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 ( 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 ( 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 ( 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. P. Gardinali ( 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 ( 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 ( 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 ( 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.

Recent Representative Publications  

1. Aceña J., S. Pérez, N. Heuett, P. Gardinali, J.L. Abad, P. Eichhorn, D. Barceló. Structure elucidation of phototransformation products of unapproved analogs of the erectile dysfunction drug sildenafil in artificial freshwater with UPLC-Q Exactive-MS. In press Journal of Mass Spectrometry (8/14).

2. Berry, John P., Gibbs, P. D. L., Gantar, M. and Schmale, M. C. (2007). Identification of developmental toxins from marine and freshwater algae using the zebrafish embryo as a model of vertebrate development. Comp. Biochem. Physiol. C Toxicol. Pharmacol., 145 (1): 61-72.

3. Berry, J.P., Gantar, M., Perez, M. H., Berry, G. and Noriega, F. G. (2008). Cyanobacterial Toxins as Allelochemicals with Potential Applications as Algaecides, Herbicides and Insecticides. Mar. Drugs, 6: 117-146.

4. Berry, J. P., Lee, E., Walton, K., Wilson, A. and Bernal-Brooks, F. (2011) Bioaccumulation of microcystins by fish associated with a persistent cyanobacterial bloom in Lago de Patzcuaro (Michoacan, Mexico). Environ. Toxicol. Chem., 30: 1621-1628.

5. Cawley K., Campbell J., Zwilling M., and Jaffé R. (2014). Evaluation of Forest Disturbance Legacy Effects on Dissolved Organic Matter Characteristics in Streams at the Hubbard Brook Experimental Forest, New Hampshire. Aquatic Sciences. DOI: 10.1007/s00027-014-0358-3.

6. Chen M., and Jaffé R. (2014). Photo- and bio-reactivity patterns of dissolved organic matter from biomass and soil leachates and surface waters in a subtropical wetland. Water Research. 61: 181-190.

7. Chao Tai, Yanbin Li, Yongguang Yin, Leonard Scinto, Guibin Jiang, and Yong Cai (2014). Methylmercury photodegradation in surface water of the Florida Everglades: Importance of Dissolved Organic Matter-Methylmercury Complexation. Environ. Sci. Technol. 48, 7333-7340.

8. Ding Y., Watanabe A., and Jaffé R. (2014). Dissolved black nitrogen (DBN) in freshwater environments: Source and land to ocean flux assessment. Organic Geochemistry 68, 1-4.

9. Echols, B. S.; Smith, A. J.; Gardinali, P. R.; Rand, G. M. (2014). Acute aquatic toxicity studies of Gulf of Mexico water samples collected following the Deepwater Horizon incident (May 12, 2010 to December 11, 2010). Chemosphere 120, (0), 131-137.

10. He D., Mead R.N., Belicka L., Pisani O., and Jaffé R. (2014). Assessing biomass contributions to particulate organic matter in a subtropical estuary: a biomarker approach. Organic Geochemistry. DOI:10.1016/

11. Heuett N., S. Rani, P. R. Gardinali (2014). Understanding the magnitude of emergent contaminant releases through target screening and metabolite identification using high resolution mass spectrometry: illicit drugs in raw sewage influents. Journal of Hazardous Materials (8/14); In press.

12. Jaffé R., Y. Ding, J. Niggemann, A. Vähätalo, Stubbins A., Spencer R., J. Campbell, and T. Dittmar (2013). Global mobilization of charcoal from soils via dissolution and subsequent riverine transport to the oceans. Science, doi:10.1126/science.

13. Jaja-Chimedza, A., Gantar, M., Gibbs, P.D.L., Schmale, M.C. and Berry, J. P. (2012) Polymethoxy-1-alkenes from Aphanizomenon ovalisporum inhibit vertebrate development in the Zebrafish (Danio rerio) embryo model. Mar. Drugs, 10: 2322-2336

14. Jiang W., Q Cai, W Xu, M Yang, Y Cai, DD Dionysiou, KE O'Shea (2014). Cr (VI) Adsorption and Reduction by Humic Acid Coated on Magnetite. Environmental Science & Technology, in press.

15. Lucy Yehiayan, Szabina Stice, Guangliang Liu, Shannon Matulis, Lawrence H. Boise, and Yong Cai (2014). Dimethylarsinothioyl Glutathione as a Metabolite in Human Multiple Myeloma Cell Lines upon Exposure to Darinaparsin. Chem. Res. Toxicol. 27, 754-764.

16. Mayer, A. M. S., Clifford, J., Aldulescu, M., Frenkel, J., Holland, M. A., Hall, M. L., Glaser, K. B., Berry, J. P. (2011) Cyanobacterial Microcystis aeruginosa lipopolysaccharide elicits release of superoxide anion, thromboxane B2, cytokines, chemokines, and matrix metalloproteinase-9 by rat microglia. Toxicol. Sci., 121: 63-72.

17. O'Shea K.E., Dionysios D. Dionysiou (2012). Advanced Oxidation Processes for Water Treatment. Journal of Physical Chemistry Letters 3(15), 2112-2113.

18. Ramirez Cesar E; Sarah Bellmund; Piero R Gardinali (2014). A simple method for routine monitoring of glyphosate and its main metabolite in surface waters using lyophilization and LC-FLD+MS/MS. Case study: canals with influence on Biscayne National Park. Science of the Total Environment 496, 389-401.

19. Ramirez, C.; Wang, C.; Gardinali, P.(2014). Fully automated trace level determination of parent and alkylated PAHs in environmental waters by online SPE-LC-APPI-MS/MS. Analytical and Bioanalytical Chemistry 406(1), 329-344.

20. Song W., Shuwen Yan, William J. Cooper, Dionysios D. Dionysiou, and Kevin E. O'Shea (2012). Hydroxyl Radical Oxidation of Cylindrospermopsin (Cyanobacterial Toxin) and Its Role in the Photochemical Transformation. Environ. Sci. Technol. 46(22), 12608-12615.

21. Suchy, P. and Berry, J. P. (2012) Detection of total microcystin in fish tissue based on Lemieux oxidation and recovery of 2-methyl-3-methoxy-4-phenylbutanoic acid (MMPB) by solid-phase microextraction/gas chromatography/mass spectrometry (SPME-GC-MS). Int. J. Environ. Anal. Chem., 92 (12): 1443-1456.

22. Timko S., Romera-Castillo C., Jaffé R., and Cooper W. (2014). Photo-reactivity of natural dissolved organic matter from fresh to marine waters in the Florida Everglades, USA. Environmental Sciences: Processes and Impacts 16:866-878.

23. Wang, J., and Gardinali, P. R. (2014). Identification of phase II pharmaceutical metabolites in reclaimed water using high resolution benchtop Orbitrap mass spectrometry. Chemosphere 107(0), 65-73.

24. Yongguang Yin, Yanbin Li, Chao Tai, Yong Cai, and Guibin Jiang (2014). Methyl iodide, a recently registered fumigant, can methylate inorganic mercury species to toxic methyl mercury in natural waters. Nature Communication. 5:4633 doi: 10.1038/ncomms5633.

25. Yuxiang Mao, Yanbin Li, Jennifer Richards, and Yong Cai (2013). Investigating Uptake and Translocation of Mercury Species by Sawgrass (Cladium jamaicense) Using a Stable Isotope Tracer Technique. Environ. Sci. Technol. 47, 9678−9684.

26. Zhao C., M Pelaez, DD Dionysiou, SC Pillai, JA Byrne, KE O'Shea (2014). UV and visible light activated TiO2 photocatalysis of 6-hydroxymethyl uracil, a model compound for the potent cyanotoxin cylindrospermopsin. Catalysis Today 224, 70-76.

For additional information contact:

Dr. Rudolf Jaffé
Graduate Program Director – Environmental Chemistry Track
Department of Chemistry and Biochemistry – BBC Campus
3000 NE 151 Str., Marine Sciences Building 250C
North Miami, Fl 33181 Phone: 305-348.2456