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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Ways to encourage water to protonate an amine: superbasing.

April 8th, 2016
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Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1) and is thus more basic than hydroxide anion in this medium.

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Celebrating Paul Schleyer: searching for hidden treasures in the structures of metallocene complexes.

April 2nd, 2016
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A celebration of the life and work of the great chemist Paul von R. Schleyer was held this week in Erlangen, Germany. There were many fantastic talks given by some great chemists describing fascinating chemistry. Here I highlight the presentation given by Andy Streitwieser on the topic of organolithium chemistry, also a great interest of Schleyer's over the years. I single this talk out since I hope it illustrates why people still get together in person to talk about science.

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Does combining molecules with augmented reality have a future?

March 28th, 2016
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Augmented reality, a superset if you like of virtual reality (VR), has really been hitting the headlines recently. Like 3D TV, its been a long time coming! Since ~1994 or earlier, there have been explorations of how molecular models can be transferred from actual reality to virtual reality using conventional computers (as opposed to highly specialised ones). It was around then that a combination of software (Rasmol) and hardware (Silicon Graphics, and then soon after standard personal computers with standard graphics cards) became capable of such manipulations. VRML (virtual reality modelling language) also proved something of a false start So have things changed?

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How many water molecules does it take to form ammonium hydroxide from ammonia and water?

March 20th, 2016
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This is a corollary to the previous post exploring how many molecules are needed to ionise HCl. Here I am asking how many water molecules are required to form the ionic ammonium hydroxide from ammonia and water.

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Research data: Managing spectroscopy-NMR.

March 16th, 2016
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At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here.

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Global initiatives in research data management and discovery: searching metadata.

March 7th, 2016
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The upcoming ACS national meeting in San Diego has a CINF (chemical information division) session entitled "Global initiatives in research data management and discovery". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session.

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Discovery based research experiences: gauche effects in group 16 elements.

March 2nd, 2016
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The upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses. I had previously explored what I called extreme gauche effects in the molecule F-S-S-F. Here I take this a bit further to see what else can be discovered about molecules containing bonds between group 16 elements (QA= O, S, Se, Te). 

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Earth’s missing chemistry.

February 24th, 2016
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At the precise moment I write this, there is information about 108,230,950 organic and inorganic chemical substances from the World's disclosed chemistry. So it was with a sense of curiosity that I came across this article in the American Mineralogist[1] entitled "Earth’s “missing” minerals" (the first in a series of articles apparently planned on the topic of the missing ones). The abstract is particularly interesting and whilst I encourage you to go read the article itself, I will quote some eye-catching observations from just this abstract:

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References

  1. R.M. Hazen, G. Hystad, R.T. Downs, J.J. Golden, A.J. Pires, and E.S. Grew, "Earth’s “missing” minerals", American Mineralogist, vol. 100, pp. 2344-2347, 2015. http://dx.doi.org/10.2138/am-2015-5417