For a brief time during and after the German reunification (1990–1991) he was the deputy technical director (catalysis and sorption) for BIOSYM Technologies in San Diego, California (now BIOVIA).

His computational studies have allowed for a better understanding of the structures and activities of some catalysts such as zeolites, specifically their acid sites,[7] as well as the interpretation of solid state NMR spectra of nucleus Si-29, and quadrupolar nuclei such as Na-23,[8] Al-27 and O-17.

On 30 December 1998, he married Angela Merkel (herself a doctor of physics who had once worked in quantum chemistry research), who later became the chairwoman of the Christian Democratic Union.

Due to the fact that Merkel became the first female chancellor of Germany on 22 November 2005, Sauer also assumed a role in diplomatic protocol as third-highest ranking spouse.

Even during his wife's election in the Bundestag, her inauguration, and later her taking the oath of office, Sauer was not present but reportedly briefly followed the event on TV from his university chemistry lab.