Once he turned 10 his family and he moved back to Japan, where he would attend Yamate primary for a year before transferring over to the junior division of Konan High school.

[2] Nakanishi was a founding member and one of the six directors of research at the International Centre of Insect Physiology and Ecology in Kenya, the first director of the nonprofit Suntory Institute for Bioorganic Research (Sunbor), Osaka, and he assisted the Brazilian government to set up a center of excellence in the Amazons, the Institute of Medicinal and Ecological Chemistry with its headquarters in São Paulo.

Nakanishi's research encompassed isolation, structural and bioorganic studies of bioactive compounds, retinal proteins, interaction between ligands and neuroreceptors, development of various spectroscopic methods, especially circular dichroic spectroscopy.

These include ginkgolides from the ancient ginkgo tree, first insect molting hormones from plants, new nucleic acid bases, insect antifeedants, antibiotics, first meiosis inducing substance from starfish, crustacean molt inhibitors, shark repellents from fish, tunicate blood pigments, brevetoxins from red-tide dinoflagellates, philanthotoxin (glutamate and nicotinic acetylcholine receptor antagonist) from a wasp, and the human eye pigment involved in macular degeneration.

It also established the structure and biosynthesis of the fluorescent pigment A2E that leads to the incurable eye disease age-related macular degeneration (AMD) and its involvement in apoptosis.

Nakanishi's spectroscopic contributions included the first applications of the NMR nuclear Overhauser effect in structure determination during the ginkgolide studies (1967), and in particular development of the exciton coupled circular dichroic method (1969), a non-empirical sub-microgram scale technique for determining various aspects of molecular chirality of organic molecules in solution, an extremely versatile technique applicable to compounds ranging from small molecules to various types of ligand/receptor complexes.

[5] When Nakanishi appeared at a reception where he was scheduled to receive an award or to present a scientific paper, the audience could most generally expect an added spectacular surprise treat, as he was also an accomplished, amateur magician.