The Directory of Open Access Journals (DOAJ) currently lists 2420 Open Access scholarly journals. Of these, 52 currently fall under the category of chemistry. Although the organic chemistry subcategory only currently lists three journals, the general chemistry category actually contains several journals containing organic chemistry content, such as the Bulletin of the Korean Chemical Society, Chemical and Pharmaceutical Bulletin, and Molbank.
Clearly, the chemistry journals included in DOAJ's listings would not be considered to be in "the mainstream" by experts in the field. And that's exactly the point. Innovation always happens at the margins.
As Clayton Christensen puts it in his landmark book, The Innovator's Dilemma:
As we shall see, the list of leading companies that failed when confronted with disruptive changes in technology and market structure is a long one. … One theme common to all of these failures, however, is that the decisions that led to failure were made when the leaders in question were widely regarded as among the best companies in the world.
Replacing the word "company" with "scientific journal" leads to an important hypothesis about the future of scientific publishing.
And on the subject of disruptive innovation itself, Christensen writes:
Occasionally, however, disruptive technologies emerge: innovations that result in worse product performance, at least in the near-term. Ironically, in each of the instances studied in this book, it was disruptive technologies that precipitated the leading firms' failure.
It seems very unlikely that scientific publishing operates according to a different set of rules than any other technology-driven business. The coming wave of disruptive innovation will be dramatic, and the outcome completely predictable.