Molecules is published by a registered non-profit organization in Switzerland called Molecular Diversity Preservation International, or MDPI, founded by Dr. Shu-Kun Lin, a physical organic chemist. The first issue of the journal came out in 1996. At the time there were a lot of chemistry publications, but an awful lot of data was not being published. Journals were publishing short communications with very little detail about how to actually do the chemistry—there weren’t a lot of venues for full papers with a lot of experimental details.

“The whole advent of open-access publication and the Internet allowed for the proliferation of electronic journals. Molecules is perhaps unique in that it is one of the first and survived so long.”

Dr. Lin was concerned that all this information was being lost, so he decided to start an online journal, with quick publication and full experimental details. Dr. Lin also set up a repository for authors to deposit samples of chemicals, which could be shared by the scientific community. If anybody saw something in a paper and wanted to test it or do some chemistry with it, they could either contact the authors directly or got to MDPI and obtain a sample for scientific use.

I think it’s both. One of the banes of publication, at least in chemistry, is having something interesting to report but not having the space to publish the details. Then other people try to reproduce it and they’re not able to, because they don’t have all the information.

One, the volume of papers over the past few years has steadily increased. We have made an effort to do this, sending out invitations to authors to submit papers to the journal, making it known that it publishes fast—typically within a few weeks of submission, if the papers don’t require too many corrections. Over the past few years, we’ve published more than a thousand pages per year.

One reason we can get these papers is that publication is relatively inexpensive compared with other journals with the same publication model—meaning free for readers. Authors or institutions pay for publications. Molecules charges $500 U.S., which is far less than comparable journals following the same models. In other journals, the publication costs tend to run in the $2000 to $3000 range. So $500 is affordable to a wider range of scientists.

We assure that all papers are entirely peer reviewed. They go out to three or more reviewers, who read the papers, suggest corrections, make comments, and/or decide that the paper is not worth publishing.

Well, everything is done electronically. And then the authors themselves are asked to suggest possible reviewers who might be familiar with that area of chemistry. Although the editors don’t always use the suggestions—we don’t want friends down the hallway reviewing the papers. So authors are asked for referees, typically not associated with the same institutions.

We also have a large database of potential referees in all areas of chemistry. If we don’t like the ones the author suggests, we know other referees to consult. Then these referees are sent an electronic copy of the paper along with a form to fill out for comments. They’re also asked if they can reply within a week or so, and if they can’t, then to let us know and perhaps to suggest an alternative reviewer. We get a fairly good response to this kind of request.

The main one has been the decision to go entirely to open access with the author or institution pay model. Over the years, we tried a variety of models. We tried a subscription base, for instance, that would financially support the journal, but that didn’t work terribly well. We had mixed models, in which papers whose authors did not want to pay fees could either contribute samples to the repository or their articles could be subscription-only access—pay per view. Those would be password-protected and so nobody could read them without paying for them. But we found that with so much free literature out there, that’s a hard sell. So over the past couple of years, we’ve moved to be completely free to readers, with all payments coming from authors or institutions. Although because we get submissions often from developing countries, where $500 is a lot of money, in many instances the fees are waived.

We publish a lot of special issues. We recruit well-known scientists in particular fields to put together an entire issue. In those issues, we waive publication fees for deserving papers, and those are the issues that tend to get the high-impact papers.

It varies—maybe three or four. Right now, we have calls out for four such special issues in 2007. One is called "Pro-drugs: from design to application." Pro-drugs are substances that turn into drugs in the body. Another one is on bile acids. Another is on phenolics, which are substances found in plants that are valuable in making coatings and molded products.

We also publish conference proceedings. We publish the proceedings from a biannual conference in Australia on synthesis. And we publish the proceedings from ECSOC, which is the Electronic Conference on Synthetic Organic Chemistry, which was founded and is sponsored by MDPI, and is in its tenth edition. In September of each year, the authors submit papers to an open forum on the Internet —it’s like a blog. They can send in comments and read the papers. These papers tend to be short communications. After the conference we ask authors to add experimental details to the papers, and then we publish them in a special issue of the journal.

It made a big difference in the beginning. It was quite popular. But 9/11 changed things and made it quite difficult. Ten years ago, postal authorities didn’t look that askance at little envelopes full of white powders moving around between countries. Now there are all kinds of restrictions on what can be shipped, all kinds of documentation needed, and it makes it very hard to ship these samples around the world. Also the storage of samples itself has become an issue. In that sense, the repository was a victim of its own initial success.

Now we try to minimize it. We will accept a limited amount of samples, but they have to be very carefully identified and shipped and there’s not that many people willing to go through the trouble. The repository still exists, though. The database is still online and we still get requests for samples. More and more, though, we just put a line in the article saying that readers can contact the authors directly for samples or that samples are no longer available.

Not in the field itself so much as in electronic publishing as a whole. The whole advent of open-access publication and the Internet allowed for the proliferation of electronic journals. Molecules is perhaps unique in that it is one of the first and survived so long. In fact, if I can digress a little bit, after volume one or two, one of the major scientific publishers offered to take over publication of Molecules and publish it as a traditional journal as well as an electronic one. But there was falling out over editorial policy between Dr. Lin and this publisher. As a result, this publisher started its own journal called Molecules Online and for a while there were two journals with almost the same name. The other one (Molecules Online) vanished after a year or so; there weren’t enough papers submitted, despite it having a big-name editorial board and the backing of a large publisher. Molecules, however, survived and has been slowly expanding over the years.

I can certainly see it continuing to expand just in the sheer number of papers we publish. Looking at the number of special issues we have planned and the response we’re getting, we could probably even double our volume for 2007 – surpassing 2,000 pages. We’re also beginning to attract bigger names. We have had some papers from Nobel Laureates for the first time in the past year. Those papers will attract interest, and attract other significant papers—it snowballs. As long as we can continue to maintain a fast turn-around service, the journal will continue to prosper.

The proliferation of electronic journals. It’s hard to stand out in the crowd. It also dilutes the number of good papers available for publication. This isn’t as much of a problem for the big-name journals, but for the newer journals like us, it makes it a struggle to keep up the quality of the publications. In this sense, the main challenge for us is to maintain the quality of the peer-review process. We had a rejection rate of more than 2/3 in 2006: two out of three papers submitted were rejected.

I think we fill a unique niche between the journals that publish short communications and those that publish full papers but have an excessive lead time. By combining a very fast turnaround with a lower cost than most commercial operations, we hope to be an attractive venue for scientists to reveal their results.