Sometimes, as a break from describing chemistry, I take to describing the (chemical/scientific) creations behind the (WordPress) blog system. It is fascinating how there do seem increasing signs of convergence between the blog post and the journal article. Perhaps prompted by transclusion of tools such as Jmol and LaTex into Wikis and blogs, I list the following interesting developments in both genres.
The blog post as a scientific article: citation management
February 27th, 2012The hydroboration-oxidation mechanism: An updated look.
February 26th, 2012One thing almost always leads to another in chemistry. In the last post, I described how an antiperiplanar migration could compete with an antiperiplanar elimination. This leads to the hydroboration-oxidation mechanism, the discovery of which resulted in Herbert C. Brown (at least in part) being awarded the Nobel prize in 1979. Read the rest of this entry »
E2 elimination vs ring contraction: anti-periplanarity in action.
February 20th, 2012The anti-periplanar principle permeates organic reactivity. Here I pick up on an example of the antiperiplanar E2 elimination (below, blue) by comparing it to a competing reaction involving a [1,2] antiperiplanar migration (red). Read the rest of this entry »
An exothermic E2 elimination: an unusual intrinsic reaction coordinate.
February 6th, 2012The previous post explored why E2 elimination reactions occur with an antiperiplanar geometry for the transition state. Here I have tweaked the initial reactant to make the overall reaction exothermic rather than endothermic as it was before. The change is startling.
An orbital analysis of the stereochemistry of the E2 elimination reaction
February 4th, 2012The so-called E2 elimination mechanism is another one of those mainstays of organic chemistry. It is important because it introduces the principle that anti-periplanarity of the reacting atoms is favoured over other orientations such as the syn-periplanar form; Barton used this principle to great effect in developing the theory of conformational analysis. Here I explore its origins. Read the rest of this entry »
Secrets of a university tutor: dissection of a reaction mechanism. Part 2, the stereochemistry.
January 30th, 2012In the previous post, I went over how a reaction can be stripped down to basic components. That exercise was essentially a flat one in two dimensions, establishing only what connections between atoms are made or broken. Here we look at the three dimensional arrangements. It all boils down to identifying what the stereochemistry of the bonds marked with a wavy line are. Read the rest of this entry »
Secrets of a university tutor: dissection of a reaction mechanism.
January 25th, 2012Its a bit like a jigsaw puzzle in reverse, finding out to disassemble a chemical reaction into the pieces it is made from, and learning the rules that such reaction jigsaws follow. The following takes about 45-50 minutes to follow through with a group of students.
The “shocking” Xe-Au bond.
January 21st, 2012Chemistry rarely makes it to the cover of popular science magazines. Thus when this week, the New Scientist ran the headline “Forbidden chemistry. Reactions they said could never happen“, I was naturally intrigued. The examples included Woodward and Hoffmann’s “symmetry-forbidden” reactions, which have been the subject of several posts here already. But in the section on nobel gas chemistry, the same Hoffmann is reported as having been shocked to hear of a compound of xenon and gold, both of which in their time were thought of as solidly inert, and therefore even more unlikely to form a union.
Secrets of a university tutor: tetrahedral intermediates.
January 8th, 2012The tetrahedral intermediate is one of those iconic species on which the foundation of reaction mechanism in organic chemistry is built. It refers to a (normally undetected and hence merely inferred) species formed initially when a nucleophilic reagent attacks a carbonyl compound. Its importance to understanding the activity of enzymes cannot be overstated. An example of this genre is shown below, in which a thiol reacts with an acyl cyanide to form the species ringed in green.
Shared space (in science).
January 6th, 2012I thought I would launch the 2012 edition of this blog by writing about shared space. If you have not come across it before, it is (to quote Wikipedia), “an urban design concept aimed at integrated use of public spaces.” The BBC here in the UK ran a feature on it recently, and prominent in examples of shared space in the UK was Exhibition Road. I note this here on the blog since it is about 100m from my office.