“A nucleophilic incursion
In polar aprotic submersion,
With leaving group egress
As synchronous process:
It’s SN2 (Walden inversion).”
The 4 April 2022 limerick was the first in a week of posts that summarized specific organic chemistry mechanisms: step-by-step depictions of how molecules transform over the course of a given reaction.
I remember my introduction to chemical mechanisms as involving a tremendous amount of specialized vocabulary: with exams perpetually on the near horizon, it seemed like I needed to memorize several complicated terms long before I could process what each of them truly meant. This poem and the ones that follow are intended to put some of the key trends and words together in a memorable way for someone trying to learn the basics.
In a first for these essays, I think it will be useful to have a small illustration for a few of these, over the next five weeks. Some additional introductory words are likely useful here, too, since one of the few things I suspect of being even more off-putting than unexpected chemistry jargon would be an unexpected chemistry diagram!
In these diagrams, curved arrows show electron flow, which is the underlying impetus for all of these processes. The curved arrow starts where the excess electrons are and points to where they end up, in a given reaction step; electrons typically move in pairs (two at a time). Lines represent covalent bonds. Dash-wedge notation shows three-dimensional (3-D) arrangements of these bonds. A “wedged” triangle shows that the bond is coming towards the viewer, and a “dashed” triangle shows that the bond is behind the screen.
(This illustration is brought to you courtesy of the whiteboard setup still present in my kitchen, which has never quite recovered from being a Spring 2020 classroom.)
Finally, to turn back to today’s mechanism and limerick: one of the simplest mechanisms of interest in Organic Chemistry is the SN2 process, depicted above. Overall, it is a depiction of how Molecule A turns into Molecule B: how a negatively charged nucleophile (abbreviated generically as Nuc above) replaces the bromine atom in the original molecule; as part of the same process, the bromine atom “leaves” the original molecule, becoming a negatively charged bromide ion, also characterized as the leaving group.
“A nucleophilic incursion /
In polar aprotic submersion…”
Two mechanisms commonly taught to organic chemistry students are SN1 and SN2: two types of nucleophilic substitution (abbreviated as SN) that were both celebrated during NaPoWriMo2022. Both involve a nucleophilic attack, or “incursion.” SN1 reactions occur via a two-step process; SN2 reactions occur via a single, concerted step. (This non-intuitive naming is because one species is involved in the rate-determining step of an SN1 mechanism, whereas two species are involved in the rate-determining step of an SN2 mechanism… since its single step is the only one!)
A perennial, early challenge for students is discerning via which mechanism a nucleophilic substitution occurs. One clue is the solvent (the reaction medium). SN2 reactions are favored by polar aprotic solvents (polar solvents that lack a proton; acetone is a common choice), while SN1 reactions are favored by polar protic solvents (such as water). “Polar aprotic submersion” denotes that the reaction occurs in polar aprotic solvent, hinting at SN2.
“With leaving group egress /
As synchronous process…”
As shown above, in an SN2 process, the nucleophile attacks simultaneously with the departure of the leaving group (“leaving group egress”), since everything happens at once (a “synchronous process”).
“It’s SN2 (Walden inversion).”
The closing line reveals the SN2 label and a corresponding inversion of stereochemistry: the 3-D arrangement of the atoms. The inversion is named for Paul Walden, the chemist who studied the process in 1896, and can be detected when the reaction occurs at a chiral center (which is not the case shown above).