Science Poetry

Grammar of Elements

“Unerring, preparing is 
James Andrew Harris: 
T’ward isotopes heavy, his
Labwork maintains.  
Methods intrepid for 
Element 104
Find rutherfordium,
Now to be named.”  

The 12 April 2022 post was a Twitter biography poem noting some of the accomplishments of James Andrew Harris (1932-2000), whose research was integral to the discovery of multiple new elements.  Harris was a Black chemist who faced discrimination in his own career before his significant achievements at what is now Lawrence Berkeley National Laboratory.  Throughout his career, he supported many African-American students in their pursuit of STEM coursework and research.    

“Unerring, preparing is /
James Andrew Harris: / 
T’ward isotopes heavy, his /
Labwork maintains…”  

James Andrew Harris was an outstanding nuclear scientist who led the Heavy Isotopes Production Group in the Lawrence Radiation Laboratory at UC Berkeley during the 1960s.  This lab group worked on synthesizing precursor species necessary for the bombardment experiments that would yield new elements.  Careful, meticulous preparation (i.e., “preparing” that was “unerring”) of the heavy-isotope precursors was necessary for the success of subsequent steps.  

“Methods intrepid for / 
Element 104 /
Find rutherfordium, /
Now to be named.”

This work ultimately led to the identification of two new elements, through the intrepid preparation methods of Harris’s team, followed by subsequent experiments and analyses by the research team led by Albert Ghiorso.  The elements in question had the atomic numbers 104 and 105 (meaning an element with 104 protons and an element with 105 protons, respectively).  Near the same period of time, a research team at the Joint Institute for Nuclear Research (JINR) in Russia also identified these two elements in the lab.  

Each lab group used their own names with each of the two elements, and it took many years for the International Union of Pure and Applied Chemistry (IUPAC) to resolve this naming controversy.  The IUPAC is the worldwide authority for chemists in terms of standardized nomenclature and communication.  As recounted in the poem, the IUPAC decided that Element 104 would be known as rutherfordium, after Ernest Rutherford; further, that Element 105 would be known as dubnium, after the town of Dubna, which is where the JINR is located. 

(This detailed discussion process yielded new, consistent reference points for chemists… and a title for this post!)     

Science Poetry

Flat Confirmation

Cogitate, calculate: 
Dame Kathleen Lonsdale,
Through X-ray spectroscopy,
Compound discerns.
Insight incipient: 
Hex-methyl-ation will 
Benzene’s geometry 
Flatly confirm.

As a new year and new semester are now officially underway, I will return to the weekly routine of these posts.  The 11 April 2022 poem began the 2022 week of “Twitter biographies.”  The first was a pseudo-double-dactyl poem summarizing a key experimental insight in chemistry from Kathleen Lonsdale, who lived from 1903-1971.  

“Cogitate, calculate: /
Dame Kathleen Lonsdale, /
Through X-ray spectroscopy, /
Compound discerns…”

Dame Kathleen Lonsdale was the first woman elected as president of the International Union of Crystallography, in addition to many, many other honors.  

X-ray crystallography is a technique in which, by sending high-energy X-rays at a sample of a compound, a chemist can examine how those X-rays are scattered: a useful analogy might be inferring the shape of an object from the shadow it casts, although X-ray crystallography techniques are far more involved and exacting.  Many compounds’ structures have been discerned through this technique, generalized in the poem as “X-ray spectroscopy” (again, a less precise characterization than is ideal, this time for the sake of the meter).          

“Insight incipient: /
Hex-methyl-ation will / 
Benzene’s geometry /
Flatly confirm.”

The specific experiment commemorated in this poem was Lonsdale’s use of X-ray crystallography to determine the geometry of benzene, a compound which had interested chemists for many years.  Before this insight, it was known that a benzene molecule contained six carbon atoms and six hydrogen atoms and arranged these atoms cyclically, in a ring.  However, scientists had still disagreed for decades as to its planarity: was the ring flat?  (Did it have all of its carbon atoms in the same plane?)    

Lonsdale determined an answer to this question by analyzing a derivative of benzene called hexamethylbenzene, which has a methyl group (-CH3) attached to each carbon in the benzene ring.  She noted that the central benzene ring had to be flat to account for the results seen via her X-ray crystallography experiment.  Thus, the geometry was “flatly confirm[ed]”: benzene was shown to be planar, via significant and convincing evidence.  

Science Poetry

Winter Break

Semester autumnal concluding
With Finals Week tasks, grade-computing…
Pause pathway reactive 
For routine refractive 
In spring-academic-preluding.  

This is a non-Twitter limerick written specifically to wrap up the Fall 2022 semester and look ahead to the Spring 2023 term.  

Semester autumnal concluding /
With Finals Week tasks, grade-computing…

This is Finals Week on campus, which means the number of assessments to evaluate skyrockets, as the number of class meetings dwindles.  “Grade-computing” is the order of most days, as assignments and exams accumulate.  

Pause pathway reactive /
For routine refractive…

The image of a reaction coordinate diagram— which chemists use to map out the energetics of a reaction— comes to mind often during the peaks and valleys of an autumn semester, which can combine to provide the sense of an academic roller coaster.  The “Finals Week tasks” mentioned in the previous lines can build into a fearsome metaphorical maximum, and at winter break, the “pathway reactive” can find a brief energetic minimum, even if the academic year is not fully complete.   

 A “routine refractive” is one that changes direction slightly, via some significant poetic license.  (In a STEM context, refraction is a term describing the bending of light rays.)  For a few weeks, the academic-year routine is briefly interrupted, and focus shifts elsewhere.  

In spring-academic-preluding.  

Part of that refractive routine involves turning attention towards the new semester and its new classes.  Class preparation is always a significant part of winter break, in the “spring-academic-preluding,” but it will be helpful to rest at least briefly before that begins.  I will likewise pause these posts for a few weeks!

Science Poetry

Matter of Degrees

“A molecule’s turning rotations;
Its stretching and bending vibrations—
To calculate, heed them:
The degrees of freedom.
(Forget not three types of translation!)”

The 10 April 2022 limerick addressed a concept related to molecular motions and energetics.  The main idea here is that a molecule can undergo 3N types of motion, where N is the number of atoms in a molecule.  The types of motion are more precisely termed “degrees of freedom” in chemistry analyses.  

“A molecule’s turning rotations; /
Its stretching and bending vibrations…”

We can consider water as a sample molecule.  Water, with its V-shape, has the formula H2O: thus, three atoms and nine (3N) degrees of freedom.  

We can think of the ways that a water molecule could move.  It could “translate” (move in space) in three dimensions: the x, y, and z axes in a Cartesian system.  As we look at a water molecule, we see that it could also “rotate” in three ways: first, so that the H atoms spin to the “left and right” around the O atom; second, in the direction perpendicular to the first direction (so the H atoms spin “over and under” relative to the O atom); third, within the plane of the screen itself.  

The possible “vibrations” correspond to the remaining number of degrees of freedom possible for water as a non-linear molecule.  These can be calculated via the equation 3N-6 (since six degrees of freedom are already occupied: three translations and three rotations).

From that equation, we can confirm that water has three vibrational modes: a symmetric stretch, in which both O-H bonds stretch and compress at once; an asymmetric stretch, in which the O-H bonds alternate their motion; and a bending mode, in which the molecule’s H-O-H bond angle changes.  

“To calculate, heed them: /
The degrees of freedom. /
(Forget not three types of translation!)”

The concept of degrees of freedom facilitates many calculations in chemistry, such as those related to infrared spectroscopy

Interestingly, this essay is slightly misaligned with the poem: the “three types of translations” provide the poetic punchline, but it doesn’t work to omit that prose-based explanation until the end.  

Science Poetry

Solution Composition

“A solute plus solvent: solution.  
We quantify its constitution:
Numeric relation;
Expressed concentration,
Decreasing upon its dilution.”

The 9 April 2022 Twitter limerick returned to far less dense material than the mechanistic deciphering of the last few verses and posts!  As the title suggests, this post (composition) translates a poem related to solution chemistry.

“A solute plus solvent: solution…”

A solution is a homogeneous (uniform) mixture of two substances: the substance present in the lesser amount is the solute, and the substance present in the greater amount is the solvent.  

If we take one gram of table salt (sodium chloride, NaCl) and dissolve it in enough water to form exactly 150 mL of the solution, we generate an aqueous solution of sodium chloride: the salt is the solute and the water is the solvent.  

“We quantify its constitution: /
Numeric relation; /
Expressed concentration…”

Chemists have several ways to quantify the constitution of a solution (to answer the question of how much solute and how much solvent will be present in the solution) and find its concentration.  Concentrations are calculated through “numeric relations,” or equations. The most common concentration expression is molarity: moles of solute divided by liters of solution (M = mol / L).  

In the solution described above, 1.00 g of sodium chloride (NaCl) is equal to 0.0171 moles of NaCl, due to its molar mass of 58.4 g/mol. By taking 0.0171 mol NaCl divided by 0.150 L of solution, we obtain a molarity of 0.114 M here.  

“Decreasing upon its dilution.”

If a solution is diluted, more solvent is added, while the amount of the solute stays the same.  

For instance, in our example, if enough water is subsequently added to generate exactly 300 mL total, then the solution’s volume is doubled, and the molarity becomes half what it was: the solution’s concentration “decrease[s] upon its dilution.”  

Some analogy likely applies here about how the clarity of this simpler post, compared to the last few, benefits from its succinctness (its “smaller volume”)!

Science Poetry

Taking Shape

“A simplified rhyming summation:
Chem concept of hybridization.  
From orbitals’ mixing;
Molecular bonding formation.”

The 3 April 2022 Twitter limerick addressed some key topics related to molecular geometries: the shapes molecules adopt, which impact their reactivities.  Molecular geometries are explained by chemists via several different theories and concepts, depending on which lens is most useful for the situation at hand.    

“A simplified rhyming summation: / 
Chem concept of hybridization.” 

The first two lines state that this poem will summarize the chemical concept called hybridization, acknowledging that this will be a simplification!  

“Geometry-fixing /
From orbitals’ mixing: / 
Molecular bonding formation.” 

VSEPR Theory is the simplest explanation of three-dimensional molecular geometries, via concepts of “valence-shell electron-pair repulsion.”  Via VSEPR Theory, a methane molecule (CH4) would be predicted to have its geometry (shape) because of four regions of electron density (the four C-H bonds) around the central carbon; this shape would be called tetrahedral

However, that geometry does not make sense with carbon’s electron configuration: the way in which a carbon atom has its electrons distributed among its orbitals, via its subshells and shells.  Carbon’s electron configuration as an individual neutral atom is represented as [He] 2s2 2p2 (an arrangement suggesting that carbon will form only two bonds).    

The concept of orbital hybridization is introduced via a different approach called valence bond (VB) theory.  Via hybridization, orbitals mix together to generate what are called “hybrid orbitals,” capable of forming bonds of equal energy.  Methane’s orbitals undergo “sp3 hybridization,” which means the one s orbital and the three p orbitals in the n=2 shell are averaged together to yield four sp3 orbitals of equivalent energy, rationalizing why methane can form the four equivalent bonds necessary for the tetrahedral shape.  

This can be summarized poetically as “geometry-fixing from orbitals’ mixing,” resulting in “molecular bonding formation.”  The last lines can be read in two reasonable ways: either as “a given geometry (formation) is rationalized via hybridization” or as “hybridization results in the formation of several molecular bonding interactions” (i.e., the chemical bonds of interest).  

Science Poetry

Trend Fashions

“To rank-classify chem collections,
Note elements’ relative directions;
Sort kaleidoscopic
With chart Periodic.
(Beware, though, of trending exceptions!)”

The 2 April 2022 Twitter limerick described the concept of periodic trends, or periodic properties: qualitative information that can be inferred from the relative location of elements on the Periodic Table of Elements (PTE).

“To rank-classify chem collections, /
Note elements’ relative directions

The first two lines provide an overview of some ways in which the Periodic Table of Elements (PTE) provides an enormous amount of information. Collectively, sets of elements can be “rank-classif[ied]” with respect to many of their properties: for instance, it can be discerned which of a given pair of elements has the larger atomic radius (atomic size) or first ionization energy, based on their relative placement (“relative directions”) on the PTE. Similar analyses can be completed for many other periodic properties; the practice of doing so is called analyzing periodic trends.

For instance, iodine (I) is lower than bromine (Br) in the column for the halogens (Group 7A) on the PTE. Without looking up any specific data, we can predict from our knowledge of periodic trends that an atom of iodine is larger than an atom of bromine and that iodine has a lower first ionization energy (a lower energetic cost for forming a singly-positively-charged ion) than bromine.

Sort kaleidoscopic /
With chart Periodic. /
(Beware, though, of trending exceptions!)

One of the most amazing aspects of the PTE (the “chart Periodic”) is the way that it allows chemists to arrange a wide array of chemical information in a meaningful way: to “sort [the data] kaleidoscopic,” in this limerick’s phrasing.

However, not every trend described is a perfectly linear one, as nuances in elements’ electron configurations can lead to exceptions from the trends in question. Often, the question I ask of my General Chemistry class is not to “predict this trend” but rather to “rationalize the exception to this trend.” This can be a complex topic to encounter, meriting an accentuating “beware”!

Science Poetry

Fourth Dimensions

“To month of light verses, returning;
Fourth year of this fourth month’s discerning. 
Attempt quaternary:
Chem rhymes ancillary,
With goal of supporting STEM learning.”  

This post returns to the more familiar routine of translating past Twitter chemistry poems.  This particular limerick was posted on 1 April 2022 and marked the beginning of National Poetry Writing Month (NaPoWriMo) 2022.  

“To month of light verses, returning; /
Fourth year of this fourth month’s discerning.” 

April 2022 was the fourth NaPoWriMo for me (which is difficult to believe).  My first year of April poems fell in 2019 during the overlap of National Poetry Writing Month and the International Year of the Periodic Table.  The subsequent April routines have marked various stages of progress through the COVID-19 pandemic and thus provided stability during some strange times.

The combination of the fourth attempt at this routine and the theme of passing time (with time as the fourth dimension) together gave rise to this post’s title.  In these poems, I use the forms of light verse as structures through which to communicate chemistry concepts; most commonly, these forms are limericks or double dactyls.  This April routine provides a “fourth month’s discerning”: a way to practice understanding and communicating chemistry concepts in a different way. 

“Attempt quaternary: /
Chem rhymes ancillary, /
With goal of supporting STEM learning.”  

This month was my fourth attempt (“attempt quaternary”) at this routine, in which “chem rhymes ancillary” were a useful addition to my academic routine.  As can be seen throughout this website, my goal is to use this approach to scientific content to “support STEM learning.”  

I suspect I’m primarily writing to the student I once was: interested in the unusual vocabulary and etymologies of chemistry… to a sometimes-distracting extent! However, I hope these essays might be more generally interesting to others as well. 

Science Poetry

Act of Learning

Astronomer, learnéd… expounding
Through proofs, figures: dense and confounding.  
The student, receptive
To nature’s perspective,
Will exit the lecture resounding.  

This week’s poem is a non-Twitter one; I had initially drafted it during the summer, when I was focused on a series of posts inspired from lines from works of literature, as a limerick-framed restatement of some of the images and themes of Walt Whitman’s “When I Heard the Learn’d Astronomer.”  However, as this poem is primarily a paraphrase, it did not seem to fit as well with the others, which used direct quotes or allusions to initiate the new verses and essays, so I tabled it for a few weeks.

Astronomer, learnéd… expounding
Through proofs, figures: dense and confounding.  

Walt Whitman’s “When I Heard the Learn’d Astronomer” famously describes a speaker’s encounter with a lecture from a renowned scientist.  The speaker first notes the overwhelming amount of data presented in the auditorium: “When the proofs, the figures, were ranged in columns before me, / When I was shown the charts and diagrams, to add, divide, and measure them…

I teach many content-heavy chemistry courses.  I appreciate their roles in various disciplinary curricula, but I am also aware that the first presentations undoubtedly seem “dense and confounding” to new students.    

The student, receptive
To nature’s perspective,
Will exit the lecture resounding.  

Whitman’s poem concludes with lines describing how the speaker seeks refuge from the information-dense presentation in a primary encounter with astronomical observation: “[R]ising and gliding out I wander’d off by myself, / In the mystical moist night-air, and from time to time, / Look’d up in perfect silence at the stars.”  

The student is clearly open to appreciating the subject matter at hand (in the limerick phrasing: “receptive / [t]o nature’s perspective”), but via a direct, self-initiated study: the truest example of active learning

I expect that the limerick form might seem trivializing here, but I had intended this verse as a tribute.  Whitman’s poem is one I remember when teaching, where my goal is primarily that students progress toward becoming independent life-long learners, regardless of their responses to the chemistry content presented.  In reading, I find the effect of the speaker’s shift from the passive voice (“When I was shown”) to the active observation (“I… [l]ook’d up in perfect silence at the stars”) to be unfailingly moving.   

Science Poetry

Isolation Incident

“A simplified Chem situation,
Analysis by isolation:
One species in excess 
So rate law is expressed 
In pseudo-nth-order notation.”

The 22 October 2021 Twitter limerick was the last in the poetic series for National Chemistry Week 2021.  It summarized a technique called the isolation method, which (as with other approaches highlighted in the last few poems) is a technique used by chemists to simplify a complicated rate law.  

“A simplified Chem situation, /
Analysis by isolation…”

The first two lines note that this is another simplifying scenario in the discipline of chemistry, pertaining to kinetics.  

Isolation method” is a phrase that came to mind often in 2020’s early days of the pandemic, as the terms “social distancing” and “isolation guidelines” suddenly were added to everyone’s lexicon.  In the chemistry setting, though, the approach allows an investigator to examine the kinetic role of one reactant at a time as it affects a rate law.

“One species in excess /
So rate law is expressed /
In pseudo-nth-order notation.”

The last three lines summarize a typical example.  One experiment I cite often in class involves the fading of a pink-colored solution over time, where the solution takes on a vibrant color because excess base is present (a case of “one species in excess”) with a chemical indicator (phenolphthalein).  By monitoring the fading of the pink color, students determine information about how the reaction depends specifically on the presence of the phenolphthalein.  

Rate laws are typically classified as first-order, second-order, etc. with respect to a given reactant.  When the isolation method is used, the phrasing changes to pseudo-first-order, etc., acknowledging that this is a finding that has yet to be fully clarified to explore the role of the excess reactant.  “Pseudo-nth-order” means the value of n is under investigation (and is a phrase that fits neatly into a metric rhythm!).

In the case of the experiment described above, the experimental finding is that the rate law is pseudo-first-order with respect to phenolphthalein.  When the entire rate law is determined, it is first-order with respect to both phenolphthalein and the base, so second-order overall.