Posts Tagged ‘Tutorial material’

A short history of molecular modelling: 1860-1890.

Saturday, February 5th, 2011

In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century. It had all started 93 years earlier in 1860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as real entities was to remain controversial for another 45 years (for example Faraday, perhaps the most famous scientist alive in 1860 did not believe atoms were real). So the idea of constructing a molecular model from atoms as the basis for understanding chemical behaviour was perhaps bolder than we might think. It is shown below, part of a set built for August Wilhelm von Hofmann as part of the lectures he delivered at the Royal College of Chemistry in London (now Imperial College).

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Shorter is higher: the strange case of diberyllium.

Friday, January 21st, 2011

Much of chemistry is about bonds, but sometimes it can also be about anti-bonds. It is also true that the simplest of molecules can have quite subtle properties. Thus most undergraduate courses in chemistry deal with how to describe the bonding in the diatomics of the first row of the periodic table. Often, only the series C2 to F2 is covered, so as to take into account the paramagnetism of dioxygen, and the triple bonded nature of dinitrogen (but never mentioning the strongest bond in the universe!). Rarely is diberyllium mentioned,  and yet by its strangeness, it can also teach us a lot of chemistry.

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The melting points from benzene to cyclohexane: a prime example of dispersion forces in action?

Thursday, December 30th, 2010

One of the delights of wandering around an undergraduate chemistry laboratory is discussing the unexpected, if not the outright impossible, with students. The >100% yield in a reaction is an example. This is sometimes encountered (albeit only briefly) when students attempt to recrystallise a product from cyclohexane, and get an abundant crop of crystals when they put their solution into an ice-bath to induce the crystallisation. Of the solvent of course! I should imagine 1000% yields are possible like this.

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Do marauding electrons go in packs?

Monday, December 27th, 2010

Is there a preferred pack size for electrons on the move? Or put less flamboyantly, is there an optimum, and a maximum number of arrows (electron pairs) that one might push in revealing the mechanism of a concerted reaction? A sort of village-instinct for electrons. Consider the following (known, DOI: 10.1016/S0040-4039(00)98289-3) reaction

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(anti)aromaticity avoided: a tutorial example

Tuesday, December 7th, 2010

More inspiration from tutorials. In a lecture on organic aromaticity, the 4n+2/4n Hückel rule was introduced (in fact, neither rule appears to have actually been coined in this form by Hückel himself!). The simplest examples are respectively the cyclopropenyl cation and anion. The former has 2 π-electrons exhibiting cyclic delocalisation, and the 4n+2 (n=0) rule predicts aromaticity. Accordingly, all three C-C distances are the same (1.363Å).

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Secrets of a university tutor: (curly) arrow pushing

Thursday, October 28th, 2010

Curly arrows are something most students of chemistry meet fairly early on. They rapidly become hard-wired into the chemists brain. They are also uncontroversial! Or are they? Consider the following very simple scheme.

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Conformational analysis of biphenyls: an upside-down view

Friday, April 2nd, 2010

One of the (not a few) pleasures of working in a university is the occasional opportunity that arises to give a new lecture course to students. New is not quite the correct word, since the topic I have acquired is Conformational analysis. The original course at Imperial College was delivered by Derek Barton himself about 50 years ago (for articles written by him on the topic, see DOI 10.1126/science.169.3945.539 or the original 10.1039/QR9561000044), and so I have had an opportunity to see how the topic has evolved since then, and perhaps apply some quantitative quantum mechanical interpretations unavailable to Barton himself.

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The conformation of cyclohexane

Thursday, January 28th, 2010

Like benzene, its fully saturated version cyclohexane represents an icon of organic chemistry. By 1890, the structure of planar benzene was pretty much understood, but organic chemistry was still struggling somewhat to fully embrace three rather than two dimensions. A grand-old-man of organic chemistry at the time, Adolf von Baeyer, believed that cyclohexane too was flat, and what he said went. So when a young upstart named Hermann Sachse suggested it was not flat, and furthermore could exist in two forms, which we now call chair and boat, no-one believed him. His was a trigonometric proof, deriving from the tetrahedral angle of 109.47 at carbon, and producing what he termed strainless rings.

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Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog

Saturday, April 12th, 2008