Chemical & Materials Sciences Staff information

Biography

James E. Amonette, Ph.D., specializes in the areas of environmental geochemistry and soil mineralogy. He has a strong interest in the structure and chemistry of minerals and in the application of spectroscopic techniques, such as laser photoacoustic, Mössbauer, electron paramagnetic, infrared, and x-ray absorption/scattering, to characterize the solid phases and to predict and monitor the reactions associated with the presence of hazardous wastes in soil environments. In recent years he has expanded his interests to include ways of capturing and sequestering C in soils and geological formations. Currently, he is currently involved in projects related to 1) the redox chemistry of iron-bearing clays and nanoparticles and its impact on the reductive degradation pathways of chlorinated hydrocarbons, 2) terrestrial soil carbon sequestration with a focus on amendments (such as fly ash and charcoal), management regimes (moisture), and soil gas monitoring, and 3) monitoring of leakage rates from geologic carbon sequestration.

Dr. Amonette’s contributions include dissertation work on the role of structural iron in mica weathering, analytical techniques for the determination of ferrous iron and for the semi-quantitative modal analysis of clay minerals in soils, reduction of iron-bearing smectites for remediation processes, synthesis and properties of hydrotalcites for adsorption of anions, modification of natural layer silicates for adsorption of Cs and Sr, and a chapter on the environmental chemistry of iron that includes a theoretical approach for estimating reduction potentials for iron in silicate minerals. He continues to focus much of his work on zerovalent and ferrous iron chemistry, and its potential use for environmental remediation.

For nearly a decade, Dr. Amonette co-led a team working on the fundamental molecular-scale aspects of carbonate mineral dissolution and growth processes using a combination of atomic-force microscopy and theoretical calculations. More recently, Dr. Amonette has focused on the catalytic mechanisms that promote the formation of humic materials. The chemistry of charcoal and fly ash are of particular interest as these common materials could be applied as soil amendments to promote carbon equestration. He is particularly interested in the potential use of bio-char (i.e., charcoal produced during biomass pyrolysis) as a promising way to sequester carbon in a stable form for thousands of years.

Dr. Amonette has worked on the precipitation/dissolution chemistry of Cr(III) and Cr(VI) in soils. He identified the solid solution Ba(S,Cr)O4 as a possible phase controlling the aqueous concentrations of Cr(VI) species and determined the solubility products of several Ba(S,Cr)O4 solids. He also provided infrared spectroscopic evidence for the existence of the amorphous (Fe,Cr)(OH)3 solid solution and for the association of carbonate with Cr in the structure of this compound. Recently, he used laser photoacoustic spectroscopy to measure the kinetics and thermodynamics of trace-level chromate sorption to iron oxides.

Dr. Amonette has more than 28 years of research experience and has been with the Pacific Northwest National Laboratory (PNNL) since 1986. He has authored or coauthored more than 57 peer reviewed scientific journal publications, 20 book chapters, 40 technical reports, six patents mainly in the area of photoacoustic spectroscopy, and a book on quantitative methods in soil mineralogy.

A list of recent publications appears at the end of this page.

Research Interests

• Environmental geochemistry
• Soil mineralogy
• Application of spectroscopic techniques, such as laser photoacoustic, Mössbauer, electron paramagnetic,
• infrared, and x-ray absorption/scattering, to characterize the solid phases and to predict and monitor the reactions that occur in soil environments.
• Carbon sequestration (terrestrial and geological)

Education and Credentials

• Ph.D., Soil Chemistry, Iowa State University
• M.S., Soil Chemistry, Iowa State University
• B.S., Soil Science, New Mexico State University

Affiliations and Professional Service

• Chair, Soil Mineralogy Division, Soil Science Society of America, 1994
• Associate Editor, Soil Mineralogy Division, Soil Science Society of America Journal, 1994-1996
• Bouyoucos Conference Co-Organizer, Soil Science Society of America, 2004
• Associate Editor, Clays and Clay Minerals, 1998 - present
• Council Member, Clay Minerals Society, 1996-1998; 2006-2008
• Meeting Co-Chair, Clay Minerals Society, 2004
• American Chemical Society

Awards and Recognitions

• 2008 Fitzner/Eberhardt Award for Outstanding Contributions to Science and Engineering Education
• R&D100 Award for "In-Situ Redox Manipulation," 1998
• "Chet Cooper Mentor of the Year, 2000" Presented by the Environmental and Health Sciences Division at PNNL for Dr. Amonette’s work with students, teachers and postdoctoral appointees over many years.

PNNL Publications

2009

• Amonette JE, and JL Barr. 2009. Multi-Channel Auto-Dilution System for Remote Continuous Monitoring of High Soil-CO2 Fluxes. PNNL-18229, Pacific Northwest National Laboratory, Richland, WA. 
• Fang Y, SB Yabusaki, SJ Morrison, JE Amonette, and PE Long. 2009. "Multicomponent reactive transport modeling of uranium bioremediation field experiments." Geochimica et Cosmochimica Acta 73(20):6029-6051. 
• Wang CM, DR Baer, JE Amonette, MH Engelhard, J Antony, and Y Qiang. 2009. "Morphology and Electronic Structure of the Oxide Shell on the Surface of Iron Nanoparticles." Journal of the American Chemical Society 131(25):8824-8832.  doi:10.1021/ja900353f

2008

• Bachelor PP, JI McIntyre, JE Amonette, JC Hayes, BD Milbrath, and P Saripalli. 2008. "Potential method for measurement of CO2 leakage from underground sequestration fields using radioactive tracers." Journal of Radioanalytical and Nuclear Chemistry 277(1):85-89.  doi:10.1007/s10967-008-0713-8
• Baer DR, JE Amonette, MH Engelhard, DJ Gaspar, AS Karakoti, SVNT Kuchibhatla, P Nachimuthu, J Nurmi, Y Qiang, V Sarathy, S Seal, A Sharma, PG Tratnyek, and CM Wang. 2008. "Characterization Challenges for Nanomaterials." Surface and Interface Analysis 40(3-4):529-537.  doi:10.1002/sia.2726
• Borch T, AK Camper, JA Biederman, P Butterfield, R Gerlach, and JE Amonette. 2008. "Evaluation of Characterization Techniques for Iron Pipe Corrosion Products and Iron Oxide Thin Films." Journal of Environmental Engineering (ASCE) 134(10):835-844. 
• Hayes JA, DM Schubert, JE Amonette, P Nachimuthu, and RS Disselkamp. 2008. "Ultraviolet stimulation of hydrogen peroxide production using aminoindazole, diaminopyridine, and phenylenediamine solid polymer complexes of Zn(II)." Journal of Photochemistry and Photobiology. A, Chemistry 197(2-3):245-252.  doi:10.1016/j.jphotochem.2007.12.031
• Sarathy V, PG Tratnyek, J Nurmi, DR Baer, JE Amonette, CL Chun, RL Penn, and EJ Reardon. 2008. "Aging of Iron Nanoparticles in Aqueous Solution: Effects on Structure and Reactivity." Journal of Physical Chemistry C 112(7):2286-2293.  doi:10.1021/jp0777418

2007

• Jastrow JD, JE Amonette, and VL Bailey. 2007. "Mechanisms controlling soil carbon turnover and their potential application for enhancing carbon sequestration ." Climatic Change 80(1-2):5-23. 
• Marsili E, H Beyenal, L Di Palma, C Merli, A Dohnalkova, JE Amonette, and Z Lewandowski. 2007. "Uranium immobilization by sulfate-reducing biofilms grown on hematite, dolomite, and calcite." Environmental Science & Technology 41(24):8349-8354.  doi:10.1021/es071335k
• Palumbo AV, JR Tarver, LA Fagan, MS McNeilly, R Ruther, LS Fisher, and JE Amonette. 2007. "Comparing metal leaching and toxicity from high pH, low pH, and high ammonia fly ash." Fuel 86(10-11):1623-1630.  doi:10.1016/j.fuel.2006.11.018
• Thompson KM, SW Petersen, JS Fruchter, CC Ainsworth, VR Vermeul, DM Wellman, JE Szecsody, MJ Truex, JE Amonette, and PE Long. 2007. "Supplemental Groundwater Remediation Technologies to Protect the Columbia River at Hanford, WA." In Waste management symposium 2007 : Global Accomplishments in Environmental and Radioactive Waste Management - Education and Opportunity for the Next Generation of Waste Management Professionals : February 25 March 1, 2007, Tucson, Arizona.  Waste Management Symposia, Tucson, AZ. 
• Wang CM, DR Baer, JE Amonette, MH Engelhard, JS Anthony, and Y Qiang. 2007. "Electron Beam Induced Thickening of the Protective Oxide Layer around Fe Nanoparticles ." Ultramicroscopy 108(1):43-51.  doi:10.1016/j.ultramic.2007.03.002
• Wang CM, DR Baer, JE Amonette, MH Engelhard, Y Qiang, and JJ Antony. 2007. "Morphology and Oxide Shell Structure of Iron Nanoparticles Grown by Sputter-Gas-Aggregation." Nanotechnology 18(25):Art. No. 255603.  doi:10.1088/0957-4484/18/25/255603

2006

• Amonette JE, MJ Truex, and JS Fruchter. 2006. Project Work Plan Carbon Tetrachloride and Chloroform Attenuation Parameter Studies: Heterogeneous Hydrolytic Reactions. PNNL-SA-51843, Pacific Northwest National Laboratory, Richland, WA. 
• Arvidson RS, M Collier, KJ Davis, MD Vinson, JE Amonette, and A Luttge. 2006. "Magnesium inhibition of calcite dissolution kinetics." Geochimica et Cosmochimica Acta 70(3):583-594. 
• Fulton JL, DW Matson, KH Pecher, JE Amonette, and JC Linehan. 2006. "Metal-based Nanoparticle Synthesis from the Rapid Expansion of Carbon Dioxide Solutions." Journal of Nanoscience and Nanotechnology 6(2):562-567. 
• Hua B, B Deng, EC Thornton, J Yang, and JE Amonette. 2006. "Incorporation of Chromate into Calcium Carbonate Structure during Coprecipitation." Water, Air, and Soil Pollution.  doi:10.1007/s11270-006-9242-7
• Saripalli P, JE Amonette, FC Rutz, and N Gupta. 2006. "Design of Sensor Networks for the Long term Monitoring of Geological Sequestration." Energy Conversion and Management 47(13-14):1968-1974.  doi:10.1016/j.enconman.2005.09.010
• Thompson CJ, RG Riley, JE Amonette, and PL Gassman. 2006. "Quantification of Volatile Organics in Soil Aging Experiments Using Fourier Transform Infrared Spectroscopy." Applied Spectroscopy 60(8):914-919.  doi:10.1366/000370206778062156

2005

• Gonzalez-Gil G, JE Amonette, MF Romine, YA Gorby, and G Geesey. 2005. "Bioreduction of Natural Specular Hematite under Flow Conditions." Geochimica et Cosmochimica Acta 69(5):1145-1155. 
• Marsili E, H Beyenal, L Di Palma, C Merli, A Dohnalkova, JE Amonette, and Z Lewandowski. 2005. "Uranium removal by sulfate reducing biofilms in the presence of carbonates ." Water Science and Technology 52(7):49-55. 
• Nurmi JT, PG Tratnyek, V Sarathy, DR Baer, JE Amonette, KH Pecher, CM Wang, JC Linehan, DW Matson, RL Penn, and MD Driessen. 2005. "Characterization and Properties of Metallic Iron Nanoparticles: Spectroscopy, Electrochemistry, and Kinetics." Environmental Science and Technology 39(5):1221-1230. 
• Sani RK, BM Peyton, A Dohnalkova, and JE Amonette. 2005. "Reoxidation of Reduced Uranium with Iron(III) (Hydr)Oxides under Sulfate-Reducing Conditions." Environmental Science and Technology 39(7):2059-2066. 
• Wang CM, DR Baer, LE Thomas, JE Amonette, J Anthony, Y Qiang, and G Duscher. 2005. "Void Formation during Early Stages of Passivation: Initial Oxidation of Iron Nanoparticles at Room Temperature." Journal of Applied Physics 98(9):094308(7).  doi:10.1063/1.2130890

2004

• Beyenal H, RK Sani, BM Peyton, A Dohnalkova, JE Amonette, and Z Lewandowski. 2004. "Uranium Immobilization by Sulfate-reducing Biofilms." Environmental Science and Technology 38(7):2067-2074 . 
• Foster NS, NB Valentine, SE Thompson, TJ Johnson, and JE Amonette. 2004. "FTIR Transmission and Photoacoustic Spectroscopy for the Statistical Identification of Bacteria ." In Proceedings of SPIE - Chemical and Biological Point Sensors for Homeland Defense, vol. 5269, ed. Arthur J. Sedlacek III, Richard Colton, Tuan Vo-Dinh, pp. 172-182.  SPIE (International Society for Optical Engineering), Bellingham , WA. 
• Foster NS, SE Thompson, NB Valentine, JE Amonette, and TJ Johnson. 2004. "Identification of Sporulated and Vegetative Bacteria using Statistical Analysis of Fourier Transform Mid-Infrared Transmission Data ." Applied Spectroscopy 58(2):203-211. 
• Norberg NS, KR Kittilstved, JE Amonette, RK Kukkadapu, DA Schwartz, and DR Gamelin. 2004. "Synthesis of Colloidal Mn2+:ZnO Quantum Dots and High-TC Ferromagnetic Nanocrystalline Thin Films." Journal of the American Chemical Society 126(30):9387-9398. 
• Palumbo AV, JF Mccarthy, JE Amonette, LS Fisher, SD Wullschleger, and WL Daniels. 2004. "Prospects for Enhancing Carbon Sequestration and Reclamation of Degraded Lands with Fossil-fuel Combustion By-products." Advances in Environmental Research 8(3-4):425-438. 
• Post WM, RCC Izaurralde, JD Jastrow, BA McCarl, JE Amonette, VL Bailey, PM Jardine, TO West, and J Zhou. 2004. "Enhancement of Carbon Sequestration in US Soils." BioScience 54(10):895-908. 
• Sani RK, BM Peyton, JE Amonette, and G Geesey. 2004. "Reduction of Uranium(VI) under Sulfate-reducing Conditions in the Presence of Fe(III)-(hydr)oxides." Geochimica et Cosmochimica Acta 68(12):2639-2648. 
• Strawn DG, NE Palmer, LJ Furnare, C Goodell, JE Amonette, and RK Kukkadapu. 2004. "Copper Sorption Mechanisms on Smectites." Clays and Clay Minerals 52(3):321-333. 
• Williford RE, DR Baer, JE Amonette, and AS Lea. 2004. "Dissolution and Growth of (10(1) over-bar4) Calcite in Flowing Water: Estimation of Back Reaction Rates via Kinetic Monte Carlo Simulations." Journal of Crystal Growth 262(1-4):503-518. 

2003

• Amonette JE, RK Kukkadapu, EE Alp, W Sturhahn, and TS Toellner. 2003. "Heterogeneous Electron-Transfer Kinetics with Synchrotron 57Fe Mossbauer Spectroscopy." Geochimica et Cosmochimica Acta 67(12):2109-2116. 
• Amonette JE, CK Russell, KA Carosino, NL Robinson, and JT Ho. 2003. "Toxicity of Al to Desulfovibrio desulfuricans." Applied and Environmental Microbiology 69(7):4057-4066. 
• Amonette JE, SM Heald, and CK Russell. 2003. "Imaging the heterogeneity of mineral surface reactivity using Ag(I) and synchrotron X-ray microscopy." Physics and Chemistry of Minerals 30(9):559-569. 
• Arvidson RS, IE Ertan, JE Amonette, and A Luttge. 2003. "Variation in Calcite Dissolution Rates: A Fundamental Problem? ." Geochimica et Cosmochimica Acta 67(9):1623-1634. 
• Lea AS, TT Hurt, A El-Azab, JE Amonette, and DR Baer. 2003. "Heteroepitaxial Growth of a Manganese Carbonate secondary Nano-Phase on the (101_4) Surface of Calcite in Solution." Surface Science 524(1-3):63-77. 
• Miao J, JE Amonette, Y Nishino, T Ishikawa, and KO Hodgson. 2003. "Direct determination of the absolute electron density of nanostructured and disordered materials at sub-10 nm resolution ." Physical Review. B, Condensed Matter and Materials Physics 68(012201):1-3. 
• Thompson SE, NS Foster, TJ Johnson, NB Valentine, and JE Amonette. 2003. "Identification of Bacterial Spores using Statistical Analysis of Fourier Transform Infrared Photoacoustic Spectroscopy Data ." Applied Spectroscopy 57(8):893-899. 
• Wang J, AG Kalinichev, JE Amonette, and RJ Kirkpatrick. 2003. "Interlayer Structure and Dynamics of Cl-Bearing Hydrotalcite: Far Infrared Spectroscopy and Molecular Dynamics Modeling." American Mineralogist 88(Feb-Mar 2003):398-409. 

2002

• Amonette JE. 2002. "Methods for Determination of Mineralogy and Environmental Availability ." Chapter 5 in Soil Mineralogy with Environmental Applications, SSSA Book Series, vol. 7, ed. J.B. Dixon and D.G. Schulze, pp. 153-197.  Soil Science Society of America, Madison , WI. 
• Baer DR, Y Liang, AS Lea, JE Amonette, and NG Colton. 2002. "Scanning Force Microscopy Measurements of Dissolution and Growth Processes: CaCO3 Examples." In State-of-the-Art Applications of Surface and Interface Analysis Methods to Environmental Material Interactions: In Honor of James E. Castle's 65th Year, vol. 2001-5, ed. D.R. Baer, C.R. Clayton, G.D. Davis, et. al., pp. 139-148.  The Electrochemical Society, Inc., Pennington, NJ. 
• Vermeul VR, MD Williams, JE Szecsody, JS Fruchter, CR Cole, and JE Amonette. 2002. "Creation of a Subsurface Permeable Reactive Barrier Using In Situ Redox Manipulation." Chapter 6 in Handbook of Groundwater Remediation using Permeable Reactive Barriers: Applications to Radionuclides, Trace Metals, and Nutrients, ed. David L. Naftz, et al, pp. 163-192.  Academic Press, San Diego, CA. 
• Yoon S, PA Helmke, JE Amonette, and WF Bleam. 2002. "X-ray absorption and magnetic studies of trivalent lanthanide ions sorbed on pristine and phosphate-modified boehmite surfaces." Langmuir 18 (26)(Dec 24, 2002):10128-10136. 

2001

• Foster NS, JE Amonette, T Autrey, and JT Ho. 2001. "Detection of Trace Levels of Water in Oil by Photoacoustic Spectroscopy." Sensors and Actuators. B, Chemical 77(3):620-624. 
• Lea AS, JE Amonette, DR Baer, Y Liang, and NG Colton. 2001. "Microscopic Effects of Carbonate, Manganese, and Strontium ions on Calcite Dissolution." Geochimica et Cosmochimica Acta 65 (3):369-379. 
• Matocha CJ, DL Sparks, JE Amonette, and RK Kukkadapu. 2001. "Kinetics and Mechanism of Birnessite Reduction by Catechol." Soil Science Society of America Journal 65:58-66. 
• Zachara JM, NS Foster, JE Amonette, EJ Bylaska, AR Felmy, PL Gassman, SM Heald, RK Kukkadapu, C Liu, MJ Mason, KM Rosso, CK Russell, JR Rustad, SC Smith, Z Wang, and TW Wietsma. 2001. Annual Report 2000 Environmental Dynamics and Simulation. PNNL-13456, Pacific Northwest National Laboratory, Richland, WA. 

2000

• Amonette JE, DJ Workman, DW Kennedy, JS Fruchter, and YA Gorby. 2000. "Dechlorination of Carbon Tetrachloride by Fe(II) Associated with Goethite." Environmental Science and Technology 34:4606-4613. 
• Brown GE, SA Chambers, JE Amonette, JR Rustad, T Kendelewicz, P Liu, CS Doyle, D Grolimund, NS Foster, SA Joyce, and S Thevuthasan. 2000. "Interaction of Aqueous Chromium Ions with Iron Oxide Surfaces." Chapter 14 in Nuclear Site Remediation: First Accomplishments of the Environmental Management Science Program. ACS Symposium Series, vol. 778, ed. Eller, P. Gary; Heineman, William R., pp. 212-246.  American Chemical Society, Washington DC. 
• Fruchter JS, CR Cole, MD Williams, VR Vermeul, JE Amonette, JE Szecsody, JD Istok, and MD Humphrey. 2000. "Creation of a Subsurface Permeable Treatment Zone for Aqueous Chromate Contaminatioin Using In Situ Redox Manipulation." Ground Water Monitoring and Remediation 20(2):66-77. 
• Small JR, NS Foster, JE Amonette, and T Autrey. 2000. "Listening to Colloidal Silica Samples: Simultaneous Measurement of Absorbed and Scattered Light Using Pulsed-Laser Photoacoustics." Applied Spectroscopy 54(8):1142-1150. 
• Zachara JM, NS Foster, JE Amonette, EJ Bylaska, AR Felmy, PL Gassman, SM Heald, RK Kukkadapu, C Liu, MJ Mason, KM Rosso, CK Russell, JR Rustad, SC Smith, Z Wang, and TW Wietsma. 2000. Annual Report 1999 Environmental Dynamics & Simulation . PNNL-13206, Pacific Northwest National Laboratory, Richland, WA. 

1999

• Amonette JE, FA Khan, H Gan, JW Stucki, and AD Scott. 1999. "Comparison of Oxidimetric, Spectrophotometric, and Mossbauer-Spectroscopic Methods for Determination of Fe(II) in Nonrefractory Minerals." In Clays for our Future: Proceeding 11th International Clay Conference 1997, ed. H. Kodama, A.R. Mermut, and J.K. Torrance, pp. 277-286.  ICC97 Organizing Committee, Ottawa, ON, CANADA. 
• Foster NS, T Autrey, JE Amonette, JR Small, and EW Small. 1999. "Laser Photoacoustic Spectroscopy: A Versatile Absorption-Spectroscopic Technique." American Laboratory 31(4):96S-108S. 
• Foster NS, JE Amonette, and T Autrey. 1999. "In-situ Detection of Chromate Using Photoacoustic Spectroscopy." Applied Spectroscopy 53(6):735-740. 
• Istok JD, JE Amonette, CR Cole, JS Fruchter, MD Humphrey, JE Szecsody, SS Teel, VR Vermeul, MD Williams, and SB Yabusaki. 1999. "In Situ Redox Manipulation by Dithionite Injection: Intermediate-Scale Laboratory Experiments." Ground Water 37(6):884-889. 
• Kloprogge JT, S Komarneni, and JE Amonette. 1999. "Synthesis of Smectite Clay Minerals: A Critical Review." Clays and Clay Minerals 47(5):529-554. 
• Mattigod SV, D Rai, and JE Amonette. 1999. "Concentrations and Distribution of Major and Selected Trace Elements in Size-Density Fractionated Fly Ashes." In Biogeochemistry of Trace Elements in Coal and Coal Combustion Byproducts, ed. K.S. Sajwan, A.K. Alva and R.F. Keefer, pp. 115-131.  Kluwer Academic/Plenum Publishers, New York, NY. 
• Maxwell RS, RK Kukkadapu, JE Amonette, and HM Cho. 1999. "2H Solid-State NMR Investigation of Terephthalate Dynamics and Orientation in Mixed-Anion Hydrotalcite-like Compounds." Journal of Physical Chemistry B 103:5197-5203. 
• Thornton EC, and JE Amonette. 1999. "Hydrogen Sulfide Gas Treatment of Cr(VI)-Contaminated Sediment Samples from a Plating-Waste Disposal Site-Implications for In-Situ Remediation." Environmental Science and Technology 33:4096-4101.