5th Annual Report of the Stanford Environmental Molecular Science Institute: a focus on Chemical and Microbial Processes at Environmental Interfaces




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5th Annual Report of the Stanford Environmental Molecular Science Institute: A Focus on Chemical and Microbial Processes at Environmental Interfaces


August 16, 2009


Gordon E. Brown, Jr.1,2,3, Anders Nilsson2, Alfred M. Spormann3, Karim Benzerara4, Hendrik Bluhm5, Bryan A. Brown6, Georges Calas4, Anne M. Chaka7, Brent R. Constantz8, Francois Farges9, Scott E. Fendorf 1, Andrea L. Foster10, Farid Juillot4, Guillaume Morin4, Satish C.B. Myneni11, Georges Ona-Nguema4, Lars G.M. Pettersson12, Kevin M. Rosso13,

James J. Rytuba10, Miquel Salmeron14, Jennifer Saltzman15, Mark P. Taylor16,

Thomas P. Trainor17, and Jennifer Wilcox18

1Dept. of Geological & Environmental Sciences, Stanford University, Stanford, CA 94305-2115, USA

2Dept. of Photon Science and Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, SLAC National Accelerator Laboratory, MS 69, Menlo Park, CA 94025, USA

3Dept. of Chemical Engineering, Stanford University, Stanford, CA 94305, USA

4Institut de Minéralogie et de Physique des Milieux Condensés (IMPMC) - UMR 7590 - CNRS – Université Paris 6 & 7 - IPGP, 140, rue de Lourmel, 75015 Paris, France

5Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

6School of Education, Stanford University, Stanford, CA 94305, USA

7Physics Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA

8Calera Corporation, 100A Albright Way, Los Gatos, CA 95032, USA

9Muséum National d'Histoire Naturelle, USM 201 and CNRS UMR 7160, Paris, France

10Geologic Division, U.S. Geological Survey, 345 Middlefield Road, MS 91, Menlo Park, CA 94025, USA

11Dept. of Geosciences, Princeton University, Princeton, NJ 08540, USA

12FYSIKUM, Stockholm University, Albanova University Center, S-10691 Stockholm, Sweden

13W.R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA

14Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

15School of Earth Sciences, Stanford University, Stanford, CA 94305, USA

16Science & Technology Division, Corning Incorporated, Sullivan Park DV-01-9, Corning, NY 14831, USA

17Dept. of Chemistry and Biochemistry, University of Alaska, Fairbanks, AK 99775-6160, USA

18Dept. of Energy Resources Engineering, Stanford University, Stanford, CA 94305, USA


I. GOALS, ORGANIZATIONAL STRUCTURE, ACTIVITIES, AND RESEARCH HIGHLIGHTS


The Stanford Environmental Molecular Science Institute (EMSI) is completing its fifth year of operation and continues to pursue fundamental and applied studies of chemical and microbial processes at complex environmental interfaces. The Stanford EMSI was founded in September 2004 as a multidisciplinary, multi-institutional, multi-investigator research, graduate training, and education/outreach program funded by the NSF Chemistry Division, with additional funding from the NSF Earth Sciences Division and the DOE Biological & Environmental Research Division through their Environmental Remediation Science Program.

Goals – The overall goals of the Stanford EMSI are to (1) develop a quantitative molecular-level understanding of chemical and biological processes occurring at environmental interfaces and how they affect contaminant and pollutant speciation, toxicity, mobility, and potential bioavailability; (2) explore how such interactions studied in the laboratory relate to the complexity found in natural environments; (3) provide platforms for new approaches to address environmental challenges involving contaminants; (4) recruit a diverse group of qualified graduate, undergraduate, and post-doctoral students; (5) create a stimulating multidisciplinary research/learning environment in which students and post-Ph.D. participants can tackle complex systems and questions relevant to problems in environmental chemistry, ranging from molecular to field scales; and (6) effectively disseminate our research results and approach to the broader public and to future generations of scientists, engineers, and policy makers and to engage K-12 science teachers in current topics in environmental chemistry. As the remainder of this report will show, we are addressing each of these goals.


Organizational Structure – The Stanford EMSI team includes 24 senior investigators from three countries (USA, France, and Sweden,), six universities (Stanford University, University of Alaska-Fairbanks, Princeton University, University of Paris VI, University of Paris VII, and Stockholm University, Sweden), three U.S. national laboratories (SLAC National Accelerator Laboratory, Lawrence Berkeley National Laboratory, and Pacific Northwest National Laboratory), two U.S. government agencies (National Institute of Standards & Technology and U.S. Geological Survey), the French National Natural History Museum, and two U.S. technology companies (Corning, Inc. and Calera Corporation). Our team also includes about 40 graduate students, postdoctoral scholars, and undergraduate and high school interns. A listing of these participants for the 2008-2009 period can be found in Appendix C. The activities of the Stanford EMSI can be broken down into nine research areas, many of which have strong cross-links. They are [with SEMSI senior investigators listed after each area in which they are involved] (A) Structural Studies of Bulk Water [Anders Nilsson (SSRL) and Lars G. M. Pettersson (Stockholm University)]; (B) Interaction of Water with Environmental Substrates [Hendrik Bluhm (LBNL), Gordon Brown (Stanford University and SSRL), Anne Chaka (NIST), Nilsson, Pettersson, Kevin Rosso (PNNL), and Miquel Salmeron (LBNL)]; (C) Structure of Metal Complexes in Aqueous Solutions [Myneni, Chaka, and Nilsson]; (D) Structure and Reactivity of Hydrated Metal Oxide Surfaces [Tom Trainor (University of Alaska, Fairbanks), Bluhm, Brown, Chaka, Rosso, Salmeron, and Michael Toney (SSRL)]; (E) Sorption Processes at Solid-Aqueous, Microprobe-Aqueous, and Solid-Biofilm Interfaces and Biomineralization [Brown, Brent Constantz (Calera Corporation); Francois Farges (Muséum National d'Histoire Naturelle, France), Scott Fendorf (Stanford University), Andrea Foster (U.S. Geological Survey), Satish Myneni (Princeton University), Alfred Spormann (Stanford University), Mark Taylor (Corning, Inc.), Trainor]; (F) Theoretical Modeling of Solid-Aqueous Solution Interfaces and Interfacial Reactions [Chaka, Nilsson, Pettersson, Rosso, Trainor, Brown, and Jennifer Wilcox (Stanford University)]; (G) Dynamics in Biofilms at Solid-Aqueous Solution Interfaces, and Molecular Genomics and Biofilm Physiology [Spormann, Brown, Fendorf, and Rosso]; (H) Environmental Applications [Fendorf, Brown, Georges Calas (University of Paris VI), Foster, Farid Juillot (University of Paris VII), Guillaume Morin (University of Paris VI), Myneni, James J. Rytuba (US Geological Survey), Spormann, and Trainor]; (I) New Experimental Developments in Synchrotron Radiation-Based Spectroscopies and Micro-Imaging [Nilsson, Bluhm, and Salmeron].

In addition to the research areas listed above, the Stanford EMSI has strong education and outreach components led by Dr. Jennifer Saltzman, Educational Outreach Coordinator for the Stanford School of Earth Sciences and the Stanford EMSI, and Prof. Bryan Brown, Assistant Professor, Stanford School of Education and Stanford EMSI Educational Outreach Supervisor. We have organized and run four four-day summer workshops for high school science teachers with a focus on the environmental chemistry of mercury, including a workshop on July 22-25, 2009, which is discussed in section III.A.2. The Stanford EMSI has also run three science journalist workshops over the past three years with a focus on the environmental chemistry of arsenic and mercury, including a workshop on October 24, 2008. We also co-organized and sponsored the 6th annual Stanford-Berkeley Summer School on Applications of Synchrotron Radiation in the Physical Sciences on August 18-22, 2008 at Stanford University. In addition, we have summer intern programs for high school students and college undergraduates at Stanford and our partner institutions (University of Alaska, Fairbanks and Princeton University).


The 4th annual meeting of the Stanford EMSI was held at Stanford University on August 25-26, 2008 and was attended by 42 SEMSI members, four members of the SEMSI External Advisory Committee (Prof. George R. Helz, Chair (Dept. of Chemistry, University of Maryland), Dr. Brent Constantz (Calera Corporation, Los Gatos, CA), Dr. Yuri Gorby (J. Craig Venter Institute, San Diego, CA), and Dr. David Shuh (Chemical Sciences Division, Lawrence Berkeley National Laboratory)), and three guests (Dr. John Bargar (SSRL), Prof. Rossitza Pentcheva and Ms. Katrin Otte (University of Munich)). The meeting consisted of 19 oral and 17 poster presentations as well as a general session in which members of the research areas listed above discussed research needs and opportunities. A copy of the 4th Annual Stanford EMSI Meeting Program with Abstracts can be found in Appendix D. In place of the annual meeting this year, we will hold a special workshop at Stanford University for selected senior investigators in early September 2009 at which we will prepare a review article for submission to Chemical Reviews that will focus on progress made in the area of chemical and biological interactions at environmental interfaces over the past decade. This review article is intended to update a 1999 Chemical Reviews article entitled “Metal oxide surfaces and their interactions with aqueous solutions and microbial organisms” (Brown et al., Chem. Rev. 1999, 99, 77-174), which has been cited 325 times since its publication.

Research Highlights – Selected highlights of Stanford EMSI-funded research include the following: (1) x-ray spectroscopic and x-ray scattering studies of water under ambient conditions have led to the proposal of a new structure of water involving a fluctuating equilibrium between low density and high density regions in the water structure with different types of H-bonding and a new understanding of the “structure-making” and “structure-breaking” role of cations of different valence in water; (2) the first ambient pressure x-ray photoelectron spectroscopy studies of the interaction of water with metal oxide surfaces under in situ, near-ambient conditions have led to new understanding of hydroxylation of these surfaces involving cooperative effects among adjacent water molecules; (3) the first ambient pressure XPS studies of the structuring of water on Cu surfaces explains the very different wetting properties of Cu(110) and Cu(111) surfaces; (4) theoretical studies of the dissociation of water in the presence of Cr3+ and Fe3+ ions show the importance of dynamical effects involving Zundel and Eigen proton complex formation; (5) theoretical studies of the structure of hydrated Fe-oxide surfaces and their interaction with water and aqueous Pb(II) ions explain why aqueous Pb(II) forms stronger chemical bonds to the a-Fe2O3 (0001) surface rather than the a-Al2O3 (0001) surface; (6) crystal truncation rod diffraction studies of hydrated iron oxide surfaces have provided the first details about the surface structures of these important environmental substrates and show how Fe(II) adsorbs on the (0001) and (1-102) hematite surfaces where it behaves as Fe(III) but still acts as a powerful reductant; (7) total x-ray scattering, thermogravimetric analyses, and magnetic susceptibility studies of ferrihydrite aged at 175°C in the presence of citrate have resulted in the discovery of a new ordered ferrihydrite phase intermediate between disordered ferrihydrite and hematite, confirmation of the controversial structure of disordered ferrihydrite proposed by Michel et al. in 2007, new understanding of the defect structure of ferrihydrite, a new chemical formula for the disordered and ordered ferrihydrite phases, and an explanation of the ferromagnetic properties of ordered ferrihydrite; (8) spectroscopic, quantum chemical, and surface complexation studies of the interaction of environmentally common carboxylic acids (oxalic, maleaic, malonic, and lactic) and humic acid with Al-(oxyhydr)oxide nanoparticles that have helped elucidate reasons for differences in solid dissolution caused by different acids; (9) x-ray spectroscopic studies of the interactions of aqueous arsenite and arsenate with iron (oxyhydr)oxide surfaces have resulted in new molecular-level models for the sequestration of As(III) and As(V) on these common environmental substrates; (10) x-ray and FTIR spectroscopic studies of the interaction of aqueous Zn(II) and oxalate with hematite nanoparticle and microparticle surfaces showed major differences in sorbate structure and shed new light on reasons for differences in reactivity of hematite particles of different size; (11) long-period x-ray standing wave studies of the partitioning of aqueous Pb(II), Zn(II), and As(V) on oriented single crystal surfaces of -Fe2O3 and -Al2O3 coated by organic polymers and Shewanella oneidensis biofilms show that there are significant differences in the binding of different ions on the metal oxide surfaces and in the microbial biofilms; (12) a major advance was made in quantifying x-ray fluorescence intensities from long-period XSW measurements with respect to element partitioning between phases; (13) studies of the speciation, transformation, and cycling of arsenic in various contaminated field settings, including France, Bangladesh, and Cambodia, show that the long-held model of As(V) release from iron oxide particles is not as simple as previously believed; (14) studies of the speciation, transformations, and cycling of mercury in mercury mining environments in the California Coast Range led to new models that help explain the atmospheric evasion of Hg(0) from these deposits and the release of Hg(II) from microbially enhanced dissolution of HgS solids; (15) development and application of a new scanning transmission x-ray microscopy (STXM) beamline at the Advanced Light Source led to new understanding of microbial weathering and calcification as well as the behavior of arsenic in acid mine drainage environments; and (16) development of a new ambient pressure XPS spectrometer at SSRL that will extend the water pressure range that can be explored in equilibrium with oxide surfaces.


The research efforts of the Stanford EMSI over the past five years have resulted in 180 papers published or in press in peer-reviewed scientific journals, conference proceedings, or research monographs. A list of these publications can be found in Appendix A. A breakdown of publications in terms of type of journal is given below.


chemistry (ACS and IUPAC) journals and conference proceedings – 75 (42%)

geochemistry/mineralogy journals and conference proceedings – 41 (23%)

physics journals and conference proceedings – 22 (12%)

high impact journals (Science, Nature, Phys. Rev. Lett., PNAS) – 9 (5%)

microbiology/geobiology journals – 8 (5%)

surface science journals – 8 (5%)

surface chemistry and agronomy monographs – 8 (5%)

materials science/glass science journals – 4 (2%)

environmental science journals (other than ES&T) and conference proceedings – 2 (1%)

medical journals – 1 (0.5%)


In addition, 23 manuscripts have been submitted to peer-reviewed journals during the past year. A listing of these manuscripts can also be found in Appendix A (section b). Members of the Stanford EMSI have presented over 250 keynote addresses, invited talks, contributed talks, and posters at international and national meetings during the period Sept. 2004-June 2009. A listing of these presentations can be found in Appendix B.

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