Tag: chemistry

“An arrow deemed retrosynthetic
Portrays a reflective aesthetic:
Reverse contemplation
To starting location
In pondering routes hypothetic.”

The next type of reaction arrow highlighted in verse, in the 19 April 2023 Twitter limerick, was the “retrosynthetic arrow,” which visually indicates a specific type of analysis most typically completed by organic chemists.  

“An arrow deemed retrosynthetic /
Portrays a reflective aesthetic…”

The retrosynthesis arrow has one of the most distinctive appearances of the arrows described in these poems, indicating the need for retrosynthesis: thinking backwards, via a “reflective aesthetic.”  It is a hollow arrow pointing from the left to the right.  It is probably most illustrative to contrast it with the other left-to-right arrow we’ve seen thus far. 

Reaction 1 (above) is the typical case we’ve seen before: Reactant A forms Product B. 

By contrast, Reaction 2 below indicates that we consider Species A as the target molecule in an organic synthetic project (the molecule that we want to synthesize in the lab). Species B in this case is the precursor: something that could be used as a reactant to form target Species A as a product. The unusual arrow communicates this thought process.  

“Reverse contemplation /
To starting location…”

Typically, then, we would continue thinking backwards, as in simplified Reaction 3: all the way to starting materials that were readily available (either easy-to-synthesize or listed in a catalog), generalized here as Species D.  

In poetic terms, our “reverse contemplation” would continue all the way back to “starting location.”

“In pondering routes hypothetic.”

Chemist E. J. Corey won the Nobel Prize in 1990 for formally developing the technique of retrosynthesis.  This “pondering [of] routes hypothetic” has led to many insights in organic chemistry. 

Here, the subtle difference in arrow notation indicates a specific and valuable technique for an organic chemist to understand. 

“A route’s back-and-forth versatility:
A question again for agility
Of arrow notation:
Tell-tale variation
Can indicate reversibility.”

The 18 April 2023 Twitter limerick continued a sequence of poems that aimed to highlight different types of arrows used in chemistry communication.  

“A route’s back-and-forth versatility: /
A question again for agility /
Of arrow notation…”

We typically consider reactions as going only in the forward direction, from Point A to Point B, from reactants to products.  However, it is more precise to say most reactions are reversible, so that either direction (Point A to Point B…OR Point B to Point A!) can technically be favored by considering the reaction conditions of interest.  (Varying the temperature, pressure, and amounts of species involved in the reaction equilibrium would be a few ways to achieve this.)  

This aspect of a chemical reaction (“the route’s back-and-forth versatility”) can be specifically shown in a few ways.  The most characteristic denotation is two half-headed arrows, one pointing left and one pointing right, stacked on top of one another.  That is, rather than A → B, we would write A ⇌ B.  We would describe this reaction as “shifting left” if the pertinent conditions tended to form more of species A or “shifting right” if the pertinent conditions tended to form more of species B.    

“Tell-tale variation /
Can indicate reversibility.”

This poem and the next few will highlight increasingly specific notation variations that indicate increasingly specific chemical principles: in this case, the “tell-tale” reaction arrow of interest highlights the reversibility of the reaction.  The double-headed arrow tells us something different than a “left-to-right” arrow would.    

As with last week, this post will be relatively brief, since the aim of each limerick in this series is simply to highlight (and describe) how the featured type of arrow is distinct from the others.  

“The arrow’s most classic citation
Provides chem reaction’s narration:
Reactants yield products;
Denoting said progress,
The “verb” in the balanced equation.”

The 17 April 2023 limerick discussed the most traditional use of an arrow within a chemical reaction’s setting: showing the reaction progress moving forward from reactants to products.   

“The arrow’s most classic citation /
Provides chem reaction’s narration…”

If a student has encountered previous chemistry coursework, the first arrow of interest is likely familiar; it is a relatively “classic citation,” as such discussions go.  

When a reaction is written on a sheet of paper, reactants are written on the left-hand side, while products are written on the right-hand side. In between them is a single-headed arrow pointing from left to right.  

This arrow thus “narrates” the process by showing that the reactants on the left will form the products on the right, over the course of the chemical reaction.  

“Reactants yield products; /
Denoting said progress, /
The ‘verb’ in the balanced equation.”

These last three lines are a rhymed restatement of the last point from the previous section. This arrow in the reaction is what conveys the actual progress of the chemical step underway, becoming the “verb,” as one translates a chemical reaction’s notations to words.

Below is a reaction I’ve written about previously in this space, carbonatation (or carbonation), in which a fresco surface reacts with carbon dioxide in the air to provide a work of art notable for its longevity.  

Ca(OH)₂ (aq) + CO₂ (g) → CaCO₃ (s) + H₂O (l)

This reaction can be translated to words: aqueous calcium hydroxide and gaseous carbon dioxide react to form solid calcium carbonate and liquid water.  

The chemical formulas each correspond to a precise compound name; the letters in parentheses, to a description of each compound’s phase; the arrow corresponds to the phrase “react to form.”  

Future poems on this theme will examine arrows that represent more complicated phenomena, but this first example is relatively simple. 

“In reading reaction’s drawn evidence,
Consider notational relevance: 
What seems like a muddle
Of differences subtle
Resolves through an arrow analysis!”

I am back to campus for a new semester, and so it is helpful to also return to this writing routine. The second half of NaPoWriMo 2023 began with a set of Twitter poems highlighting “chemical notation week” in the hashtags, a theme that seems like a bit of a hard sell as I revisit these in early 2024!  I’ll plan on one post per poem, through the next several weeks; however, if the writing starts getting extremely dense, I might combine and summarize a few.

“In reading reaction’s drawn evidence, /
Consider notational relevance…”

The goal of this series of poems was to highlight how seemingly small differences in reaction arrow notation can play major roles in chemistry settings: how a “reaction’s drawn evidence” (its interpretation by another chemist) relies heavily on its specific “notational relevance” (the precise usage of the correct notation for the process of interest).  

This is a point that often can be frustratingly unexpected for chemistry learners: where what appears to be a small error results in what seems like a disproportionate effect on a graded assessment.  My goal was that this set of limericks would be an accessible and fun way to deliberately introduce and emphasize these important differences in notation.  

“What seems like a muddle /
Of differences subtle /
Resolves through an arrow analysis!”

The last three lines address what the themes of the next few poems and posts will be: first, that chemical reactions can communicate information that seems confusingly dense; second, that careful attention to these subtleties can resolve the confusion.  In particular, the many types of reaction arrows will be explored over the next several poems.

The last line relies on a pun between “error analysis,” which is a common theme of many lab reports, as the propagation of error throughout an experiment is quantified, and “arrow analysis”: the close examination of reaction arrows that these poems will involve. 

On precipice of winter-breaking,
With final-exam-prep painstaking,
These lines anapestic
Are far from majestic
(Last rhymed autumn-term undertaking).  

This non-Twitter poem probably requires little interpretation, near the close of a hectic semester, but I will give it a bit of additional context. 

On precipice of winter-breaking, /
With final-exam-prep painstaking…

We are in the last week of classes here, prior to Finals Week (and then the Grading/Meeting Weeks…), before a brief winter break. 

In the academic timeline, attention has thus shifted primarily to preparations for the final exams: reviewing and reflecting on the chemistry content from a busy semester.      

These lines anapestic /
Are far from majestic…

The metric feet used in limericks are anapests and amphibrachs. In this setting, the adjective form of the first lends itself particularly well to a sardonic rhyme, since my end-of-term work tends to focus primarily on simply accomplishing tasks, rather than achieving any sort of impressiveness in doing so!  The close of autumn term can seem particularly draining as the daylight wanes throughout the semester, whereas in spring, the shift back to longer daylight hours often provides a welcome boost in the last few weeks of the semester.         

(Last rhymed autumn-term undertaking).  

While it’s possible I might aim for a more extensive essay before year’s end, this will nonetheless be the last post during the autumn term itself, as highlighted in the last line. 

Together, the “precipice” of the first line and the semester’s drawing to a close are what prompted the title of this specific piece.

“A compound in classrooms to celebrate,
As one writes, reflects, notes, or calculates:
A session’s board-chalking
Can supplement talking
Through cases of calcium carbonate!”

The 15 April 2023 limerick commemorated a chemical compound commonly found in academic spaces: calcium carbonate, as part of chalk.  

“A compound in classrooms to celebrate, / 
As one writes, reflects, notes, or calculates…”

I have been through decades of classes at this point, as a student and a teacher, so I have seen chalk employed for a variety of purposes in a variety of settings (for a variety of years).  The utility of chalk and a chalkboard for documenting a process— solving an equation, balancing a reaction, diagramming a sentence, outlining a story— is particularly pronounced.  While classroom chalk can also sometimes consist of other compounds, calcium carbonate is the focus of this particular poem, as the final line will reveal. 

“A session’s board-chalking /
Can supplement talking /
Through cases of calcium carbonate!”

One of the reasons I rely on the chalk/chalkboard combination in my teaching is that I can pace myself more reasonably, providing clear context for each step of solving a problem rather than going too rapidly toward the answer.  The “session’s board-chalking can supplement talking” and ensure I do not rush ahead.  (“Cases of calcium carbonate” is a needlessly complex phrasing for “boxes of chalk”!)  

As with many aspects of day-to-day academic life, the origins of both using chalk with a chalkboard and erasing chalk with a chalkboard eraser are more complex than I had previously realized.  A past exhibition in the Smithsonian highlights the importance of the chalkboard in math education and its use in the USA since the early 1800s, although similar uses had been established around the world for centuries previous.    

“In chemistry’s schemes mechanistic,
Find blend analytic-artistic…
See bonds’ breaking/forming;
Electrons’ unmooring:
All shown through line drawings, logistic.”

The 14 April 2023 limerick summarized an interesting overlap of chemistry and art, in terms of the drawings that chemists use to depict reactions.

“In chemistry’s schemes mechanistic, /
Find blend analytic-artistic… “

I’ve written often about my interest in the chemistry underlying artistic techniques, such as frescoes and cyanotypes.  Another way in which chemistry and art overlap is with respect to the symbolic representations used to describe the step-by-step progress of chemical reactions; these representations are called mechanisms (or “schemes mechanistic”).  

Organic chemists, especially, spend much time learning to draw these “blend[s] analytic-artistic,” in which the logical flow of a set of steps can be followed from reactants to products.  

“See bonds’ breaking/forming; /
Electrons’ unmooring: /
All shown through line drawings, logistic.”

Mechanisms are also called “electron-pushing diagrams” or “arrow-pushing diagrams.”  Pioneered by Robert Robinson (1886-1975), the drawings allow a chemist to easily show the breaking and forming of bonds between atoms, as well as the movement of electrons within and between molecules, using curved arrows.  The arrows begin where the electrons are and point to where they will go, as shown in the substitution- and elimination-themed poems from last autumn.  

I’ve written recently on the power of line drawings in organic chemistry, where even a simple hyphen can be reasonably read by a chemist as the molecule ethane.  To read through a multi-step mechanism is to see the immense utility of these “line drawings, logistic” when used in communication among chemists.  

Interestingly, throughout NaPoWriMo 2023, I found it a fun challenge to describe in verse the considerable variety of arrows in chemistry, so I plan to return to this topic, with some additional poem-expanding essays, in early 2024.  “Aims of arrows” can thus be read as both summarizing the goals of these mechanistic drawings and pointing towards themes in the spring term.  

“Depicting a shape three-dimensional: 
For chemists, a process intentional, 
As dash-wedge notation, 
A visual narration, 
Finds clarity through the conventional.”

The 13 April 2023 limerick described dash-wedge notation, a common drawing convention used by chemists to approach the challenge of representing three-dimensional structures in two-dimensional settings (in other words, how they deal with the “depiction restrictions” of the post title).  

“Depicting a shape three-dimensional: /
For chemists, a process intentional…”

The three-dimensional structures (shapes) of molecules help explain their functions.  A major goal in undergraduate chemistry coursework is learning to read and draw representations of these 3-D shapes from and in two-dimensional settings (e.g., chalkboards and notebook paper).  

Some of the drawing conventions are named for the chemists who devised them.  The Newman projection and the Haworth projection are named for Melvin Newman and Norman Haworth, respectively.  Newman projections allow chemists to consider conformational analysis, and Haworth projections help model concepts related to carbohydrate chemistry.  

“As dash-wedge notation, 
A visual narration, 
Finds clarity through the conventional.”

Several other such conventions, though, are not named for a specific scientist.  Indeed, it seems intriguingly hard (at least via the cursory searches that supplement these poems!) to track down a solid reference regarding the scientists who devised the sawhorse projection or the dash-wedge notation.  

The latter, named in this poem, is a “visual narration [that] finds clarity through the conventional.”  If a bond is written as a “wedge,” it is meant to be read by a chemist as coming towards the viewer, out of the plane of the screen/page/chalkboard.  If a bond is written as a “dash,” it is read as going away from the viewer, behind the plane of that surface.  This is a common notation that students learn to represent 3-D molecular structure.  

This limerick was a fun chance to simply highlight the rationale behind learning this visual and representational skill in chemistry coursework.  Overall, the historical saga of molecular representation in chemistry is fascinating and deserves many more words than the 280 assigned to this poem translation!  

“A process creative: foundation
In wide-ranging, deep preparation.  
Then: steps incubating,
Scenes illuminating, 
And subsequent verification.”

The 12 April 2023 limerick summarized Graham Wallas’s model of creative cognition.  Wallas was a psychologist who lived from 1858-1932, and this specific discussion was presented in his 1926 book The Art of Thought, stating that creative insights occur via a four-step process.  

“A process creative: foundation / 
In wide-ranging, deep preparation.” 

The first step of Wallas’s model of creative cognition is preparation: the accumulation of knowledge and understanding over a long period of study.  

“Then: steps incubating, /
Scenes illuminating, /
And subsequent verification.”

The second step is incubation: a period of time wherein the individual is not consciously considering the question or topic as intentionally as in the preparation period.  The third is illumination, where the flash of inspiration or insight arrives in a moment (I often think of this as the most cinematic step).  Finally, the fourth step, that of verification, involves the idea’s testing and eventual validation by the larger community.  All four steps lend themselves quite well to the meter and rhyme scheme of a limerick!   

***

Interestingly, while such a narrative would not be part of a scientific journal article, this is often a pattern that can be seen in the stories of scientists’ discoveries, such as physicist Lise Meitner’s inspiration regarding nuclear fission (during a winter walk with another physicist, her nephew Otto Frisch) or chemist August Kekulé’s discovery of the structure of benzene (legend holds that he realized the key insight after waking up from a nap in front of the fireplace).    

These “illuminations” are the sort of moments I enjoy highlighting in limerick and double dactyl forms.  Moreover, these types of stories and Wallas’s model both suggest echoes of Louis Pasteur’s famous 1854 quote, always a favorite: “In the fields of observation, chance favors only the prepared mind.” Since this is (unbelievably) my 200th post here, it seems a fitting opportunity to revisit some of these words.    

“The process of ionization:
A charge-causing classification;
Electrons lost/gained
Yield an ion proclaimed
From an atom once neutral in station.”

The 11 April 2023 limerick returned to familiar themes seen on this website, building on a common chemistry term with a variety of flexible rhymes!  

“The process of ionization: /
A charge-causing classification…”   

Ionization is the process of converting a neutral atom to a charged ion: it is thus “a charge-causing classification.”  

The “first ionization energy” of an element refers to the energy required to accomplish the process shown here, where the neutral element X is converted to the singly-positively-charged cation X⁺, by losing an electron (e^– ).  As defined, this is a gas-phase process (shown here via the phase label of (g)).  

X (g) → X⁺ (g) + e^–

One of the most reliable periodic trends is that first ionization energy increases for elements going across a row (left to right) of the periodic table and decreases going down a column.  This is because it becomes easier to remove an electron from an atom as the atom increases in size, and atomic radius decreases across a row (left to right) and increases down a column.    

“Electrons lost/gained /
Yield an ion proclaimed /
From an atom once neutral in station.”

In a neutral atom, the number of protons (which are positively charged) balances out the number of electrons (which are negatively charged).  If an atom loses or gains electrons, this balance is upset, and an ion results!  In other words, an “ion [is] proclaimed, from an atom once neutral in station.” If an atom loses electrons, it forms a positively charged ion, which has more protons than electrons and is called a cation.  If an atom gains electrons, it forms a negatively charged ion, which has more electrons than protons and is called an anion.