My previous post on the topic of mauveine left the outcome dangling. Put simply, λ _max is measured at about 549nm for mauveine A, but was calculated at about 440nm using a modern method for predicting colour (TD-DFT). According to the colour table below, that would make it orange, not mauve. Can the theoretical prediction be out by 110nm, or might it be the structure of the molecule itself that has been wrongly described?

As the title hints, I have been here before. The S _N 1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism.

I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled “ The past, present and future of Scientific discourse ” (DOI: 10.1186/1758-2946-3-46). Here I take two articles, one published 58 years ago and one published last year, and attempt to reinvent some aspects.

Organic chemists have been making (more or less pure) molecules for the best part of 180 years. Occasionally, these ancient samples are unearthed in cupboards, and then the hunt for their origin starts. I have previously described tracking down the structure of a 120 year-old sample of a naphthalene derivative. But I visited a colleague's office today, and recollected having seen a well-made wooden display cabinet there on a previous visit.

Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The Cahn-Ingold-Prelog convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule on the left below.

I asked a while back whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism.

Bonds are a good example of something all chemists think they can recognise when they see them. But they are also remarkably dependent on context. We are running a molecular modelling course at the moment, and I found myself explaining to someone how very context-sensitive they can be. I thought it might be useful to collect my thoughts here.

In two previous posts, I have looked at why cis -butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “ topological ” bond, rather than attraction between the H…H region to form a weak chemical “ bond ”. Here I take a look at what happens when that central C=C bond is gradually removed.

I wrote earlier about the strangely close contact between two hydrogen atoms in cis -butene. The topology of the electron density showed characteristics of a bond, but is it a consensual union?

Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption . Here I describe from my own perspective some of the disruptions to chemistry I experienced (for another commentary, see here). Chemical diagram, circa 1983.

The properties of electrons are studied by both chemists and physicists. At the boundaries of these two disciplines, sometimes interesting differences in interpretation emerge. One of the most controversial is that due to Bader (for a recent review, see DOI: 10.1021/jp102748b) a physicist who brought the mathematical rigor of electronic topology to bear upon molecules.