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, B40 to be specific.[cite]10.1038/nchem.1999[/cite] My interest was in how the σ and π-electrons were partitioned. In a C40, one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that. Having one electron less per atom, one might imagine that a fullerene-like boron cluster would have no π-electrons. But the element has a propensity[cite]10.1039/B911817A[/cite] to promote its σ-electrons into the π-manifold, leaving a σ-hole. So how many π-electrons does B40 have? These sorts of clusters are difficult to build using regular structure editors, and so coordinates are essential. The starting point for a set of coordinates with which to compute a wavefunction was the supporting information. Here is the relevant page: 
The coordinates are certainly there (that is not always the case), but you have to know a few tricks to make them usable.
The 5σ-confidence level: how much chemistry achieves this?
July 5th, 2014I 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? Today, I read Steve Bachrach’s post on the structure of Citrinalin B and how “use of Goodman’s DP4 method indicates a 100% probability that the structure of citrinalin B is (the structure below)”. Wow, that is even higher than the physicists. Of course, 100% has been obtained by rounding 99.7 (3σ is 99.73%) or whatever (this is one number that should never be so rounded!). 
But there was one aspect of this that I did want to have a confidence level for; the absolute configuration of citrinalin B. Reading the article Steve quotes[cite]10.1038/nature13273[/cite], one sees this aspect is attributed to ref 5[cite]10.1021/jo051499o[/cite], dating from 2005. There the configuration was assigned on the basis of “comparison of the electronic circular dichroism (ECD) spectra for 1 and 2 with those of known spirooxiindole alkaloids“. However, this method can fail[cite]10.1002/chem.201101129[/cite]. Also, one finds “comparison of the vibrational circular dichroism (VCD) spectra of 1 with those of model compounds“[cite]10.1021/jo051499o[/cite]. Nowadays, one would say that there is no need for model compounds, why not measure and compute the VCD of the actual compound? Even a determination using the Flack crystallographic method can occasionally be wrong![cite]10.1021/jo401316a[/cite]. Which leads to asking what typical confidence levels might be for these three techniques, and indeed whether improving instrumentation means that the confidence level gets higher with time. OK, I am going to guess these.
The price of information: Evaluating big deal journal bundles
July 3rd, 2014Increasingly, our access to scientific information is becoming a research topic in itself. Thus an analysis of big deal journal bundles[cite]10.1073/pnas.1403006111[/cite] has attracted much interesting commentary (including one from a large scientific publisher[cite]10.1038/510447f[/cite]). In the UK, our funding councils have been pro-active in promoting the so-called GOLD publishing model, where the authors (aided by grants from their own institution or others) pay the perpetual up-front publication costs (more precisely the costs demanded by the publishers, which is not necessarily the same thing) so that their article is removed from the normal subscription pay wall erected by the publisher and becomes accessible to anyone. As the proportion of GOLD content increases, it was anticipated (hoped?) that the costs of accessing the remaining non-GOLD articles via a pay-walled subscription would decrease.
Amides and inverting the electronics of the Bürgi–Dunitz trajectory.
June 26th, 2014
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. 
My first thought was to calculate the wavefunction and identify the location and energy (= electrophilicity) of the lone pairs (the presumed attractor of an electrophile). But a better more direct approach soon dawned. A search of the crystal structure database. Here is the search definition, with the C=O-E angle, the O-E distance and the N-C=O-E torsion defined (also specified for R factor < 5%, no errors and no disorder). 
The first plot is of the torsion vs the distance, for E = H-X (X=O,F, Cl) 
Anchoring chemistry.
June 18th, 2014I 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.
Test of JSmol in WordPress: the background story.
June 8th, 2014A 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. Like most software technologies, much has changed, and Java itself (as a compiled language) has had to move to improve its underlying security. In the last year, the Java code itself (in this case Jmol) has needed to be digitally signed in a standard manner, and this meant that many an old site that used unsigned older versions has started to throw up increasingly alarming messages.
Kekulé’s vibration: A modern example of its use.
June 6th, 2014Following 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. The idea was sparked by Steve Bachrach’s latest post, where the “zero-point” structure of the molecule has recently been clarified as having D2 symmetry.[cite]10.1002/chem.201304972[/cite]
Benzene: an oscillation or a vibration?
May 28th, 2014In 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. The original article is in german, but more significantly, obtainable only with difficulty. Thus I cannot access[cite]10.1002/jlac.18721620110[/cite] the article directly since my university does not have the appropriate “back-number” subscription.‡ So it was with delight that I tracked down an English translation in a journal that I could easily access.[cite]10.1039/JS8722500605[/cite] Here I discuss what I found (on pages 614-615, the translation does not have its own DOI).