The first major contribution of Woodwards career in the early 1940s was a series of papers describing the application of ultraviolet spectroscopy in the elucidation of the structure of natural products. Woodward collected together a large amount of empirical data, and then devised a series of rules later called the Woodwards rules, which could be applied to finding out the structures of new natural substances, as well as non-natural synthesized molecules. The expedient use of newly developed instrumental techniques was a characteristic Woodward exemplified throughout his career, and it marked a radical change from the extremely tedious and long chemical methods of structural elucidation that had been used until then.
In 1944, with his post doctoral researcher, William von Eggers Doering, Woodward reported the synthesis of the alkaloid quinine, used to treat malaria. Although the synthesis was publicized as a breakthrough in procuring the hard to get medicinal compound from Japanese occupied southeast Asia, in reality it was too long and tedious to adopt on a practical scale. Nevertheless, it was a landmark for chemical synthesis. Woodward's particular insight in this synthesis was to realise that the German chemist Paul Rabe had converted a precursor of quinine called quinotoxine to quinine in 1905. Hence, a synthesis of quinotoxine (which Woodward actually synthesized) would establish a route to synthesizing quinine. When Woodward accomplished this feat, organic synthesis was still largely a matter of trial and error, and nobody thought that such complex structures could actually be constructed. Woodward showed that organic synthesis could be made into a rational science, and that synthesis could be aided by well-established principles of reactivity and structure. This synthesis was the first one in a series of exceedingly complicated and elegant syntheses that he would undertake.