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Donald Cotter's scientific research focuses on the mechanism of transmetalation, specifically the processes by which organic groups are transferred from the main-group metal tin to the transition metal palladium.

Cotter has received grants for his research in transmetalation from the Petroleum Research Fund, as well as funding from the Henry and Camille Dreyfus Special Grant Program in the chemical sciences to support updating the computer interface and operating system of one of the chemistry department's NMR spectrometers and to network the device making NMR data available from any Ethernet port on campus.

In a 1995 edition of Science, Cotter is featured in an article discussing why more and more young researchers are attracted to smaller liberal arts institutions as opposed to research universities. In "Scientists Enjoy Life in the Not-So-Fast Lanes," Cotter discusses the freedom that working at Mount Holyoke gives him to develop new courses and to pursue research and teaching.

Recently, Cotter has turned his scholarly attentions to the study the history of chemistry, focusing on the American chemical community between 1890 and 1920. He has reported his findings at meetings of the Chemical Heritage Foundation; the International History, Philosophy, and Science Teaching Group; and the Society for the Social Study of Science. In 2004, Cotter will add a course in history of chemistry to the department's offerings.

Cotter is former member of the team-taught Unity of Science course, an interdisciplinary, introductory-level science course at Mount Holyoke that emphasizes the methods and relevance of scientific inquiry. He is the author of numerous scholarly papers and presentations, many of them coauthored by Mount Holyoke students.