Henry Rzepa's Blog Chemistry with a twist

April 22, 2020

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

Filed under: reaction mechanism — Henry Rzepa @ 9:04 am

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.

Each example takes the form of two movie animations, one showing the classical IRC path and the other the “major trajectory” (DT) resulting from a molecular dynamics calculation. The latter representation incorporates molecular vibrations into the picture, showing how they evolve from reactants into a reaction product over a time period. Dynamics are a more realistic picture of how a molecule actually reacts. Any given trajectory can follow its own path, but the most common path for it to take is indeed that defined by the IRC and here you can compare the two approaches. What is interesting of course are those examples where the IRC and DT differ, with perhaps the latter not necessarily following the minimum energy path charted by the former. Even more fascinating are those non-classical reactions where a given IRC path, as defined by a single unique transition state at the top of the energy barrier, can nonetheless result in two or more different reaction outcomes. [1] See my analysis.

This databank is still young, with eight reactions at the time this blog was written. Suggestions for new reactions are invited, and I do hope it grows rapidly. Also I look forward to a section describing the technicalities of how the DT are computed and what sorts of resources are required to do this routinely (an article describing the databank is being prepared). In particular, how do the computer time resources needed for IRC and DT compare? It is good indeed to see this dynamic picture entering into the undergraduate taught curriculum.


For an example of a differing outcome, see here.

References

  1. X.S. Bogle, and D.A. Singleton, "Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction", Organic Letters, vol. 14, pp. 2528-2531, 2012. http://dx.doi.org/10.1021/ol300817a

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