Yes, actually. The answer that comes to mind is Gilbert and the Chemystical Island - a game I spent a lot of hours with as a kid together with my parents. It's basically a Myst-like point-and-click adventure game with the usual trappings of "combine items and drag them onto problems on screen to solve", but where every problem has a solution rooted in science and chemistry intended to be a teaching aid.

I had a great time as a kid making batteries out of lemons and nails and learning about paper being made from trees and many more little discoveries.