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Metallic hydrogen

27 January 2017 - Or not

metallichydrogen2017.PNGThis week Dias and Silvera have reported the discovery of metallic hydrogen in the journal Science and not without controversy (DOI). A diamond anvil cell was used to compress hydrogen gas at cryogenic temperatures and a record-high pressure. Problems to overcome were diamond tip failure and hydrogen diffusion into the diamond tip.Solutions: really low operating temperature, special treatment of the diamond tip and coating it with alumina. The laser used for illumination and for measuring the pressure inside the anvil was of low power in order to minimise damage to the sample. At 335 GPa the pressure was increased further by manually rotating the screw and at 495 GPa the hydrogen sample (8 by 10 by 1 micron in volume) as viewed through a microscope turned from black to reflecting, indicating metallic properties.

But there is controversy. Davide Castelvecchi in a Nature article sums up the criticism. Pressure miscalculated, the actual material observed is not hydrogen metal but the alumina. Most of all, the experiment is apparently only performed once, Dias and Silvera have been holding on to their precious sample in the anvil for several months until their publication was out. Well, as of this week they are back in business. The really interesting premise is that with heating up and de-pressurising the anvil, the hydrogen sample is predicted to be metastable and metallic properties should be retained. To be continued!

Update 23-02-2017: crap, the sample disappeared (The Independent article)

Dark reactions

26 January 2017 - Chemical reaction databases.

darkreactions.PNGWe can add a new chemical reaction database to our list of chemical reaction databases. See previous database coverage here. Not a brand new one, it has been around since 2016.

This Haverford College initiative aims to use machine learning to predict the success of chemical reactions. This concept has been described in a 2016 Nature letter (DOI): an algorithm was trained on a set of successful reactions and a set of so-called dark reactions - unsuccessful and failed -, more specifically a hydrothermal synthesis. With training done, the algorithm was then set to work and it proved better in devising new synthesis strategies than humans!

The aim of the dark reactions project (website here) is to collect failed reactions that together with successful reactions can serve as test sets for further machine learning. Failed reactions do generally not make it to publications and hence the repository. The site has a public reactions database. A csv file is available once you have registered as a user. The file contains around 4000 reactions. Curiously the published database only contains sets of reactants: no reaction conditions or products. Not sure why that is. There is also a piece of software downloadable from github here. Not sure yet what that is about either.

Pyramidal carbon

15 January 2017 - Molecule of the year 2016

pyramidalcarbonMalischewski2016.PNGThanks to the New Scientist article here for reminding us but the discovery of a pyramidal carbon dication by Malischewski and Seppelt (DOI) must be the chemistry event of the last year (work published 26 November, yeah this blog missed it completely). It is common knowledge that carbon will partner in chemical bonds with up to 4 partners but definitely not more. In fact, if a molecule is depicted in any way with 5 bonds going away from it (clearly an error made) the author is met with ridicule and a specific reserved phrase : Texas carbon, a reference to the Texas five-pointed lone star. As it turns out this ridicule is misplaced! It is possible to create Texas carbon molecules after all. Malischewski and Seppelt made theirs starting from the Dewar benzene of hexamethylbenzene (by a cyclotrimerisation of 2-butyne with aluminum chloride). This compound was epoxidized and then reacted with magic acid. This very strong acid basically strips away O2- leaving behind C6(CH3)62+(SbF6-)2. Read the supplementary info to learn the very thin line between reaction success and reaction black tar. The crystal end-product (produced by adding HF and cooling) is stable at -78°C ready for X-ray diffraction. And how to describe the molecule? It is the adduct of the pentamethylcyclopentadienylium cation and the 1-ethylium-1-ylidene cation CH3C+ cation with 6 bonding electrons shared between them. There is of course the issue of precedence, the dication was already observed by NMR in 1973 (DOI) but an actual crystal structure is always a next step.

Spot the hydrogen atoms

14 January 2017 - Image of the week

paracetamolbyPEDT.PNGDoes the phrase "hydrogen atoms omitted for clarification" sound familiar to you? It is the default text accompanying every crystal structure depiction. The reason? it may be that the presence of the hydrogen atoms is obvious so that there is no need to show them. The actual truth: the accuracy of the position of the hydrogen atoms in a crystal structure is very inaccurate and any depiction of them will hopelessly clutter the picture. Problem is, hydrogen has just one electron, reducing scattering power. But thank science we now have precession electron diffraction tomography (PEDT), a brand new technique pioneered by Czech/French team headed by L. Palatimus as first author who practised it on straightforward paracetamol (DOI). To paint the picture old-fashioned X-ray crystallography has been superseded by electron crystallography which has been superseded by precession electron diffraction and then by its tomography child. Technology moves fast. The instrument is especially suited for working with micro crystals. Challenge: any crystal submitted to PEDT suffers from the radiation and will deteriorate. Solution: build up a picture by moving the electron beam over the crystal and build up the image. Results: the measured C-H distances in paracetamol are 1.15 angstroms (textbook value 1.09 angstroms) and the measured angles deviate by 10 degrees.