October 23rd, 2015
Steve Bachrach on his own blog has commented on a recent article[1] discussing the structure of the trimer of fluoroethanol. Rather than the expected triangular form with three OH—O hydrogen bonds, the lowest energy form only had two such bonds, but it matched the microwave data much better. Here I explore this a bit more.
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References
- J. Thomas, X. Liu, W. Jäger, and Y. Xu, "Unusual H‐Bond Topology and Bifurcated H‐bonds in the 2‐Fluoroethanol Trimer", Angewandte Chemie International Edition, vol. 54, pp. 11711-11715, 2015. https://doi.org/10.1002/anie.201505934
Tags: Atoms in molecules, chemical bonding, Diagram, Hydrogen bond, low energy structure, lowest energy form, microwave, Steve Bachrach
Posted in Interesting chemistry | 4 Comments »
October 23rd, 2015
Posted in Historical | 1 Comment »
October 14th, 2015
In Jingdezhen an Imperial Kiln was built in 1369 to produce porcelain that was “white as jade, thin as paper, bright as a mirror and tuneful as a bell”. It’s the colours of the glazes that caught my eye, achieved by a combination of oxidative and reductive firing in the kiln, coupled with exquisite control of the temperature.
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Posted in Historical, Interesting chemistry | No Comments »
October 9th, 2015
This comes to you from China, and the city of Suzhou. To set the scene, cities in China have a lot of motorbikes. Electric ones. With their own speed units, a % of Panda speed. 
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Posted in Interesting chemistry | 1 Comment »
October 1st, 2015
A fascinating re-examination has appeared[1] of a reaction first published[2] in 1960 by Wittig and then[3] repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g. a nickel spatula?). In this recent article[1] a mechanism for the catalytic cycle is proposed. Here I thought I might explore this mechanism using calculations to see if any further insights might emerge.
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References
- S.A. Künzi, J.M. Sarria Toro, T. den Hartog, and P. Chen, "Nickel‐Catalyzed Cyclopropanation with NMe<sub>4</sub>OTf and <i>n</i>BuLi", Angewandte Chemie International Edition, vol. 54, pp. 10670-10674, 2015. https://doi.org/10.1002/anie.201505482
- V. Franzen, and G. Wittig, "Trimethylammonium‐methylid als Methylen‐Donator", Angewandte Chemie, vol. 72, pp. 417-417, 1960. https://doi.org/10.1002/ange.19600721210
- G. Wittig, and D. Krauss, "Cyclopropanierungen bei Einwirkung von <i>N</i>‐Yliden auf Olefine", Justus Liebigs Annalen der Chemie, vol. 679, pp. 34-41, 1964. https://doi.org/10.1002/jlac.19646790106
Tags: activation free energy barriers, Cambridge, energy, energy relative, nickel-carbene product
Posted in Interesting chemistry, reaction mechanism | No Comments »
September 24th, 2015
How does an anaesthetic work? Surprisingly, it is only recently[1] that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling.[2] A propofol analogue was constructed[1] by replacing one of the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen and forms a carbene as a reactive species, which with further chemistry binds covalently[2] to adjacent amino acids in the binding pocket.These modified segments could then be analysed by mass spectrometry.[1] An isomer of diazirine is diazomethane, which is some 11 kcal/mol lower in free energy, but fortunately the diazirene is preventing from thermally isomerising to this species by a large kinetic barrier. That was the intro; now for a connection.‡ I recently attended a presentation on another medical topic, the therapeutic uses of carbon monoxide.[3] In higher concentrations it is notoriously lethal, but with appropriate delivery it can be therapeutic. So, intertwingling, I asked myself what the properties of the carbon monoxide isoelectronic analogue of a diazirine might be (X=C, Y=O below).
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References
- G.M.S. Yip, Z. Chen, C.J. Edge, E.H. Smith, R. Dickinson, E. Hohenester, R.R. Townsend, K. Fuchs, W. Sieghart, A.S. Evers, and N.P. Franks, "A propofol binding site on mammalian GABAA receptors identified by photolabeling", Nature Chemical Biology, vol. 9, pp. 715-720, 2013. https://doi.org/10.1038/nchembio.1340
- L. Dubinsky, B.P. Krom, and M.M. Meijler, "Diazirine based photoaffinity labeling", Bioorganic & Medicinal Chemistry, vol. 20, pp. 554-570, 2012. https://doi.org/10.1016/j.bmc.2011.06.066
- R. Motterlini, and L.E. Otterbein, "The therapeutic potential of carbon monoxide", Nature Reviews Drug Discovery, vol. 9, pp. 728-743, 2010. https://doi.org/10.1038/nrd3228
Tags: anaesthetic, Diazirine, GABAA receptors, photo affinity labelling, propofol
Posted in Interesting chemistry, reaction mechanism | No Comments »
September 13th, 2015
Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.
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Tags: chemical phenomena
Posted in Chemical IT, crystal_structure_mining | No Comments »
September 6th, 2015
An article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds"[1] was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate carbon.
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References
- L. Yang, E. Ganz, Z. Chen, Z. Wang, and P.V.R. Schleyer, "Four Decades of the Chemistry of Planar Hypercoordinate Compounds", Angewandte Chemie International Edition, vol. 54, pp. 9468-9501, 2015. https://doi.org/10.1002/anie.201410407
Tags: Angle, Cambridge, chemical bonding, Cycloalkane, Cyclopropane, HTML, HTML element, Ligand, metal, search definition, search results, search software, Steve Bacharach
Posted in Chemical IT, crystal_structure_mining | No Comments »
September 5th, 2015
The previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides.
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Tags: Amide, Functional groups, Thioamide
Posted in Chemical IT, crystal_structure_mining | No Comments »