David in Chihuahua
David M. Singer
PhD candidate
Surface and Aqueous Geochemistry Group

Department of Geological and Environmental Sciences
Stanford University


telephone: (650) 723-7513
fax: (650) 725-2199

(David, at left, on a field trip to Chihuahua, Mexico - Dec. '06)

Research Experience

Project Title:  “Geochemical and biogeochemical controls on radionuclide cycling in soils and sediments”

Project incorporates large-scale experiments, with molecular-scale Synchrotron X-ray techniques to understand the mechanisms and types of interactions by which biominerals form and how the effect metal
mobility and speciation.  Two such bio minerals are calcium oxalate (formed within plants and soils), and uraninite (formed by the bioreduction of U(VI) by bacteria).

(1) Sequestration of Sr(II) by Calcium Oxalate – A Batch Uptake Study and EXAFS Analysis of Reaction Products

    Calcium oxalate (CaOx) is produced by 2/3 of all plant families, comprising up to 80 wt.% of the plant tissue and is found in many surface environments.  It is unclear, however, how CaOx in plants and soils interacts with metal ions and possibly sequesters them.  This study examines the speciation of Sr2+ following its reaction with CaOx.  Batch uptake experiments were conducted over the pH range 4-10 and an ionic strength of 100 mM, using NaCl as the background electrolyte, and at initial Sr concentrations, [Sr], ranging from 0.01mM to 1 mM.  Experimental results indicate that Sr2+ uptake by CaOx is independent of pH and correlates positively with Ca release, with higher initial [Sr] resulting in increased Ca release. Extended X-ray absorption fine structure (EXAFS) spectroscopy was used to determine the molecular-level speciation of Sr2+ in the wet reaction products.  Because of potential problems caused by asymmetric distributions of Sr-O distances when fitting Sr K-edge EXAFS data using the standard harmonic model, we also employed a cumulant expansion model and an asymmetric analytical model to account for anharmonic effects.  For Sr-bearing phases with low to moderate first-shell anharmonicity, the cumulant expansion model is sufficient for EXAFS fitting; however, for higher degrees of anharmonicity, an analytical model is required.  Deconvolutions of the Sr K-edge EXAFS were performed to identify features due to multi-electron excitation (MEE).  MEE was found to give rise to low-frequency peaks in the Fourier Transform before the first shell of oxygen atoms, which do not affect EXAFS fitting results.  Based on the batch uptake results and the EXAFS analyses of reaction products, we conclude that Sr2+ exchanges with Ca2+ at the CaOx surface to form a Sr-oxalate coating under the conditions of our experiments.  As Sr-oxalate is two orders of magnitude less soluble that CaOx, this difference could potentially be a significant factor in the biogeochemical cycling of Sr2+ in soils and sediments or in plants or plant litter where CaOx is present.  The formation of Sr-oxalate in these environments under conditions similar to those of our experiments should therefore retard Sr movement.

(2) Biogenic UO2 - characterization and surface reactivity

    Nano-scale biogenic UO2 is easier to oxidize and more reactive to aqueous metal ions than bulk UO2.  In an attempt to understand these differences in properties, we have used a suite of bulk and surface characterization techniques to examine differences in the reactivity of biogenic UO2 versus bulk UO2 with respect to sorption of aqueous Zn(II).  Precipitation of biogenic UO2 was mediated by Shewanella putrefaciens CN32, and the precipitates were washed using two protocols: (1) 5% NaOH, followed by 4 mM KHCO3/KCl (NA-wash; “NAUO2”, to remove surface organic matter), and (2) 4 mM KHCO3-KCl (BI-wash; “BIUO2”, to remove soluble uranyl species).  BET surface areas of biogenic-UO2 prepared using the two protocols are 128.63 m2g-1 and 92.56 m2g-1, respectively; particle sizes range from 2-10 nm as determined by FEG-SEM.  Surface composition was probed using XPS, which showed a strong carbon 1s signal for the BI-washed samples; surface uranium is > 90% U(IV) for both washing protocols.  U LIII-edge XANES spectra also indicate that U(VI) is the dominant oxidation state in the biogenic UO2 samples.  Fits of the EXAFS spectra of these samples yielded half the number of uranium second-shell neighbors relative to bulk UO2, and no detectable oxygen neighbors beyond the first shell. At pH 7, the sorption of Zn(II) onto both biogenic and bulk UO2 is independent of electrolyte concentration, suggesting that Zn(II) sorption complexes are dominantly inner-sphere.  Fits of Zn K-edge EXAFS spectra for biogenic UO2 indicate that Zn(II) sorption is dependent on the washing protocol.  Zn-U pair correlations are observed for both the bulk UO2 and the NA-washed nanoparticulate samples, but not for the BI-washed nanoparticulate samples, suggesting that Zn(II) sorbs directly to the UO2 surface in the absence of organic matter (independent of size), and possibly to organic matter when present.  These results suggest that the types of reactive sites on nanoparticulate biogenic UO2 are the same as for bulk UO2, although with a much higher surface area and a greater number of reactive sites.  The presence of organic matter on the surface of biogenic UO2 appears to block the sorption of Zn(II) directly with the particle surface.  This coating would likely also inhibit oxidants from attacking the biogenic UO2 surface.

(3) Using synchrotron X-ray techniques to examine uranium speciation as a function of depth in contaminated Hanford Sediments

    Processing ponds at the Hanford, Washington Area 300 site were used for storing basic sodium aluminate and acidic U(VI)-Cu(II)-containing waste from 1943 to 1975. One result of this usage is a groundwater plume containing elevated levels of uranium and copper beneath the dry ponds and adjacent to the Columbia River.  We have used synchrotron-based micro-X-ray diffraction (mXRD), micro-X-ray fluorescence (mXRF) mapping, and mXAFS spectroscopic techniques to probe the distribution and speciation of uranium and copper through the vadose and groundwater zones beneath North Processing Pond #2 (NPP2).  Sediment samples were collected from the vadose zone (8’ and 12’ depths), and the groundwater sample was collected just below the water table (12’-14’ depth).  U LIII-edge XANES spectroscopy indicates that uranium is primarily (> 95%) in the 6+ valence state. mXRF mapping revealed two major uranium populations within the vadose and groundwater zones: (1) diffuse uranyl associated with the surface of most of the minerals present, and (2) U(VI)-hotspots associated with surface coatings on muscovite and chlorite. These U(VI)-hotspots are frequently spatially correlated with Cu(II)-hotspots and were identified by mXRD as cuprosklodowskite (cps) and metatorbernite (mtb) in the groundwater zone. In contrast, the U(VI)-Cu(II)-containing precipitates are X-ray amorphous in the vadose zone.  These results complement those from Catalano et al. (2007) who found that the dominant uranium-bearing phase was metatorbernite in the upper vadose zone (4’ depth) and uranyl sorbed onto phyllosilicates in the groundwater zone.  Our recent findings suggest that U(VI) and Cu(II) remain strongly correlated with depth beneath NPP2, and that U(VI)-Cu(II) phases are potentially undergoing dissolution/re-precipitation reactions with changing water influx with depth.  These findings suggest that the fate and transport of uranium are controlled in part by uranyl desorption and potentially dominated by dissolution of U-Cu precipitates.

(4) Uranyl-chlorite interactions (coming soon)
Sequestration of soluble uranium (U) by clay minerals is a potentially major sink for U in contaminated environments.  We have used a series of batch sorption/desorption experiments combined with U LIII-edge EXAFS spectroscopy to investigate the dominant sorption mechanism(s) governing uranyl uptake by chlorite. Sorption was independent of ionic strength, suggesting a dominantly inner-sphere sorption mechanism. At pH 6.5, U(VI) uptake as a function of solution chemistry followed the trend CO3-Ca-free system > CO3-Ca-bearing system > CO3-bearing system.  Conversely at pH 10, U(VI) uptake as a function of solution chemistry followed the trend CO3-Ca-bearing system > CO3-Ca-free system » CO3-bearing system. The minimum sorption loading was 0.28 mmoles U g﷓1 chlorite at pH 4, whereas the sorption loading was 6.3 mmoles U g-1 chlorite pH 6.5 and pH 10.  Sequential desorption experiments suggest that  (1) there was little to no weakly bound U(VI) or U(VI) coprecipitated with ferrihydrite, and (2) U(VI) inner-sphere sorption complexes can be desorbed with 0.1 M HCl, but desorption is less kinetically inhibited with 1.0 M HCl.  Fits of the EXAFS spectra of the sorption samples indicate that U(VI) forms inner-sphere sorption complexes at [Fe(O,OH)6] octahedral sites in a bidentate manner.  When CO3 and Ca were included, the EXAFS spectra fits indicate that U(VI)-CO3 sorption complexes were present, although there was no evidence for U(VI)-CO3-Ca sorption complexes.  Long-term exposure of chlorite to U(VI) to promote ferrihydrite formation or reduction of U(VI) by Fe(II) was performed under both aerobic and anaerobic conditions to determine the role these uptake mechanisms might play.  EXAFS spectra of these samples indicated the presence of 25% U(IV), where as no U(IV) was detected for the sorption samples. An additional contribution to the spectra was observed that is consistent with the U-U pair correlation in uraninite.  However, the presence of Ca in solution prohibited U(VI) reduction.  These results suggest that long-term exposure of chlorite to uranyl could result in U sequestration as the relatively insoluble UO2, versus more transient sorption complexes.  The results presented in this study can aid surface complexation models of uranyl sorption on clay minerals by accounting for the change in sorption mechanisms as a function of solution chemistry.

   Project Title:  “Fate of metal-EDTA complexes during plant uptake”
  Project included greenhouse studies of plant uptake of metal-EDTA solutions, and bench-top and synchrotron Fourier Transform Infrared (FT-IR) spectroscopy of plant samples at the NSLS.  FT-IR showed metal-EDTA complexes stay intact during plant uptake, which would enable plants to remove higher concentrations of toxic metals with the phytotoxic effect of the metals masked.
   Student abstracts are available at the Department of Energy's Office of Education site

    Project Title:  “Highly oxidized rocks from the San Gorgonio Pass, California; Petrology and thermodynamic calculations”
Project included electron microprobe chemical analyses of mineralogically exotic minerals and thermodynamic calculations of model systems of the effect of oxygen fugacity on Mn-end member garnet-epidote equilibrium.  The paper is available here.

   Project Title:  “Phytoremediation:  the use of plants to remove contaminants from soils – economic and environmental considerations”.
Project included greenhouse and field experiments of plant uptake of heavy metals and radionuclides.  Analytical techniques included ICP-AES of heavy metals, Gamma radiation counting for radio-cesium and americium and Synchrotron X-ray Absorption Spectroscopy of plant samples to determine redox state of metals taken up by hyperaccumulating plants.

   For more information about Phytoremediation, click here for a review about how phytoremediation has been applied.


Teaching Experience
   view my teaching portfolio

*Recipient of the 2004-2005 Centennial Teaching Assistant Award*

GES 1 "Introduction to Geology" (Spring 2003)
   Responsibilities; lead weekly laboratory session including leading three field trips, weekly office hours, grade laboratory projects and lecture exams and quizzes.

GES-80 "Earth Materials" (Fall 2002, 2003, and 2004
   Responsibilities; as head T.A, lead weekly laboratory session including 15 lecture, weekly office hours, lead three reviews sessions over the course of a quarter and grading laboratory projects, laboratory finals, and bi-weekly lecture homework, and assist in overnight field trip.

GES 90 "Introduction to Geochemistry" (Winter 2003)
   Responsibilities; weekly office hours, grade bi-weekly homework, lead review session prior to midterm and final.

GES-170 "Environmental Geochemistry" (Winter 2003)
   Responsibilities; weekly office hours, grade bi-weekly homework, lead review session prior to midterm, and assist in grading of final project.