These papers include correspondence from over 180 individuals, lecture notes and essays on mathematics, astronomy, and electricity, and his diaries from journeys through Germany (1798) and Switzerland (1802).

The collection consists of diaries, 1890-1938, containing brief records of professional work and family events (49 vols.); also autobiography entitled "Memories for my boys," 1930 (B D713m), referring to his childhood and to his professional career and mentioning Franz Boas, William Comstock, Livingston Farrand, William W. Keen, S. Weir Mitchell, Elihu Root, and W. T. Sedgewick and also APS, University of Chicago, Johns Hopkins University, Yale University, and Wistar Institute (1 vol.); also a few miscellaneous papers, 1869-1932, chiefly letters to and from members of his family, and also Poultney Bigelow, Simon Henry Gage, and W. B. Van Ingen; two essays ("The Days of Man" and "A Venetian Night"): genealogical data; verses dedicated to his wife; extracts of letters to supplement his diaries.

These papers include diaries (1777-1782), expense books (1794-1804), notebooks, a commonplace book, drafts of essays, excerpts from minutes of Friends' Monthly Meeting, Tortola (1741-1761), newspaper clippings, sketches, and correspondence. Also included are letters and papers of Mrs. Thornton.