Archive for the ‘General’ Category

A tourist trip around London Overground with a chemical theme.

Saturday, August 29th, 2015
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Most visitors to London use the famous underground trains (the “tube”) or a double-decker bus to see the city (one can also use rivers and canals). So I thought, during the tourism month of August, I would show you an alternative overground circumnavigation of the city using the metaphor of benzene.

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Single Figure (nano)publications, reddit AMAs and other new approaches to research reporting

Wednesday, August 5th, 2015
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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 ?).

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The 2015 Bradley-Mason prize for open chemistry.

Friday, June 26th, 2015
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Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote openness. Jean-Claude Bradley was a young scientist who was passionately committed to practising open chemistry, even though when he started he could not have anticipated any honours for doing so. A year ago a one day meeting at Cambridge was held to celebrate his achievements, followed up with a special issue of the Journal of Cheminformatics. Peter Murray-Rust and I both contributed and following the meeting we decided to help promote Open Chemistry via an annual award to be called the Bradley-Mason prize. This would celebrate both “JC” himself and Nick Mason, who also made outstanding contributions to the cause whilst studying at Imperial College. The prize was initially to be given to an undergraduate student at Imperial, but was also extended to postgraduate students who have promoted and showcased open chemistry in their PhD researches.

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How many water molecules does it take to ionise HCN/HNC? An NCI exploration.

Monday, March 2nd, 2015
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HCN 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.

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How many water molecules does it take to ionise HI?

Saturday, February 28th, 2015
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Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.

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How many water molecules does it take to ionise HF and HBr?

Friday, February 27th, 2015
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No 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.

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How-open-is-it?

Thursday, February 12th, 2015
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The 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.

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A convincing example of the need for data repositories. FAIR Data.

Thursday, January 15th, 2015
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Derek 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.

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The demographics of a blog readership – updated

Thursday, January 8th, 2015
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About 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! 2015
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”.

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Why is mercury a liquid at room temperatures?

Saturday, July 12th, 2014
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Computational quantum chemistry has made fantastic strides in the last 30 years. Often deep insight into all sorts of questions regarding reactions and structures of molecules has become possible. But sometimes the simplest of questions can prove incredibly difficult to answer. One such is how accurately can the boiling point of water be predicted from first principles? Or its melting point? Another classic case is why mercury is a liquid at room temperatures? The answer to that question (along with another, why is gold the colour it is?) is often anecdotally attributed to Einstein. More accurately, to his special theory of relativity.[1] But finally in 2013 a computational proof of this was demonstrated for mercury.[2] The proof was built up in three stages.

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References

  1. A. Einstein, "Ist die Trägheit eines Körpers von seinem Energieinhalt abhängig?", Ann. Phys., vol. 323, pp. 639-641, 1905. http://dx.doi.org/10.1002/andp.19053231314
  2. F. Calvo, E. Pahl, M. Wormit, and P. Schwerdtfeger, "Evidence for Low-Temperature Melting of Mercury owing to Relativity", Angewandte Chemie International Edition, vol. 52, pp. 7583-7585, 2013. http://dx.doi.org/10.1002/anie.201302742