Secrets of a university tutor. An exercise in mechanistic logic: first dénouement.

October 28th, 2012

The reaction described in the previous post (below) is an unusual example of nucleophilic attack at an sp2-carbon centre, reportedly resulting in inversion of configuration[cite]10.1021/ja00765a062[/cite]. One can break it down to a sequence of up to eight individual steps, which makes teaching it far easier. But how real is that sequence?

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Secrets of a university tutor. An exercise in mechanistic logic, prequel.

October 27th, 2012

The reaction below plays a special role in my career. As a newly appointed researcher (way back now), I was asked to take tutorial groups for organic chemistry as part of my duties. I sat down to devise a suitable challenge for the group, and came upon the following reaction[cite]10.1021/ja00765a062[/cite]. I wrote it down on page 2 of my tutorial book, which I still have. I continue to use this example in tutorials to this day, some 35 years later.

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Trimethylenemethane Ruthenium benzene

October 17th, 2012

Every once in a while, one encounters a molecule which instantly makes an interesting point. Thus Ruthenium is ten electrons short of completing an 18-electron shell, and it can form a complex with benzene on one face and a ligand known as trimethylenemethane on the other[cite]10.1039/C39910001457[/cite].

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How is the bromination of alkenes best represented?

October 14th, 2012

I occasionally delve into the past I try to understand how we got to our present understanding of chemistry. Thus curly arrow mechanistic notation can be traced back to around 1924, with style that bifurcated into two common types used nowadays (on which I have commented and about which further historical light at the end of this post). Here I try to combine these themes with some analysis of wavefunctions for a particularly troublesome reaction to represent, the dibromination of an alkene, which I represented in the previous post as shown below.

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Text-books and the bromination of ethene.

October 14th, 2012

There is often a disconnect between how a text-book (schematically) represents a reaction and a more quantitive “reality” revealed by quantum mechanics. Is the bromination of ethene to give 1,2-dibromoethane one such example?

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Ring-flipping in cyclohexane in a different light

October 12th, 2012

The conformational analysis of cyclohexane is a mainstay of organic chemistry. Is there anything new that can be said about it? Let us start with the diagram below:

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Alkyne metathesis: a comparison with alkene metathesis.

October 8th, 2012

Metathesis reactions are a series of catalysed transformations which transpose the atoms in alkenes or alkynes. Alkyne metathesis is closely related to the same reaction for alkenes, and one catalyst that is specific to alkynes was introduced by Schrock (who with Grubbs won the Nobel prize for these discoveries) and is based on tungsten (M=W(OR)3).

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Alkene metathesis springs a surprise.

October 1st, 2012

Alkene metathesis is part of a new generation of synthetic reaction in which a double C=C bond is formed from appropriate reactants where no bond initially exists (another example is the Wittig reaction), with the involvement of a 4-membered-ring metallacyclobutane ring 1 (again, very similar to the Wittig). I thought it might make a good addition to my collection of reaction mechanisms and so as the first step I set about locating the transition state (TS or TS’) for the reaction, using in this case a model for Grubbs’ catalyst. I have located a fair few transition states in my time, and was frankly not expecting a surprise. This is the story that showed otherwise …

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Oxime formation from hydroxylamine and ketone. Part 2: Elimination.

September 25th, 2012

This is the follow-up to the previous post exploring a typical nucleophilic addition-elimination reaction. Here is the elimination step, which as before requires proton transfers. We again adopt a cyclic mechanism to try to avoid the build up of charge separation during those proton movements.

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Oxime formation from hydroxylamine and ketone: a (computational) reality check on stage one of the mechanism.

September 23rd, 2012

The mechanism of forming an oxime from nucleophilic addition of a hydroxylamine to a ketone is taught early on in most courses of organic chemistry. Here I subject the first step of this reaction to form a tetrahedral intermediate to quantum mechanical scrutiny.

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