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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings. Edward Valeev talked about the scaling problem in coupled cluster theories, the so-called gold standard for computing the energy and properties of small molecules.

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It is always interesting to observe conference experiments taking place. The traditional model involves travelling to a remote venue, staying in a hotel, selecting sessions to attend from a palette of parallel streams and then interweaving chatting to colleagues both old and new over coffee, lunch, dinner or excursions.

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Bees are having a tough time around the world. Oddly, they are surviving very well in cities. One reason are the wild flower meadows in London and for some summer relief I thought I would tell you the story of the one shown below. We live in west London, in an area that was farmland as recently as the 1930s and used to produce vegetables and milk for the population of London.

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There is much focus at the moment on how to ensure experimental replicability in e.g. the molecular sciences. An important aspect of that is having access to FAIR data; data which is findable, accessible, inter-operable and re-usable. One of the “gold standards” in chemistry is the data associated with crystal structures.

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The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5Å of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other combinations of two atoms, say H and F? Here I briefly explore this notion.

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In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule.

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About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[cite]10.1021/ja407398w[/cite]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings.

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The iron complex shown below forms the basis for many catalysts.[cite]10.1002/anie.200502985[/cite] With iron, the catalytic behaviour very much depends on the spin-state of the molecule, which for the below can be either high (hextet) or medium (quartet) spin, with a possibility also of a low spin (doublet) state. Here I explore whether structural information in crystal structures can reflect such spin states.

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In an earlier post, I lamented the modern difficulties in running old instances of Jmol, an example of an application program written in the Java programming language. When I wrote that, I had quite forgotten a treasure trove of links to old Java that I had collected in 1996-7 and then abandoned. Here I browse through a few of the things I found. The collection is at DOI: 10.14469/hpc/2657.