Data-free research data management? Not an oxymoron.

May 24th, 2016
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I occasionally post about "RDM" (research data management), an activity that has recently become a formalised essential part of the research processes. I say recently formalised, since researchers have of course kept research notebooks recording their activities and their data since the dawn of science, but not always in an open and transparent manner. The desirability of doing so was revealed by the 2009 "Climategate" events. In the UK, Climategate was apparently the catalyst which persuaded the funding councils (such as the EPSRC, the Royal Society, etc) to formulate policies which required all their funded researchers to adopt the principles of RDM by May 2015 and in their future researches. An early career researcher here, anxious to conform to the funding body instructions, sent me an email a few days ago asking about one aspect of RDM which got me thinking.

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What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?

May 11th, 2016
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I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[1] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.

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References

  1. G. Klopman, K. Tsuda, J. Louis, and R. Davis, "Supernucleophiles—I", Tetrahedron, vol. 26, pp. 4549-4554, 1970. http://dx.doi.org/10.1016/S0040-4020(01)93101-1

Autoionization of hydrogen fluoride.

April 24th, 2016
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The autoionization of water involves two molecules transfering a proton to give hydronium hydroxide, a process for which the free energy of reaction is well known. Here I ask what might happen with the next element along in the periodic table, F.

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Deuteronium deuteroxide. The why of pD 7.435.

April 22nd, 2016
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Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.

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Collaborative FAIR data sharing.

April 17th, 2016
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I want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article.[1]

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References

  1. C. Romain, Y. Zhu, P. Dingwall, S. Paul, H.S. Rzepa, A. Buchard, and C.K. Williams, "Chemoselective Polymerizations from Mixtures of Epoxide, Lactone, Anhydride, and Carbon Dioxide", J. Am. Chem. Soc., vol. 138, pp. 4120-4131, 2016. http://dx.doi.org/10.1021/jacs.5b13070

Oxane oxide: a tautomer of hydrogen peroxide.

April 15th, 2016
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If H3N+-O is viable compared with its tautomer H2N-OH when carrying water bridges, then why not try H2O+-O vs HO-OH?

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Azane oxide, a tautomer of hydroxylamine.

April 15th, 2016
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In the previous post I described how hydronium hydroxide or H3O+…HO, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O, a tautomer of the better known hydroxylamine (H2N-OH).

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References

  1. M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen-Bonded Complex of Hydronium and Hydroxide Ions", Chemistry - A European Journal, vol. 21, pp. 6350-6354, 2015. http://dx.doi.org/10.1002/chem.201406383

Hydronium hydroxide: the why of pH 7.

April 14th, 2016
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Ammonium hydroxide (NH4+…OH) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+…OH. The measured concentrations [H3O+] ≡ [OH] give rise of course to the well-known pH 7 of pure water, and converting this ionization constant to a free energy indicates that the solvated ion-pair must be some ~19.1 kcal/mol higher in free energy than water itself. So can a quantum calculation reproduce pH7 for water?

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Publishing embargoes.

April 13th, 2016
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Publishing embargoes seem a relatively new phenomenon, probably starting in areas of science when the data produced for a scientific article was considered more valuable than the narrative of that article. However, the concept of the embargo seems to be spreading to cover other aspects of publishing, and I came across one recently which appears to take such embargoes into new and uncharted territory.

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