Though not quite germane to this blog (Computational Organic Chemistry), the recent commentary by Rzepa1 does deserve mention. Henry takes on, in a nice breezy style (note the title: The importance of being bonded), the nature of bonding in 1, which initially was thought to be of structure 1a but subsequent x-ray structural analysis suggested the presence of an S-S bond, i.e. 1b. Schleyer has applied NICS analysis to suggest that the compound is bishomoaromatic.2 Henry utilizes AIM and ELF analysis to discuss the nature of the bonding, including the possibility of H…H interaction between the methyl groups and trishomoaromatic character. What I liked about the article is that Henry rightly makes the case that exploration of the notion of “bonding” can be quite opaque and often leads to stretching the models we commonly employ. Well worth the read!
References
(1) Rzepa, H. S., "The importance of being bonded," Nat. Chem., 2009, 1, 510-512, DOI: 10.1038/nchem.373.
(2) Zhang, Q.; Yue, S.; Lu, X.; Chen, Z.; Huang, R.; Zheng, L.; Schleyer, P. v. R., "Homoconjugation/Homoaromaticity in Main Group Inorganic Molecules," J. Am. Chem. Soc., 2009, 131, 9789-9799, DOI: 10.1021/ja9029285
Henry Rzepa responded on 11 Nov 2009 at 3:32 am #
Apologies for commenting (again), especially about my own article (but I guess this is no surprise to readers of this blog). I wanted to delve into how the article actually came about, since it represents in some ways an interesting departure from the conventional journal scene. Nature Chemistry, being a new journal, have adopted a model of employing a very pro-active editorial team. This team (so I understand) attends scientific conferences regularly, and have as their brief the task of identifying interesting new reports of science. So it was with the genesis of the article Steve has blogged about. An article by Paul Schleyer and co-workers was so identified by the Nature team, and they invited me to write 1000 or so words in the form of a News and Views opinion. After a brain dump, I found that even 1400 words did not really produce a self-contained argument. What is more, I felt I needed to add a little bit of further analysis to that presented by Paul and others. The article evolved into a bit of a chimera, being in part a view, in part a review and in part a bit of original research. When the editor staff got back to me, they thought this blend departed somewhat from their own concept of a News and Views item. I responded by mulling over whether the entire item should instead appear on my blog! Perhaps they did not anticipate this particular, perhaps idiosyncratic response! In the event, we settled for another type of article introduced by the journal, called a commentary, which has almost double the word limit.
But was I happy yet? Well no. I decided I also wanted to present the results in the form of an Exploratorium. Full marks to the Nature chemistry team; they responded magnificently by mounting this on their site (if you do explore, the actual page is a bit wide, which causes problems with the molecules on the far right. But its early days!). And for good measure, a Digital repository entry to the original calculation is also included. The outcome is certainly different from the norm!
I do find we are entering a most interesting period, where the conventional scientific article is being dismantled, and re-assembled (mutated) into quite different forms. With other newcomers, such a Google Wave, further threatening the conventional, I wonder where scientific publishing will go over the next few years? Steve, what are your views on this?
Steven Bachrach responded on 11 Nov 2009 at 9:10 am #
Well, you and I (and Peter and many others) have been arguing about this idea and presenting alternative models and concept for well over 10 years now! I am a firm believer that the Internet has yet to be properly exploited by chemists – we have used the net as a delivery means (we now get our articles as pdf files and exchange these amongst ourselves), but we have not revolutionized the way we communicate.
My philosophy now is to embrace all experiments and hope that someone comes up with an idea that creates the critical support mass. So I support OA initiatives (for example, I wrote the OA policy statement for my university, modeled after the Harvard policy, which we adopted 2 weeks ago). Obviously, I do a lot of blogging and support other blogs. I support OA journals and have published in them. I hope that the Open Science Initiative of JC Bradley catches on. And your example of blogging original research has inspired me to do the same – look for a follow-up to one of my previous posts. (I had been thinking of writing this up as a more traditional article but thought let’s join in on the bandwagon!)
So, we need to continue evangelize and provide alternative models and hope that our examples inspire others to follow suit. But what will be the primary means of scientific communication 10 years from now? I fear it will remain exactly where we are at: the traditional research article published in traditional journals online in some non-reusable, non-semantic form with supporting materials in similarly non-reusable format.
Henry Rzepa responded on 11 Nov 2009 at 10:55 am #
Yes Steve, it is more difficult to change people than technology. But take a look at the surprising success of eg Twitter (which I have avoided! Imagine having only 140 characters in which to craft this response). Take a look at some of the surprising iPhone apps emerging (iPaper, the journal reader app, etc). That is all technology of course. As for the people, well, in a faculty of 52 academics here, I am the only one that blogs (or produces enhanced articles using Jmol). No-one goes onto the chemistry islands in Second Life (including myself). Having said that, for those articles where I collaborate with colleagues, they do seem to be genuinely appreciative of how their resulting articles have been enhanced. But it is seen as a dark arcane art, and I doubt they would have the confidence to attempt it themselves.
Finally, we run a course where students have to report their experiments on a Wiki. There is little complaint, and not a little imagination used. They seem happy. But their minds are still open. They will be mature researchers (some of them) in 10 years time, and perhaps some of what they learn now will rub off!
Steven Bachrach responded on 11 Nov 2009 at 11:08 am #
I am ever hopeful that the next generation will sweep out the old ones and adopt the new technologies within the discipline. Let’s hope that faculty to beat them into submission that the only way to do science is the old stodgy way….
That said, I don’t twitter; I am on facebook but I don’t know why; I have never gone into Second life; and I rarely enhance my articles. Now for the first three, I just don’t see what advantages those technologies offer scientists – but I am certainly open to be informed! With the last issue, I keep advocating with software companies and publishers that we need better tools for enhancing our articles. We need to turn the job of enhancing an article from “a dark arcane art” into something no more difficult and as routine as embedding a Symyx Draw (my new favorite chemical drawing program) structure into a word document!
Stuart responded on 11 Nov 2009 at 1:46 pm #
Henry – thanks for the generous comments regarding the manner in which your Commentary article evolved and was handled as it went through the publication process here at Nature Chemistry – you put us through our paces, and the result is a wonderful contribution (I especially like the title ;-)). At NPG we’re trying to innovate as much as we can, but I realise we probably do not go as far as some people would like. That being said, I do get the impression that there is a large silent majority who while they may not be ‘happy’ with the current system of scholarly communication in chemistry, they are nonetheless satisfied with it to such an extent that it thrives in its current form. Maybe as new generations of web 2.0 scientists sweep through academic departments, things will change – but I get the impression that how one’s paper is published is – for a lot of people – much less important than getting their paper published… That being said, we should always be striving to innovate in publishing and come up with better ways of disseminating results and data. So, who knows what it will be like in 10 years time? But perhaps by then the editors of other chemistry journals may start engaging the community too – Stuart