Archive for the ‘reaction mechanism’ Category
Tuesday, 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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References
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C. Willgerodt, "Ueber die Einwirkung von gelbem Schwefelammonium auf Ketone und Chinone", Berichte der deutschen chemischen Gesellschaft, vol. 20, pp. 2467-2470, 1887. http://dx.doi.org/10.1002/cber.18870200278
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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. http://dx.doi.org/10.1021/ja01157a034
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Wednesday, 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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References
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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. http://dx.doi.org/10.1002/anie.201805511
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Friday, 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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Wednesday, 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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References
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K. Miyamoto, S. Narita, Y. Masumoto, T. Hashishin, M. Kimura, M. Ochiai, and M. Uchiyama, "Room-Temperature Chemical Synthesis of C2", 2019. http://dx.doi.org/10.26434/chemrxiv.8009633.v1
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Wednesday, 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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Monday, April 13th, 2020
A reaction can be thought of as molecular dancers performing moves. A choreographer is needed to organise the performance into the ballet that is a reaction mechanism. Here I explore another facet of the Michael addition of a nucleophile to a conjugated carbonyl compound. The performers this time are p-toluene thiol playing the role of nucleophile, adding to but-2-enal (green) acting as the electrophile and with either water or ammonia serving the role of a catalytic base to help things along.†
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Sunday, March 29th, 2020
In the previous post, I looked at the mechanism for 1,4-nucleophilic addition to an activated alkene (the Michael reaction). The model nucleophile was malonaldehyde after deprotonation and the model electrophile was acrolein (prop-2-enal), with the rate determining transition state being carbon-carbon bond formation between the two, accompanied by proton transfer to the oxygen of the acrolein.
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Wednesday, March 25th, 2020
In 2013, I created an iTunesU library of 115 mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here. That collection is still available and is viewable in the iTunesU app on an iPhone or an iPad. The realisation struck me now‡ that one of the types not described in that library was Michael-type 1,4-nucleophilic addition to an activated alkene, as described at Wikipedia. So here is that addition.
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Wednesday, October 9th, 2019
If, as a synthetic chemist, you want to invert the configuration of an alcohol in which the OH group is at a chiral centre, then the Mitsunobu reaction has been a stalwart for many years. Now a catalytic version has been published, [1] along with a proposed mechanism. Here I apply computation as a reality check to see what the energetics of this mechanism might be.
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References
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R.H. Beddoe, K.G. Andrews, V. Magné, J.D. Cuthbertson, J. Saska, A.L. Shannon-Little, S.E. Shanahan, H.F. Sneddon, and R.M. Denton, "Redox-neutral organocatalytic Mitsunobu reactions", Science, vol. 365, pp. 910-914, 2019. http://dx.doi.org/10.1126/science.aax3353
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Thursday, May 2nd, 2019
Ken Houk’s group has recently published this study of cycloaddition reactions, using a combination of classical transition state location followed by molecular dynamics trajectory calculations,[1] and to which Steve Bachrach’s blog alerted me. The reaction struck me as being quite polar (with cyano groups) and so I took a look at the article to see what both the original[2] experimental conditions were and how the new simulations compared. The reaction itself is shown below.
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References
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X. Xue, C.S. Jamieson, M. Garcia-Borràs, X. Dong, Z. Yang, and K.N. Houk, "Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity", Journal of the American Chemical Society, vol. 141, pp. 1217-1221, 2019. http://dx.doi.org/10.1021/jacs.8b12674
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C.Y. Liu, and S.T. Ding, "Cycloadditions of electron-deficient 8,8-disubstituted heptafulvenes to electron-rich 6,6-disubstituted fulvenes", The Journal of Organic Chemistry, vol. 57, pp. 4539-4544, 1992. http://dx.doi.org/10.1021/jo00042a039
Tags:Chemistry, computational chemistry, Implicit solvation, Ken Houk, Molecular dynamics, Molecular modelling, Natural sciences, Physical sciences, Solutions, Solvent, Solvent model, Solvents, Steve Bachrach, Theoretical chemistry
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