The wrong trousers: the anti-Markovnikov addition of borane to 2-methylpropene.

March 2nd, 2014

A staple of introductory undergraduate teaching in organic chemistry is Markovnikov’s rule, which states: “the addition of a protic acid HX to an alkene results in the acid hydrogen (H) becoming attached to the carbon with fewer alkyl substituents and the halide (X) group to the carbon with more alkyl substituents“. Shortly thereafter,  students are exposed to the “anti-Markovnikov” addition of borane to e.g. 2-methylpropene. In order to achieve a consistent explanation for both reactions, I normally show students the following mechanism.  Here I introduce a “reality check” to the first component of that mechanism (for the oxidative step, see this post).

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Intersecting paths in molecular energy surfaces.

February 16th, 2014

The potential energy surface for a molecule tells us about how it might react. These surfaces have been charted for thousands of reactions using quantum mechanics, and their basic features are thought to be well understood. Coming across an entirely new feature is rare. So what do you make of the following?

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A congruence of concepts: conformations, configurations, amides and enzymes

February 9th, 2014

This is the time of year when I deliver two back-2-back lecture courses, and yes I do update and revise the content! I am always on the look-out for nice new examples that illustrate how concepts and patterns in chemistry can be joined up to tell a good story. My attention is currently on conformational analysis; and here is an interesting new story to tell about it.

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3D-rendered molecular models on this blog: an update.

January 16th, 2014

So much to do, so little time to do it. That is my excuse at least. Right from my first post on this blog in 2008 I have tried to enhance it using Jmol, a Java-based applet (normally indicated with the caption Click for 3D). This has been pretty stable for some five years now, but a recent spate of security-based releases of the JRE (Java runtime environment) for desktop computers has impacted, the latest of which was released yesterday (Java 7, V 51).  Put simply, when I started, an unsigned applet was fine. Now to run, it can only be a properly signed applet. Fortunately, there are two solutions:

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Three-for-one: a pericyclic brain teaser.

January 12th, 2014

A game one can play with pericyclic reactions is to ask students to identify what type a given example is. So take for example the reaction below.

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A simple pericyclic reaction encapsulating the four thermal selection rules.

January 2nd, 2014

As my previous post hints, I am performing my annual spring-clean of lecture notes on pericyclic reactions. Such reactions, and their stereochemistry, are described by a set of selection rules. I am always on the lookout for a simple example which can most concisely summarise these rules. The (hypothetical) one shown below I think nicely achieves this, and raises some interesting issues in the process.14vs12

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Refactoring my lecture notes on pericyclic reactions.

December 29th, 2013

When I first started giving lectures to students, it was the students themselves that acted as human photocopiers, faithfully trying to duplicate what I was embossing on the lecture theatre blackboard with chalk. How times have changed! Here I thought I might summarise my latest efforts to refactor the material I deliver in one lecture course on pericyclic reactions (and because my notes have always been open, you can view them yourself if you wish).

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Does forming a Wheland intermediate disrupt all aromaticity?

December 6th, 2013

Text books will announce that during aromatic electrophilic substitution, aromaticity is lost by the formation of a Wheland intermediate (and regained by eliminating a proton). Is that entirely true?wheland

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A curly-arrow pushing manual

December 4th, 2013

I have several times used arrow pushing on these blogs. But since the rules for this convention appear to be largely informal, and there appears to be no definitive statement of them, I thought I would try to produce this for our students. This effort is here shared on my blog. It is what I refer to as the standard version; an advanced version is in preparation. Such formality might come as a surprise to some; arrow-pushing is often regarded as far too approximate to succumb to any definition, although it is of course often examined.

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Chemistry data round-tripping. Has there been ANY progress?

December 2nd, 2013

This is one of those topics that seems to crop up every three years or so. Since then, new versions of operating systems, new versions of programs, mobile devices and perhaps some progress? 

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