Previously, I explored the Graham reaction to form a diazirine. The second phase of the reaction involved an Sn2′ displacement of N-Cl forming C-Cl. Here I ask how facile the simpler displacement of C-Cl by another chlorine might be and whether the mechanism is Sn2 or the alternative Sn1.

At rOpenSci we are developing on a suite of packages that expose powerful graphics and imaging libraries in R. Our latest addition is av – a new package for working with audio/video based on the FFmpeg AV libraries. This ambitious new project will become the video counterpart of the magick package which we use for working with images.

The gifski package which was demonstrated in May at eRum 2018 in Budapest is now on CRAN. Gifski is a simple but powerful package which can hopefully take away an important performance bottleneck for generating animated graphics in R. What is Gifski Gifski is a multi-threaded high-quality GIF encoder written in Rust. It can create animated GIF images with thousands of colors per frame and do so much faster than other software.

I noted in my WATOC conference report a presentation describing the use of calculated reaction barriers (and derived rate constants) as mechanistic reality checks. Computations, it was claimed, have now reached a level of accuracy whereby a barrier calculated as being 6 kcal/mol too high can start ringing mechanistic alarm bells.

A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C).[cite]10.1073/pnas.1709586114[/cite] The mechanism involves an initial equilibrium between React and Int1 , followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate ( Int2 below, as per

It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key.

The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally. The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO ⁵⁺ cation, giving a tri-cationic complex. There are no examples of the resulting motif in the Cambridge structure database.

The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD). I have used ethane instead of methane, since it is now possible to

Is asking a question such as “what is the smallest angle subtended at a chain of three connected 4-coordinate carbon atoms” just seeking another chemical record, or could it unearth interesting chemistry?

In answering tutorial problems, students often need skills in deciding how much time to spend on explaining what does not happen, as well as what does. Here I explore alternatives to the mechanism outlined in the previous post to see what computation has to say about what does (or might) not happen.