Derek Lowe reports the story[cite]10.1126/science.abq0516[/cite] that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube. So I thought it would be fun to compute exactly where that electron sits!
Archive for August, 2022
Octafluorocubane radical anion – where does the extra electron sit?
Monday, August 29th, 2022Four stages in the evolution of interactive ESI as part of articles in chemistry journals.
Thursday, August 25th, 2022A previous post was triggered by Peter alerting me that interactive electronic supporting information (IESI) we had submitted to a journal in 2005[cite]10.1021/ic0519988[/cite] appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient IESIs were in 2022. I have now reached 2014 in this journey, which is being recorded as it happens in the comments page of the post. I discovered there were four distinct stages in that evolution of IESI which I thought it would be of interest to record here.
Unexpected Isomerization of Oxetane-Carboxylic Acids – an alternative autocatalytic mechanism evaluated.
Wednesday, August 17th, 2022Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result. Here I look at an alternative mode where the oxetane-carboxylate itself acts as the transfer chain, via a H-bonded dimer shown below.
Unexpected Isomerization of Oxetane-Carboxylic Acids – substrate design.
Sunday, August 14th, 2022Having established a viable model for the unexpected isomerism of oxetane carboxylic acids to lactones[cite]10.1021/acs.orglett.2c01402[/cite], and taken a look at a variation in the proton transfer catalyst needed to accomplish the transformation, I now investigate the substrate itself.
Unexpected Isomerization of Oxetane-Carboxylic Acids – catalyst design.
Saturday, August 13th, 2022Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring. 
Web page decay and Journals: How an interactive “ESI” from 2006 was rescued.
Friday, August 12th, 2022In 2006[cite]10.1021/ic0519988[/cite] we published an article illustrating various types of pseudorotations in small molecules. It’s been cited 20 times since then, so reasonable interest! We described rotations known as Lever and Turnstile as well as the better known Berry mode. Because the differences between these rotations are quite subtle, we included an interactive electronic supporting information to illustrate them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a long time in the Web ecosystem (some early wag suggested, like dogs, that one year in normal time approximates to about 7 years in Web time) and inevitably, like e.g. both Rasmol[cite]10.1039/P29950000007[/cite] and Chime before it, Jmol no longer works when invoked from a Web browser; Java applets are very much dead and we are now on the fourth generation of molecule viewer, JSmol. Two days ago I was contacted by someone (thanks Peter!) who had noticed that the journal landing page did not seem to point to any ESI. Here I tell the story of what happened next.
Unexpected Isomerization of Oxetane-Carboxylic Acids – a viable mechanism
Friday, August 12th, 2022In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives.
Unexpected Isomerization of Oxetane-Carboxylic Acids – a first look at the mechanism
Sunday, August 7th, 2022Derek Lowe’s blog has a recent post entitled A Downside to Oxetane Acids which picks up on a recent article[cite]10.1021/acs.orglett.2c01402[/cite] describing how these acids are unexpectedly unstable, isomerising to a lactone at a significant rate without the apparent need for any catalyst. This is important because these types of compound occur frequently in the medicinal chemistry literature.