B.Sc. (Hons), PhD

Instructor, Chemistry
Faculty of Arts and Sciences
School of STEM

604.986.1911 ext. 2506
Fir Building, room FR492


PhD, Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry, University of Waterloo, 2003.

B.Sc. (Honours), Biochemistry, Dalhousie University, 1998.


Mark Vaughan's (PhD, University of Waterloo, 2003) scientific interests lie in the domain where chemistry meets biology. His particular focus is on investigating and altering the inner workings of enzymes, the remarkable protein machines that catalyze virtually all of the chemical reactions of life.

Originally from Nova Scotia, Vaughan completed his undergraduate studies in biochemistry at Dalhousie University. He then moved to the University of Waterloo for his doctoral degree in chemistry, working on the synthesis of modified forms of amino acids for use in protein engineering. During his post-doctoral work at the University of British Columbia, he developed an enzymatic system for the synthesis of glycosphingolipids, a class of molecules that have therapeutic potential in the treatment of Alzheimer's disease, Parkinson's disease and other neurodegenerative disorders.

Vaughan joined the Department of Chemistry at Capilano University in 2007. He accepted a position at Quest University Canada in 2014 and worked there for three years before returning to Capilano U in 2017.

In addition to being a scientist, Vaughan is also a professional musician and has performed across Canada, the United States and Europe. Some of the more unusual venues in which he has performed include a lighthouse on the northernmost tip of mainland Scotland, a centuries-old barn in Wales, a bluegrass festival in Switzerland and on a train travelling from coast to coast across Canada. He has also composed musical scores for several animated short films.

As a scientist, I take joy in the process of discovery, and I try to incorporate this sense of discovery into my classes. My focus is on a first-principles approach to teaching, developing the fundamental concepts from which we can extrapolate broader ideas, rather than memorizing factual information. My approach is driven by problem-solving and scientific inquiry.

In recent years, I have worked to incorporate increasingly dynamic visual models to illustrate the central concepts of chemistry. As the entities which comprise chemistry (i.e., atoms and molecules) are inherently invisible to us, I use molecular modelling software to provide a visual sense of the behaviour of chemical species.

As a biochemist, I am interested in the intersections between biology and chemistry. My primary focus is on the study of enzymes, the remarkably proficient biological catalysts responsible for carrying out virtually all of the chemical reactions of life. Much of my work has focused on the manipulation of enzyme structure to confer new properties, such as the ability to catalyze desirable chemical reactions. I am also interested in abiogenesis, the process by which life on Earth originated from non-living chemical processes.

More recently, I have been focused on chemical education research, particularly in the areas of molecular modelling and discovery-based learning.

Refereed Journal Publications

Vaughan, M. D., Su, Z., Daub. E., and Honek, J. F. Intriguing cellular processing of a fluorinated amino acid during protein biosynthesis inEscherichia coli, Organic and Biomolecular Chemistry, 14, 8942-8946, 2016.

Caines, M. E., Vaughan, M. D., Tarling, C. A., Hancock, S. M., Warren, R. A., Withers, S. G., and Strynadka, N. C. Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms, Journal of Biological Chemistry, 282, 14300-14308, 2007.

Vaughan, M. D., Robertson, V. J., and Honek, J. F. Experimental and theoretical studies on inversion dynamics of dichloro(L-difluoromethionine-N,S)platinum(II) and dichloro(L-trifluoromethionine-N,S)platinum(II) complexes, Journal of Fluorine Chemistry, 128, 65-70, 2007.

Garner, D. K., Vaughan, M. D., Hwang, H. J., Savelieff, M. G., Honek, J. F., and Lu, Y. Examining reduction potential tuning by the axial methionine in the blue copper centre with unnatural amino acids, Journal of the American Chemical Society, 128, 15608-15617, 2006.

Hancock, S. M.*, Vaughan, M. D.*, and Withers, S. G. Engineering of glycosidases and glycosyl transferases, Current Opinion in Chemical Biology, 10, 509-519, 2006. (* co-first authors)

Vaughan, M. D., Johnson, K., DeFrees, S., Tang, X., Warren, R. A. J., and Withers, S. G. Glycosynthase-mediated synthesis of glycosphingolipids, Journal of the American Chemical Society, 128, 6300-6301, 2006.

Vaughan, M. D., Sampson, P. B., Daub, E., and Honek, J. F. Investigation of Bioisosteric Effects on the Interaction of Substrates/Inhibitors with the Methionyl-tRNA Synthetase from Escherichia coli, Medicinal Chemistry, 1, 227-237, 2005.

Crepin, T., Schmitt, E., Mechulam, Y.., Sampson, P. B., Vaughan, M. D., Honek, J. F., and Blanquet, S. Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase, Journal of Molecular Biology, 332, 59-72, 2003.

Salopek-Sondi, B., Vaughan, M. D., Skeels, M. C., Honek, J. F., and Luck, L. A. 19F NMR Studies of the Leucine-Isoleucine-Valine Binding Protein: Evidence That a Closed Conformation Exists in Solution, Journal of Biomolecular Structure and Dynamics, 21, 235-246, 2003.

Vaughan, M. D., Sampson, P. B., and Honek, J. F. Methionine in and out of proteins: Targets for drug design, Current Medicinal Chemistry, 9, 385-409, 2002.

Vaughan, M. D., Cleve, P., Robinson, V., Duewel, H. S., and Honek, J. F. Difluoromethionine as a novel 19F NMR structural probe for internal amino acid packing in proteins, Journal of the American Chemical Society, 121, 8475-8478, 1999.

Bearne, S. L., St-Maurice, M., and Vaughan, M. D. An assay for mandelate racemase using high performance liquid chromatography, Analytical Biochemistry, 269, 332-336, 1999.


Johnson, K. F., DeFrees, S., Withers, S. G., and Vaughan, M. D. Mutant endoglycoceramidases with enhanced synthetic activity. PCT Int. Appl. WO 2005118798, 125 pp.


Supplemental materials for Organic Chemistry: Mechanistic Patterns, 1st Ed. by Igilvie et al. Nelson Higher Education, 2018.

Hatnean, G., and Vaughan, M. Solutions Manual and Answer Key for Chemistry: Human Activity, Chemical Reactivity, 2nd Ed. Mahaffy et al. Nelson Higher Education, 2014.

Solutions Manual for Newfoundland High School Chemistry text, Nelson Higher Education, to be published in 2019.

Notice of Special Recognition, Capilano University, 2012 and 2014.