Question for the day – Einstein, special relativity and atomic weights.

July 25th, 2020

Sometimes a (scientific) thought just pops into one’s mind. Most are probably best not shared with anyone, but since its the summer silly season, I thought I might with this one.

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The Willgerodt-Kindler Reaction: mechanistic reality check 1.

July 21st, 2020

The Willgerodt reaction[1], discovered in 1887 and shown below, represents a transformation with a once famously obscure mechanism. A major step in the elucidation of that mechanism came[2] using the then new technique of 14C radio-labelling, shortly after the atom bomb projects during WWII made 14CO2 readily available to researchers. Here I am going to start the process of applying the far more recent technique of quantitative quantum mechanical modelling to see if some of the proposed mechanisms stand up to its scrutiny.

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  1. C. Willgerodt, "Ueber die Einwirkung von gelbem Schwefelammonium auf Ketone und Chinone", Berichte der deutschen chemischen Gesellschaft, vol. 20, pp. 2467-2470, 1887.
  2. W.G. Dauben, J.C. Reid, P.E. Yankwich, and M. Calvin, "The Mechanism of the Willgerodt Reaction1", Journal of the American Chemical Society, vol. 72, pp. 121-124, 1950.

Curly arrows in the 21st Century. Proton-coupled electron transfers.

June 10th, 2020

One of the most fascinating and important articles dealing with curly arrows I have seen is that by Klein and Knizia on the topic of C-H bond activations using an iron catalyst.[1] These are so-called high spin systems with unpaired electrons and the mechanism of C-H activation involves both double headed (two electron) and fish-hook (single electron) movement. Here I focus on a specific type of reaction, the concerted proton-coupled-electron transfer or cPCET, as illustrated below. These sorts of reactions happen also to be of considerable biological importance, including e.g. the mechanism of photosynthesis and many other important transformations.

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  1. J.E.M.N. Klein, and G. Knizia, "cPCET versus HAT: A Direct Theoretical Method for Distinguishing X-H Bond-Activation Mechanisms", Angewandte Chemie International Edition, vol. 57, pp. 11913-11917, 2018.

Fascinating stereoelectronic control in Metaldehyde and Chloral.

June 9th, 2020

Metaldehyde is an insecticide used to control slugs. When we unsuccessfully tried to get some recently, I discovered it is now deprecated in the UK. So my immediate reaction was to look up its structure to see if that cast any light (below, R=CH3, shown as one stereoisomer).

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The first ever curly arrows. Revisited with some crystal structure mining.

May 27th, 2020

With the current global lockdown, and students along with everyone else staying at home, I have noticed some old posts of mine are getting more attention than normal. One of these is an analysis I did in 2012 of Robinson’s original curly arrow illustration.[1] That and the fact that I am about to give a lecture on what I call my autobiographical journey discovering them, to our own students here (remotely of course), has prompted me to revisit my original discussion.

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  1. "Forthcoming events", Journal of the Society of Chemical Industry, vol. 43, pp. 1295-1298, 1924.

The strongest bond in the universe: A crystallographic reality check?

May 25th, 2020

My previous two posts on the topic of strongest bonds have involved mono and diprotonating N2 and using quantum mechanics to predict the effect this has on the N-N bond via its length and vibrational stetching mode. Such species are very unlikely to be easily observed for verification. But how about a metal M+ instead of H+? It turns out that structures containing the fragment Ru-N≡N-Ru are a small but well studied class of organometallic. Here is a search of the CSD crystal database for this motif.

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The strongest bond in the universe: revisited ten years on.

May 23rd, 2020

I occasionally notice that posts that first appeared here many years ago suddenly attract attention. Thus this post, entitled The strongest bond in the universe, from ten years back, has suddently become the most popular, going from an average of 0-2 hits per day to 92 in a single day on May 22nd (most views appear to originate from India). I can only presume that a university there has set some course work on this topic and Google has helped some of the students identify my post. Well, re-reading something you wrote ten years ago can be unsettling. Are the conclusions still sound? Would I establish my claim the same way now? After all, one picks up a little more experience in ten years. So here is my revisitation.

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Choreographing a chemical ballet: what happens if you change one of the actors?

May 8th, 2020

Earlier, I explored the choreography or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated imine rather than carbonyl compound (scheme 2). 

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Discussion of (the) Room-temperature chemical synthesis of dicarbon – open and transparent science.

May 6th, 2020

A little more than a year ago, a ChemRxiv pre-print appeared bearing the title referenced in this post,[1] which immediately piqued my curiosity. The report presented persuasive evidence, in the form of trapping experiments, that dicarbon or C2 had been formed by the following chemical synthesis. Here I describe some of what happened next, since it perhaps gives some insight into the processes of bringing a scientific result into the open.

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  1. K. Miyamoto, S. Narita, Y. Masumoto, T. Hashishin, M. Kimura, M. Ochiai, and M. Uchiyama, "Room-Temperature Chemical Synthesis of C2", 2019.

A databank of molecular dynamics reaction trajectories (DDT) focused on undergraduate teaching.

April 22nd, 2020

In a previous post, I talked about a library of reaction pathway intrinsic reaction coordinates (IRCs) containing 115 examples of organic and organometallic reactions. Now (thanks Dean!) I have been alerted to a brand new databank of dynamics trajectories (DDT), with the focus on those reactions taught in undergraduate organic chemistry courses, some of which are shown below.

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