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When we submitted our last paper for publication, we also posted the manuscript on the pre-print server arXiv.  This has several advantages:

(1) It makes the work freely accessible to everyone while the paper is being reviewed
(2) It makes the work freely accessible to everyone after its been published
(3) It establishes priority

However, journals will not accept manuscripts that have already been published.  Will depositing a paper on a preprint server like arXiv.org or Nature Precedings prevent me from submitting my paper to a journal?

That depends on the journal, and you can check using this site call SHERPA/RoMEO

Our paper went PLoS ONE.  Not surprisingly, SHERPA/RoMEO tells you that PLoS ONE is a "green journal" that allows you to pretty much to anything with your manuscript before and after it is published.  This makes sense since PLoS ONE is an open access journal.

Journal of Physical Chemistry A and Journal of Chemical Theory and Computations
But what if the paper doesn't get  into PLoS ONE for some reason?  In my pre-OA days I probably would have sent this paper to JPC-A or JCTC.  SHERPA/RoMEO tells me both are "white journals" meaning  I have to get permission from the publisher first, before I submit my pre-print.

I wasn't sure exactly what that meant so I wrote the managing editor of both journals, which happens to be the same person, whether I could submit to JPC-A and JCTC if I had deposited my manuscript in arXiv of Nature Precedings.  The answer is "yes" for JPC-A (and B, C, and Letters) in both cases, and in the case of JCTC: "yes" for arXiv and "undecided" for Nature Precedings.

In all cases you have to state in the cover letter where you have posted your preprint.

Physical Chemistry Chemical Physics
SHERPA/RoMEO lists PCCP as a "blue journal" meaning pre-print deposition is not allowed.  However, the RSC License to Publish clearly states that deposition in arxiv is OK.  So I contacted them.  Deposition in ArXiv is allowed, but deposition in Nature Precedings is not!

Lessons Learned
(1) If you want to deposit your pre-print prior to submission, check SHERPA/RoMEO.  If in doubt, check with the journal.  But be patient, getting an answer can take a while.
(2) Even non-profit society journals (and their editors!) have their own interests in mind, not yours or science in general.
(3) Rational thinking doesn't seem to apply here in general.  Why would arXiv be OK, but not Nature Precedings?

This work is licensed under a Creative Commons Attribution 3.0 Unported License.

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