Whilst clusters of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B ₄₀ to be specific.[cite]10.1038/nchem.1999[/cite] My interest was in how the σ and π-electrons were partitioned. In a C ₄₀ , one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that.

Computational quantum chemistry has made fantastic strides in the last 30 years. Often deep insight into all sorts of questions regarding reactions and structures of molecules has become possible. But sometimes the simplest of questions can prove incredibly difficult to answer. One such is how accurately can the boiling point of water be predicted from first principles? Or its melting point?

I was lucky enough to attend the announcement made in 2012 of the discovery of the Higgs Boson. It consisted of a hour-long talk mostly about statistics, and how the particle physics community can only claim a discovery when their data has achieved a 5σ confidence level. This represents a 1 in 3.5 million probability of the result occurring by chance. I started thinking: how much chemistry is asserted at that level of confidence?

Increasingly, our access to scientific information is becoming a research topic in itself.

The Bürgi–Dunitz angle describes the trajectory of an approaching nucleophile towards the carbon atom of a carbonyl group. A colleague recently came to my office to ask about the inverse, that is what angle would an electrophile approach (an amide)? Thus it might approach either syn or anti with respect to the nitrogen, which is a feature not found with nucleophilic attack.

I was reminded of this article by Michelle Francl[cite]10.1038/nchem.1733[/cite], where she poses the question “What anchor values would most benefit students as they seek to hone their chemical intuition?” She gives as common examples: room temperature is 298.17K (actually 300K, but perhaps her climate is warmer than that of the UK!), the length of a carbon-carbon single bond, the atomic masses of the more common elements.

A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first introduced in 1996), or almost 20 years ago.

Following the discussion here of Kekulé’s suggestion of what we now call a vibrational mode (and which in fact now bears his name), I thought I might apply the concept to a recent molecule known as [2.2]paracyclophane.

In the preceding post, a nice discussion broke out about Kekulé’s 1872 model for benzene.[cite]10.1002/jlac.18721620110[/cite] This model has become known as the oscillation hypothesis between two extreme forms of benzene (below). The discussion centered around the semantics of the term oscillation compared to vibration (a synonym or not?) and the timescale implied by each word.

Continuing my european visits, here are two photos from Bonn. First, a word about how the representation of benzene evolved, attributed to Kekulé. The sausage formula Above is his first effort, made in 1865. The bent bond formula This one above is better, offered in 1866.

Not a computer in sight! I refer to a chemistry lab from the 1800s I was recently taken to, where famous french chemists such as Joseph Gay-Lussac, Michel Chevreul and Edmond Fremy were professors. Although not used for chemistry any more, it is an incredible treasure trove of objects. Here are photos of some.