When I first heard about organic reaction mechanisms, I was convinced that it was something coming out of my teacher’s imagination. I did not want to learn them (and bombed the exam). Fortunately, that feeling did not last. I quickly realized that arrow-pushing, although cartoonish, was the best way for organic chemists to illustrate how molecules behaved. Most importantly, these cartoons are not simply projections of our imagination. They are the best theories we have based on experimental evidence.
During my Ph.D. in experimental organic chemistry, my chemical intuition got better. I improved at proposing and writing mechanisms, but they were still but mere drawings on a board. I knew they represented something real, but I couldn’t see that something. It’s only when I joined the Houk group for my post-doc that it finally clicked. Watching a Diels-Alder transition structure vibrate for the first time, I was hooked. We shouldn’t say that arrows portray the movement of electrons (even if it’s true)! We should emphasize that arrows show bonds forming and breaking, and with them molecules changing. With some help from computational software, it is even possible to model how that looks like.
For the last six years of my career, my research has brought me to look at 3D representations of molecules reacting. It has greatly improved my mastery of organic chemistry and I now hope that it can do the same for others. Organic reaction mechanisms make so much sense once you’ve seen them happen on a screen. Connecting the movement of atoms to the arrows on the paper is much simpler then. I truly believe that visualizing organic reactions makes learning organic chemistry easier.
So while we were doing remote work in 2020, my team and I got to work to design this resource. Our first tasks will be to create animations of many textbook organic reactions so that students taking introductory organic chemistry will better understand organic mechanisms. And based on my successful transition from experimental to computational chemist in 2015, I wish to encourage more synthetic chemists to pick up computational chemistry. Soon, we will share some detailed tutorials on how to get started, in case it can push anyone to try it.
If you have any suggestions on how to improve the site, or want to suggest reactions you would like covered, leave a comment below!
