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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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Chemical ITBob HansonJavaJavaScriptJim HuChemical Sciences
Published

A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first introduced in 1996), or almost 20 years ago.

HistoricalHenry ArmstrongKekule VibrationPaul SchleyerChemical Sciences
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In the preceding post, a nice discussion broke out about Kekulé’s 1872 model for benzene.[cite]10.1002/jlac.18721620110[/cite] This model has become known as the oscillation hypothesis between two extreme forms of benzene (below). The discussion centered around the semantics of the term oscillation compared to vibration (a synonym or not?) and the timescale implied by each word.

HistoricalEdmond FremyJoseph Gay-LussacMichel ChevreulChemical Sciences
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Not a computer in sight! I refer to a chemistry lab from the 1800s I was recently taken to, where famous french chemists such as Joseph Gay-Lussac, Michel Chevreul and Edmond Fremy were professors. Although not used for chemistry any more, it is an incredible treasure trove of objects. Here are photos of some.

Chemical ITBeta SoftwareGeneric Data SearchMolecular Search EnginesSearch EngineChemical Sciences
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I remember a time when tracking down a particular property of a specified molecule was an all day effort, spent in the central library (or further afield). Then came the likes of STN Online (~1980) and later Beilstein. But only if your institution had a subscription.

Chemical ITCrystal_structure_miningGeneralFe And CoSearch DefinitionChemical Sciences
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This is rather cranking the handle, but taking my previous post and altering the search definition of the crystal structure database from 4- to 5-coordinate metals, one gets the following. Fe … Co … Ni … Cu … Trigonal bipyramidal coordination has angles of 90, 120 and 180°. Square pyramidal has no 120° angles, and the 180° angles might be somewhat reduced.

Chemical ITCrystal_structure_miningGeneralDataPt[/caption] SquareChemical Sciences
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I love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about ten minutes. The (CCDC database) search definition required is shown above.

Interesting ChemistryGrignard ReagentChemical Sciences
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I have just noticed unexpected links between two old posts, one about benzene, one about diphenyl magnesium and a link to August Kekulé. Click for 3D The post about benzene dealt with the apparently simple issue of why all the C-C bonds are of equal length. The answer, in brief is purely because of the σ-electrons. If the π-electrons had their way, benzene would have three short and three long C-C bonds.