Tag: chemistry

“Consider the lim’rick emphatic;
Mark feet anapestic-syllabic.
(Aside– parenthetic;
Perhaps exegetic.)
Deliver the punchline dramatic!”

This is the second part of what I imagine will be a five-post project in total, developing a conference talk I gave last summer into a piece of prose.  This post will discuss how I have used the limerick form in some science poetry endeavors.   Serendipitously, it works well to use a Twitter poem I’ve never “expanded” here before, posted on 12 May 2022 for National Limerick Day, as an introduction.   

“Consider the lim’rick emphatic; /
Mark feet anapestic-syllabic…”   

This Twitter poem was one in which some of the rules of the “limerick emphatic” were presented via the familiar structure of the limerick itself.  The metric feet used in the limerick are anapests (e.g., “in-ter-VENE”) or amphibrachs (e.g., “con-DI-tions”), depending on where the line breaks occur.  Moreover, lines 1-2 in a limerick are often those that set out the premise or subject of the verse (as in Edmund Lear’s “There was an old man of Thermopylae” and many others).   

“(Aside– parenthetic;
Perhaps exegetic.)
Deliver the punchline dramatic!”  

The rest of this poem presents a commentary on the humorous, light nature of the limerick, noting how the AABBA rhyme scheme can allow particularly well for a parenthetical or explanatory side comment in lines 3-4, as well as a punchline or insight in line 5.  

***

I’ve written previously about how April 2019 was a fortuitous month in that it was the overlap of National Poetry Month and the International Year of the Periodic Table: the juxtaposition was enough motivation to deliberately celebrate my interest in both chemistry and poetry.  I joined Twitter that spring and enjoyed the specific challenge of posting 30 poems in 30 days, relating the limericks to some of the science stories and concepts I had taught most often over the past several years.  

The limerick form has been in use for centuries; its famous structure was crucial in facilitating this initial interdisciplinary step.  It had previously been challenging, in my own experience, to find a way to combine chemistry and language as two fields of interest; indeed, that sentiment could someday be expanded into its own set of essays.  However, to keep the comment more germane to this theme: an academic career in STEM involves much writing, but that writing is primarily informative, rather than creative.  Moreover, the tension of accessibility and precision is one I still work to balance when presenting scientific vocabulary as a teacher, and I’m confident this will be a challenge throughout my career.  Knowing the “rules” for the limerick, as well as the limerick’s humorous nature, provided enough structure, yet flexibility (speaking of tension!), with which to begin this science writing endeavor.  

I was pleased to succeed at writing 30 poems in that initial April project.  It was striking how reframing my understanding of varied chemistry concepts (such as covalent bonding and the gold foil experiment) in these poems distilled such topics down to their essentials, which would also benefit my teaching in subsequent years. 

Revisiting past presentation
Of time-limit/slide-share persuasion;
Extending dispersive 
In next month’s four verses: 
Throughout summer, prose motivation.  

Once again, June 30 has somehow already arrived; once again, it is worth taking some deliberate time to plan for more creative writing in July, to make sure I don’t lose track of the entire season.  This year, I will use the next four weeks to expand on a conference presentation that I gave last summer, which overlaps with several of the topics discussed on this website.  

Revisiting past presentation / 
Of time-limit/slide-share persuasion…

As noted above, this will be a chance to expand on an academic presentation in a less formal mode.  For me, such talks can be challenging given their time constraints and the accompanying need to create a set of slides (PowerPoint, etc.) for a central focus; they are a medium of the “time-limit/slide-share persuasion.” 

The title of this post alludes to the fact that these essays will have a similar theme to last year’s conference presentation, although revisiting the theme in this form has involved a delay: this second look has been “tabled” for a while.          

Extending dispersive /
In next month’s four verses…

Over the course of the next four weeks, I will expand on each of four general points from the talk: limericks in science poetry; double dactyls in science poetry; main themes of science communication; and general references and resources.

As has become the norm for these posts, I will introduce each of these themes in a brief verse, then “extend [the theme] dispersive,” including more supporting nuance via a brief essay.  This routine will ideally continue through each Friday in July.  

Throughout summer, prose motivation.  

It is even more remarkable this year than in some previous summers how quickly the month of June flew by, via academic-year-ending paperwork and previously postponed appointments.  The past two summers’ mini-projects have been useful in converting brief poems from the stuff of marginalia to more substantive writing, using July as effectively as possible; ideally, such “prose motivation” will continue again in the month ahead.  

“Month’s poems, chem-themed, are completing
This April’s fourth trial, repeating;
A welcome colliding
Of science and writing,
Towards May and the summer, proceeding.”  

The last limerick from the April 2022 iteration of National Poetry Writing Month was posted on 30 April 2022.  After a limerick-structured salute to Finals Week the day before; the April 30 post was likewise predictable in theme, focusing on the end of the month.  It provides a good place to pause here at the end of the Spring 2023 semester, as well.     

“Month’s poems, chem-themed, are completing / 
This April’s fourth trial, repeating…”

Though I’ve never kept one, I have always noted the appeal of the five-year diary, in which the writer records only one line per date, but then has a chance to automatically return to (for instance) the April 26 of “year x” in “year x + 1,” “year x + 2,” etc., in completing the subsequent lines assigned to the same date.  The cyclical reflection inherent in keeping up with a written record for such a long time has always seemed appealing.  Realistically, this writing routine is the closest I’ll come to a record like that one; it’s been interesting to look back over the past four Aprils, via these essays.  

The first time I attempted this practice was April 2019, for the overlap of the Year of the Periodic Table and National Poetry Writing Month.  By the time April 2020 arrived, the world had fundamentally changed, due to the pandemic, and the poems reflected that.  Each subsequent April has seemed a bit more familiar, to the point that this year’s parallel poetic posts, over on Twitter, focus almost completely on chemistry notation and concepts yet again.        

“A welcome colliding /
Of science and writing, /
Towards May and the summer, proceeding.”  

The end of the semester is predictably challenging, as deadlines, due dates, and celebrations all collide in academic buildings and events.  It has consistently helped to have a deliberate writing structure in these two spaces, with the Twitter poems from a given April informing the following April’s essays here. 

As with previous years, I will pause posts in this space for a few weeks, as the calendar moves on to the summer. 

“These chem terms are far from generic:
First noted with acids, tartaric;   
The handed behaviors 
That explain endeavors: 
R/S forms, enantiomeric.”

The 28 April 2022 Twitter limerick described some context and vocabulary related to enantiomers: compounds that are identical in connectivity but in terms of their three-dimensional structures are non-superimposable mirror images. 

“These chem terms are far from generic: /
First noted with acids, tartaric…”

The first few lines note that this poem will introduce some precise vocabulary, “far from generic,” for stereochemical properties of chemical species.  

The properties described here were observed by Louis Pasteur in 1847 with crystal samples derived from tartaric acid.  Using a magnifying glass, a pair of tweezers, and (presumably) no small amount of patience, he separated the pertinent crystals into two piles based on their optical properties: one set of crystals rotated plane-polarized light in a clockwise direction, while the other rotated plane-polarized light in a counter-clockwise direction.  

This difference in optical activity is the only difference in physical properties for enantiomers: in other physical properties (like melting or boiling points), they are identical.  

“The handed behaviors /
That explain endeavors: / 
R/S forms, enantiomeric.”

Stereochemistry involves the three-dimensional (3-D) arrangement of atoms in a molecule, rather than the molecule’s composition or connectivity.  Enantiomers, specifically, demonstrate “handed behaviors”; they are non-superimposable mirror images of one another, just as hands are.  This 3-D-specific information can be delineated in a variety of ways; a common shorthand is called R or S notation.  

As stated above, enantiomers have identical physical properties aside from their optical activity; however, their chemical reactivities differ in chiral environments.  In those cases, the R enantiomer of a molecule would react differently than the S enantiomer: “the handed behaviors… explain endeavors,” or chemical reactivities.  

The depictions of these “mirror-image” compounds can seem simple and often can look identical at first glance (resulting in the post’s title!).  However, once discerned, the “handed” differences in their three-dimensional compositions would have significant implications for how such molecules behave.   

“Three C and six H and 
Shape most triangular:
Name given sample as
Cyclopropane.
Simple example for
Nomenclatorial 
Rules, regulations.
(Ring, meter: both strained.)”

The 27 April 2022 Twitter poem focused on information related to cyclopropane as a representative hydrocarbon molecule.  

“Three C and six H and /
Shape most triangular: /
Name given sample as /
Cyclopropane…”

Cyclic hydrocarbon compounds (those that contain only carbon and hydrogen atoms) can be represented with skeletal formulas.  Given the nuances of drawing such structures, the compounds’ representations yield simple shapes.  

Cyclohexane has the molecular formula C₆H₁₂, and its skeletal structure looks like a hexagon.  Cyclopentane has the molecular formula C₅H₁₀, and its skeletal structure looks like a pentagon.  Cyclobutane has the molecular formula C₄H₈, and its skeletal structure looks like a square.  Cyclopropane has the molecular formula C₃H₆, and its skeletal structure looks like a triangle.  

Seeing a “shape most triangular” in an organic chemistry setting indicates that the molecule of interest is cyclopropane.  

“Simple example for /
Nomenclatorial /
Rules, regulations. /
(Ring, meter: both strained.)”

Each part of cyclopropane’s name describes important information, as portrayed by the “nomenclatorial rules [and] regulations” involved.  

“Prop” communicates that three carbon atoms are in the structure; “ane” indicates that only single carbon-carbon bonds are present in the molecule (and thus also communicates the number of hydrogen atoms, since it is known that carbon will form four bonds overall).  “Cyclo” explains that the structure takes the shape of a ring, with the carbons circling back to bond to one another, rather than an acyclic chain. 

Cyclopropane is a “strained” structure: it is not possible for the carbon atoms in the ring to each take on the exact dimensions predicted for tetrahedral molecular geometries and still lead overall to the triangular shape.  The last line acknowledges this and also notes that the pseudo-double-dactyl poem strains a bit on its own, with an imperfect central rhyme and some metric flaws.

“A threefold kinetic provision:
Reactants in proper position
With energy sufficient
And run-ins efficient 
Achieve a successful collision.” 

The 26 April 2022 Twitter limerick provided an overview of collision theory, which is used in chemical kinetics.  The field of chemical kinetics is concerned with the rates at which and mechanisms by which chemical reactions occur.  

“A threefold kinetic provision…”

 Kinetic theories are those that rationalize gas behaviors based on the motion of the molecules involved.  These theories consider gas molecules as hard spheres to simplify their treatment, essentially treating molecules as infinitesimally tiny billiard balls.  This helps explain why “collision” is the primary term used to describe molecular encounters.     

Collision theory points to three main criteria (“a threefold kinetic provision”) for considering whether a chemical reaction will successfully transpire. 

“Reactants in proper position /
With energy sufficient /
And run-ins efficient…”

The idea of collision theory is that for molecules to react with one another, they have to successfully collide with (encounter) one another. 

The three criteria explored in collision theory are generally referred to as the collision requirement (are molecules encountering one another in the first place?); the energetic requirement (will a pertinent collision occur with enough energy to overcome the activation barrier?); and the steric requirement (will the molecules that collide with one another have the proper three-dimensional arrangement in doing so)?  

In verse form, the collision requirement becomes “run-ins efficient”; the energetic requirement becomes “energy sufficient”; and the steric requirement becomes “in proper position.”  

“Achieve a successful collision.” 

If all three of these criteria are met, the particular molecular encounter can proceed from reactants to products: the collision has been a “successful” one.   

(As in the case of many other posts on this site, a primary goal with this poem is to help chemistry learners organize a great deal of information!  The nuances and details, of which there are many, can follow once the big picture makes more sense.) 

“Adapt a Midsummer quotation…
Airy nothing gains name, habitation;  
Poet’s pen thus aligning
With a STEM start inclining: 
Things unknown framed through shared observation.”

I am backtracking a bit to the 23 April 2022 Twitter limerick, which I inadvertently overlooked in a busy spring semester!  This poem was posted in honor of William Shakespeare’s birthday and highlights a famous passage from A Midsummer Night’s Dream.  

“Adapt a Midsummer quotation… /
Airy nothing gains name, habitation…”  

The first line of the limerick cites the specific play of interest; the second line highlights the pertinent passage of interest, from Act Five of A Midsummer Night’s Dream: 

“The poet’s eye, in fine frenzy rolling, / Doth glance from heaven to earth, from earth to heaven; / And as imagination bodies forth / The forms of things unknown, the poet’s pen / Turns them to shapes and gives to airy nothing / A local habitation and a name.”

“Poet’s pen thus aligning /
With a STEM start inclining: / 
Things unknown framed through shared observation.”

I heard an insightful discussion of the Shakespeare passage during a wonderful online colloquium on science, imagination, and poetry in 2021, via the University of York’s Festival of Ideas.  Several of the points raised stayed with me until the following April, when I again was completing the National Poetry Writing Month routine on April 23, specifically.  (This date has been a particularly fun one to work towards, throughout my four years of attempting NaPoWriMo.)

The general theme is highlighted in the poem’s final line: that both scientists and poets employ new language and metaphor with which to describe the previously unseen world, sharing their observations of the “things unknown” of heaven and earth, in Shakespeare’s writing. 

This has been a fascinating idea to explore in some of my general education courses, examining creativity in both the sciences and the humanities.  Careful observation and detailed description are crucial in multiple fields, and those interdisciplinary overlaps continue to be favorite themes in this space.    

“Michaelis-Menten-ly,
Enzymes will catalyze.   
Key derivation from 
Briggs and Haldane:
[ES] defined with approach 
Quasi-steady-state.
Lineweaver-Burk yields a
Graphical gain.”

The 25 April 2022 poem was similar to the “aromaticity ode” from a few days prior, in that its primary aim was to compile a significant amount of information in a memorable way.  It was posted on “DNA Day,” so a biochemistry theme seemed particularly appropriate. 

The poem compiles several names and big-picture findings of several scientists who studied enzyme catalysis.    

“Michaelis-Menten-ly, /
Enzymes will catalyze.” 

Enzymes are biological catalysts, remarkable in their specificity and efficiency: they speed up reactions but are not consumed in these reactions.  Many enzyme-related reactions can be modeled via the Michaelis-Menten mechanism, a step-by-step depiction that biochemists use to understand the kinetics (rates) of enzyme-catalyzed reactions.  

In 1913, biomedical researchers Leonor Michaelis and Maud Menten proposed this important mechanism.  In these first few lines, their famous names are adapted into an adverb for use in this pseudo-double-dactyl poem.  

The mechanism can be seen at this link and rationalizes how an enzyme (abbreviated E) interacts with a substrate (abbreviated S) to ultimately yield a product (abbreviated P).        

“Key derivation from /
Briggs and Haldane:/
[ES] defined with approach / 
Quasi-steady-state…”

George Briggs and J.B.S. Haldane published their work on a subsequent investigation of Michaelis-Menten kinetics in 1925, involving an innovation regarding the enzyme-substrate complex (ES) formed as a reaction intermediate, noting that its concentration in solution (designated in the poem by the square brackets) stays relatively constant (“quasi-steady-state”).    

“Lineweaver-Burk yields a /
Graphical gain.” 

Hans Lineweaver and Dean Burk proposed a graphical analysis of the Michaelis-Menten mechanism in 1934.  This type of analysis allows efficient interpretation of some of the important rate-related data under investigation, which can be quickly ascertained via algebraic manipulation, yielding a “gain” of key kinetic parameters. 

The post title notes that all three pairs of names relate to models that are useful in understanding biochemical processes; it alludes to Maud Menten’s name, specifically, in doing so.

“A mid-spring occasion of birthday;
The celebrant, one Charlotte Brontë.  
Her fiction direction 
From Haworth projection 
Yields Eyre literary as mainstay.”

The 21 April 2022 Twitter poem was a limerick that commemorated some common vocabulary terms seen in chemistry and literature.  

“A mid-spring occasion of birthday; /
The celebrant, one Charlotte Brontë…“  

This particular poem was written in honor of and posted on Charlotte Brontë’s birthday.  Brontë was a renowned English writer who lived from 21 April 1816 to 31 April 1855.  She and her sisters (Emily and Anne) authored several classic novels during their careers.     

“Her fiction direction /
From Haworth projection /
Yields Eyre literary as mainstay.”

The poem notes the overlap in language between a drawing convention used in chemistry and the name of a famous home from the history of British literature.  The Haworth projection is used to quickly communicate information about the three-dimensional structure of saccharides (sugar molecules); this is similar to the ways in which Newman projections and Fischer projections can efficiently share structural information. Different projections have different benefits for different types of molecules.  Haworth House was the name of the Brontë family’s parsonage.  

I remember the similarity in terms striking me when I encountered the chemical drawings for the first time, years ago, and it was fun to find a way to finally highlight that.  The suitability of “Haworth projection” as an appropriate descriptor for a book that originated in some way from the Brontë home (in addition to its chemically precise meaning!) has been with me for a while.  

Finishing up the last few lines, “fiction direction” is a wordy but reasonable rephrasing of the concept of a book’s central theme.  “Eyre literary” is a pun on “literary air” and, of course, a nod to the title of Jane Eyre, since the poem was posted for Charlotte Brontë’s birthday specifically. 

“Classifying aromatic?  
Benzene ring, one emblematic
Structure seen; its systematic 
Look yields answer automatic.   
Tougher cases?  Check prolongéd:
‘4n plus two’ pi electrons; 
Conjugated; planar; cyclic.
(Faulty rhymes but fair mnemonic.)”

The 20 April 2022 poem was a checklist-style poem intended to highlight some of the many questions for discerning whether or not an organic molecule is aromatic: an adjective that, in a chemistry context, designates increased stability, compared to what would be predicted from its structure. (Chemists use the terms aromatic, antiaromatic, and non-aromatic as useful classifications of molecular structure.)  

Historically, it was seen that many compounds that had distinct aromas were some of the first to be classified as chemically aromatic; however, now, the two meanings are distinct.    

“Classifying aromatic? / 
Benzene ring, one emblematic /
Structure seen; its systematic /
Look yields answer automatic…”

The first lines ask whether the molecule of interest contains a benzene ring or not, given that benzene is the iconic example of an aromatic molecule.  A molecule could have both aromatic and non-aromatic (aliphatic) regions, but the benzene ring would always be aromatic.  

“Tougher cases?  Check prolongéd: /
‘4n plus two’ pi electrons; / 
Conjugated; planar; cyclic. /
(Faulty rhymes but fair mnemonic.)”

The latter lines include more complex discussions (i.e., a “prolonged check”).  Is the molecule conjugated (alternating single and double bonds, as drawn in an electron dot structure)?  Planar (flat)?  Cyclic (ring-shaped)? If the answer to all three is yes, how many pi electrons (those populating the delocalized “pi bond” system) does the molecule have?   Learning to count these electrons and apply Hückel’s rule is a traditional organic chemistry endeavor. 

If a planar, cyclic, conjugated molecule contains “4n + 2” pi electrons, where n is any number including zero (so that the formula yields two, six, ten, fourteen, etc.), then the molecule would be aromatic.  If the answer to the electron count is “4n” (four, eight, twelve, sixteen, etc.), then the molecule would be antiaromatic: decreased stability, compared to expectation from structure alone.  Benzene (six pi electrons) is aromatic; cyclobutadiene (four pi electrons) is antiaromatic.

This poem uses imperfect rhymes, and it rivals the mechanism-themed verses for density of jargon, but it was fun to try to create here a useful mnemonic.  The title borrows (and misspells) a lyric from Lerner and Loewe’s “The Rain in Spain,” noting a molecule characterized as aromatic overall would be “mainly in the plane,” among other criteria.