I recently received two emails each with a subject line new approaches to research reporting. The traditional 350 year-old model of the (scientific) journal is undergoing upheavals at the moment with the introduction of APCs (article processing charges), a refereeing crisis and much more. Some argue that brand new thinking is now required. Here are two such innovations (and I leave you to judge whether that last word should have an appended ?).
Archive for the ‘General’ Category
How many water molecules does it take to ionise HCN/HNC? An NCI exploration.
Monday, March 2nd, 2015HCN is a weak acid (pKa +9.2, weaker than e.g. HF), although it does have an isomer, isocyanic acid or HNC (pka < +9.2 ?) which is simultaneously stronger and less stable. I conclude my halide acid series by investigating how many water molecules (in gas phase clusters) are required for ionisation of this “pseudo-halogen” acid.
How many water molecules does it take to ionise HI?
Saturday, February 28th, 2015How many water molecules does it take to ionise HF and HBr?
Friday, February 27th, 2015No doubt answers to the question posed in the previous post are already being obtained by experiment. Just in case that does not emerge in the next day or so, I offer a prediction here.
How-open-is-it?
Thursday, February 12th, 2015The title of this post refers to the site http://howopenisit.org/ which is in effect a license scraper for journal articles. In the past 2-3 years in the UK, we have been able to make use of grants to our university to pay publishers to convert our publications into Open Access (also called GOLD). I thought I might check out a few of my recent publications to see what http://howopenisit.org/ makes of them.
A convincing example of the need for data repositories. FAIR Data.
Thursday, January 15th, 2015Derek Lowe in his In the Pipeline blog is famed for spotting unusual claims in the literature and subjecting them to analysis. This one is entitled Odd Structures, Subjected to Powerful Computations. He looks at this image below, and finds the structures represented there might be a mistake, based on his considerable experience of these kinds of molecules. I expect he had a gut feeling within seconds of seeing the diagram.
The demographics of a blog readership – updated
Thursday, January 8th, 2015About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage! 
Of course, it is the nature of the beast that whilst we can track countries, very little else is known about such readerships. Is the readership young or old, student or professor, chemist or not (although I fancy the latter is less likely). Another way of keeping tabs on some of the activity are aggregators such as Chemical Blogspace, which has been rather quiet recently. Perhaps we have become too obsessed by metrics, and with the Internet-of-things apparently the “next-big-thing”, the metrics are only likely to increase. This will only encourage “game playing“, and I urge you to see a prime example of this in the UK REF (research excellence framework), the measure which attempts to rank UK universities in terms of their “excellence”.
The 5σ-confidence level: how much chemistry achieves this?
Saturday, July 5th, 2014I was lucky enough to attend the announcement made in 2012 of the discovery of the Higgs Boson. It consisted of a hour-long talk mostly about statistics, and how the particle physics community can only claim a discovery when their data has achieved a 5σ confidence level. This represents a 1 in 3.5 million probability of the result occurring by chance. I started thinking: how much chemistry is asserted at that level of confidence? Today, I read Steve Bachrach’s post on the structure of Citrinalin B and how “use of Goodman’s DP4 method indicates a 100% probability that the structure of citrinalin B is (the structure below)”. Wow, that is even higher than the physicists. Of course, 100% has been obtained by rounding 99.7 (3σ is 99.73%) or whatever (this is one number that should never be so rounded!). 
But there was one aspect of this that I did want to have a confidence level for; the absolute configuration of citrinalin B. Reading the article Steve quotes[cite]10.1038/nature13273[/cite], one sees this aspect is attributed to ref 5[cite]10.1021/jo051499o[/cite], dating from 2005. There the configuration was assigned on the basis of “comparison of the electronic circular dichroism (ECD) spectra for 1 and 2 with those of known spirooxiindole alkaloids“. However, this method can fail[cite]10.1002/chem.201101129[/cite]. Also, one finds “comparison of the vibrational circular dichroism (VCD) spectra of 1 with those of model compounds“[cite]10.1021/jo051499o[/cite]. Nowadays, one would say that there is no need for model compounds, why not measure and compute the VCD of the actual compound? Even a determination using the Flack crystallographic method can occasionally be wrong![cite]10.1021/jo401316a[/cite]. Which leads to asking what typical confidence levels might be for these three techniques, and indeed whether improving instrumentation means that the confidence level gets higher with time. OK, I am going to guess these.
The price of information: Evaluating big deal journal bundles
Thursday, July 3rd, 2014Increasingly, our access to scientific information is becoming a research topic in itself. Thus an analysis of big deal journal bundles[cite]10.1073/pnas.1403006111[/cite] has attracted much interesting commentary (including one from a large scientific publisher[cite]10.1038/510447f[/cite]). In the UK, our funding councils have been pro-active in promoting the so-called GOLD publishing model, where the authors (aided by grants from their own institution or others) pay the perpetual up-front publication costs (more precisely the costs demanded by the publishers, which is not necessarily the same thing) so that their article is removed from the normal subscription pay wall erected by the publisher and becomes accessible to anyone. As the proportion of GOLD content increases, it was anticipated (hoped?) that the costs of accessing the remaining non-GOLD articles via a pay-walled subscription would decrease.