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Charles Macdonald was born in Aberdeen in 1828 to Elizabeth and John Macdonald, a builder. He graduated from the University of Aberdeen in 1850, where he distinguished himself as the recipient of the Hutton Prize for the arts curriculum. After receiving his M.A., he studied divinity and became a licentiate in the Church of Scotland, but turned his energies to teaching. Macdonald was at the Aberdeen Grammar School in 1862 when he was selected by the Church of Scotland in Nova Scotia as its nominee for the chair of mathematics at the newly re-opened Dalhousie College in Halifax.
Macdonald was a gifted and beloved teacher as well as a popular public speaker, giving lectures on such whimsical topics as “On Fun” as well as more contentious addresses on evolution and education. In 1882 he married Susan Morrow, who died after childbirth one year later. Macdonald did not remarry, raising his son as a single father.
Charles Macdonald passed away in 1901 at the age of seventy-two after contracting pneumonia. In his will he left $2,000 to buy books for the university library, which prompted a movement among alumni to build a proper library in his honour. The Macdonald Library was built in 1914 and served as the university library until the 1970s.