PhD in Chemistry with an Environmental Chemistry Track

I. Track description

The Ph.D. program in Environmental Chemistry is situated within the current doctoral program in the Department of Chemistry and Biochemistry. This track will prepare students with an interest in the chemical aspects of environmental science with coursework and research experience at the doctoral level. Graduates of the program will have developed a strong expertise in both environmental science and chemistry, and will therefore be able to find employment in these areas in industry, government and academia.

The proposed track consists of both academic classes and research. The requirements of the track are similar to those that presently exist for doctoral students in chemistry. The difference between the current doctoral program and the new track lie in the requirement that the majority of the coursework and the thesis research be in the general area of environmental chemistry.

II. Rationale, types of students, expected numbers of students in the first five years, community need/relevance

There is an increasing need for doctoral training in Environmental Science based both on surveys of employers and on student interest. Thus many universities are at present developing and implementing interdisciplinary doctoral level programs in Environmental Science and related fields. The model chosen for the FIU doctoral Environmental Science program is for the Environmental Science Program (housed in SEAS) to work with science departments, namely Biological Sciences, Chemistry and Biochemistry, and Earth and Environment, to develop Environmental Science majors within their existing Ph.D. or M.S. programs. This will help in recruiting high quality doctoral students to populate those majors. FIU has a well-established reputation in the field of Environmental Science, and through SERC and faculty in the science departments has gained significant research support and infrastructure to support such interdisciplinary programs.

The types of students we expect to enter this program are those who have a current interest in the chemical and biochemical aspects of environmental science and wish to earn a doctoral degree indicating specific expertise in these areas. The program fits well with current areas of emphasis of the University. Both local students and those from out of area will be attracted to this program because of the combination of specific expertise of current faculty in areas of environmental science and the additional training they will receive in chemistry at the graduate level. There is a strong local market for students with advanced training in the general area of environmental science. As a consequence, graduates of this program should find that there is a demand for people with their skills. The increasing importance of the environment on the national level means that there should also be a general demand for students with an interest and training in environmental science and specific expertise in environmental chemistry and biogeochemistry.

III. Required courses

  1. A minimum of 81 credit hours of coursework. A grade of C or higher must be obtained in all courses, and a cumulative GPA of 3.0 or higher must be maintained. The course of study must include:
    1. 12 credit hours of required classes including four of the following six environmental chemistry core courses, each of which is worth three credit hours.
      • CHM 5423 – Atmospheric Chemistry
      • CHM 5765 – Aquatic Chemistry
      • CHM 6281 – Environmental Organic Chemistry
      • CHM 6340 – Organic Geochemistry
      • OCC 5050 – Chemical Oceanography
      • CHM 6088 – Environmental Chemistry of Trace Elements
    2. 6 credit hours of required classes including two chemistry core courses chosen from the following:
      • CHM 5156 – Advanced Chromatography
      • CHM 5138 – Advanced Mass Spectrometry
      • CHM 5236 – Spectroscopic Techniques and Structure Determination
      • CHM 6157 – Advanced Analytical Chemistry
      • CHM 5165 – Chemometrics and Sampling
      • CHM 5260 – Physical Organic Chemistry
    3. At least one elective. The list of approved electives is maintained by the Chemistry and Environmental Science Major Graduate Committee. This committee consists of the Environmental Science Graduate Program Director, the Chemistry and Biochemistry Graduate Program Director, and two Departmental faculty members active in research in environmental science.
    4. Full time graduate students are required to register for one credit of CHM 6940 (Supervised Teaching) each semester they serve as a teaching assistant.
    5. Full time graduate students are required to register for one credit of CHM 6935 (Graduate Seminar) and one credit of CHM 6936 (Chemistry Colloquium) each fall and spring semester.
    6. At least one credit of CHM 6936 (Chemistry Colloquium) is required. Each student must present a seminar on their proposed research at the colloquium for a letter grade by the end of their third semester of graduate study.
    7. At least eight credit hours of CHM 7910 (Dissertation Research) involving independent dissertation research under the direction of a faculty member in the Department.
    8. At least 20 credits of CHM 7980 (Ph.D. Dissertation) is to be taken after the student has advanced to candidacy.
    9. A maximum of 36 credits may be transferred from another graduate program with the approval of the Graduate Committee. However, only six credit hours can be counted towards the formal post-baccalaureate coursework. Students must elect an appropriate course load in accordance with their research topic, and in agreement with their Graduate Committee and the Departmental Graduate Advisor.
  2. Satisfactory completion of cumulative exams. The students will begin taking the cumulative examinations after completing the proficiency requirements but no later than the beginning of the student’s second semester. Six exams, each lasting three hours, will be given each year. The student must pass four out of 10 consecutively offered exams for admission to candidacy. Cumulative exams in the area of Environmental Chemistry will be added to existing specialties.
  3. Satisfactory presentation and defense of an original research proposal, and satisfactory completion of a preliminary oral examination. The presentation and examination occur consecutively in a single session and must be completed before the end of the fifth semester (excluding summers). The examination will be conducted by the Dissertation Committee, be based on the student’s dissertation research, and include questions from the student’s major field and cognate fields. After fulfilling this requirement, passing the cumulative examinations, and completing all required course work, the student advances to candidacy.
  4. Satisfactory public presentation and defense of a research dissertation, evaluated by the Dissertation Committee. The student’s Dissertation Committee will consist of the research advisor (an FIU graduate faculty member who holds dissertation advisor status), a member from outside the Department or School but within FIU, a randomly selected member appointed by the Graduate Program Director from the Department’s graduate faculty, and at leat two additional committee members with expertise in the student’s research area. At least three members of the Dissertation Committee, including the major research advisor, must be graduate faculty members from the Department of Chemistry and Biochemistry, and at least two of these three members must be tenured. The Committee may include additional members, but they will be non-voting.

IV. Participating faculty (not restricted to those listed below)

  • Dr. J. Berry ( berryj@fiu.edu) Marine and freshwater algae are a rich source of toxic or otherwise biologically active compounds. As part of the Department of Chemistry and Biochemistry, as well as the Marine Science Program at FIU, my research focuses on the identification, isolation and characterization of these bioactive compounds, particularly including those from the cyanobacteria (or "blue-green algae"), as they relate to both environmental health and biomedicine.
  • Dr. Y. Cai (cai@fiu.edu) Dr. Cai’s research is in the field of environmental bioinorganic chemistry, biogeochemistry, and bioanalytical chemistry. The research in his group addresses many interrelated, molecular-level questions regarding the environmental fate and health effect of biomedically and environmentally important metals, including metalloids, such as mercury (Hg) and arsenic (As).
  • Dr. A. DeCaprio (adecapr@fiu.edu) Dr. DeCaprio's areas of research interest include the use of of biomonitoring and biomarkers in forensic toxicology and human exposure assessment, methods for ultra-trace analysis of drugs, pollutants, and their metabolites, and investigation of protein adducts as exposure/risk biomarkers and as mediators of the mechanism of toxicity of pollutants and drugs.
  • Dr. Francisco Fernandez-Lima (fernandf@fiu.edu) Dr. Fernandez-Lima research group focuses on the development of versatile new technologies and methods that help the scientific community address research problems using post-ionization separation based on ion mobility spectrometry and mass spectrometry. We have special interest in the development of new fast separation/identification techniques that can be easily implemented for the dissection, at the molecular level, of complex mixtures
  • Dr. P. Gardinali (gardinal@fiu.edu) Dr. Gardinali’s areas of research include analytical chemistry, environmental chemistry, and environmental toxicology. His work is particularly focused on source fate and transport of organic pollutants in marine and coastal ecosystems, environmental monitoring and risk evaluation. His lab has concentrated on the use of novel mass spectrometry techniques for the trace detection of emergent contaminants, wastewater indicators and exotic chemicals in surface waters.
  • Dr. R. Jaffé (jaffer@fiu.edu) Dr. Jaffé's research is in the area of environmental organic geochemistry and biogeochemistry. He is particularly interested in the environmental dynamics of dissolved, particulate and sedimentary organic matter in aquatic ecosystems as it relates to carbon cycling. Study sites range from headwater streams, sub-tropical wetlands, tropical rivers and estuarine and oceanic environments. Laboratory work heavily relies on Excitation Emission Matrix fluorescence, size exclusion chromatography, HPLC, GC/MS and stable isotope analyses.
  • Dr. J. Joens (joensj@fiu.edu) Measurement and interpretation of UV-visible gas phase absorption spectra of small molecules. Thermodynamics and spectroscopic properties of weakly bound molecular complexes in both the gas phase and condensed phase. Spectroscopic studies of carbonyl compounds in aqueous solution. Kinetic and photochemical processes in planetary atmospheres.
  • Dr. K. O’Shea (osheak@fiu.edu) Professor O'Shea's current research focuses on biological implications and environmental applications of reactive oxygen species (ROS).  His research group investigates the reactions of ROS with organic pollutants and toxins related to potential water treatment and purification strategies.  Our primary goal is to develop a fundamental mechanistic understanding the reactions between ROS and problematic toxins and pollutants in ground, surface and drinking water. His research group is also studying reactions in biological systems where ROS create havoc through radical oxidative processes, leading to a variety of diseases and disorders from heart disease to arthritis to skin cancer.
  • Dr. Kathleen Rein (reink@fiu.edu) Dr. Kathleen (Kelly) Rein is a bioorganic and natural products chemist with a particular interest in algal toxins, their biosynthesis, metabolism, pharmacology, fate in the environment and endogenous function. These may be cyanobacterial toxins such as the hepatotoxic microcystins or marine dinoflagellate toxins such as the brevetoxins from the Florida Red Tide organism Karenia brevis.

Recent Publications Environmental Track faculty:

Benigni, P., Marin, R., Sandoval, K., Gardinali, P., & Fernandez-Lima, F. (2017). Chemical Analysis of Water-accommodated Fractions of Crude Oil Spills Using TIMS-FT-ICR MS. JoVE (Journal of Visualized Experiments), (121), e55352-e55352.

Benigni P., Porter J., Ridgeway M.E., Park M.A., Fernandez-Lima F. (2018). "Increasing analytical separation and duty cycle with non-linear analytical mobility scan functions in TIMS-FT-ICR MS". Anal Chem. 90 (4), 2446–2450.

Benigni P., Sandoval K., Thompson C.J., Ridgeway M.E., Park M.A., Gardinali P., Fernandez-Lima F. (2017). ”Analysis of Photo-irradiated Water Accommodated Fractions of Crude Oils Using Tandem TIMS and FT-ICR MS”, Environ. Sci. Technol., 51 (11), pp 5978–5988.

Benigni P., DeBord J.D., Thompson C.J., Gardinali P., Fernandez-Lima F. (2016). "Increasing Polyaromatic Hydrocarbon (PAH) Molecular Coverage during Fossil Oil Analysis by Combining Gas Chromatography and Atmospheric-Pressure Laser Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS)". Energy and Fuels, 30 (1), 196–203.

Benigni P., Thompson C.J., Ridgeway M.E., Park M.A., Fernandez-Lima F. (2015). "Targeted high resolution ion mobility separation coupled to ultra-high resolution mass spectrometry of endocrine disruptors in complex mixtures". Anal. Chem. 87 (8), 4321–4325.

Berry, J.P., Roy, U., Jaja-Chimedza, A., Sanchez, K., Matysik, J. and Alia, A. (2016) High-resolution magic angle spinning nuclear magnetic resonance of intact zebrafish embryos detects metabolic changes following exposure to teratogenic polymethoxyalkenes from algae. Zebrafish, 13: 456-465.

Campeão, M. E., Reis, L., Leomil, L., de Oliveira, L., Otsuki, K., Gardinali, P. & Thompson, C. C. (2017). The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation. Frontiers in microbiology, 8, 1019.

Cassell, R. T., Chen, W., Thomas, S., Liu, L. & Rein, K. S. (2015). Brevetoxin, the Dinoflagellate Neurotoxin, Localizes to Thylakoid Membranes and Interacts with the Light‐Harvesting Complex II (LHCII) of Photosystem II. ChemBioChem, 16(7), 1060-1067.

Chen, W., Colon, R., Louda, J. W., Rodriguez del Rey, F., Durham, M., & Rein, K. S. (2018). Brevetoxin (PbTx-2) influences the redox status and NPQ of Karenia brevis by way of thioredoxin reductase. Harmful Algae, 71, 29-39.

Chen, W., Tuladhar, A., Rolle, S., Lai, Y., Rodriguez del Rey, F., Zavala, C. E., Liu, Y. & Rein, K. S. (2017) Brevetoxin-2, is a unique inhibitor of the C-terminal redox center of mammalian thioredoxin reductase-1. Toxicology and Applied Pharmacology, 329, 58-66.

Cui D., Mebel A.M., Arroyo-Mora L.E., Holness H., Furton K.G., O'Shea K. (2017). Kinetic, product, and computational studies of the ultrasonic induced degradation of 4-methylcyclohexanemethanol (MCHM), Water Research, 126, 164-171.

Gallo, M.V., Deane, G.D., DeCaprio, A.P., Schell, L.M., and Akwesasne Task Force on the Environment (2015). Changes in persistent organic pollutant levels from adolescence to young adulthood. Environ. Res., 140, 214-224.

Gonzalez-Raymat H., Liu G., Liriano C., Li Y., Yin Y., Shi J., Jiang G., Cai Y. (2017). Elemental mercury: Its unique properties affect its behavior and fate in the environment. Environmental Pollution, 229, 69-86.

Haq, M., Gonzalez, N., Mintz, K., Jaja-Chimeda, A., De Jesus, C. L., Lydon, C., Welch, A. and Berry, J.P. (2016) Teratogenicity of ochratoxin A and the degradation product, ochratoxin a, in the zebrafish (Danio rerio) embryo model of vertebrate development. Toxins, 8: 40.

He D., Ladd N., Sachs J.P. and Jaffé R. (2017). Inverse relationships between salinity and 2H/1H fractionation in leaf wax n-alkanes from Florida mangroves. Org. Geochem. 110, 1-12.

Hu, P., Dubinsky, E.A., Probst, A.J., Wang, J., Sieber, C.M., Tom, L.M., Gardinali, P.R., Banfield, J.F., Atlas, R.M. and Andersen, G.L., (2017). Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proceedings of the National Academy of Sciences, 114(28), pp.7432-7437.

Jaja-Chimedza, A., Sanchez, K., Gantar, M., Gibbs, P.D.L., Schmale, M. C. and Berry, J. P. (2017) Carotenoids glycosides from cyanobacteria are teratogenic in the zebrafish (Danio rerio) embryo model. Chemosphere, 174: 478-489.

Mckay G., Huang W., Romera-Castillo C., Crouch J., Rosario-Ortiz F.L. and Jaffé R. (2017). Assessing dissolved organic matter photo-reactivity in a subtropical wetland ecosystem: Correlations between optical properties, antioxidant capacity, and the photochemical formation of reactive intermediates. Environ. Sci. Technol. 51, 5404–5413

Meng B., Li Y., Cui W., Jiang P., Liu G., Wang Y., Richards J., Feng X., Cai Y. (2018). Tracing the Uptake, Transport, and Fate of Mercury in Sawgrass (Cladium jamaicense) in the Florida Everglades Using a Multi-isotope Technique. Environ. Sci. Technol., 52, 3384–3391.

Möller, C., Clark, E., Safavi-Hemani, H., DeCaprio, A.P., and Marí, F. (2017). Isolation and characterization of Conohyal-P1, a hyaluronidase from the injected venom of Conus purpurascens, J. Proteomics, 164, 73-84.

Möller, C., Davis, W.C., Marí, F., Thompson, V.R., and DeCaprio, A.P. (2017). Proteomic analysis of thiol modifications and assessment of structural changes in hemoglobin induced by aniline metabolites N-phenylhydroxylamine and nitrosobenzene. Sci. Rep., 4, 14794.

Mulet, C.T., Arroyo-Mora, L.E., Leon, L.A., Gnagy, E., and DeCaprio, A.P. (2018). Rapid quantitative analysis of methylphenidate and ritalinic acid in oral fluid by liquid chromatography triple quadrupole mass spectrometry (LC-QqQ-MS), J. Chromatogr. B, 1092, 313-319.

Oehrle, S.; Rodriguez-Matos, M.; Cartamil, M.; Zavala, C.; Rein, K. S. (2017) Toxin composition of the 2016 Microcystis aeruginosa bloom in the St. Lucie Estuary, Florida. Toxicon, 138, 169-172.

Pisani O., Gao M., Maie N., Miyoshi T., Childers D.L. and Jaffé R. (2018). Compositional aspects of herbaceous litter decomposition in the freshwater marshes of the Florida Everglades. Plant & Soil. 423, 87-98. DOI: 10.1007/s11104-017-3495-3.

Rashid M., Sterbinsky G.E., Gracia Pinilla M.A., Cai Y., O’Shea K.E. (2018). Kinetic and Mechanistic Evaluation of Inorganic Arsenic Species Adsorption onto Humic Acid Grafted Magnetite Nanoparticles, The Journal of Physical Chemistry C, https:/pubs.acs.orgdoi/abs/10.1021/acs.jpcc.7b12438

Roebuck JA, Podgorski D., Wagner S. and Jaffé R. (2017). Photo-dissolution of charcoal and fire-impacted soil as a potential source of dissolved black carbon in aquatic environments. Organic Geochemistry. 112, 16-21.

Roy, U., Conklin, L., Schiller, J., Matysik, J., Berry, J. P. and Alia, A. (2017) Metabolic profiling of zebrafish (Danio rerio) embryos by NMR spectroscopy reveals multifaceted toxicity of beta-methylamino-L-alanine (BMAA). Scientific Reports, 7: 17305.

Sandoval, K., Ding, Y., & Gardinali, P. (2017). Characterization and environmental relevance of oil water preparations of fresh and weathered MC-252 Macondo oils used in toxicology testing. Science of the Total Environment, 576, 118-128.

Sun, P., Leeson, C., Zhi, X., Leng, F., Pierce, R. H., Henry, M. S. & Rein, K. S. (2016). Characterization of an epoxide hydrolase from the Florida red tide dinoflagellate, Karenia brevis. Phytochemistry, 122, 11-21.

Seither, J.Z., Arroyo-Mora, L.E., Hindle, R. and DeCaprio, A.P. (2018). Systematic toxicological analysis of novel psychoactive substances. I. Development of a compound database and HRMS spectral library, Forensic Chem., 9, 12-20.

Tai C., Zhang S., Yin Y., Dai Z., Li Y., Jiang G., Cai Y., Huang C., and Shi J. (2018). Facile Photoinduced Generation of Hydroxyl Radical on a Nitrocellulose Membrane Surface and its Application in the Degradation of Organic Pollutants. ChemSusChem., 11, 1 – 6.

Tose L.V., Benigni P., Leyva D., Sundberg A., Ramírez C.E., Ridgeway M.E., Park M.A., Wanderson Romão, Jaffé R., Fernandez-Lima F. (2018). "Coupling Trapped Ion Mobility Spectrometry to Mass Spectrometry: TIMS-TOF MS vs TIMS-FT-ICR MS", Rapid Commun. Mass Spectrom. 32, 1287-1295 (doi:10.1002/rcm.8165).

Wagner S., Jaffé R., Stubbins A. (2018). Dissolved black carbon in aquatic ecosystems: A review. Limnology & Oceanography Methods. DOI: 10.1002/lol2.10076.

Wang, J., Sandoval, K., Ding, Y., Stoeckel, D., Minard-Smith, A., Andersen, G., Dubinsky, D., Atlas, R., and Gardinali,P., (2016) "Biodegradation of dispersed Macondo crude oil by indigenous Gulf of Mexico microbial communities", Science of the Total Environment, 557-558: 453-468.

Wang Y., Li Y., Liu G., Wang D., Jiang G., and Cai Y. (2015). Elemental Mercury in Natural Waters: Occurrence and Determination of Particulate Hg(0). Environ. Sci. Technol., 49, 9742–9749.

Weiss-Errico M.J., Ghiviriga I., O’Shea K.E. (2017). 19F NMR Characterization of the Encapsulation of Emerging Perfluoroethercarboxylic Acids by Cyclodextrins, The Journal of Physical Chemistry B 121 (35), 8359-8366.

Weiss-Errico, M., Berry, J. P. and O’Shea, K. (2017) Beta-cyclodextrin attenuates perfluorooactanoic acid toxicity in the zebrafish embryo model. Toxics, 5: 31.

Yang M., Matulis S., Boise L.H., McGoron A.J. and Cai Y. (2017). Potential Application of SERS for Arsenic Speciation in Biological Matrices. Analytical and Bioanalytical Chemistry. DOI 10.1007/s00216-017-0434-3.

Zhao C., Peller J.R., Mezyk S.P., Kamat P.V., O’Shea K.E. (2017). Oxidative remediation of 4-methylcyclohexanemethanol (MCHM) and propylene glycol phenyl ether (PPh). Evidence of contaminant repair reaction pathways, Physical Chemistry Chemical Physics 19 (20), 13324-13332.

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For additional information, please contact:

Dr. John Berry
Graduate Program Director – Environmental Chemistry Track
Department of Chemistry and Biochemistry – BBC Campus
3000 NE 151 Str., Marine Sciences Building 354
North Miami, Fl 33181
berryj@fiu.edu Phone: 305-919-4569