Abstracts
February 13, 2004
Stony Brook University
Benjamin Hornberger
Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800
Development of segmented silicon detector for phase contrast imaging
Soft x-ray spectromicroscopy (roughly 250-1000 eV) provides high contrast, high resolution (sub-50 nm) absorption images of wet organic and inorganic specimens with sensitivity to the molecular binding of elements including carbon, nitrogen, oxygen, nickel, and iron. Hard x-ray microprobes (~10 keV energy) can be used for the mapping of trace amounts of many elements. However, in both microscopes it is desirable to use phase contrast to see fine structure with greater detail, and in particular with hard x-rays the only way one can see structural detail in soft tissues is via phase contrast. We report the development of a segmented silicon detector to record absorption, phase and darkfield images simultaneously in a scanning transmission X-ray microscope (STXM). The method shows particular strength in combination with other techniques like fluorescence, e.g. for estimating the total carbon content in a sample from absolute phase shift measurements, or in showing the underlying biological structure when measuring trace metal concentrations.
Corey A. Cohn and Martin A. Schoonen
Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
Mineral driven non-adsorption loss of RNA
Pyrite has been shown to produce hydrogen peroxide (H2O2) and hydroxyl radical (.OH). All biomolecules are susceptible to .OH attack. RNA has been shown to decompose in a Fenton reaction that generates OH and in the presence of pyrite. However, the stability of RNA in the presence of other minerals has not been determined. RNA stability in the presence of minerals has been examined using batch experiments and molecular-scale techniques (Fourier transform infrared spectroscopy). RNA is lost from solution when mixed with all of the minerals except quartz and with H2O2 only. Differentiating adsorption from decomposition is the current goal.
Jeff Gillow
Environmental Sciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000
Microbial Transformation of the Chemical Association and Mobility of Actinides in Contaminated Soil
The fate of plutonium was examined after microbial activity in two soils from the Rocky Flats Environmental Technology Site. The soils were characterized by sequential selective extraction for the mineralogical association of Pu and incubated under anaerobic conditions with glucose or lactate. Reductive dissolution of iron occurred in glucose-amended samples. Plutonium was detected in fluid from soil in which the Pu was initially associated with the residual fraction. This shows that fermentative microbial activity can mobilize Pu in contaminated soil possibly due to dissolution of iron phases and stabilization of Pu as a colloid. Studies underway include Pu oxidation state by solvent extraction and XANES.
Marianna A. Kissell1, Richard J. Reeder1, Mark Fuhrmann2
1Department of Geosciences, Stony Brook University, Stony Brook, New York 11794-2100
2Environmental Sciences Department, Brookhaven National Laboratory, Upton, New York 11973-5000
XAS studies of arsenic cycling in an As-hyperaccumulating plant: kinetics of uptake, translocation, and redox chemistry We use XAS to study the kinetics of arsenic uptake, translocation and redox chemistry as well as the spatial and temporal distribution of arsenic in Pteris cretica. XANES experiments have allowed us to directly probe the oxidation state of arsenic as a function of time and of location in the soil-plant system (root, leaf, soil). The valence state and speciation (and therefore the toxicity and bioavailability) of arsenic can be determined by detailed analysis of the arsenic K-edge in previously doped plant samples, while the potential for remobilization of sequestered arsenic can be predicted from careful interpretation of elemental mapping.
M. Lerotic and C. Jacobsen
Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800
Cluster analysis of soft x-ray spectromicroscopy data
Soft x-ray spectromicroscopy provides spectral data on the chemical speciation of light elements at sub-100 nanometer spatial resolution.When all chemical species in a specimen are known and separately characterized, existing approaches can be used to measure the concentration of each component at each pixel. In other situations such as in biology or environmental science, this approach may not be possible. A method to find natural groupings of data without prior knowledge of the spectra of all components will be presented. Principal component analysis is used to orthogonalize spectromicroscopy data, and discard much of the noise present in data set. Then cluster analysis is used to find a hierarchical classification of pixels with similar spectra, to extract representative, cluster-averaged spectra with good signal-to-noise ratio, and to obtain gradations of concentration of these representative spectra at each pixel. The method is illustrated with a simulated data set of organic compounds, and a mixture of lutetium in hematite used to understand colloidal transport properties of radionuclides. We gratefully acknowledge funding from the National Institutes for Health under contract R01 EB00479-01A1, and from the National Science Foundation under contracts OCE-0221029 and CHE-0221934.
Ashaki A. Rouff1, Evert J. Elzinga1, Richard J. Reeder1, Nicholas S. Fisher2
1Department of Geosciences, Stony Brook University, Stony Brook, New York 11794-2100
2Marine Sciences Research Center, Stony Brook University, Stony Brook, NY 11794-5000
Demonstrating mechanistic variation in Pb(II)-calcite interactions
Metal contaminants in near-surface settings may be sequestered by naturally occurring mineral phases. Sequestration can occur via several mechanisms including adsorption, precipitation and co-precipitation. This study complements batch sorption studies with X-ray absorption spectroscopy to demonstrate the dependence of occurrent mechanisms on solution chemistry in the Pb(II)-calcite-water system. At 1 mM Pb and pH 8.2, adsorption of mononuclear inner-sphere complexes to the calcite surface dominates. Varying pH results in combined adsorption and co-precipitation at 7.4 and 9.4 with more pronounced incorporation at the higher pH. At Pb > 1 mM, simultaneous adsorption and precipitation occurs, with the dominance of precipitation at Pb > 20 mM. These results highlight the role of a variety of mechanistic processes in the immobilization of Pb(II) by calcitic phases.
POSTERS
Vasso Alexandratos
Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
Spectroscopic studies of Arsenate uptake by Calcite
Spatially resolved spectroscopic observations reveal that surface properties play an important role in controlling arsenate interaction with calcite. Operation of the spiral growth mechanism on the calcite (10 4) surface results in the formation of two characteristic non-equivalent pairs of vicinal faces denoted as "+" and "-" respectively, which differ in the structure of growth steps. Synchrotron m -XRF reveals that "-" vicinal faces are distinctively enriched in AsO43- compared to the "+" vicinals. This interaction causes formation of macrosteps on the - vicinal faces of the calcite surface. Macrosteps increase in density as the concentration of arsenate increases. EXAFS analysis confirmed that As is present in the calcite structure as tetrahedral AsO43- complex possibly substituting in CO32- sites and causing distortion to the local environment. Results imply that bulk partition coefficients for As(V) depend on the availability of different calcite surface sites.
Ivor Bull
Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
Microcrystal diffraction studies of novel structures with applications in ion-exchange
The study of structurally and chemically diverse open framework and cluster solids is flourishing in an attempt to increase and improve application of such materials in areas such as shape selective catalysis, absorption and ion-exchange. These materials often crystallize with crystals too small for laboratory X-ray sources, and so microcrystal diffraction at a synchrotron source allows us to obtain structural information necessary to provide a greater understanding of the applications of these materials. One area for the discovery of new materials is the synthesis of mixed-geometry frameworks such as several new scandium phosphate. In addition, we report the structure of a potassium niobium germanate cluster structure synthesized by our collaborator at SANDIA national labs which has proven ion-exchange capability.
R. Kramer Campen1, James D. Kubicki1, Eric Borguet2
1Department of Geosciences, Pennsylvania State University
2Department of Chemistry, University of Pittsburgh
Understanding the Adhesion of Gram Negative Bacteria to Mineral Surfaces
Most extant microorganisms are surface bound at some point during their life cycle. Typically, at some time after initial adhesion cells undergo physiological changes including the excretion of copious amounts of extracellular polysaccharides (the formation of a biofilm), the loss of flagella and the altering of controls on metabolism. Cells gain from this surface adhesion in nutrient rich environments because the biofilm allows protection against predation as well as the ability to exercise precise chemical control over the local microenvironment. While beneficial to cells, this adhesion and biofilm formation has such adverse effects as the persistence of infection of prosthetic limbs and the near impossibility of economic remediation of contaminated groundwater by injection of microorganisms.
In this work we focus on the molecular mechanism of the adhesion of gram negative bacteria to mineral surfaces. The gram negative cell surface is festooned by several types of proteins and polysaccharides. Prior work suggests that the polysaccharides may be most important in adhesion. Our work, then, focuses on description of the physical chemistry of the interaction of polysaccharide brushes with mineral surfaces. We address this problem on two spatial scales, that of functional group/functional group interaction and that of whole molecule conformation. To answer this multiscale question we apply a number of different experimental and theoretical approaches including macroscopic adsorption experiments, ATR-FTIR, second harmonic generation and electronic structure, classical atomistic and coarse grained simulation. The current paper will provide an overview of our progress on each of these fronts.
Aaron J. Celestian1, Dmitri G. Medvedev2, Akhilesh Tripathi2, J ohn Parise1, Abraham Clearfield2, John Hanson3
1Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
2Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, TX 77843-3255
3Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973
Synchrotron Time resolved X-ray diffraction of Cs exchange into molecular sieve H-CST
Titanosilicate (TS) with mineral sitinakite topology (referred to as CST in literature) is an effective Sr and Cs ion exchange molecular sieve in highly concentrated alkaline solutions (Poojary et al. 1996). To understand how Cs exchanges into this structure and to determine the mechanism of Cs uptake in the H form of CST, time resolved X-ray diffraction techniques were used. The process in going from H-CST to Cs,H-CST is the distortion of the [001] 8 member ring channel in the H-CST form, to a more circular geometry as required for the Cs form. In H-CST, these channels are elliptical with a long axis to short axis ratio of 1.27. We theorize that as Cs2 fills the channel, it forces the 8-member rings to become more circular to accommodate the Cs size and the higher 8-fold bonding coordination of Cs1.
Evert J. Elzinga
Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
Spectroscopic investigation of U(VI) sorption at the calcite-water interface
The interaction of U(VI) species with the calcite surface was characterized in situ using EXAFS and luminescence spectroscopies. Results indicate that U(VI) forms mononuclear triscarbonate-like surface complexes at uranyl solution concentrations below 500 mM, with a change in interaction with calcite surface sites as the surface loading increases, whereas the formation of U(VI) hydroxide precipitates is observed at higher concentrations. Consequently, multiple uranyl species are likely to exist at the calcite surface during interaction of U(VI)-containing waters in the near-surface environment. As a result, complex sorption/desorption behavior and kinetics may be associated with differing stabilities of sorbed U(VI) species in calcite-containing materials.
Charlotte Eng
Department of Material Sciences and Engineering, Stony Brook University, Stony Brook, NY
The Spectroscopic Study of Uranyl Species Bound to Simple Organic Analogsto Simulate Uranium Behavior in the Natural Environment
The Department of Energy (DOE) has sought the help of the scientific community to develop inexpensive and efficient remedial technologies that remove radionuclides from the environment. This research aims to study uranium association to both organic and inorganic compounds found in the contaminated environment, in the hopes that the information gathered can be applied to the development and optimization of remediation techniques. Spectroscopic techniques (e.g. infrared, raman, x-ray photoelectron spectroscopy) will be used in conjunction with molecular modeling to examine the behavior of uranyl ions complexed to various organic ligands (e.g. catecholate, salicylate) in given conditions to further our understanding of uranium's impact on the environment.
Younkee Paik1, Cole KE3, Reeder RJ2, Schoonen MAA2, Grey CP1
1Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
2Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
3CEMS Summer Research Student, Fairfield University
2H MAS NMR Studies of Dueterated Goethite (a-FeOOD)
2H magic angle spinning (MAS) NMR spectroscopy was used to study goethite (a-FeOOH). Both hydrogenated and deuterated forms of goethite were synthesized at a same condition except the use of deuterated water for a-FeOOD. Here we report high resolution 2H MAS NMR spectra, for the first time, which were acquired from the dueterated goethite above its Neel Temperature by using a variable temperature NMR technique. Further characterizations of the materials were discussed by using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and Scanning electron micrograph (SEM).
Luming Peng1, Hyunsoo Park1 and Clare P. Grey1 and John B. Parise2
1Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
2Department of Geosciences, State University of New York at Stony Brook, Stony Brook, NY 11794-2100
Solid State NMR Studies of Zeolites and Zeotype Materials
Ion-exchange materials, including zeolites and various types of microporous materials, have great potential for solving environmental problems, such as radioactive waste removal. We use NMR to characterize the local structures of these materials. For example, we use 31P MAS NMR to look at the P local environments of the novel scandium phosphate materials synthesized by Prof. Parise's group. 17O MAS NMR is used to investigate the framework oxygen in zeolite LSX and Y. Future studies will involve 17O NMR studies of novel zeolitic materials.
Alexander Smirnov and Martin A. A. Schoonen
Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100
Ammonium Immobilization in Ocean Floor Rocks and Minerals
Ammonia (NH3) and ammonium (NH4+) may have been present in hydrothermal circulation systems on the early Earth. These reduced forms of nitrogen are important prerequisites for abiotic synthesis of various organic compounds such as amines, amino acids or polypeptides. While oxidation state of the early mantle and atmosphere (thus the ratio of reduced/oxidized nitrogen species) remains a subject of debate, it is important to evaluate the fate of ammonium ion in the presence of rocks and minerals of the ocean floor and provide further constraints on possibilities of abiotic organic synthesis in submarine hydrothermal vent systems. It is plausible that a fraction of the ammonium was immobilized after formation (e.g., abiotic mineral-catalyzed N2 reduction) and unavailable for further reaction. The objective of our research is to assess the capacity of selected rocks and minerals to immobilize ammonium ion via surface sorption and/or ion exchange. In a series of batch and flow-through experiments we will examine the sorption and ion exchange capabilities of various minerals relevant to the ocean-floor and submarine hydrothermal systems environments. The uptake experiments will be conducted in simulated seawater solutions (NaCl, KCl, NH4Cl). Selected materials will be analyzed using flow-through Horizontal Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy to determine sorption mechanisms, effects of pH, temperature and ion competition.
Gillian M. Stewart1; Cochran JK1; Masque P2; Miguel JC3; Rodriguea AM3; Fisher NS1
1Marine Science Research Center, Stony Brook University, Stony Brook, NY 11794-5000
2ICTA, University Autonoma de Barcelona, Bellaterra, Spain
3Marine Environment Laboratory, IAEA, Monaco
210Po concentrations, fluxes, and particle settling velocities at the DYFAMED site, Northwest Mediterranean
As part of the MEDFLUX project, vertical profiles of the natural radionuclide 210Po were collected from March to May 2003 at the DYFAMED site (Ligurian Sea). Novel settling velocity sediment traps and an elutriator were employed along with the traditional IRS sediment traps, Niskin bottles, and in situ pumps to explore the physical and temporal characteristics of sinking and suspended material. The activity of polonium will be compared with both organic carbon and protein in samples to assess 210Po's usefulness as a potential organic carbon tracer. This is the first time that this radionuclide has been examined in samples separated by sinking velocity and may further elucidate the magnitude and composition of particulate flux.
Benjamin S. Twining1, Stephen B. Baines1, Nicholas S. Fisher1, and Michael R. Landry2
1Marine Sciences Research Center, Stony Brook University, Stony Brook, NY 11794-5000
2University of Hawaii at Manoa, 1000 Pope Road, MSB 307, Honolulu, HI 96822
Fe:C ratios within the plankton community during the Southern Ocean Iron Experiment (SOFeX)
Two techniques were used to measure the Fe:C ratios of various components of the plankton community during the Southern Ocean Iron Experiment (SOFeX). Long-term (6 d) deck incubations with 55Fe and 14C allowed us to measure bulk Fe:C ratios in picoplankton (0.2-1mm), as well as larger size classes (3-20mm,>20mm). Samples were collected simultaneously for measurements of Fe (as well as Si, Ca, Mn, Cu, and Zn) in individual phytoplankton and protozoa cells using a synchrotron x-ray fluorescence (XRF) microprobe. This technique allows us to map the distribution of bioactive trace elements within cells from this region, in addition to providing quantitative measurements of whole-cell metal concentrations. Radioisotope experiments conducted at the south patch pre-fertilization station (Sta. 19) provide internal cell quotas for bacteria (Ti/citrate-EDTA rinsed cells, 19.5 +/- 0.6 mmol Fe:mol C) that are higher than those measured in other Fe-limited regions. The 3-20mm and >20mm size classes show lower bulk Fe concentrations (11.5 +/- 1.1 and 9.2 +/- 0.6 mm:mol, respectively). The overall Fe content of bacterial cells from this station was notably higher (seawater-rinsed cells, 71.2 +/- 0.4), though larger cells had a smaller fraction of externally-bound Fe. XRF analyses of single cells from this station reveal higher Fe:C ratios in flagellated cells (16.5) than diatoms (10.8), with heterotrophic species showing higher mean concentrations than autotrophic/mixotrophic cells (as determined by presence of Chl a autofluorescence). Iron appears to be associated with chloroplasts, while zinc tends to map onto P (assumed to be the nucleus). Highly localized regions of Si within some dinoflagellates suggest that phagotrophic cells may have grazed on small diatoms in the south patch. Following iron fertilization, total bacterial Fe content rose substantially (seawater-rinsed cells, 99.1-110.9), but increases in internal Fe quotas were less dramatic (18.8-25.4). In contrast, total Fe:C ratios of phytoplankton and protozoa (as measured with XRF increased ~ 7-fold following Fe fertilization, though this increase was less dramatic in the radioisotope incubations (2-3 fold increase). We plan to use these cellular Fe contents, along with grazing rates measured with simultaneous dilution experiments to estimate Fe recycling rates as mediated by protozoan grazing.