His research interests are devoted to the synthesis of complex natural products, particularly those of the terpene, polyphenol, and alkaloid classes, seeking to identify new strategies and tactics of broad significance. Particular emphasis has been placed on dimeric and higher-order natural products of these classes. In addition, Scott and his group have developed a unique group of halogenating reagents that are used in both academia and industry, with one sold by Sigma-Aldrich to create natural and designed compounds.

Overall, Scott has trained more than 70 scientists in his laboratory from the high school through postdoctoral levels, and has delivered more than 175 lectures to date worldwide. He is dedicated to chemical education in its broadest sense as denoted by a Cottrell Scholar Award from the Research Corporation for Science Advancement (2009). Scott is also helping to shape the face of undergraduate education worldwide as co-author (with T. W. G. Solomons and C. B. Fryhle) of the 11th and 12th editions of Organic Chemistry (Wiley). Scott has also edited a set of volumes on domino chemistry that was just published by Thieme, and finally, Scott has also co-authored, with P. J. Beuning and D. Z. Besson, a book on teaching and mentoring in science entitled Teach Better, Save Time, and Have More Fun.