Science Poetry

Climb Ev’ry Mountain

“To isolate state of transition,
Note how E relies on position: 
The resulting stratagem 
Seeks energy’s maximum
In calc’s geometric submission.”

The 16 April 2022 Twitter limerick returned to more conceptual material, summarizing a specific type of chemistry calculation called a transition-state optimization.

“To isolate state of transition, /
Note how E relies on position…”

A transition-state optimization calculates the energy of a molecule (or chemical entity, more broadly) as a function of its molecular geometry; molecular geometry is a shorthand communicating the position of all the atoms in a given molecule.  The overall shape of most reaction coordinates resembles a hill; it represents an energetic barrier, which must be overcome for the reaction to occur and the products to be formed.  The transition state is at the top of this “hill.”    

To figure out the energy that a reaction needs to proceed, it is necessary to determine the height of the peak that must be scaled: to find the transition state (to “isolate state of transition”).  To achieve this, a chemist generates a drawing or a set of data representing a molecule and submits it to a computational software package.  The ensuing calculations determine energy (E) as a function of the position-related data: aiming to see how the energy changes as positions of the atoms change.    

“The resulting stratagem /
Seeks energy’s maximum /
In calc’s geometric submission.”

The verses in this site have summarized an energy minimization before: how to identify a reaction’s reactants and products, by looking for the lowest-possible energy arrangement of a molecule: the minimized molecular shapes on either side of the reaction barrier.  

A transition-state optimization is the opposite; this “strategem” seeks to find the greatest-possible energy arrangement for the species of interest.  In other words, this is an energy maximization process, aiming to identify the species at the top of the energetic barrier, “climbing the mountain,” in the famously melodic words of this post’s title.