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The Nature, Origin and Preservation of Amide Organic Nitrogen in Organic Matter

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The Nature, Origin and Preservation of Amide Organic Nitrogen in Organic Matter Old Dominion University ODU Digital Commons Chemistry & Biochemistry Theses & Dissertations Chemistry & Biochemistry Summer 2011 The Nature, Origin and Preservation of Amide Organic Nitrogen in Organic Matter Georgina Anne McKee Old Dominion University Follow this and additional works at: https://digitalcommons.odu.edu/chemistry_etds Part of the Analytical Chemistry Commons, Geochemistry Commons, and the Organic Chemistry Commons Recommended Citation McKee, Georgina A.. "The Nature, Origin and Preservation of Amide Organic Nitrogen in Organic Matter" (2011). Doctor of Philosophy (PhD), Dissertation, Chemistry & Biochemistry, Old Dominion University, DOI: 10.25777/ng41-5t14 https://digitalcommons.odu.edu/chemistry_etds/39 This Dissertation is brought to you for free and open access by the Chemistry & Biochemistry at ODU Digital Commons. It has been accepted for inclusion in Chemistry & Biochemistry Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. THE NATURE, ORIGIN AND PRESERVATION OF AMIDE ORGANIC NITROGEN IN ORGANIC MATTER by Georgina Anne McKee M. Chem. July 2006, University of Sheffield, United Kingdom A Dissertation Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY CHEMISTRY OLD DOMINION UNIVERSITY August 2011 Approved by: Patrick G. Hatcher (Director) Andrew S. Gordon (Member) Thomas Isenhour (Member) ABSTRACT THE NATURE, ORIGIN AND PRESERVATION OF AMIDE ORGANIC NITROGEN IN ORGANIC MATTER Georgina Anne McKee Old Dominion University, 2011 Director: Dr. Patrick G. Hatcher 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. IV This dissertation is dedicated to my family. V ACKNOWLEDGMENTS The completion of this dissertation was only possible by the guidance and support of many people. I would firstly like to thank my advisor, Dr. Hatcher, who suggested I embark upon the journey of completing a PhD, and for being there for me every step of the way. His patient teaching of all the skills I have learnt as being a graduate student in his group will immensely assist my future research. I am especially grateful for the opportunity to learn and become adept at a wide variety of techniques not available to many graduate students. In addition, his careful and thoughtful critic of my writing has much improved my style. The high level of funding I received throughout my degree, enabled me to attend many conferences, teaching me about effective presentation skills and allowing me to network with my peers. He has provided me with an amazing start to my career, and I will always be grateful. I would also like to thank my committee members, Dr. Isenhour, Dr. Gordon and Dr. Mao for their continued advice throughout my degree, and for dedicating many hours to the improvement of this document. Completion of my degree would not have been possible without the support of my research group. I would like to thank each of them for their advice through the years that have enabled me to pursue my degree. I would like to thank in particular, Dr. Rachel Sleighter who has spent many hours answering my questions and assisting in all aspects of my research. Her friendly face when I first arrived at ODU made me feel welcome and at home immediately in my new state of Virginia. I would also like to Dr. Zhanfei Liu who worked with me to learn the intricacies of peptide synthesis from scratch and advised me on many topics, both related to my research and on my personal life. Another individual who has been an incredible help for my research is Megan Kobiela, whose vi outstanding organisation and planning skills made much of the syntheses and analyses of the compounds used in this dissertation possible. The amazing dynamic of the Hatcher group has made me feel so grateful for coming to ODU and consequently, I am able to call so many my friends. I will never forget the annual 'purple elephant' parties, the Larchmont gatherings, intramural football and the annual writing retreats. My time at ODU truly will be remembered with fond and happy memories. There are many additional people I would like to thank who have made my research possible with their advice and assistance including Dr. Elodie Salmon, and Dr. Hussain Abdulla. I particularly thank Susan Hatcher of the College of Sciences major instrument cluster (COSMIC) whose patient answering of my many questions and assistance with all aspects of FT-ICR-MS analysis enabled me to be successful in my research. I would also like to thank Mahasilu Amunugama for his assistance with FT- ICR-MS and Dr. Junyan Zhong for teaching me how to analyse my samples and answering my questions related to nuclear magnetic resonance (NMR) spectroscopy. Particular thanks go to Dr. Aron Stubbins and Joshua Marsh for accompanying me on the field trip to Bermuda, and their help in collecting my samples. I would also like to thank Dr. Mopper and Dr. Mullholland for the occasional use of the instruments in their labs. In addition, I would like to thank many individuals at the Bermuda Institute of Ocean Sciences (BIOS), who greatly assisted in all aspects of collecting my samples in Bermuda in particular Jane Burrows, Steven Bell, and Bruce Williams. The use of one of their labs, and many pieces of their equipment allowed me to collect and process my samples within my allotted time efficiently. I would also like to acknowledge the R/V HSBC Atlantic Explorer for use of their freezer to transport some of my samples back to ODU. Many people of USDA assisted in obtaining the appropriate permits that allowed me to vii transport my samples back to ODU. In addition, many companies that I worked with in organising the trip to Bermuda provided the necessary equipment I needed and I am grateful for their services. I would also like to thank the Dean of the College of Sciences for providing much of the funding for the Bermuda trip. Funding for my research was also provided by the Frank Batten Endowment Fund and the National Science Foundation Grant number OCE-0726759. Lastly I would like to thank my family for providing the support I needed to complete my degree. Their encouragement during the many difficult times I encountered, gave me the strength I needed to continue. My sister, Sarah, in particular has always been my inspiration to be a success in all aspects of my life with her amazing examples of courage when times are challenging. I have no doubt that my husband, Steven, has made it possible for me to become the person I am today by his continuous support. His ability to still appear enthusiastic about my research on a daily basis even if he has heard it thousands of times before makes me appreciate how important he is for achieving my life goals. He is an unwavering supporter of all my work even if it means that he has to make sacrifices for me. I am truly lucky to have such a fantastic support network that I can rely on in all circumstances. NOMENCLATURE % Ce Percent of C in the extract % Cr Percent of C in the residue % Cs Percent of C in the original sediment % Ne Percent
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