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:

Read the rest of this entry »

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.

Read the rest of this entry »

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

Read the rest of this entry »

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).

Read the rest of this entry »

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

Read the rest of this entry »

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.

Read the rest of this entry »

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? 

Read the rest of this entry »

Caesium trifluoride: could it be made?

November 23rd, 2013

Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[cite]10.1002%2Fanie.200703710[/cite] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[cite]http://dx.doi.org/10.1021%2Fed085p1182[/cite]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[cite]10.1038/nchem.1754[/cite] Here I report some further calculations inspired by this report.

Read the rest of this entry »

Avoided (pericyclic) anti-aromaticity: Reactions of t-butyl-hydroxycarbene.

November 13th, 2013

Not long ago, I described a cyclic carbene in which elevating the carbene lone pair into a π-system transformed it from a formally 4n-antiaromatic π-cycle into a 4n+2 aromatic π-cycle. From an entirely different area of chemistry, another example of this behaviour emerges; Schreiner’s[cite]10.1039/C2SC21555A[/cite] trapping and reactions of t-butyl-hydroxycarbene, as described on Steve Bachrach’s blog. A point I often make is that chemistry is all about connections, and so here I will discuss such a connection.schreiner

Read the rest of this entry »

The subtle effect of dispersion forces on the shapes of molecules: benzyl magnesium bromide.

November 10th, 2013

In the previous post I mentioned in passing the Grignard reagent benzyl magnesium bromide as having tetrahedral coordination at Mg. But I have now noticed, largely through spotting Steve Bachrach’s post on “Acene dimers – open or closed?” another geometric effect perhaps worthy of note, certainly one not always noted in the past; that of dispersion forces.

Read the rest of this entry »