Rich Apodaca posted the definitive version of the ACS position on the NIH mandate:
ACS and the NIH Public Access Policy: Clarification at Last (permalink)An alert Depth-First reader pointed me to the new ACS policy for authors receiving NIH funding. The details are contained in a document outlining two ways authors can choose to comply with the new law requiring recipients of NIH funds to deposit a copy of their peer-reviewed manuscripts into PubMed Central. The choices are:
- Publish the article under ACS Author Choice by paying a fee. The ACS will then automatically deposit the article on behalf of the author. 
- Publish the article using the standard procedure, but with the ACS granting authors the right (and responsibility) to deposit their manuscripts in compliance with the NIH Public Access Policy.
Under Option 2, copyright remains with the ACS – authors are simply granted an exception to enable them to comply with federal law. This means, among other things, that ACS retains the right to prevent third parties (including authors themselves) from creating derivative works of deposited manuscripts, and from redistributing them.
 ACS Author Choice states:
The ACS AuthorChoice option establishes a fee-based mechanism for individual authors or their research funding agencies to sponsor the open availability of their articles on the Web at the time of online publication. Under this policy, the ACS as copyright holder will enable unrestricted Web access to a contributing author’s publication from the Society’s website, in exchange for a fixed payment from the sponsoring author. ACS AuthorChoice also enables such authors to post electronic copies of published articles on their own personal websites and institutional repositories for non-commercial scholarly purposes.
PMR: My understanding is that the Open choice payment (which I believe for non-members is of the order of 2000-3000 USD) gives relatively few rights over option (2):
- it allows authors to have a copy of the manuscript on their own website and IR (but not to allow re-use)
- it gives the article full visibility on the ACS website (i.e. in context of the TOC) and – as I read it – to be posted in PMC by the ACS
Whether this is worth thousands of dollars authors can now decide.
It would be interesting to see (though probably never revealed) whether exposure on the ACS site or on PMC (which will become the primary site for research bioscientists to visit) gets most traffic.
Remember that Entrez and Pubmed have some great indexing tools and these will continue to increase (I hope to post more on my personal involvement here later). Whereas ACS has the power of Chemical Abstracts to search its material. CAS has many years’ of experience but has a large subscription (many many thousands of dollars per year). Pubmed and Pubchem is free.
It will be interesting to see the comparative use of these sites over the next few years. A reasonably fair test of Open Access.
Unless of course the publishers forbid the indexing of chemistry in Pubmed Central.