources of nutrients and unnatural hydrologic regimes. If employed adaptively in ecosystem management, this tool can be used to both detect and react to change before the system has been irreparably altered.

Comparative study of dissolved organic matter from groundwater and surface water in the Florida coastal Everglades using multi-dimensional spectrofluorometry combined with multivariate statistics

Dissolved organic matter (DOM) in groundwater and surface water samples from the Florida coastal Everglades were studied using excitation–emission matrix fluorescence modeled through parallel factor analysis (EEM-PARAFAC). DOM in both surface and groundwater from the eastern Everglades S332 basin reflected a terrestrial-derived fingerprint through dominantly higher abundances of humic-like PARAFAC components. In contrast, surface water DOM from northeastern Florida Bay featured a microbial-derived DOM signature based on the higher abundance of microbial humic-like and protein-like components consistent with its marine source. Surprisingly, groundwater DOM from northeastern Florida Bay reflected a terrestrial-derived source except for samples from central Florida Bay well, which mirrored a combination of terrestrial and marine end-member origin. Furthermore, surface water and groundwater displayed effects of different degradation pathways such as photodegradation and biodegradation as exemplified by two PARAFAC components seemingly indicative of such degradation processes. Finally, Principal Component Analysis of the EEM-PARAFAC data was able to distinguish and classify most of the samples according to DOM origins and degradation processes experienced, except for a small overlap of S332 surface water and groundwater, implying rather active surface-to-ground water interaction in some sites particularly during the rainy season. This study highlights that EEM-PARAFAC could be used successfully to trace and differentiate DOM from diverse sources across both horizontal and vertical flow profiles, and as such could be a convenient and useful tool for the better understanding of hydrological interactions and carbon biogeochemical cycling.

Vegetation dynamics and their implications for the management of wetlands in the lowlands of Nepal

The maintenance of species richness is often a priority in the management of nature reserves, where consumptive use of resources is generally prohibited. The purpose of this research was to improve management by understanding the vegetation dynamics in the lowlands of Nepal. The objectives were to determine vegetation associations in relation to environments and human-induced disturbances that affect vegetation dynamics on floodplains, where upstream barrages had altered flooding patterns, and consumptive use of plant resources was influencing natural processes. Floodplain vegetation in relation to physical environments and disturbances were studied along transects, perpendicular to the course of the Mahakali River in the western Terai, Nepal. Forest structural changes were studied for three years in ten plots. A randomized split-block experiment with nine burning and grazing treatments was performed in seasonally flooded grasslands. A semi-structured questionnaire was used to assess people's socio-economic status, natural resource use patterns and conservation attitudes. ^ Elevation, soil organic matter, nitrogen, percentage of sand and grazing intensity were significant in delineating herbaceous vegetation assemblages, whereas elevation and livestock grazing were significant in defining forest type boundaries. On the floodplain islands, highly grazed Dalbergia sissoo-Acacia catechu forests were devoid of understory woody vegetation, but the lightly grazed D. sissoo-mixed forests had a well-developed second canopy layer, comprising woody species other than D. sissoo and A. catechu. In grasslands, species richness and biomass production were highest at intermediate disturbance level represented by the lightly grazed and ungrazed early-burned treatments. Ethnicity, education and resource use patterns were important in influencing conservation attitudes. A succession towards the mixed forests would occur in D. sissoo-dominated floodplain forests, where dams and barrages reduce flooding and associated fluvial processes, and if livestock grazing is stopped, as occasionally suggested by nature conservationists. In seasonally flooded grasslands, early burning with moderate grazing would enhance the species diversity and productivity. There is a need to implement a participatory integrated wetland management plan, to include community development, education and off farm income generation, to assure participatory conservation and management of wetlands in Nepal. ^

Biogeochemical factors affecting the fate and transport of mercury in the terrestrial environment at Oak Ridge, Tennessee

Mercury (Hg) contamination problem in the United Sates has been an important issue due to its potential threat to human and ecological health. This thesis presents a study of two Hg-contaminated sites along the East Fork Poplar Creek (EFPC) at Oak Ridge. The top soils from the terrestrial areas, along with the soils from three vertical soil horizons at the EFPC bank were sampled and analyzed for total-Hg (THg), methyl-Hg, total-organic-carbon (TOC), and pH. The stream bank soils were also analyzed for the stable-Hg-isotopes (198Hg, 199Hg, 200Hg, 201Hg, and 202Hg). Furthermore, some of the soil samples (n=7) from the same study sites were investigated for phytoavailability of mercury as measured by degree of Hg translocation in aboveground biomass of Impatiens walleriana plants grown in the soils.^ The results showed a significant difference (p<0.001) in THg concentrations for the forest soils (42.40±4.98 mg/kg) and the grassland soils (8.71±2.30 mg/kg). The higher THg and methyl-Hg concentrations were commensurate with the higher TOC content in the soils (p<0.001). Also, the THg concentrations for the upstream site was higher (129.08±34.14 mg/kg) than the downstream site (24.31±3.47 mg/kg). The two sites also differed in their stable Hg isotope compositions (p<0.001 for δ199Hg). The stable isotope analysis indicated the increased level of mass dependent isotopic fractionation with increasing depths along the EFPC bank. The difference between the two study sites was also prominent in case of the Hg uptake by the plants, with higher Hg uptake from the upstream soils compared to that from the downstream soils. A significant correlation, r=0.93 p<0.01, was observed between the Hg uptake and the soil-THg concentrations. THg was higher in the leaves (1161.87±310.01 μg/kg) than in the flowers (206.13±55.23 μg/kg) or the stems (634.54±403.35μg/kg). ^ The level of Hg contamination increased with decreasing distance from the point source and was highly influenced by plants/microbes, soil-organic-content, and Hg-speciation. The isotopic study indicated the existence of an additional Hg source in the EFPC watershed, possibly atmospheric Hg-deposition. These findings are worth taking into account while planning any Hg remediation effort and developing Hg loading criteria as per the National Pollutant Discharge Elimination System (NPDES) Program.^

Landscape patterns of periphyton in the Florida Everglades

Periphyton is an abundant and ubiquitous feature of the Florida Everglades, often forming thick mats that blanket shallow sediments and submersed plants. They are considered to be primary ecosystem engineers in the Everglades by forming and stabilizing soils, controlling concentrations of nutrients and gases, and supplying food and structure for other organisms. Distribution patterns are related to underlying physicochemical gradients as well as those hydrologic changes imposed by water management. Because communities respond rapidly to environmental change, their use has been advocated to provide indication of system degradation or restoration. The authors review studies on the distribution of periphyton in the Everglades, highlighting major findings relevant to water management, and also areas where additional exploration is necessary.

Hydrogeophysical characterization of anisotropy in the Biscayne Aquifer using geophysical methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.^

Hydrogeophysical Characterization of Anisotropy in the Biscayne Aquifer Using Geophysical Methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.