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April 2019 Limerick Project

Earth Day

“Via STEM, we explore what’s attainable,
Our efforts towards world more sustainable.
We must seek to strive:
Find ways for Earth to thrive,
For ‘to yield’ would be act unexplainable.”  

In the week beginning with 22 April 2019, I changed my approach slightly, writing a set of five poems geared towards the American Chemical Society’s “Chemists Celebrate Earth Week” celebration, focusing on green chemistry and other efforts in environmental sustainability. The specific motto for 2019 was “Take Note: The Chemistry of Paper,” and this was enough motivation to bring in some direct allusions to some beloved poets and poems.  (After all, these poems were recorded on paper in their moments of inspiration!)    

Thus, in this limerick and the four following (from April 22-26, 2019), I alluded to famous poems or poetic works that could be read to address a scientific theme, paying appropriate tribute in the hashtags.  This first was written for Earth Day itself; the 22 April 2019 limerick echoes some of the words of a favorite poem by Alfred, Lord Tennyson.   

“Via STEM, we explore what’s attainable,/
Our efforts towards world more sustainable.”

The first two lines acknowledge the work underway by many scientists in efforts of sustainability: ecological and other interdisciplinary investigations of the complexity of our increasingly interconnected world.  

“We must seek to strive:/ Find ways for Earth to thrive,/
For ‘to yield’ would be act unexplainable.”  

The end of the limerick borrows from the closing of Tennyson’s “Ulysses”:

“…tho’ / We are not now that strength which in old days/
Moved earth and heaven, that which we are, we are;/
One equal temper of heroic hearts,/
Made weak by time and fate, but strong in will/
To strive, to seek, to find, and not to yield.”

I referenced the famous final sequence of verbs (“to strive, to seek, to find, and not to yield”) in my last three lines, using Tennyson’s words in exhorting scientists never to give up in “seek[ing] a newer world.”       

It is challenging to write more than an explanation of the limerick’s verbiage.  I cannot share any academic expertise about Tennyson’s poem; it is simply one I cherish. That the poem ends with a negative infinitive is perhaps my favorite aspect: the last three syllables do not say “to succeed” (or some more poetic positive phrase!), but rather “not to yield.”  In so many situations, the temptation to succumb to fear is immense; the image of the king– idle no longer, choosing NOT to yield, resolutely rejoining the fray– is tremendously moving. (See also: Théoden.)  

Looking back at this limerick one year later, from a challenging April 2020: may we all continue to be strong in will, through the days ahead.

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April 2019 Limerick Project

Electrolytes

“The salt of the earth, role emergent;
Strong electrolytes, their traits observant.
Compounds’ crystals dissolve
In pure water. Resolved:
Now the water will conduct a current.”

Aqueous chemistry– the chemistry that occurs in water– constitutes yet another common topic in introductory textbooks.  Species that are ionized in water are called electrolytes: these ions can go on to a variety of reactions, such as precipitations, redox, and neutralizations (acid-base reactions).  The 21 April 2019 limerick explains the characteristic properties of electrolytes in aqueous solutions. Characterizing compounds as strong, weak, or non electrolytes is a useful skill to learn in introductory chemistry coursework.   

“The salt of the earth, role emergent; /
Strong electrolytes, their traits observant.”  

Ionic compounds are commonly called salts.  If an ionic compound is water-soluble (dissolving in water rather than remaining a solid), it ionizes completely: dissociating completely into its component ions.  This behavior characterizes it as a strong electrolyte.  

The most famous salt is table salt: sodium chloride, a compound referenced in a wide range of contexts throughout history!  It is useful to consider as a representative strong electrolyte. Table salt exists as the neutral (uncharged) chemical compound NaCl.  When dissolved in water, it ionizes completely into sodium ions (represented as Na+) and chloride ions (represented as Cl).    

A weak electrolyte ionizes partially in water.  Keeping our focus on the kitchen: one component of vinegar is acetic acid, a weak electrolyte with the molecular formula CH3COOH.  When dissolved in water, acetic acid ionizes only partially to its component ions (CH3COO and H+).  Most of the acetic acid molecules stay in their neutral forms (as CH3COOH).

Finally, a non-electrolyte does not ionize in water.  Table sugar (sucrose, C12H22O11), for instance, is a non-electrolyte.  It dissolves in water, but if we looked at the compound at the molecular level, we would see that the sugar molecules all stay intact in their neutral forms.       

“Compounds’ crystals dissolve/
In pure water. Resolved: /
Now the water will conduct a current.”

Where does the name “electrolyte” come from?  When an electrolyte dissolves in water, the resulting solution can conduct an electric current.  This is more pronounced with a strong electrolyte than a weak one, a fact which is the substance of many chemistry demonstrations!  An aqueous solution of a non-electrolyte does not conduct any electric current.

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April 2019 Limerick Project

Covalent Bonds

“Covalent bonds: electrons’ sharing, 
In two orbitals’ overlap, pairing. 
H2’s bond length can be 
Found via minimized E 
As a function of H atoms’ bearings.”

Chemical compounds form when their component elements can stabilize one another via energetic interactions.  The 20 April 2019 limerick summarizes several important pieces of information related to one such type of interaction: a covalent bond.  In particular, the poem describes a hydrogen molecule and how its geometry is related to the energy of its covalent bond.  

“Covalent bonds: electrons’ sharing,/
In two orbitals’ overlap, pairing.” 
Chemical compounds bond in two main ways: ionic bonds, in which oppositely charged ions attract, and covalent bonds, in which atoms share their valence electrons.  This poem focuses on the latter case.  

To share electrons to form a covalent bond, two atoms’ orbitals (regions of space in which electrons are likely to be found) must overlap.  This is the substance of valence bond theory: as these orbitals overlap, the electron of one atom pairs with the electron of another in a covalent bond, stabilizing the molecule overall.  

“H2’s bond length can be/ Found via minimized E/
As a function of H atoms’ bearings.”
The simplest molecule is the hydrogen molecule, written as H2 and containing two hydrogen atoms covalently bonded together (again, my Twitter notation fails to subscript the numeral two!).  

These last three lines of the poem narrate the potential energy surface of a hydrogen molecule, with energy as a function of internuclear distance (bond length).  As we look at the graph, we can find the bond length of H2 by finding the minimum energy (the minimum point on the y-axis) and looking at what bond length corresponds (on the x-axis).  In other words, we look for “minimized E as a function of H atoms’ bearings”: minimized energy as a function of the hydrogen atoms’ distance from one another.  

Such a graph can be found in any introductory chemistry textbook and gives us two important pieces of information: the bond dissociation energy of H2 (how much energy is required to break the bond?), which is 432 kJ/mol, and the bond length of H2, which is 74 picometers (pm).     

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April 2019 Limerick Project

Laws of Thermodynamics

The forward momenta of Thermo,
Through progress from Physics and Chem, show
Laws named One, Two, and Three,
Then seek to define T,
So backtrack to a fourth law deemed Zero.

In learning chemistry, I was often distracted by the etymologies of some of the terms of interest presented in my courses.  The 19 April 2019 limerick addresses one such linguistic oddity, one of the topics I now teach each year: the “zeroth” law of thermodynamics.  

“The forward momenta of Thermo,
Through progress from Physics and Chem, show…”

Thermodynamics is a field that generally examines heat energy and thus is of interest to many types of scientists.  This particular poem highlights the field’s development by physicists and chemists as commemorated in the four laws of thermodynamics, which were articulated during the mid-nineteenth to early-twentieth centuries.  

“Laws named One, Two, and Three,
Then seek to define T,
So backtrack to a fourth law deemed Zero.” 

The fundamental principles of thermodynamics are collected in the four laws of thermodynamics.  The first law explains the conservation of energy: energy cannot be created or destroyed; it can only change forms.  For chemists, this is generally presented as: ΔU = q + w. This equation states that a system exchanges its energy (ΔU) with its surroundings via two energetic “currencies”: heat (q) and work (w).  The second law contextualizes a property called entropy, which has been poetically dubbed “time’s arrow”; in terms of processes, entropy governs their spontaneity: the direction in which these processes naturally occur.  The third law states that as temperature approaches absolute zero (0 K), the entropy of a system approaches zero.   

The meaning of this limerick hinges on the unusual fact that the law of thermodynamics that was fourth to be formulated is named the zeroth law!  This is because the first, second, and third laws all rely on the property of temperature (T)… but to use temperature, it’s necessary to first define it.  The zeroth law defines temperature; when it was formulated, scientists decided it would be simpler to denote it as zeroth rather than renumber the existing three laws.      

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April 2019 Limerick Project

In the Abstract

“In writing a lab report’s abstract,
Report data found, in form exact.
Descriptions avoid,
Lest your reader’s annoyed:
Be succinct so the details don’t distract.” 

The April 18 limerick returns to the topic of scientific writing, looking at in detail at the first section of a lab report, which is called the abstract.  “Lab report” is a shorthand for “laboratory report,” a common assignment in undergraduate science coursework. Via these assignments, science students report on experimental work completed in the laboratory setting and gain experience with the conventions and challenges of academic scientific writing.   

“In writing a lab report’s abstract,/
Report data found, in form exact.”    

An abstract is a brief summary of a scientific document’s key findings.  (It is worth first an acknowledgement that it’s non-intuitive to think of this concrete type of writing via a word that often means anything but concrete!  However, the Latin term abstractus is cited as denoting a variety of meanings, and two that are particularly pertinent here are “extracted” and “summarized.”) 

When I teach lab courses, I emphasize that students should highlight the key experimental data obtained as clearly as possible, in a given abstract, so that readers can decide as easily as possible whether or not the larger report is worth the considerable time investment.  

Lab reports are not identical to scientific journal articles, but they are an introduction to writing in that challenging, information-dense format, which was previously discussed in the 11 April 2019 limerick.  As I mentioned there, it’s simplest to leave writing the abstract until the end, as an understanding of “what the key findings are” emerges during the report-writing process itself.   

“Descriptions avoid,/ Lest your reader’s annoyed:/
Be succinct so the details don’t distract.” 
Along the same lines, the abstract is not a place for creative writing.  “Annoyed” is probably too strong a true descriptor for a potential reader, but the last line sums up the key idea: an abstract should point directly to the main findings of an experiment, rather than try to tell the story of how those findings were obtained.  The remainder of the report or article provides space for placing the work in context, describing the experimental details, and fully explaining the implications of these key findings.       

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April 2019 Limerick Project

Hess's Law

“A puzzle-like problem: expunction
Of like terms from reactions’ adjunction
Towards a target process…
Keep in mind: Law of Hess! 
Find solution since H is state function.”  

The April 17 limerick is the third of three limericks focused on enthalpy.  So far we’ve seen both enthalpy’s empirical implications (what does it mean for a chemical reaction run in the lab?) and its mathematical relationships.  This third limerick examines one of the most common applications of enthalpy-related concepts: a calculation called Hess’s Law. It is named after chemist Germain Hess, who was the first to publish this mathematical approach in 1840.  

“A puzzle-like problem: expunction/
Of like terms from reactions’ adjunction/

Towards a target process…/”
The essence of Hess’s Law is that if we want to know the Delta H (𝛥H, or change in enthalpy) for a reaction for which that quantity isn’t yet known, we can manipulate other, related reactions for which the Delta H values ARE known and then add those values to obtain the Delta H of the target reaction (“target process”).  

Much more detailed explanations are available, but the paragraph above gives the gist of the limerick’s wording: when we add up the manipulated, related reactions (and thus examine their “adjunction”), we end up “expunging” terms that are identical on either side of the reaction arrow until we reach the target reaction.       

I tend to present this type of problem as a puzzle when I lecture on it: we know the picture on the front of the jigsaw puzzle box (the target reaction) and we fit together the pieces (the given reactions) to get there.    

“Keep in mind: Law of Hess!/
Find solution since H is state function.”   
The last two lines reveal the name of this specific type of calculation and point to the mathematical properties of enthalpy (H) as key to facilitating this type of solution.  

Since enthalpy is a state function, all that matters is the final state of the reaction (having the correct products) and the initial state (having the correct reactants).  Once we have them, we can determine the Delta H of the target reaction. It doesn’t matter how we got to that target (that is, the order in which we put the puzzle pieces together is irrelevant), because enthalpy is a state function. 

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April 2019 Limerick Project

Enthalpy

“Delta H represents change in enthalpy,
A chemic’lly convenient quantity.
Vessel’s open to air?
Find the Delta T there,
And thus heat transferred in pressure’s constancy.” 

The April 16 limerick likely comes the closest of these April 2019 poems to a lecture explanation; I cover all these points “in prose” when I teach chapters on thermochemistry (the chemical bookkeeping of the quantities via which reactions absorb or release heat energy).  

“Delta H represents change in enthalpy.”
The Greek letter delta represents a change in a type of function called a state function.  We can subtract the initial value (state) of a function from the final value (state) of that function to obtain the change in that function; altitude is a simple example.  The letter H represents the state function of enthalpy.   

“A chemically convenient quantity.”
When I introduce enthalpy to my students, it is with a direct acknowledgement that many functions (as well as symbols and units more generally, as discussed in Andy Weir’s excellent book The Martian) throughout history were derived to provide convenient shorthands for a group of chemists working at a given time.  Generations later, students are tasked with making sense of this polyglot science!  

Here, enthalpy is the heat energy transferred at constant pressure. Most chemistry lab work is done at constant (atmospheric) pressure; heat energy is particularly convenient to monitor, via temperature changes. Enthalpy is itself a state function, while heat energy is a path function (involving different types of calculations).  Equating the two under constant-pressure conditions opens the door to many useful concepts and calculations.  

“Vessel’s open to air?/  Find the Delta T there./ 
And thus heat transferred in pressure’s constancy.”
Are we running an experiment in glassware (also called a “reaction vessel”) that is open to the air?   We almost always are, when in a chemistry lab, and so the reaction in question is at constant pressure. 

We can infer the change in heat energy for the reaction from the temperature change (Delta T) in the solution in which it occurs… and thus the change in enthalpy, our “convenient quantity.” 

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April 2019 Limerick Project

Thermochemistry

“A reaction we call exothermic
Is the theme of this statement affirmic:
Wear your gloves in the lab
When the beaker you grab,
Lest you cause self a burn epidermic!”

The next few limericks, beginning with this one from 15 April 2019, address the concept of enthalpy.  Enthalpy is a science-specific vocabulary word for the heat energy transferred during a constant-pressure process.  Enthalpy is subtly different from other forms of energy; one of the upcoming poems will address this directly.     

“A reaction we call exothermic/
Is the theme of this statement affirmic:”
As we saw with an earlier limerick, the energies of reactions are described by their own vocabulary words.  This is the case for enthalpies of reaction as well; reactions can be characterized as exothermic or endothermic.   

An exothermic reaction releases heat energy.  In a chemist’s notation, we would write some variation of -𝛥H to communicate this, although the exact notation varies with specific conditions and conventions.   Overall, the “negative delta H” tells us that this corresponds to a change in enthalpy during a process/reaction: this reaction releases heat energy, meaning the reactants are at higher enthalpic content than the products.

(An endothermic reaction has a “positive delta H,” or +𝛥H.  This is analogous to the discussion of potential energy surfaces a few entries back; note the similar– but not identical– language of exothermic and endothermic, compared to exergonic and endergonic.)     

In poetic terms, this limerick introduces exothermicity, then promises to explain a bit of what that term means, via a “statement affirmic”!  

“Wear your gloves in the lab/ When the beaker you grab,/
Lest you cause self a burn epidermic!”
It is a best practice in a chemistry lab to wear disposable gloves when working with glassware, and one common piece of glassware is a beaker.  Because exothermic reactions release heat, if you pick up a piece of glassware in which one is occurring, you should take particular precautions to wear your gloves, so as not to burn your hands: your skin “epidermic.”  (That you should also be wearing safety goggles at all times in a chemistry lab goes without saying!)  

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April 2019 Limerick Project

Kekulé and Benzene

“The structure of resonant benzene
Found inception in Kekule’s daydream
As a snake seized its tail:
Vivid image availed
Him an insight once shrouded in smokescreen.”

The 14 April 2019 limerick retells a famous legend from chemical history: German organic chemist August Kekulé’s 1865 inspiration regarding the shape of the molecule benzene.

A major theme of chemistry is that the shapes (the structures) of molecules impact their behaviors (their functions); analyses of these structure-function relationships are part of many fields of chemistry research. With many compounds, their behaviors were observed in the laboratory before their chemical structures were known, and the paths to understand those structures include many interesting stories.

This story also provides a convenient overview of three types of chemical representations: empirical, molecular, and structural formulas.

“The structure of resonant benzene/
Found inception in Kekule’s daydream/
As a snake seized its tail…”
The molecule benzene contains six carbon atoms and six hydrogen atoms, as described by its molecular formula: C6H6. Before scientists understood this, they knew benzene’s empirical formula, which represents the lowest possible ratio of elements: here, CH. Since all that was known was that the molecule contained one carbon atom for every hydrogen atom, many possibilities were imagined for its shape.

According to legend, Kekulé had been pondering this question, when he had a daydream about a snake biting its tail. This inspired his idea of a cyclic compound, one in which carbon atoms formed a ring, instead of connecting to one another in a linear chain.

We now represent benzene as existing in a hexagonal shape, as succinctly shown via its structural formula. After Kekulé’s revelation, further study of benzene revealed an interesting bonding pattern called resonance, which accounts for benzene’s unusual stability.

“Vivid image availed/
Him an insight once shrouded in smokescreen.”
Kekulé later popularized the dramatic nature of his insight, writing: “One of the snakes had seized hold of its own tail, and the form whirled mockingly before my eyes. As if by a flash of lightning I awoke… I spent the rest of the night in working out the consequences of the hypothesis.”

As with many of the stories behind scientific discoveries, debates have arisen as to the veracity of the details. That said, the last line of this limerick is a final allusion to the chemical legend, since it is generally recounted that Kekulé had his daydream in front of the fireplace.

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April 2019 Limerick Project

Computational Chemistry

“Exploring with chem computational
Lets you quantify features foundational. 
Choose objectives; target
Method and basis set. 
(Some calcs close with a quote motivational!)”  

The 13 April 2019 limerick provides an overview of computational chemistry, a field that explores the overlap of chemistry, math, physics, and computer science.  

“Exploring with chem computational/
Lets you quantify features foundational.” 
Computational chemistry is a field that encompasses a wide range of research. One common type of calculation quantifies the properties and features of a chemical species based on its molecular geometry (how are the component atoms connected in space, when a molecule is in its lowest-energy arrangement?).   

For instance, water has a simple molecular structure: a central oxygen atom bonded to two hydrogen atoms, making an overall “V” shape.  What happens to the energy of a water molecule if we stretch out one of the O-H bonds?  The molecule will become less stable, and the molecule’s energy will rise.  A geometry optimization reverses this analysis: manipulating a molecule’s geometry until a minimum energy is achieved.         

Once a molecule is optimized, we can evaluate many useful, fundamental properties.  For the water example, we could calculate its geometric parameters (bond lengths, bond angles), its thermodynamic quantities (energies and related functions), and other simulated experimental data, given an optimized geometry and a related calculation called a frequency analysis.      

“Choose objectives; target/ Method and basis set.”  
Several computational approaches are possible, given the desired research question (i.e., the objectives).  For many of these approaches, you choose a method and basis set that together are best targeted to the type of research question of interest.  The method explains how the calculation will be solved; the basis set explains how many mathematical functions will be involved in that calculation.     

“(Some calcs close with a quote motivational!)”
Many different computational chemistry software packages exist; one of these famously closes each calculation with a philosophical quote