Today we're making a little step in the right direction. The International Journal of Quantum Chemistry (QUA)  is pleased to announce a collaboration between Wiley, Atypon, and Authorea which resulted in the publication of the first set of research articles featuring fully computational and interactive visualizations.
The idea of an innovative 21st century scholarly article is not new. eLife, for example, has pionereed blah blah through a pilot. What's new is that these newly published articles are real scientific papers, not just test articles.