Category: Science Poetry

“To calculate rate arithmetic
Of reaction, cite info kinetic.  
(Common error displayed: 
Writing capital K.
For rate constant, use lower-case metric!)” 

The 24 July 2019 limerick examined a particular piece of symbolic notation that often sees some misapplication in General Chemistry.   

“To calculate rate arithmetic / 
Of reaction, cite info kinetic.”  
Questions of whether a chemical reaction will occur or not involve “spontaneity,” a term with a specific meaning in chemistry.  A reaction that is spontaneous is one that occurs naturally; “spontaneous,” as a descriptor in a chemical context, is unrelated to a reaction’s speed.  (This is a case of unhelpfully mismatched chemical and everyday definitions.) 

To communicate information about the rate of the reaction, we instead use kinetic data.  The rate constant, or rate coefficient, is one piece of this data.  It is represented by a lower-case k.  The rate law of a given reaction indicates how the reaction rate depends on the rate constant and on the concentrations of species involved in the reaction.   Determining a rate law from kinetic data is a common experimental goal.     

“(Common error displayed: / 
Writing capital K. /
For rate constant, use lower-case metric!)” 
In chemistry, similar or identical symbols can be used in multiple settings with multiple meanings, a phenomenon that can be confusing.  (For instance, the capital letter H, in chemistry, can represent hydrogen, or enthalpy, or the Hamiltonian operator: each with a distinct conceptual meaning.) As learners progress from novices to experts, they become adept at reading the context clues. 

In General Chemistry coursework, students are typically introduced within the span of only a few weeks to two major topics: kinetics and equilibrium.  In the former, the lower-case k represents a rate coefficient.  In the latter, a capital K represents an equilibrium constant, a different quantity.   While the two types of constants are related to one another, it is common to see them simply used interchangeably in introductory assignments: this is an “error displayed.”

“Celebrate, elevate
Sesquicentennial
Chart periodic, the chemist’s best friend.  
Innovate, explicate
Lessons perennial,
Elements ordered in table-set trends.”  

The  23 July 2019 Twitter poem was another entry for C&E News’s “Periodic Poetry” contest, highlighting the periodic table and that table’s central role for chemists.  As with the 8 July 2019 poem, this verse doesn’t fully meet the stringent standards of the double dactyl form (a.k.a. the “higgledy piggledy”), but it comes close.  

“Celebrate, elevate / 
Sesquicentennial /
Chart periodic, the chemist’s best friend.” 
The first three lines highlight the celebratory nature of the International Year of the Periodic Table, the 150th (sesquicentennial) anniversary of Dmitri Mendeleev’s 1869 initial publication.  The periodic table is an indispensable tool for chemists, presenting a wealth of important data in an organized way.  (As a sidenote, “sesquicentennial” is one of a set of terms uniquely suited for the higgledy-piggledy form, given that it is a double-dactylic word; seeing it in a list of such words provided this poem’s inspiration.)    

“Innovate, explicate / 
Lessons perennial, /
Elements ordered in table-set trends.” 
Each fall, when teaching the history and use of the periodic table, I review my lecture notes, add in new details and examples, and generally attempt to “innovate, explicate [my] lessons perennial.” 

Mendeleev ordered the elements according to their chemical and physical properties, resulting in a chart that can predict relative information about a wide number of behaviors.  For instance, sodium (Na) and potassium (K) are in the same column, or family, in the periodic table.  Because potassium is underneath sodium in their column, a chemist thus can quickly make predictions about their relative atomic size (more precisely called atomic radius); the relative energy required to remove an electron from either atom (called the first ionization energy), and many other properties.  Periodic trends are “table-set”: in many cases, a chemist can use the periodic table to predict the relative magnitudes of elements’ physical and chemical properties.  

It is intriguing to contrast another common meaning of “higgledy-piggledy”– chaotic and disordered— with both the strict rules for this poetic form and the highly organized chemical chart which this poem celebrates!           

“Gauche interactions are 
Torsional infractions;
Likewise, groups eclipsing, so see option third…
Butane in profile
Rotates from erstwhile 
Higher-strain conformers: anti’s preferred.”

The 22 July 2019 Twitter poem examines a concept from organic chemistry, the energetic costs and benefits available to a molecule as it rotates through its conformations: specifically, the poem discusses the ways that the molecule butane can arrange itself in three-dimensional space.  This is a highly visual topic, so I’m intrigued to see what I can communicate in the 280 words below (with many links!).    

Gauche interactions are /
Torsional infractions; /
Likewise, groups eclipsing, so see option third…
The molecule butane (C₄H₁₀) consists of four carbon atoms in a line, covalently bonded.  Carbon atoms form four bonds, so butane’s terminal carbon atoms (first and last in line) each form three additional bonds to hydrogen atoms, while the middle two carbon atoms each form two additional bonds to hydrogen atoms.    

Rotation around butane’s central carbon-carbon bond leads to a variety of conformers.  Different conformers’ atoms interact with one another differently (their electron clouds repel, incurring energetic costs) through three-dimensional space.  Chemists have vocabulary to describe these torsional interactions: so named since interactions arise from the molecule’s torsion (twisting).    

The most intuitively named is the eclipsed conformer; if the methyl groups (the terminal carbon atoms, bonded to three hydrogen atoms apiece) are eclipsing, these groups line up with one another like the hands of a clock at noon. This is most easily seen through a chemistry model called a Newman projection.  Eclipsing incurs the highest possible energetic cost, or “torsional infraction,” in this molecule.  

Other energetic penalties arise in the gauche conformer, where the methyl groups are in something akin to a “2 p.m.” orientation. 

Butane in profile /
Rotates from erstwhile / 
Higher-strain conformers: anti’s preferred.
As portrayed in a rotational profile of butane, the anti conformer (an approximation of a clock’s “6 p.m.” orientation) keeps the methyl groups as far away from one another as possible and is the most energetically beneficial (“preferred”) conformation.  The anti conformer avoids torsional strain, although butane can still rotate into other conformations (“erstwhile higher-strain conformers”) as well.   

“A method from lab, mass spectrometry,
Sends sample on fragmenting odyssey.
From mass-to-charge data,
A user can rate a 
First guess as to compound’s geometry.”   

The 12 July 2019 limerick addresses another common experimental method used to identify chemical compounds: mass spectrometry.  Unlike NMR or IR spectroscopy, mass spectrometry does not examine how a chemical sample interacts with light, but rather how a sample molecule breaks into component pieces.    

“A method from lab, mass spectrometry, / 
Sends sample on fragmenting odyssey.”
One type of mass spectrometry is electron impact ionization mass spectrometry.  In the experimental apparatus, a chemical species is first vaporized: converted to a gas.  Then, as the method’s name suggests, the species is bombarded (impacted) by a high-energy stream of electrons, resulting in its ionization: the species becomes charged rather than neutral.  (In the common notation of this process, the molecule, represented as M, loses an electron through this process to form a molecular ion, represented as M⁺.  The molecular ion has a positive charge, because it lost a negatively charged electron.)  

As the molecular ion travels further through the apparatus, it fragments into common component pieces.  Through interaction with a magnet in the spectrometer, these pieces are deflected to various extents before they reach the detector of the instrument and data are collected.      

“From mass-to-charge data, / A user can rate a / 
First guess as to compound’s geometry.”  
The component pieces are also charged and thus also ions.  The mass spectrometer analyzes the mass-to-charge ratios of these smaller ions.  Generally, the ions formed in this type of instrument have a +1 charge, so the mass-to-charge ratios are equal to these ions’ masses. The resulting mass spectrum is a graph: showing the abundance (prevalence) of the component ions as a function of their masses.  

A mass spectrum provides a record of the ions generated by the fragmentation of a molecule. This helps a chemist to rate “a first guess as to [a] compound’s geometry,” providing evidence as to whether a target compound has been synthesized, by the presence or omission of expected fragments of that compound.

“Motions molecular
Lead to conjecture
Re: key architecture of functional groups…
IR spectroscopy;
Target topography:
Features are quantified through linked Law of Hooke.” 

The 11 July 2019 poem discusses another kind of spectroscopy commonly used in organic chemistry coursework: infrared (IR) spectroscopy, which uses infrared light waves.  IR waves are shorter (and higher-energy) compared to the radio waves of NMR spectroscopy, but they are still longer (and lower-energy) than the light waves associated with visible light.   

“Motions molecular/ Lead to conjecture/ 
Re: key architecture of functional groups…”
A molecule is a chemical compound in which atoms are bonded to one another covalently, by sharing electrons.  One of the ways in which chemists think about these bonds is via the model of a tiny spring.  Springs can compress and elongate: bond lengths can shorten and lengthen, in “motions molecular.”  The energies involved in these changes in bond length are characteristic depending on what types of atoms are bonded together (what is at either end of the “spring”?).   Functional groups are groups of atoms that dictate how a molecule behaves.  For instance, an ether functional group contains an oxygen atom bonded to a carbon atom on either side.  Infrared (IR) spectroscopy provides information regarding the functional groups that a molecule contains: identifying the “key architecture” of that molecule.   

“IR spectroscopy;  /  Target topography: /
Features are quantified through linked Law of Hooke.”
NMR spectroscopy can provide precise evidence in support of the structure of a chemical compound, but IR spectroscopy is more generally useful.  The metaphor I use in this poem is a topographical map: the major landmarks (here, the functional groups of the molecule) are the most evident data.  While these calculations are typically not explored in detail until more advanced chemistry classes, it is also possible to predict the specific numbers behind a given piece of IR data: to quantify the features of the molecule.  This is done by analyzing the masses of the atoms involved and the force constant of the pertinent bond.  The calculations employ a model called Hooke’s Law, often introduced in a “linked” prerequisite: a student’s physics coursework.              

“Of nuclei, resonance magnetic:
Technique useful for research synthetic.
How the sample splits, shields 
In spectrometer’s field 
Can support/reject path theoretic.”

This limerick, posted 10 July 2019, and the one that follows involve topics of spectroscopy: experimental techniques that provide information about a chemical compound based on how the compound interacts with different types of electromagnetic radiation (light).  NMR spectroscopy relies on radio waves, which have longer wavelengths and lower energies than visible light waves.    

“Of nuclei, resonance magnetic: / 
Technique useful for research synthetic.”  
The technique of interest here involves the “resonance magnetic” of nuclei; it is more prosaically known as nuclear magnetic resonance (NMR) spectroscopy.  NMR spectroscopy is particularly useful for organic synthesis research, in which scientists seek to build new molecules, because it provides significant information about molecular structure; it can help answer the question of whether or not a target compound has been achieved. Proton NMR spectroscopy and carbon NMR spectroscopy provide detailed information about the hydrogen and carbon atoms, respectively, within an organic molecule: showing how the “carbon skeleton” fits together.    

“How the sample splits, shields /
In spectrometer’s field /
Can support/reject path theoretic.”
Charged particles (including certain types of nuclei) act as tiny magnets.  Magnets affect one another, and in the presence of an externally applied magnetic field from an instrument called an NMR spectrometer, information about these nuclei can thus be discerned.  

For example, a chemist can infer several pieces of data from the appearance of a proton NMR spectrum. The number of peaks (signals) represents the types of hydrogen atoms present (for example, a spectrum with four different peaks represents a compound with four chemically distinct types of hydrogen).  The intensity of each peak provides information about the number of each type of hydrogen atom.  The splitting patterns (singlets, doublets, etc.) and the chemical shifts (how “shielded” or “deshielded” a particular signal is) seen in each spectrum result from the chemical environments of the different types of hydrogen atoms.  A chemist pieces together this information to discern the identity of a synthesized compound, providing evidence in support or rejection of the “path theoretic”: i.e., the proposed mechanism.  

“Schemes mechanistic 
Are useful heuristics 
For learning reactions organic by heart. 
Predicting new pathways, 
Then, novel skills displays: 
Part textbook-learned logic, part chemical art.”

Moving forward, I will plan to alternate my chem-education-focused essays with my Twitter poem translations.  Imprecise as the “pseudo-double-dactyl” form mentioned in the 31 May 2020 post might be, once I had its rhythm in mind, it opened up a range of chemistry words and phrases that fit better there than in the limerick’s anapestic format.  The 9 July 2019 poem highlighted one such “dactylic” topic, examining the concept of organic mechanisms: step-by-step depictions of how a reaction theoretically takes place at the molecular level.  

“Schemes mechanistic/
Are useful heuristics/
For learning reactions organic by heart.” 
“Mechanism” is an intriguingly flexible word that depends greatly on disciplinary context.  An organic chemistry mechanism is one which represents the electron flow that occurs between different reactants to achieve a chemical reaction.  These are sometimes called “electron-pushing mechanisms,” and the electrons in question are represented via the use of curved arrows.  These constitute one of the most common problem-solving types in chemistry: asking students to predict how a given reactant molecule can react to form a target product.  Generally, this is achieved by memorizing how generalized reaction scenarios occur– “learning… by heart”– and applying this knowledge to the specific molecular pathway in question.           

“Predicting new pathways, /
Then, novel skills displays: /  
Part textbook-learned logic, part chemical art.”     
“Synthesis” is another word that varies with context but generally refers to putting pieces together to form a larger whole.  In organic chemistry, it refers to the construction of new, larger molecules from smaller ones.   As an educational objective defined by Bloom’s Taxonomy, it represents a higher level of learning, in which someone uses knowledge creatively to advance a new idea.  The last three lines of this poem acknowledge the higher level of learning present in a synthetic endeavor, something advanced by an expert who has moved beyond memorization of disciplinary concepts to fluency with the use of those concepts.  It has been fascinating in developing courses of my own to learn more about how people learn; this poem attempts to articulate some of the differences in skills and objectives between a novice learner and an expert practitioner.   

“Patiently, spatially, 
D. Mendeleev 
Arranges the elements by column and row. 
Prescriptive, predictive, 
The table finds favor 
In ‘eur-eka’ moments with space apropos.” 

The 8 July 2019 poem was inspired by a call from Chemical and Engineering News for entries to a Periodic Poetry contest in mid-July.  This poem is a different form of light verse than the limericks that began this project; it is likely best characterized as a modification of the “higgledy piggledy,” or “double dactyl.”  It does not adhere particularly well to the actual rules for that poem format, which are quite specific and numerous.  However, the use of a proper name in line two, its theme regarding a historic event, and the metric feet employed are all aspects that align most closely with the double dactyl form.  

“Patiently, spatially, / D. Mendeleev /
Arranges the elements by column and row.” 
In 1869, Dmitri Mendeleev devised the first form of what we recognize today as the modern Periodic Table of the Elements (PTE).  In 2019, several events marked the 150th anniversary of that innovation.  According to some sources, Mendeleev was a card player who particularly enjoyed the game Patience, similar to Solitaire, in which cards are spatially arranged according to both suit and number.  This provided partial inspiration for his innovation regarding the periodic table’s structure: in the modern PTE, the 118 known elements are arranged according to both atomic numbers (rows) and characteristic properties (columns).        

“Prescriptive, predictive, / The table finds favor / 
In ‘eur-eka’ moments with space apropos.” 
Mendeleev took advantage of known chemical data in creating his PTE precursor, fitting elements into a pattern that placed elements into chemical families with similar properties and reactivities; he also left gaps where there wasn’t an obvious candidate to fit in a space.  The table was thus prescriptive, summarizing known information, and predictive, forecasting the properties and reactivities of newly discovered elements that would fill in the gaps.  

Mendeleev named these yet-to-be-discovered elements according to their chemical relatives.  For instance, he left a gap for an element he deemed “eka-aluminum,” with an expected placement one spot below aluminum (the Sanskrit prefix for “one” is “eka”), expecting that an element with certain properties and reactivities would be discovered and would fit there.  When gallium was isolated in 1875, its properties matched Mendeleev’s predictions for eka-aluminum (and, further, provided a “eureka” moment of scientific discovery!).  This and other “space[s] apropos” played a major role in chemists’ adoption of the periodic table. 

“The SI units, redefined today:
No longer linked to objects in a vault,
But rather fundamental constants’ slate,
To minimize experimental fault.  
The kilogram on Planck will now rely;
The kelvin will use Boltzmann to define
A temp’rature precisely and thereby
Consolidate discussions and designs.  
Five other units likewise are recast–
Candela, second, meter, mole, ampere–
From genesis in revolution past
To standards metric by which STEM coheres.  
With h, k, c, et al., assign true north;
Compare to ever-fixèd marks, henceforth.”

This sonnet, written for World Metrology Day in 2019, provides a useful transition from the April 2019 Limerick Project essays back into my general goals with this website.  Moving forward, I will still aim to post twice a week, and when the substance of a post is a single poem “translation,” I will still aim for 280 words or fewer.  Since this particular poem was spread over multiple Twitter posts, I’ll give myself 560 words as a maximum for the following discussion.   

“The SI units, redefined today: / No longer linked to objects in a vault, / But rather fundamental constants’ slate, / To minimize experimental fault.” 
Metrology is the science of measurement.  World Metrology Day is May 20 and celebrates the anniversary of the definition of the meter as a standardized unit of measurement: one on which the world could agree for purposes of scientific and commercial collaboration.  This occurred at the Metre Convention in Paris on May 20, 1875.  World Metrology Day in 2019 marked the redefinition of the metric system, or the International System of Units (denoted typically as “SI units,” given the French translation of the name: Le Système International), in terms of constants of nature.  Previously formulated in a variety of ways, these important units were redefined to rely on such quantities as the speed of light (abbreviated as c in scientific parlance) that are unchanging and universally known.  This redefinition will allow ever more precise communication and collaboration within the scientific community.    

“The kilogram on Planck will now rely; / The kelvin will use Boltzmann to define / A temp’rature precisely and thereby / Consolidate discussions and designs.”  
The SI unit of mass is the kilogram.  Previously defined by calibration against a specific physical object, one which had been kept in a locked vault, this unit was redefined in terms of Planck’s constant (h).  The SI unit of temperature is the kelvin.  While its previous definition had not relied on a physical object in the same way that the kilogram had, the redefinition linked the kelvin directly to Boltzmann’s constant (k).  Both redefinitions will enable greater cohesion in scientific communication regarding experimental designs and results, as common reference points worldwide.  

“Five other units likewise are recast– /
Candela, second, meter, mole, ampere– ”
Scientists use seven fundamental SI units in total: kilogram (mass), kelvin (temperature), meter (length), candela (luminous intensity), second (time), mole (amount), and ampere (electric current).  With the redefinition presented in 2019, all seven now depend on fundamental constants of nature for their definitions.  

“From genesis in revolution past /
To standards metric by which STEM coheres.”
The metric system was initially devised in the midst of the French Revolution (this is one of those brief statements present in introductory science textbooks that always seems worth an entire seminar course in itself).  The same system now provides a coherent reference for scientists worldwide.  

“With h, k, c, et al., assign true north; /
Compare to ever-fixèd marks, henceforth.”
The closing couplet of this sonnet denotes a few of the fundamental constants of interest to this redefinition (h, k, and c, noted above).  These last lines also allude poetically to constants as they are defined in other disciplines.  Finding true north, in geology, provides an absolute measure of directionality.  In literature, Shakespeare describes steadfast love as an “ever-fixèd mark” in a famous phrase from his Sonnet 116.  It was this last link that provided the inspiration for this particular exercise; I have always been intrigued by the centrality of “the meter” to science and poetry, in such different ways, and the focus on “constants” in different contexts was another fun theme to explore.  Moreover, it was an interesting challenge to adhere to the rules on format and rhyme for an English sonnet, after so many weeks of limericks.