Flowing Mechanisms in Chemistry


Many chemical reactions are explained by means of a mechanism. In a mechanism, the flow of electrons that cause atoms to rearrange is presented from start to finish. This is vital to all chemical reactions. The problem is that this cannot be depicted very well using drawings made by a computer. Those usually show the end-product, with all the arrows displayed at once. It is hard for students to know where to start and how to continue; it is not clear how a mechanism develops. This leads to the observation that in many advanced courses beginner mistakes are being made, even during exams. This has to be corrected during the course, which takes away time that should be spend on the actual course material. In view of the shorter teaching hours that are implemented from 2018-2019 academic year, it becomes even more important to think of smart methods to educate.  

During this project, so-called Pencasts for each mechanism will be made. Using a Livescribe pen (which contains a camera that records the writing), special A4-recording paper, and a smartphone, the teacher will record the own written mechanism (including audio). The product is a pdf-file that can be dropped-and-played on a website, played directly in the latest versions of Adobe Acrobat, and on Apps on the smartphone. The student sees a page like the one shown above, where in grey the final product is depicted, and in green the current stage of the drawing. Together with the audio comments, the student is able to see how an experienced chemist draws a chemical mechanism. This not only teaches the student how a specific mechanism develops over the course of time, but she/he can also see similar patterns being used in different mechanisms.

For each mechanism in the 1st and 2nd year Organic Chemistry classes (ORC-12803, ORC-12903, and ORC-20306), a Pencast will be made. These range from vary basic nucleophilic substitution reactions, to more complex 1,2-diol protection of carbohydrates, and the catabolism of amino acids. Simple mechanisms can be explained in short movies (up to 5 mins), whereas more complex mechanisms can be explained in longer movies, if needed spread out over multiple pages (10-15 mins).


The aim is to help students learn how to draw a chemical mechanism. In the classical method, a mechanism is depicted on the PowerPoint slide from start to finish. This does not reveal how the mechanism starts, i.e. which electrons move first / the order of electron flow and atom rearrangements. An improvement of this was to add numbers to the mechanism, but this makes the image rather complex. 

Having seen the possibility of the Livescribe Pen, which track drawings made on paper, and converts them into a (short) movie via an app on a mobile device, we realized this could be a valuable method to teach students reaction mechanisms. Since it also allows to record audio at the same time of making the drawing, it’s possible to comment on what is shown and add additional explanation. 

It is our aim that MLW-students from the WU will be known for their ability to draw sound chemical mechanisms, even if they are very complex and contain combinations of steps that students have encountered in simpler mechanisms.


We managed to make 40 Pencasts. These describe, still, some elementary principles (for example how one can understand that C-atoms make four bonds, and N-atoms only three), but also very complex multi-step mechanisms of complex metabolic pathways. Although we are satisfied with the current library of Pencasts, we still have the ambition to improve some. The Pencastst are a useful source to use in the various classes, but also to use for individual students. 61% of the students found them very helpful which underscores their added value.


For more information or recommendations, please contact Bauke Albada.


Pencasts are available for education purposes in ORC, visit our website wur.eu/orc.