Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modelled using RRKM theory, based on Eo values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k∞ values in the range 1.9 to 4.5 × 10-10 cm3 molecule-1 s-1. These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16 and 67% of the collision rates for these reactions. In the reaction of SiH2 + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalysed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H2O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

Quantum effects and dynamics in hydrogen-bonded systems: a first-principles approach to spectroscopic experiments

Computer simulations have become an important tool in physics. Especially systems in the solid state have been investigated extensively with the help of modern computational methods. This thesis focuses on the simulation of hydrogen-bonded systems, using quantum chemical methods combined with molecular dynamics (MD) simulations. MD simulations are carried out for investigating the energetics and structure of a system under conditions that include physical parameters such as temperature and pressure. Ab initio quantum chemical methods have proven to be capable of predicting spectroscopic quantities. The combination of these two features still represents a methodological challenge. Furthermore, conventional MD simulations consider the nuclei as classical particles. Not only motional effects, but also the quantum nature of the nuclei are expected to influence the properties of a molecular system. This work aims at a more realistic description of properties that are accessible via NMR experiments. With the help of the path integral formalism the quantum nature of the nuclei has been incorporated and its influence on the NMR parameters explored. The effect on both the NMR chemical shift and the Nuclear Quadrupole Coupling Constants (NQCC) is presented for intra- and intermolecular hydrogen bonds. The second part of this thesis presents the computation of electric field gradients within the Gaussian and Augmented Plane Waves (GAPW) framework, that allows for all-electron calculations in periodic systems. This recent development improves the accuracy of many calculations compared to the pseudopotential approximation, which treats the core electrons as part of an effective potential. In combination with MD simulations of water, the NMR longitudinal relaxation times for 17O and 2H have been obtained. The results show a considerable agreement with the experiment. Finally, an implementation of the calculation of the stress tensor into the quantum chemical program suite CP2K is presented. This enables MD simulations under constant pressure conditions, which is demonstrated with a series of liquid water simulations, that sheds light on the influence of the exchange-correlation functional used on the density of the simulated liquid.

The impact of different nanoparticle surface chemistry and size on uptake and toxicity in a murine macrophage cell line

This study investigated the uptake, kinetics and cellular distribution of different surface coated quantum dots (QDs) before relating this to their toxicity. J774.A1 cells were treated with organic, COOH and NH2 (PEG) surface coated QDs (40 nM). Model 20 nm and 200 nm COOH-modified coated polystyrene beads (PBs) were also examined (50 microg ml(-1)). The potential for uptake of QDs was examined by both fixed and live cell confocal microscopy as well as by flow cytometry over 2 h. Both the COOH 20 nm and 200 nm PBs were clearly and rapidly taken up by the J774.A1 cells, with uptake of 20 nm PBs being relatively quicker and more extensive. Similarly, COOH QDs were clearly taken up by the macrophages. Uptake of NH2 (PEG) QDs was not detectable by live cell imaging however, was observed following 3D reconstruction of fixed cells, as well as by flow cytometry. Cells treated with organic QDs, monitored by live cell imaging, showed only a small amount of uptake in a relatively small number of cells. This uptake was insufficient to be detected by flow cytometry. Imaging of fixed cells was not possible due to a loss in cell integrity related to cytotoxicity. A significant reduction (p<0.05) in the fluorescent intensity in a cell-free environment was found with organic QDs, NH2 (PEG) QDs, 20 nm and 200 nm PBs at pH 4.0 (indicative of an endosome) after 2 h, suggesting reduced stability. No evidence of exocytosis was found over 2 h. These findings confirm that surface coating has a significant influence on the mode of NP interaction with cells, as well as the subsequent consequences of that interaction.

Seawater carbonate chemistry and phytoplankton and eubacterial community compositions in the northwest subarctic Pacific

On-deck CO2-Fe-manipulated incubation experiments were conducted using surface seawater collected from the Western Subarctic Gyre of the NW Pacific in the summer of 2008 to elucidate the impacts of ocean acidification and Fe enrichment on the abundance and community composition of phytoplankton and eubacteria in the study area. During the incubation, excluding the initial period, the mean partial pressures of CO2 in non-Fe-added bottles were 230, 419, 843, and 1124 µatm, whereas those in Fe-added treatments were 152, 394, 791, and 1008 µatm. Changes in the abundance and community composition of phytoplankton were estimated using HPLC pigment signatures with the program CHEMTAX and flow cytometry. A DGGE fingerprint technique targeting 16S rRNA gene fragments was also used to estimate changes in eubacterial phylotypes during incubation. The Fe addition induced diatom blooms, and subsequently stimulated the growth of heterotrophic bacteria such as Roseobacter, Phaeobacter, and Alteromonas in the post-bloom phase. In both the Fe-limited and Fe-replete treatments, concentrations of 19'-hexanoyloxyfucoxanthin, a haptophyte marker, and the cell abundance of coccolithophores decreased at higher CO2 levels (750 and 1000 ppm), whereas diatoms exhibited little response to the changes in CO2 availability. The abundances of Synechococcus and small eukaryotic phytoplankton (<10 µm) increased at the higher CO2 levels. DGGE band positions revealed that Methylobacterium of Alphaproteobacteria occurred solely at lower CO2 levels (180 and 380 ppm) during the post-bloom phase. These results suggest that increases in CO2 level could affect not only the community composition of phytoplankton but also that of eubacteria. As these microorganisms play critical roles in the biological carbon pump and microbial loop, our results indicate that the progression of ocean acidification can alter the biogeochemical processes in the study area.

Seawater carbonate chemistry and coverage and dry weight of Ecklonia radiata during experiments, 2010

Predictions about the ecological consequences of oceanic uptake of CO2 have been preoccupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks the direct effects of CO2 on non-calcareous taxa, particularly those that play critical roles in ecosystem shifts. We used two experiments to investigate whether increased CO2 could exacerbate kelp loss by facilitating non-calcareous algae that, we hypothesized, (i) inhibit the recovery of kelp forests on an urbanized coast, and (ii) form more extensive covers and greater biomass under moderate future CO2 and associated temperature increases. Our experimental removal of turfs from a phase-shifted system (i.e. kelp- to turf-dominated) revealed that the number of kelp recruits increased, thereby indicating that turfs can inhibit kelp recruitment. Future CO2 and temperature interacted synergistically to have a positive effect on the abundance of algal turfs, whereby they had twice the biomass and occupied over four times more available space than under current conditions. We suggest that the current preoccupation with the negative effects of ocean acidification on marine calcifiers overlooks potentially profound effects of increasing CO2 and temperature on non-calcifying organisms.

Seawater carbonate chemistry and calcium carbonate of Padina spp., photosynthesis of Padina pavonica in nature CO2 gradients experiment

Predicting the impacts of ocean acidification on coastal ecosystems requires an understanding of the effects on macroalgae and their grazers, as these underpin the ecology of rocky shores. Whilst calcified coralline algae (Rhodophyta) appear to be especially vulnerable to ocean acidification, there is a lack of information concerning calcified brown algae (Phaeophyta), which are not obligate calcifiers but are still important producers of calcium carbonate and organic matter in shallow coastal waters. Here, we compare ecological shifts in subtidal rocky shore systems along CO2 gradients created by volcanic seeps in the Mediterranean and Papua New Guinea, focussing on abundant macroalgae and grazing sea urchins. In both the temperate and tropical systems the abundances of grazing sea urchins declined dramatically along CO2 gradients. Temperate and tropical species of the calcifying macroalgal genus Padina (Dictyoaceae, Phaeophyta) showed reductions in CaCO3 content with CO2 enrichment. In contrast to other studies of calcified macroalgae, however, we observed an increase in the abundance of Padina spp. in acidified conditions. Reduced sea urchin grazing pressure and significant increases in photosynthetic rates may explain the unexpected success of decalcified Padina spp. at elevated levels of CO2. This is the first study to provide a comparison of ecological changes along CO2 gradients between temperate and tropical rocky shores. The similarities we found in the responses of Padina spp. and sea urchin abundance at several vent systems increases confidence in predictions of the ecological impacts of ocean acidification over a large geographical range.

Seawater carbonate chemistry and survival, impairment of three phytoplankton species in a laboratory experiment

Sodium hypochlorite (NaOCl) is widely used to disinfect seawater in power plant cooling systems in order to reduce biofouling, and in ballast water treatment systems to prevent transport of exotic marine species. While the toxicity of NaOCl is expected to increase by ongoing ocean acidification, and many experimental studies have shown how algal calcification, photosynthesis and growth respond to ocean acidification, no studies have investigated the relationship between NaOCl toxicity and increased CO2. Therefore, we investigated whether the impacts of NaOCl on survival, chlorophyll a (Chl-a), and effective quantum yield in three marine phytoplankton belonging to different taxonomic classes are increased under high CO2 levels. Our results show that all biological parameters of the three species decreased under increasing NaOCl concentration, but increasing CO2 concentration alone (from 450 to 715 µatm) had no effect on any of these parameters in the organisms. However, due to the synergistic effects between NaOCl and CO2, the survival and Chl-a content in two of the species, Thalassiosira eccentrica and Heterosigma akashiwo, were significantly reduced under high CO2 when NaOCl was also elevated. The results show that combined exposure to high CO2 and NaOCl results in increasing toxicity of NaOCl in some marine phytoplankton. Consequently, greater caution with use of NaOCl will be required, as its use is widespread in coastal waters.

Seawater carbonate chemistry and combined mechanistic effects of CO2 and light on the N2-fixing cyanobacterium Trichodesmium IMS101, 2010

The marine diazotrophic cyanobacterium Trichodesmium responds to elevated atmospheric CO2 partial pressure (pCO2) with higher N2 fixation and growth rates. To unveil the underlying mechanisms, we examined the combined influence of pCO2(150 and 900 µatm) and light (50 and 200 µmol photons m-2 s-1) on TrichodesmiumIMS101. We expand on a complementary study that demonstrated that while elevated pCO2 enhanced N2 fixation and growth, oxygen evolution and carbon fixation increased mainly as a response to high light. Here, we investigated changes in the photosynthetic fluorescence parameters of photosystem II, in ratios of the photosynthetic units (photosystem I:photosystem II), and in the pool sizes of key proteins involved in the fixation of carbon and nitrogen as well as their subsequent assimilation. We show that the combined elevation in pCO2 and light controlled the operation of the CO2-concentrating mechanism and enhanced protein activity without increasing their pool size. Moreover, elevated pCO2 and high light decreased the amounts of several key proteins (NifH, PsbA, and PsaC), while amounts of AtpB and RbcL did not significantly change. Reduced investment in protein biosynthesis, without notably changing photosynthetic fluxes, could free up energy that can be reallocated to increase N2 fixation and growth at elevated pCO2 and light. We suggest that changes in the redox state of the photosynthetic electron transportchain and posttranslational regulation of key proteins mediate the high flexibility in resources and energy allocation in Trichodesmium. This strategy should enableTrichodesmium to flourish in future surface oceans characterized by elevated pCO2, higher temperatures, and high light.

Seawater carbonate chemistry and photosynthetic response of Emiliania huxleyi (CS-369) to UV radiation and elevated temperature duirng experiments, 2011

Changes in calcification of coccolithophores may affect their photosynthetic responses to both, ultraviolet radiation (UVR, 280-400 nm) and temperature. We operated semi-continuous cultures of Emiliania huxleyi (strain CS-369) at reduced (0.1 mM, LCa) and ambient (10 mM, HCa) Ca2+ concentrations and, after 148 generations, we exposed cells to six radiation treatments (>280, >295, >305, >320, >350 and >395 nm by using Schott filters) and two temperatures (20 and 25 °C) to examine photosynthesis and calcification responses. Overall, our study demonstrated that: (1) decreased calcification resulted in a down regulation of photoprotective mechanisms (i.e., as estimated via non-photochemical quenching, NPQ), pigments contents and photosynthetic carbon fixation; (2) calcification (C) and photosynthesis (P) (as well as their ratio) have different responses related to UVR with cells grown under the high Ca2+ concentration being more resistant to UVR than those grown under the low Ca2+ level; (3) elevated temperature increased photosynthesis and calcification of E. huxleyi grown at high Ca2+concentrations whereas decreased both processes in low Ca2+ grown cells. Therefore, a decrease in calcification rates in E. huxleyi is expected to decrease photosynthesis rates, resulting in a negative feedback that further reduces calcification.

Seawater carbonate chemistry and processes during experiments with phytoplankton Emiliania huxleyi (strain Bergen 2005), 2010

The response of the coccolithophore Emiliania huxleyi to rising CO2 concentrations is well documented for acclimated cultures where cells are exposed to the CO2 treatments for several generations prior to the experiment. The exact number of generations required for acclimation to CO2-induced changes in seawater carbonate chemistry, however, is unknown. Here we show that Emiliania huxleyi's short-term response (26 h) after cultures (grown at 500 µatm) were abruptly exposed to changed CO2 concentrations (~190, 410, 800 and 1500 ?atm) is similar to that obtained with acclimated cultures under comparable conditions in earlier studies. Most importantly, from the lower CO2 levels (190 and 410 ?atm) to 750 and 1500 µatm calcification decreased and organic carbon fixation increased within the first 8 to 14 h after exposing the cultures to changes in carbonate chemistry. This suggests that Emiliania huxleyi rapidly alters the rates of essential metabolical processes in response to changes in seawater carbonate chemistry, establishing a new physiological "state" (acclimation) within a matter of hours. If this relatively rapid response applies to other phytoplankton species, it may simplify interpretation of studies with natural communities (e.g. mesocosm studies and ship-board incubations), where often it is not feasible to allow for a pre-conditioning phase before starting experimental incubations.

Seawater carbonate chemistry, and Lithophyllum sp. and Feldmannia spp. coverage and dry weight during experiments, 2009

Climate-driven change represents the cumulative effect of global through local-scale conditions, and understanding their manifestation at local scales can empower local management. Change in the dominance of habitats is often the product of local nutrient pollution that occurs at relatively local scales (i.e. catchment scale), a critical scale of management at which global impacts will manifest. We tested whether forecasted global-scale change [elevated carbon dioxide (CO2) and subsequent ocean acidification] and local stressors (elevated nutrients) can combine to accelerate the expansion of filamentous turfs at the expense of calcifying algae (kelp understorey). Our results not only support this model of future change, but also highlight the synergistic effects of future CO2 and nutrient concentrations on the abundance of turfs. These results suggest that global and local stressors need to be assessed in meaningful combinations so that the anticipated effects of climate change do not create the false impression that, however complex, climate change will produce smaller effects than reality. These findings empower local managers because they show that policies of reducing local stressors (e.g. nutrient pollution) can reduce the effects of global stressors not under their governance (e.g. ocean acidification). The connection between research and government policy provides an example whereby knowledge (and decision making) across local through global scales provides solutions to some of the most vexing challenges for attaining social goals of sustainability, biological conservation and economic development.

Seawater carbonate chemistry and Emiliania huxleyi biological processes during experiments, 2010

The calcifying phytoplankton species, coccolithophores, have their calcified coccoliths around the cells, however, their physiological roles are still unknown. Here, we hypothesized that the coccoliths may play a certain role in reducing solar UV radiation (UVR, 280-400 nm) and protect the cells from being harmed. Cells of Emiliania huxleyi with different thicknesses of the coccoliths were obtained by culturing them at different levels of dissolved inorganic carbon and their photophysiological responses to UVR were investigated. Although increased dissolved inorganic carbon decreased the specific growth rate, the increased coccolith thickness significantly ameliorated the photoinhibition of PSII photochemical efficiency caused by UVR. Increase by 91% in the coccolith thickness led to 35% increase of the PSII yield and 22% decrease of the photoinhibition of the effective quantum yield by UVR. The coccolith cover reduced more UVA (320-400 nm) than UVB (280-315 nm), leading to less inhibition per energy at the UV-A band.

Graphene quantum dots and Nafion composite as an ultrasensitive electrochemical sensor for the detection of dopamine

A novel electrochemical sensor for highly sensitive and selective detection of dopamine (DA) was developed based on a graphene quantum dots (GQDs) and Nafion composite modified glassy carbon electrode (GCE). GQDs were synthesized by a hydrothermal approach for cutting graphene sheets into GQDs and characterized by TEM, UV-vis, photoluminescence, and FT-IR spectra. The GQDs had carboxyl groups with a negative charge, which not only provided good stability, but also enabled interaction with amine functional groups in DA through electrostatic interaction to enhance the specificity of DA. The interaction and electron communication between GQDs and DA can be further strengthened via π-π stacking force. Nafion was used as an anchoring agent to increase the robustness of GQDs on the electrode surface and sensor stability and reproducibility. The GQDs-Nafion composite exhibits a good linear range of 5 nM to 100 μM and a limit of detection as low as 0.45 nM in the detection of DA. The proposed electrochemical sensor also displays good selectivity and high stability and could be used for the determination of DA in real samples with satisfactory results. The present study provides a powerful avenue for the design of an ultrasensitive detection method for clinical application.