Date of Award

Summer 2011

Document Type


Degree Name

Doctor of Philosophy (PhD)


Chemistry & Biochemistry

Committee Director

Patrick G. Hatcher

Committee Member

Andrew S. Gordon

Committee Member

Thomas Isenhour

Committee Member

Jingdong Mao


Past studies have found much of nonliving sedimentary/aqueous nitrogen-containing organic matter (NCOM) is composed of amides, assumed to be peptides/proteins. Their lability calls into question their survival, and several hypotheses have been suggested to explain this. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and nuclear magnetic resonance (NMR) spectroscopy I investigated the molecular amide composition in sedimentary/aqueous systems while reassessing their preservation and formation routes.

Development of a suitable methodology is essential for successful NCOM study due to electrospray ionisation source requirements: sediment samples need to be rendered into solution. Based on NMR and FT-ICR-MS analysis, I determined that pyridine extraction was optimal. Additionally, I developed a graphical method to visualise the important components of NCOM finding that N/H versus O/C was most suitable.

Extracting with pyridine, I investigated molecular forms of NCOM in a lacustrine sediment (Mangrove Lake, Bermuda, MLB). With 2D NMR and FT-ICR-MS, I identified alkyl (di)amides, and confirmed their structure by gas chromatography MS. I suggest a formation pathway through amidation of naturally occurring glyceride esters for these newly discovered compounds. FT-ICR-MS analysis of the Lake and pore water NCOM show alkyl (di)amides prevalence throughout the Lake, and the increasing ammonia contents with depth correlates with increasing alkyl (di)amide contents downcore supporting an amidation process.

Peptide preservation hypotheses were additionally examined by synthesising designer peptides, and monitoring their fate in two natural waters, MLB and Elizabeth River, VA. Results indicate peptide length, not chemical structure, is important for determining removal rates. Additionally, removal rates are significantly affected by location, probably because of micro-organism community differences and/or adduction to naturally present Michael receptors (e.g., quinones). The adduction of a quinone to designer peptides was found to have no effect on peptide removal rates. New compounds are formed from peptide-adducts seem to incorporate parts of the peptide as a stable product demonstrating a new route for partial peptide preservation in natural waters.

Overall, advanced analytical techniques have led to new insights into amide N composition, providing further evidence of likely formation and preservation pathways in natural systems.


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