Joseph Pignatello

Department of Environmental Science and Forestry
The Connecticut Agricultural Experiment Station
123 Huntington Street
New Haven, CT 06511
Voice: (203) 974-8518 Fax:(203) 974-8502

Dr. Pignatello has expertise in physical organic chemistry; soil chemistry; environmental chemistry and engineering; fate of organic compounds in the environment; and water and soil treatment processes.

B.A., Chemistry, University of Minnesota, Minneapolis
Ph.D., Chemistry, University of California, Berkeley

Station Career: 

Assistant Scientist II, 1984-1988

Associate Scientist, 1988-1993

Scientist, 1993-2004

Senior Scientist, 2004-2013

Chief Scientist, 2013-2022

Chief Distinguished Scientist, 2022

Emeritus Scientist, 2022-present


Dr. Pignatello leads the Environmental Chemistry group, which conducts research in several areas in the environmental chemistry of pollutants and the chemistry of natural processes, including:

  • physical-chemical interactions of organic compounds with soils and soil components;
  • bioavailability of organic contaminants in natural particles;
  • physical-chemical processes for removing or degrading pollutants in soil, water and air; and
  • chemistry of natural processes in the environment.


Their research covers both fundamental and applied aspects, and deals with a diversity of agrochemicals, legacy and emerging organic contaminants, and excess nutrients. The group uses a variety of physical and chemical techniques, such as gas and liquid chromatography, solid and liquid state NMR spectroscopy, high resolution gas adsorption, diffuse-reflectance FTIR and UV/visible spectroscopies, XRD, HRTEM, SEM, AFM, radioisotope techniques, and computational molecular modeling. Many of the projects are collaborative with individuals at Federal laboratories, US and foreign universities, and others within The CAES. Outside funding has been provided over the years by USDA, NSF, EPA, SERDP, and industry sources.

Past Research:
Biodegradation of fumigants in soil and groundwater. Solvent extraction techniques for determining volatile organic compound and pesticide concentrations in soil. Field and laboratory studies to determine the causes of sequestration of pesticides and other chemicals in soil. Mechanistic modeling of sorption by soil organic matter. Rates of sorption and desorption in soil. Advanced oxidation process (especially the Fenton reaction) for degrading pesticides and many other types of compounds in soil and water.

  • Driving forces controlling sorption of organic compounds to natural organic matter and pyrogenic carbons, including special interactions, application of a glassy polymer model to soil organic matter, and the causes of sorption hysteresis and irreversibility.
  • Spectroscopic characterization of natural organic matter and chars.
  • The chemistry of peroxide-based advanced oxidation processes (AOPs) for treating wastewaters.
  • Sunlight-driven photolysis of organic pollutants and dissolved organic matter in marine and estuarine waters with emphasis on the influence of water chemistry.
  • Bioavailability of pollutants sorbed to environmental black carbon particles.
  • Electron-transfer and nucleophilic reactions mediated by pyrogenic carbons.
  • Interactions between engineered nanoparticles and biochar particles.
  • Trapping and degradation of fumigant emissions.


Present Research:
In general terms, the group’s research interests include interactions of organic compounds with soils and sediments, remediation of contaminated water and soil, and sunlight-driven reactions in the environment. Its research covers both fundamental and applied aspects of these areas and deals with a diversity of compounds within the categories of legacy pollutants, emerging pollutants such as endocrine disrupting compounds and pharmaceuticals, and nanomaterials. The group uses a variety of physical and chemical techniques, such as gas and liquid chromatography, solid and liquid state NMR spectroscopy, high resolution gas adsorption, diffuse-reflectance FTIR and UV/visible spectroscopies, XRD, HRTEM, SEM, AFM, thermomechanical and thermogravimetric analyses, radioisotope techniques, and computational molecular modeling.

Many of the projects are collaborative with individuals at CAES, Federal research laboratories, American and foreign universities, and private industry. In addition to my position at CAES, I also hold the position of Professor Adjunct of Chemical and Environmental Engineering at Yale University

Current Projects in the Group:

  • Adsorption of contaminants to pyrogenic carbons. Pyrogenic carbons include natural chars, biochars, activated carbons, and related models such as graphite, graphene, and carbon nanotubes. The group is investigating novel interactions of organic compounds on their surfaces, including, i) formation of exceptionally strong hydrogen bonds with ionizable contaminants (e.g., carboxylic acids, phenols, sulfonamides); ii) p-p electron donor-acceptor interactions with compounds containing electron-poor aromatic rings; and iii) impacts on adsorption of physical-chemical changes in carbons induced by air oxidation during pyrolysis and after aging in the environment.
  • Tailoring pyrogenic carbons for use in retention of and/or chemical transformations of contaminants. Carbons have a long history of use as adsorbents in water purification and sediment stabilization. We are modifying carbon structure and surface functionality to enhance binding capacity or to catalyze desired reactions with adsorbed pollutants. In addition, we are investigating the inherent reactivity of pyrogenic carbons to bring about hydrolytic, nucleophiic, free radical, and electron-transfer reactions of sorbed contaminants.
  • Potential roles for biochar in environmental management. Biochar is the carbonaceous byproduct of anoxic pyrolysis of biomass waste that has potential beneficial applications as a soil amendment in agriculture and environmental remediation, partially as a consequence of its strong adsorptive properties. We are tailoring biochars with superior ability to capture nutrient ions in animal wastes into less leachable forms. We are studying the use of biochar to remediate marine and land spills of crude oil, relying on its efficient absorption of crude and its ability to stimulate microbial activity. And we are investigating the interaction of nitrous oxide with biochar following reports that biochar inhibits emissions of the potent greenhouse and ozone-depleting gas, nitrous oxide, in soil.
  • Advanced oxidation processes for treating contaminated water. We are conducting fundamental chemical studies on advanced oxidation processes for ‘deep’ oxidation of organic pollutants that use hydrogen peroxide, peracetic acid, peroxymonosulfate, and peroxydisulfate as the bulk oxidant.  We are designing carbonaceous or inorganic nano-scale catalysts and photocatalyst for peroxides activation. Our emphasis is on the kinetics and mechanisms of these reactions, with special concern for the effects of water chemistry, since many treatable waters contain high levels of dissolved substances.

  • Involvement of Low-Barrier Hydrogen Bonds in Natural Environmental Processes. Hydrogen bonds between weak acid groups with similar pKa values can be much stronger and shorter than ordinary hydrogen bonds. We are examining whether such bonds play a role in bonding between soil organic matter molecules or strands, between SOM and pyrogenic carbons, and between SOM and natural and anthropogenic inorganic weak acids.

Recent publications available from the author,, (see for a full list)

  • Charge-assisted hydrogen bonding as a cohesive force in soil organic matter: water solubility enhancement by addition of simple carboxylic acids, Ni, Jinzhi and Pignatello, J.J., Environ. Sci.: Processes and Impacts, 2018; DOI: 10.1039/c8em00255j.
  • Oxidation of Organic Contaminants by Unactivated Peroxymonosulfate, Yi Yang, Gourab Banerjee, Gary W. Brudvig, Jae-Hong Kim, Joseph J. Pignatello*, Environ. Sci. Technol., 52 (10), 5911–5919 (2018); DOI: 10.1021/acs.est.8b00735.
  • Thermal Air Oxidation Changes Surface and Adsorptive Properties of Black Carbon (Char/biochar), Feng Xiao*, Alemayehu H. Bedane, Julia Xiaojun Zhao, Michael D. Mann, Joseph J. Pignatello, Science of The Total Environment, 618, 276-283 (2018).
  • Adsorption and Desorption of Nitrous Oxide on Raw and Thermally Air-Oxidized Chars,” Feng Xiao, Joseph Pignatello,* and Beatriz Gamiz, Science of The Total Environment, 643, 1436-1445 (2018);
  • Participation of the Halogens in Photochemical Reactions in Natural and Treated Waters, Yi Yang and Joseph J. Pignatello,* Molecules, 22, 1684 (2017); doi:10.3390/molecules22101684.
  • Modification of Activated Carbons for Enhanced Nucleophilic Substitution Reactions of Adsorbed Methyl Bromide, Hsin-Se Hsieh and Joseph J. Pignatello,* Appl. Catal. B: Environmental, 233, 281-288 (2018).
  • “Bioaccessibility of PAHs and PAH derivatives in a fuel soot assessed by an in vitro digestive model with absorptive sink: effects of aging the soot in a soil-water mixture,” Yanyan Zhang, Joseph J. Pignatello*, Shu Tao*. Science of the Total Environment 615, 169–176 (2018).
  • Activity and Reactivity of Pyrogenic Carbonaceous Matter Toward Organic Compounds, J.J. Pignatello*, William A. Mitch, and Wenqing Xu, Environ. Sci. Technol., 51, 8893-8908 (2017); DOI: 10.1021/acs.est.7b01088.
  • Degradation of p-Nitrophenol by Lignin and Cellulose Chars: H2O2-Mediated Reaction and Direct Reaction with the Char, Jing Yang, J.J. Pignatello*, Bo Pan,* and Baoshan Xing, Environ. Sci. Technol., 51, 8972-8980 (2017); DOI: 10.1021/acs.est.7b01087.
  • Activated Carbon Mediated Alkaline Hydrolysis of Alkyl Bromides, Hsin-Se Hsieh and Joseph J. Pignatello*, Appl. Catal. B: Environmental, 211: 68–78 (2017).
  • Feng Xiao*, Alemayehu H. Bedane, Julia Xiaojun Zhao, Michael D. Mann, and Joseph J. Pignatello, Thermal Air Oxidation Changes Surface and Adsorptive Properties of Black Carbon (Char/biochar) Science Total Environment 618, 276–283 (2018).
  • Surface Interactions between Gold Nanoparticles and Biochar, Minori Uchimiya*, Joseph J. Pignatello, Jason C. White, S. Hu, and Paulo J. Ferreira, Sci Rep-Uk, 7(1): 5027 (2017); doi:10.1038/s41598-017-03916-1.
  • Exposure of agricultural crops to nanoparticle CeO2 in biochar-amended soil, Alia D. Servin, Roberto De la Torre Roche, Hiram M. Castillo, Luca Pagano, Joseph Hawthorne, Craig Musante, Joseph Pignatello, Minori Uchimiya, and Jason C. White,* Plant Physiology and Biochemistry, 110: 147-157 (2017).
  • Bioaccumulation of nanoparticle CeO2 by earthworms in biochar amended soil, Alia D. Servin, Hiram M. Castillo, Jose A. Hernandez-Viezcas, Wout De Nolf, Roberto De la Torre-Roche, Luca Pagano, Joseph Pignatello, Minori Uchimiya, Jorge Gardea-Torresday, Jason C. White,* J. Agric. Food Chem. 66, 26, 6609-6618; DOI 10.1021/acs.jafc.7b04612.
  • Structural Transformation of Biochar Black Carbon by C60 Superstructure: Environmental Implications, Minori Uchimiya,* Joseph J. Pignatello, and Jason C. White, Scientific Reports, 7: 11787; DOI:10.1038/s41598-017-12117-9.
  • Bioaccessibility of Nitro- and Oxy-PAHs in Fuel Soot Assessed by an in vitro Digestive Model with Absorbent Sink. Yanyan Zhang, Joseph J. Pignatello,* and Shu Tao, Environmental Pollution, 218: 901-908 (2016).
  • Effects of Post-Pyrolysis Air Oxidation of Biomass Chars on Adsorption of Neutral and Ionizable Compounds, Feng Xiao and Joseph J. Pignatello,* Environmental Science and Technology, 50(12): 6276–6283 (2016). DOI: 10.1021/acs.est.6b00362.
  • Bioaccessibility of PAHs in Fuel Soot Assessed by an in vitro Digestive Model with Absorptive Sink: Effect of Food Ingestion, Yanyan Zhang, Joseph J. Pignatello*, Shu Tao, and Baoshan Xing, Environmental Science and Technology, 49: 14641–14648 (2015). DOI: 10.1021/acs.est.5b04342.
  • Activation of Hydrogen Peroxide and Solid Peroxide Reagents by Phosphate Ion in Alkaline Solution, Bing Yang, Joseph J. Pignatello*, Dong Qu*, and Baoshan Xing, Environmental Engineering Science, (2016) 33(3): 193-199. doi:10.1089/ees.2015.0460.
  • Investigation of Sorbate-Induced Plasticization by Solid-State NMR Spectroscopy, Xiaoyan Cao, Charisma Lattao, Jingdong Mao,*, Joseph J. Pignatello,*, and Klaus Schmidt-Rohr,* Journal of Soils and Sediments, (2016) 16(7): 1841-1848. DOI 10.1007/s11368-016-1378-5.
  • ISOT Calc, a versatile tool for parameter estimation in sorption isotherms, Jose Beltran, Joseph J Pignatello,  Marc Teixidó,* Computers & Geosciences, (2016) 94: 11–17.
  • Environmental fate of the fungicide metalaxyl in soil amended with composted olive-mill waste and its biochar: an enantioselective study, Beatriz Gámiz,* Joseph J. Pignatello, Lucía Cox, María C. Hermosín, Rafael Celis, Science of the Total Environment, 541, 776–783 (2016).
  • Heteroaggregation of Cerium Oxide Nanoparticles and Nanoparticles of Pyrolyzed Biomass Peng Yi, Joseph J. Pignatello,* Minori Uchimiya and Jason C. White, Environmental Science and Technology, 49: 13294-13303 (2015); DOI: 10.1021/acs.est.5b03541.
  • Interactions of Triazine Herbicides with Biochar: Steric and Electronic Effects, Feng Xiao and Joseph J. Pignatello,* Water Research, 2015, 80, 179-188.
  • Bioacessibility of PAHs in Fuel Soot Assessed by an in vitro Gastrointestinal Model: Effect of Including an Absorptive Sink, Yanyan Zhang, Joseph J. Pignatello*, Shu Tao and Baoshan Xing, Environmental Science and Technology, 2015, 49, 3905-3912.
  • Reduction of Nitroaromatics Sorbed to Black Carbon by Direct Reaction with Sorbed Sulfides, Wenqing Xu, Joseph J. Pignatello, and William A. Mitch,* Environmental Science and Technology, 2015, 49, 3419-3426.
  • Effect of Matrix Components on UV/H2O2 and UV/S2O82- Advanced Oxidation Processes for Trace Organic Degradation in Reverse Osmosis Brines from Municipal Wastewater Reuse Facilities, Yi Yang, Joseph J. Pignatello, Jun Ma, and William A. Mitch, Water Research, 89: 192-200 (2016).
  • Re-oxidation of Photo-reduced Polyoxotungstate ([PW12O40]4-) by Different Oxidants in the Presence of a Model Pollutant—Kinetics and Reaction Mechanism, Bing Yang, Joseph J. Pignatello*, Dong Qu*, and Baoshan Xing, Journal of Physical Chemistry A, 2015, 119, 1055-1065.
  • Competitive Sorption Used to Probe Strong Hydrogen Bonding Sites for Weak Organic Acids on Carbon Nanotubes, Xiaoyun Li, Beatriz Gamiz, Yiquan Wang, Joseph J. Pignatello,* and Baoshan Xing,* Environmental Science and Technology, 2015, 49, 1409-1417; DOI: 10.1021/es504019u.
  • Synthesis and Application of a Quaternary Phosphonium Polymer Coagulant to Avoid N-Nitrosamine Formation, Teng Zeng, Joseph J. Pignatello, Russell Jingxian Li, and William A. Mitch,* Environmental Science and Technology, 2014, 48 (22), 13392–13401. DOI: 10.1021/es504091s.
  • p+-p Interactions Between (Hetero-)aromatic Amine Cations and Graphitic Surfaces, Feng Xiao and Joseph J. Pignatello,* Environmental Science and Technology, 2015, 49, 906-914; DOI: 10.1021/es5043029.
  • Effect of Adsorption Nonlinearity on the pH-Adsorption Profile of Ionizable Organic Compounds, Feng Xiao and Joseph J. Pignatello,* Langmuir (in press).
  • Comparison of Halide Impacts on the Efficiency of Contaminant Degradation by Sulfate and Hydroxyl Radical-Based Advanced Oxidation Processes (AOPs), Yi Yang, Joseph J. Pignatello, Jun Ma,* William A. Mitch,* Environ. Sci. Technol. (in press).
  • Influence of salinity on triplet-state natural organic matter loss by energy transfer and electron transfer pathways, Kimberly M. Parker, Joseph J. Pignatello, and William A. Mitch,* Environ. Sci. Technol. 47: 10987-10994 (2013).
  • The role of black carbon conductivity in mediating hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation on carbon surfaces by nucleophilic substitution in the presence of sulfides, W. Xu, J. J. Pignatello, and W.A. Mitch,* Environ. Sci. Technol., 47 (13), 7129–7136 (2013).
  • Predicting Contaminant Adsorption in Black Carbon (Biochar)-Amended Soil for the Veterinary Antibiotic Sulfamethazine, M. Teixido, C. Hurtado, J.J. Pignatello*, J.L. Beltran, M. Granados and J. Peccia, Environ. Sci. Technol., 47 (12), 6197–6205 (2013).
  • New Insight into the Mechanism of Adsorption of Ionizable Compounds on Carbon Nanotubes, Xiaoyun Li, Joseph J, Pignatello,* Yiquan Wang, and Baoshan Xing;* Environ. Sci. Technol., 47, 8334-8341 (2013). DOI: 10.1021/es4011042.
  • Evidence of Micropore-filling for Sorption of Nonpolar Organic Contaminants by Condensed Organic Matter, Yong Ran,* Yu Yang, Baoshan Xing, Joseph J. Pignatello, Seokjoon Kwon, Wei Su, and Li Zhou, J. Environ. Qual. 42:806–814 (2013).
  • Catalytic Oxidation for Elimination of Methyl Bromide Fumigation Emissions Using Ceria-Based Catalysts, Chia-Ying Chen and Joseph J. Pignatello;* Applied Catalysis B: Environmental 142-143: 785–794 (2013).
  • Adsorption of Organic Compounds by Black Carbon from Aqueous Solution, J. J. Pignatello. In: “Molecular Environmental Soil Science," Jianming Xu and D.L. Sparks (Edits.); Progress in Soil Science Series; Springer; pp 359-385 (2013).
  • Laboratory Tests of Biochars as Adsorbents for Use in Recovery or Containment of Marine Crude Oil Spills, H.N. Nguyen and J.J. Pignatello,* Environ. Engineer. Sci., 30(7): 374-380 (2013).
  • Characterization of oil shale, isolated kerogen, and post-pyrolysis residues using advanced 13C solid-state nuclear magnetic resonance spectroscopy, Xiaoyan Cao, Justin E. Birdwell*, Mark Chappell, Yuan Li, Joseph J. Pignatello, and Jingdong Mao, AAPG Bulletin (Amer.  Assoc. Petroleum Geologists), AAPG Bulletin, 97(3): 421436 (2013).
  • Sorption Selectivity in Natural Organic Matter Studied with Nitroxyl Paramagnetic Relaxation Probes, C. Lattao, Y. Li, X. Cao, J. Mao, K. Schmidt-Rohr, M.A. Chappell, L.F. Miller, A.L. dela Cruz, and J.J. Pignatello,* Environ. Sci. Technol. 46: 12814-12822 (2012).
  • Advanced Solid-state NMR Characterization of Marine Dissolved Organic Matter Isolated Using the Coupled Reverse Osmosis/Electrodialysis Method, Jingdong Mao,* Xueqian Kong, Klaus Schmidt-Rohr, Joseph J. Pignatello, and E. Michael Perdue, Environ. Sci. Technol., 46, 5806–5814 (2012)
  • Impact of halide ions on natural organic matter-sensitized photolysis of 17ß-Estradiol and on singlet oxygen concentration in saline waters, Janel E. Grebel, Joseph J. Pignatello, and William A. Mitch,* Environ. Sci. Technol. 46: 7128-7134 (2012).
  • Dynamic interactions of natural organic matter and organic compounds, J.J. Pignatello*; J. Soils and Sediments, 12: 1241-1256 (2012) doi 10.1007/s11368-012-0490-4
  • Characterization of Wood Chars Produced at Different Temperatures using Advanced 13C Solid-state NMR Spectroscopic Techniques, Xiaoyan Cao, Joseph J. Pignatello, Yuan Li, Charisma Lattao, Mark A. Chappell, Na Chen, Lesley F. Miller, and Jingdong Mao,* Energy & Fuels. 26: 5983-5991 (2012).
  • Preparation and Characterization of Humic acid Cross-linked with Organic Bridging Groups, T. Schneckenburger; C.V. Lattao; J.J. Pignatello*, G.E. Schaumann, S. Thiele-Bruhn; XY Cao; JD Mao, Org. Geochem., 47 (2012) 132–138.
  • Speciation of the Ionizable Antibiotic Sulfamethazine on Black Carbon (Biochar), M. Teixido, J.J. Pignatello, J.L. Beltran, M. Grenados and J. Peccia,  Environ. Sci. Technol. 45: 10020–10027 (2011).
  • Sorbic acid as a quantitative probe for the formation, scavenging and steady-state concentrations of the triplet-excited state of organic compounds, J.E. Grebel, J.J. Pignatello, W.A. Mitch, Water Research, 45(19): 6535-6544 (2011).
  • Adsorption of Aromatic Carboxylate Ions to Charcoal Black Carbon is Accompanied by Proton Exchange with Water, Ni Jinzhi, J. J. Pignatello* and B. Xing, Environ. Sci. Technol. 45, 9240-9248 (2011). Correction: Environ. Sci. Technol. 46, 5633–5633 (2012).
  • Effect of Biochar Amendments on Mycorrhizal Associations and Fusarium Crown and Root Rot of Asparagus in Replant Soils, W.H. Elmer and J.J. Pignatello, Plant Disease 95: 960-966 (2011).
  • Effect of halide ions and carbonates on organic contaminant degradation by hydroxyl radical-based advanced oxidation processes, Janel E. Grebel, Joseph J. Pignatello, William A. Mitch; Environ. Sci. Technol., 44: 6822-6828 (2010).
  • Sources, Interactions, and Ecological Impacts of Organic Contaminants in Water, Soil, and Sediment: An Introduction to the Special Series, Joseph J. Pignatello, Brian G. Katz, and Hui Li; J. Environ. Qual., 39: 1133-1138 (2010).
  • Interactions of Anthropogenic Organic Chemicals with Organic Matter in Natural Particles, J.J. Pignatello, Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems, B. Xing, N. Senesi and P. M. Huang (eds). Volume 3 of IUPAC SERIES ON BIOPHYSICO-CHEMICAL PROCESSES IN ENVIRONMENTAL SYSTEMS; Wiley; pp 3-50.