Tag: chemistry

“Consider the protein as topic
Of int’rest most etymologic:
A vocab-themed mission 
Reflects first position
Through protean path biologic!”   

The 25 April 2024 limerick examined the etymology of the word “protein,” highlighting a topic from biochemistry in honor of the annual celebration of DNA Day.  

“Consider the protein as topic / 
Of int’rest most etymologic…”

I was interested last April in exploring a question of biochemistry vocabulary, which quickly became more complex than I expected.  After much internet searching last spring, I also found a helpful overview in Isaac Asimov’s Words of Science, in composing this essay.       

“A vocab-themed mission / 
 Reflects first position /
Through protean path biologic!”   

Asimov notes that British chemist William Prout classified three kinds of food-related substances in 1827: what would ultimately become known as carbohydrates, lipids, and proteins in subsequent years were originally deemed the “saccharins,” the “oily,” and the “albuminous,” respectively.  

The albuminous compounds (so named because they were a cloudy white, from the Latin albus for “white”– think of egg white, for instance) were seen to contain nitrogen, unlike the compounds in the other two categories.  Dutch chemist Gerardus Johannes Mulder more clearly defined the albuminous compounds, citing in 1838 their common properties and elemental compositions (percentages of carbon, hydrogen, nitrogen, and oxygen).  He corresponded with Swedish chemist Jöns Jacob Berzelius, who suggested the name “protein” for this type of substance, building on the Greek for “in the first place,” since parallel studies were showing the immense (“first-place”) importance of proteins for nutrition.      

The last line of the poem likewise notes the centrality of proteins to the complex discipline of biochemistry.  It features the similarity between “protein” and “protean”; the latter term also comes from the same Greek root for “first” and highlights the connection to the Greek god Proteus, famous for changing forms.  (This became a quite appropriate allusion, considering how challenging it was to track down a concrete answer to this seemingly simple question.)  

“A need for alkene can be fill-ed /
Through synthetic effort most skill-ed: / 
Reaction approaching, /
On ketone encroaching, /
Employing the chem of the ylide.” 

The 24 April 2024 limerick summarized the Wittig reaction, a well-known process in organic chemistry.  The structure of the poem allowed for pronunciation hints about one of the novel vocabulary terms involved.    

“A need for alkene can be fill-ed /
Through synthetic effort most skill-ed…”

The Wittig reaction is named for German chemist Georg Wittig (1897-1987), who won the Nobel Prize in Chemistry in 1979 for developing important reagents in organic synthesis.  The Wittig reaction is illustrated here.  It is famous as a synthetic pathway to alkenes: compounds with carbon-to-carbon double bonds (C=C).  

“Reaction approaching, /
On ketone encroaching, /
Employing the chem of the ylide.” 

The Wittig reaction occurs between a compound containing a carbonyl group (an aldehyde or a ketone) and a compound called a triphenylphosphine ylide.  

The ylide has both a positive and negative charge within one structure; it “encroaches” on the ketone (or aldehyde) due to this unusual reactivity.  The reaction ultimately yields an alkene and a side product of triphenylphosphine oxide.      

“Ylide” seems one of organic chemistry’s more confounding instances of jargon, at first glance; it is pronounced in such a way as to rhyme with “fill-ed” and “skill-ed,” as the poem ideally suggests.  

***

A brief postscript to this particular essay:

Speaking of “ylides,” I was intrigued as a student with the etymology of the unusual word, but I never tracked it down.  When this poem came to mind last year, I was pleased to have a new inspiration… after only fifteen-or-so years of having the question running in the background!

I’ve learned in my time preparing and teaching courses that the Nobel Prize lectures, compiled online, are unique chances to read narrative accounts of research from scientists, rather than the technical accounts found in journal articles. 

I suspected that Wittig’s lecture might include his inspiration for the novel term, and I was glad to confirm this.  In his Nobel lecture, Wittig writes: “We gave the name N-ylides to this new class of substances since the bonding of the carbon to the neighboring nitrogen is homopolar (yl) and ionic (ide) at the same time.” The phosphorus ylides from the Wittig reaction demonstrate similar chemistry, with aspects of both molecular and ionic bonding patterns.

(Wittig’s lecture title highlights this unusual chemical species and others in a creative way: “From Diyls to Ylides to My Idyll.”)

“Art, science in consonant quoting: 
Provoking, exploring, denoting;
Mirrors held up to nature. 
(Contrast nomenclatures,
But compare the efforts’ keynoting.)”

The 23 April 2024 Twitter limerick celebrated William Shakespeare’s birthday by expanding on a line from Hamlet, in which Hamlet is speaking to the troupe of actors visiting Elsinore Castle, after famously noting: “The play’s the thing/ Wherein I’ll catch the conscience of the King.” He exhorts the actors regarding the role of dramatic work, “whose end, both at the first and now, was and is, to hold as ’twere the mirror up to nature.” That last image is highlighted in this verse.    

(The title here is not particularly novel, but it is a good fit for the themes of the post!)

“Art, science in consonant quoting: /
Provoking, exploring, denoting; /
Mirrors held up to nature…”

The discussion of drama as a “mirror held up to nature” in Hamlet seemed also a fitting description for the broader endeavors of both artists and scientists.  Their efforts are shared and “consonant,” beginning from observation as a first step to “provoke, explore, [and] denote” in reporting on their subject matter. Many disciplinary differences exist, of course, but that starting commonality has been an inspiration for several years in this space.       

It is intriguing to reflect, via inevitable pun, on the various ways in which mirrors can depict images.  In an early meeting of my Chemistry in Art class, we discuss the idea that any surface reflects light. However, we only see that reflection in a shiny surface that allows the light rays to behave in a coordinated way (specular reflection), whereas a rough or irregular surface scatters the light rays at random angles (diffuse reflection), so we don’t see a recognizable image.  We also look at the difference between a regular, flat mirror and a curved mirror; students are generally familiar with the reversal effect of the former, while the latter can resolve anamorphic images into square images and is often a fun demonstration.  

A variety of reflective effects are possible, and it’s fascinating to examine a few points alongside the Hamlet quote: reflections result from behaviors of light; classifying a specific type of reflection requires an evaluation from a viewer; etc.      

“(Contrast nomenclatures, /
But compare the efforts’ keynoting.)”

Another common theme here, not limited to an annual celebration, is that science and art report on their subject matter in contrasting ways.  Their nomenclatures differ significantly from one another, but their central, “keynote” efforts are shared.  

“The Fischer esterification:
A catalyzed collaboration
‘Twixt alcohol, acid
Yields end product placid
Post sep funnel’s stratification.”

The next chemistry-themed limerick from NaPoWriMo2024 was posted on 21 April 2024 and provided an overview of a common organic chemistry reaction.    

“The Fischer esterification…”

Named for chemist Emil Fischer (1852-1919), the reaction summarized here forms an ester.  An ester is a type of functional group: a characteristic combination of atoms.  This functional group is commonly abbreviated as “R-CO₂R” and is illustrated at this outstanding website.   

“A catalyzed collaboration /
‘Twixt alcohol, acid…” 

This reaction has two reactants, one containing the functional group known as a carboxylic acid (R-COOH) and one containing the functional group known as an alcohol (R-OH).  These would be written on the left-hand side of the reaction arrow.  It can be catalyzed in the presence of a strong acid such as sulfuric acid (H₂SO₄); this could be denoted by writing the catalyst’s formula over the reaction arrow.  A good illustration of the reaction overall can be seen here.      

“Yields end product placid /
Post sep funnel’s stratification.”

The reaction forms an ester, with water as a side product; these are the compounds written on the right-hand side of the reaction arrow.  The ester product is stable (“placid”) once formed, presuming reaction conditions allow that.  [While that sounds tautological, this particular reaction is often used to explain to students how either side of a reaction equilibrium can be favored by shifting conditions, such as (here) adding excess reactants to preferentially generate the desired product.]   

The work-up process in the organic lab is what happens after a synthesis reaction is run; it removes side products and leftover reactants, allowing a chemist to obtain and characterize a single purified product.  Work-up often involves a step that separates the organic layer of the reaction mixture from the aqueous layer, using a piece of equipment called the separatory funnel: i.e., the “sep funnel’s stratification.”        

“Skies-organizingly,
Annie Jump Cannon, 
With skills astronomical, 
Science uplifts.  
Data-insighting;
Intensities, citing;
Observing and writing;
Most stellar, her gifts.”  

The next science-themed poem from the April 2024 collection was a rare “Twitter bio” from that month.  The 19 April 2024 poem focused on the career of Annie Jump Cannon (1863-1941), an astronomer at Harvard College Observatory who developed a system for classifying the stars. 

(Cannon was one of many gifted women scientists who worked as “Harvard computers” at the Observatory around the turn of the 20th century.  Dava Sobel’s superb book, The Glass Universe, is one of many that tells these astronomers’ stories in far greater detail than these brief posts can allow, and the following is only a summary.)      

“Skies-organizingly, /
Annie Jump Cannon, / 
With skills astronomical, / 
Science uplifts…”  

Annie Jump Cannon graduated in 1884 from Wellesley College, having studied astronomy and physics there.  In 1896, she was hired as a “computer” at the Harvard College Observatory, by the then-director Edward Pickering.  The observatory collected an immense amount of data, and help was needed to compile it. The expectation was that Cannon’s primary role would involve processing the existing data already collected by male astronomers (computing the answers to calculations suggested by their findings).   

However, Cannon soon made several advances as an independent scientist.  Building on her spectroscopic training, she devised an approach to classify stars in a more systematic way than in previous years, via their line spectra. [Line spectra are investigated across a range of scientific disciplines, including chemistry.  They are patterns of lines that reflect the quantized behavior of atoms: only certain energetic changes are allowed for electrons within atoms (this is a major idea discussed with quantum mechanics).  Since only certain energies are allowed, only certain wavelengths of light are correspondingly seen, causing these characteristic line patterns for each element.]   

Cannon’s skills were “astronomical” both in terms of disciplinary alignment and in the advances they allowed, as she advanced a new approach for organizing the stars in the sky.  

“Data-insighting;
Intensities, citing;
Observing and writing;
Most stellar, her gifts.”

The classification scheme that Cannon devised has been refined slightly but is still used today, linking the brightness of stars to their temperatures.  To repeat the poetic license of “astronomical” from above, her gifts were “stellar” twice over, with respect to both her subject matter and the acumen with which she completed her investigations.

“The last step seeks well-planned giornata;
Compels fresco artist to plot a 
Considered depiction 
In workday’s restriction,
Avoiding time-limit errata!”

The last of the three fresco-cycle limericks from NaPoWriMo2024 was posted on 17 April 2024 and focused on the final step: carbonation, or carbonatation.  Since I’ve used the name of this particular step as a punchline in a previous poem, I instead focused this limerick on a related concept: the time required for this last step to occur and the fresco image to thus become set.   

“The last step seeks well-planned giornata…”

Giornata means “a day’s work” in Italian.  In fresco art, it means the amount of lime plaster that an artist covers with pigment during a day.  This is due to the specific chemistry of the carbonatation step, represented symbolically here:

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

This reaction is key to the buon fresco (“true fresco”) art form.  If an artist paints on the intonaco layer of the fresco with pigments in water, the surface [consisting of calcium hydroxide, Ca(OH)₂] then reacts with the carbon dioxide (CO₂) in the surrounding air, forming a stable calcium carbonate structure around the pigments and ensuring the longevity of the work.  The artist would thus want to lay down only enough of the intonaco layer that could be covered with pigment in the same session.  

“Compels fresco artist to plot a /
Considered depiction /
In workday’s restriction…”  

I have written before about how the rules of poetic structures (such as limericks) have been a help in terms of re-starting my own creative writing processes.  I can imagine both that having to deliberately consider each giornata might help a fresco artist plan their work AND that such a restriction might be considerably more time-intense and frustrating than “five lines and an AABBA rhyme scheme.”  

“Avoiding time-limit errata!” 

Mistiming a giornata could be addressed, since fresco artists could also use the technique of fresco a secco (“dry fresco”).  As its name suggests, this technique involves painting on a dried fresco surface (directly on the already-formed calcium carbonate). 

However, the potential rhyme of “giornata” and “errata” proved impossible to resist, here.

“Step two in the fresco art-making
Is quicklime’s hydrational slaking.  
Lime plaster resulting
For next steps’ constructing:
Adhering-to-wall undertaking.”

The 16 April 2024 limerick continued the pathway of its predecessor, looking at the second step of the three-step fresco cycle, a process called slaking.   

“Step two in the fresco art-making /
Is quicklime’s hydrational slaking…” 

The reaction summarized here is symbolized as follows, as the quicklime (CaO) formed in Step 1 of the fresco cycle (calcination) is mixed with water, causing an exothermic reaction and the formation of calcium hydroxide: CaO (s) + H₂O (l) → Ca(OH)₂ (l)   

The reaction equation corresponds well to “quicklime’s hydrational slaking,” since quicklime is one reactant and water is the other.  

Two quick tangents here: first, “in the limelight,” as an idiom, refers to the intensely bright light caused by the behavior of quicklime, yet another fascinating point that I had never encountered until writing these pieces.  While unrelated to fresco, it seemed too good to pass up as a post title, since quicklime is still involved in this step.  

Second, “hydrational slaking” is admittedly redundant.  However, the latter term seems less familiar to students each time I teach.  I am sure I will persist in mentioning “slaking one’s thirst” in class as another way of saying “taking a drink of water,” since it seems a rare one-to-one correlation between everyday meaning and specialized vocabulary. 

“Lime plaster resulting /
For next steps’ constructing: /
Adhering-to-wall undertaking.”

The product in this reaction is “calcium hydroxide” to a chemist and “lime plaster” to a fresco artist.  It will be used in the next step, of constructing the fresco art itself.  A fresco consists of two plaster layers, the arriccio layer, adjacent to the wall, followed by the intonaco layer, the actual painting surface.  Both involve calcium hydroxide; the key difference between the two is the coarseness of the sand mixed into the plaster (finer sand is used for intonaco). 

“In kiln-heating limestone, occasion 
Of fresco’s first step: calcination.   
The process, applied: 
CO₂ thus ‘excised,’ 
Yielding quicklime for next needed station.”   

The 15 April 2024 Twitter limerick was the first of three sequential verses summarizing the fresco cycle.   The sequence is a fitting theme with which to begin the Spring 2025 posts: fresco is Italian for “fresh” (hence the post title), and this art form is a fascinating one to view from a chemistry perspective, among many others.  

“In kiln-heating limestone, occasion /
Of fresco’s first step: calcination.” 

The fresco cycle consists of three steps: calcination, slaking, and carbonation (also called carbonatation).  While I’ve examined the overall process before, this sequence provided a chance to explore each step in greater detail.  

The first step, calcination, is represented symbolically via the equation:
CaCO₃ (s) + heat → CaO (s) + CO₂ (g)

Alternatively, the reaction could be shown with calcium carbonate (CaCO₃) as the single reactant with a triangle, representing heat, written over the arrow (noting here what would be a fascinating tangent on its own: some sources trace this shorthand to the alchemical symbol for fire).  Calcium carbonate is also known as limestone; the more familiar name brings with it the bonus of simpler scansion.     

“The process, applied: /
CO₂ thus ‘excised,’ /
Yielding quicklime for next needed station.”        

Heating calcium carbonate to high temperatures, as in Line 1’s kiln, drives the calcination step to the right, yielding calcium oxide (CaO) and carbon dioxide (CO₂) as products.  

Calcium oxide is referred to as quicklime in the fresco process, and it will be used in the “next needed station” of the fresco cycle: the slaking step, which is what provides the slaked lime (calcium hydroxide) that will become the actual fresco surface.  

(As above, with the symbolic shorthand for heat, sitting with these terms during a break allowed me to explore an etymological question that often comes to mind in teaching this topic.  The “lime” of quicklime and lime plaster comes from the Old English lim, reflecting its stickiness as a building material, whereas the “lime” of the citrus variety comes from the Arabic limah and Persian limu.)