April 2019 Limerick Project

Literature Searches

“In searching for texts antiquarian
Or modern, seek first the librarians!
Their counsels are wise:
Research skills exercise,
While you formulate arguments clarion.”  

The April 11 limerick, written as part of National Library Week 2019, has been interestingly challenging to write about.  “Libraries and librarians are wonderful” is hardly a mysterious theme!

Since there’s not nearly as much need for translation as with some of my previous poems, I’ve opted to discuss the process of writing a scientific research article and how that can benefit from the insights of a librarian.  A chemist encounters several types of writing tasks in a career, many of which involve communicating regarding research. That communication can take place many ways; one medium is an informational piece of writing that reports on recent experiments, commonly called a journal article, research article, or scientific paper.

“In searching for texts antiquarian/ Or modern, seek first the librarians!/ Their counsels are wise:/ Research skills exercise…”
After its detailed title, a journal article typically begins with a short summary called an “Abstract,” summing up the article’s main findings; the abstract helps a reader to determine if diving into the full article would be beneficial.  Interestingly, it’s often the section written last, since it distills the article’s key points.  

The “Introduction” of the journal article (sometimes called the “Theory” section) then provides background information: what’s already been done in this area?  One aspect of writing journal articles thus involves reporting on a literature search: reviewing other scientists’ writings on the same topics, available in databases of previously published journal articles (“searching the texts antiquarian or modern”), and explaining how the new work compares to or contrasts with previously completed research.   

Librarians provide wonderful resources in navigating dense scientific literature; any author would benefit from talking with them, as a first step in the writing process. Searching for and reading journal articles can both be challenging tasks, but this type of writing follows a common format, and understanding that format can be useful.                  

“While you formulate arguments clarion.” 
The remainder of the journal article is where the chemist presents the new research, explaining what was done in the experiment (typically labeling this section as “Materials and Methods” or “Experimental Details”), the findings that were obtained (“Data and Results”), and the implications of those findings (“Discussion”).  Names can differ for all of these sections, but some common labels are presented in parentheses. These latter parts of the article constitute the author’s new contribution, ideally presented clearly, as an “argument clarion.”

April 2019 Limerick Project

Potential Energy Surfaces

“An energy surface, potential,
For reaction info: essential. 
Is shown in simplicity
Through diagram self-referential.”

The April 10 limerick summarizes a common visual shorthand used in several chemistry applications: a potential energy surface.  Potential energy surfaces are graphical representations that show the energy of a chemical compound or reaction as a function of some independent variable.  Different types of surfaces can be drawn for different chemistry-related scenarios. Some can be quite complex, but the surface described in this limerick is a simple two-dimensional graph.     

“An energy surface, potential,/
For reaction info: essential.” 

For a chemical reaction, as described in this limerick, the potential energy surface is a two-dimensional graph that represents the energy involved as a function of “reaction coordinate,” which can generally be interpreted as “reaction progress.”  Organic chemists often use these diagrams in representing chemical mechanisms (step-by-step depictions of how molecules react) to show how molecules encounter one another and absorb or release energy over the course of a reaction step. A potential energy surface is a reliable, essential tool for communicating basic information about a chemical reaction.

Is shown in simplicity/
Through diagram self-referential.”

An endoergic reaction (also called an endergonic reaction) is a reaction that requires an input of energy (as heat, light, etc.) to proceed.  It would be shown on a potential energy diagram with the reactants at lower energy than the products.  An exoergic reaction (also called an exergonic reaction) is a reaction that releases energy as it proceeds.  It would be shown on a potential energy surface with the reactants at higher energy than the products. 

In both cases, one would interpret the endoergicity or exoergicity of the reaction by looking at the placement of these products and reactants relative to one another: the energy diagram is self-referential. Furthermore, once a reader is fluent in the diagrams’ conventions and terminology, the potential energy surfaces are visually rich and relatively simple, compared to many other ways of presenting quantitative data.    

April 2019 Limerick Project

Gas Laws

“The gas laws according to Boyle,
Avogadro, and Charles embroil
P, V, n, and T– traits
Of the phase that inflates–
In equations o’er which students toil.”

I will backtrack a day with this entry, as I inadvertently skipped posting my essay on the 8 April 2019 limerick!  This poem addresses another common introductory chemistry topic: the phases of matter. General Chemistry courses typically examine properties of solids, liquids, and gases. This poem references the development of some key equations via which the gas phase, specifically, is described.         

“The gas laws according to Boyle,/
Avogadro, and Charles embroil/
P, V, n, and T– traits/ Of the phase that inflates–”

As a student, I found the names associated with introductory chemistry to often be intriguingly distracting: the history of chemistry is mostly confined to sidebars in General Chemistry textbooks, but the stories are fascinating.  

Several equations are named for scientists who worked on examining how physical properties of a gas sample are related; these are (Robert) Boyle’s Law, (Jacques) Charles’s Law, and (Amedeo) Avogadro’s Law.  The spark for this particular poem was a variation on the rules-of-cards phrase “according to Hoyle” with respect to Boyle’s name, specifically.           

Boyle’s Law states that as the pressure on a gas sample increases, its volume decreases, if amount and temperature are held constant.  Charles’s Law states that as the temperature on a gas sample increases, its volume increases, if pressure and amount are held constant.  Avogadro’s Law states that as the amount of a gas increases, its volume increases, if pressure and temperature are held constant.  

Pressure is represented with the variable P; volume, with V; amount, with n; and temperature, with T.  When linked together (“embroiled”), they comprehensively describe the properties of a gas, periphrastically described here as “the phase that inflates.” 

“In equations o’er which students toil.”  
The named laws listed above are typically combined into the Ideal Gas Law: PV = nRT, an equation that quantitatively (exactly) relates all four of a gas sample’s variables via the gas constant R.  

The last line of the limerick is simply a rueful acknowledgement that, despite the elegance of any equations involved, truly learning chemistry– or any discipline– is difficult work!      

April 2019 Limerick Project

Organic Chemistry

“ The topics in classrooms organic
Can sometimes seem roadblocks titanic.
My advice?  Simply, I’d
Heed the Hitchhiker’s Guide…
First and foremost, remember: ‘Don’t panic.’ ”   

The April 9 limerick takes a detour from General Chemistry learning objectives, taking an overall look at the traditional second-year chemistry courses through the lens of a science fiction classic.

“The topics in classrooms organic/
Can sometimes seem roadblocks titanic.”
Organic Chemistry 1 and 2 together constitute an undergraduate course sequence that can inspire significant foreboding.  “O-Chem” often is the last chemistry coursework a non-major has to complete; it is a common hurdle across many pre-professional curricula (pre-med, pre-dentistry, pre-vet, etc.); it involves the mastery of a tremendous amount of material in a two-semester lecture course; it often involves a significant lab component.  All of these facts can loom large to a student, as can the substance of the course material itself!

“My advice?  Simply, I’d/ Heed the Hitchhiker’s Guide…/
First and foremost, remember: ‘Don’t panic.’ ”   
From my own experience, I can say that Organic Chemistry can be a fun and inspiring challenge.  Where General Chemistry involves a broad range of topics; Organic Chemistry is more consistent: it’s highly visual, involving an emphasis on spatial reasoning, and it involves mastering some key techniques and rules, then applying them to several types of interesting molecules and reactions.  However, most students enter the classroom already aware of the challenges discussed above and thus more than a bit apprehensive.  

I’ve thus always thought the textbooks would benefit from a treatment similar to The Hitchhiker’s Guide to the Galaxy, the central text from Douglas Adams’s 1979 novel of the same name.  Adams describes the interstellar encyclopedia: “It looked insanely complicated, and this was one of the reasons why the snug plastic cover it fitted into had the words DON’T PANIC printed on it in large friendly letters.” 

Most textbooks have molecular structures or chemistry-related pictures on the front; while certainly not intentionally alienating, they are not as reassuring as Adams’s famous motto!     

April 2019 Limerick Project

Redox Reactions

“The ‘oil rig,’ a helpful mnemonic
For redox’s challenges chronic.
Mind errors, potential.
This note is essential:
View of loss/gain must be electron-ic.”

The 7 April 2019 limerick addresses another reaction classification topic, this time looking at “reduction-oxidation” chemistry. Reduction and oxidation are themselves names that correspond to specific processes; they always happen in tandem, so the chemical shorthand becomes “Red-Ox,” or “redox.” Redox is a term that can apply to a wide range of subclasses of reactions; combustion (from the 6 April 2019 limerick) is one of these.  

In particular, the poem clarifies the use of a common memory trick for describing redox processes. The discussion focuses on the most obvious type of redox reaction, a displacement reaction, to keep the discussion as straightforward as possible.

“The “oil rig,” a helpful mnemonic/
For redox’s challenges chronic.”
Redox reactions involve electron movement.  Because electrons are negatively charged, the elements to which and from which electrons flow experience a change in their own charges over the course of the reaction.  These can be challenging reactions to consider, as redox concepts can manifest themselves in several ways.    

In the simplified reaction below, the notation used for the reactants (left of the arrow) shows us that Element A starts out as a neutral metal and Element B starts out with a positive charge, in their reactant forms.  In their product forms (right of the arrow), Element A has a positive charge and Element B is a neutral metal. 

This is also called a displacement reaction because A “displaces” B in terms of forming a compound with C.  

A + BC → B + AC   

The “mnemonic” in question links the movement of electrons to the chemical vocabulary: “Oxidation Is Loss; Reduction Is Gain.”  This statement is abbreviated as “OIL RIG.”

In the reaction above, Element A is oxidized, losing electrons to go from neutral to positively charged; Element B is reduced; gaining electrons to go from positively charged to neutral.   

“Mind errors, potential./ This note is essential:/
View of loss/gain must be electron-ic.”
A common error with these reactions is viewing “loss” and “gain” in terms of the values of the charges on the elements, neglecting the fact that electrons are negatively charged.  (In the example above, the ERROR would be saying: A’s charge becomes more positive; thus, it “gains”; thus, it is reduced.)

The application of the “oil rig” mnemonic relies on considering loss/gain in terms of electrons.  

April 2019 Limerick Project

Combustion Reactions

“A process denoted combustion
Results in methodic production:
H2O, CO2;
Common products ensue
From a fuel hydrocarbon’s consumption.”

As with the April 5 limerick, the 6 April 2019 limerick addresses another reaction class and how to easily identify it. This specific poem examines combustion reactions and the chemical formulas used to represent specific compounds involved therein.    

“A process denoted combustion/ Results in methodic production:”
This limerick outlines the class of reaction of interest, pointing out that we’ll be able to classify a reaction as a combustion reaction by looking at its characteristic reactants and products (its “methodic production”). The remainder of the poem defines these species more directly.      

“H2O, CO2;/ Common products ensue/
From a fuel hydrocarbon’s consumption.”  
This is the first limerick in my project to exploit chemical notation to obey the rhythmic rules of the poetic form! For the syllables to work here, the third line is read as “H two O, C O two.”  These abbreviations have specific meanings for chemists.

Notably, “H2O” and “CO2” are not formatted correctly, due to Twitter constraints (or at least my lack of knowledge of how to format subscripts and superscripts via that medium!); they should be properly written as H2O and CO2.  These are the chemical formulas for water and carbon dioxide, respectively. The formula for water tells us that each H2O molecule contains two hydrogen atoms and one oxygen atom; the formula for carbon dioxide tells us that each CO2 molecule contains one carbon atom and two oxygen atoms. 

Water and carbon dioxide are the characteristic products when a hydrocarbon fuel [a molecule consisting only of carbon and hydrogen, such as butane (C4H10) or propane (C3H8)] reacts with oxygen to undergo combustion.        

The overall pattern can be seen in the balanced reaction shown below, which represents the complete combustion of propane. 
C3H8 + 5 O2 →  3 CO2 + 4 H2O

April 2019 Limerick Project

Precipitation Reactions

“Reactions with solid formation,
We classify precipitation:
Mix solutions (aq),
And the (s) formed anew
Will crash out to observer’s elation.”

The next few limericks address specific classes of chemical reactions and how to identify and interpret them: again, a common theme of many General Chemistry courses.  The first, from 5 April 2019, is a reaction type that figures heavily in both introductory chem courses and my interdisciplinary course, Chemistry in Art.   

“Reactions with solid formation,/ We classify precipitation:” 
Much like balancing reactions, another intro-level skill is identifying types of reactions; chemical reactions often have tell-tale reactants or products that allow their classification.  Reactions in different classes follow set patterns, so once we’ve done our classification, we can explore more interesting aspects of the pertinent chemistry.

For instance, a precipitation reaction involves the formation of a solid product called a precipitate; this product “falls” out of solution (parallelling the everyday definition of precipitation).  

“Mix solutions (aq),/ And the (s) formed anew/
Will crash out to observer’s elation.”
To identify a precipitation reaction, we look for a process with two identifying characteristics.  First, the reactants are aqueous solutions (compounds dissolved in water); they are designated as such by the (aq) abbreviation after their chemical formulas.  Second, one product is a solid, which is designated by the (s) abbreviation after its chemical formula. The final line of the poem notes that precipitation reactions are fun to watch, as the solid product “crashes out” of the solution.

Here’s a sample reaction, in which aqueous solutions of potassium chloride (KCl) and silver nitrate (AgNO3) yield a precipitate of silver chloride (AgCl) and a side product of aqueous potassium nitrate (KNO3); we can see the pattern described in lines 3-5 of this limerick:  
KCl (aq) + AgNO3 (aq) → AgCl (s) + KNO3 (aq)   

Precipitation reactions have implications for the interdisciplinary overlap of chemistry and art.  Silver chloride itself is light-sensitive and participates in reactions associated with black-and-white photography.  Some solid precipitates formed in other precipitation reactions are brightly colored and can be used as pigments in mixing and using paints.       



This virtual space: still uncharted;
My first few attempts have been thwarted.
But thoughts keep repeating:
The time here is fleeting;
Get moving; get writing; get started.

I’ve always thought of myself as both a chemist and a writer, but little evidence exists of the latter role, compared to the former. I’m hoping to change that in terms of my creative routine this year.

The last few years have brought some tentative steps in that direction. Most concretely, I greatly enjoyed a poetic experiment in April 2019, wherein I celebrated the overlap of the International Year of the Periodic Table and National Poetry Month, “five lines at a time,” with a set of thirty limericks over thirty days, shared on my Twitter account. I’ve been meaning for several months to go back and provide some additional context and content, so that the limericks could conceivably be useful/educational, as well as format-appropriate. That intent is my most specific and immediate aim, here. I plan to keep each of these initial entries constrained to 280 words, given their origin in Twitter’s 280-character limit: hoping to keep the discussion distinct and direct.

More generally, the “what I wish I’d known” list gets a bit longer every year, as it applies to both 2000 (as a chemistry student in college) and 2010 (as a new chemistry professor). I’ve thought for a while about attempting to compile and communicate some of that information, and this could be a space for that purpose.

And finally, at the risk of this entry’s becoming a bit of a Mobius strip, I’ve found the rediscovery of creative writing to be restorative during the past few years: writing about writing will be a third common topic here, I imagine. While the techniques or resources I’ve discovered are not remotely new, they have all at some recent point been new to me. I’d thus like to create my record of what has helped, in the hopes that it might conceivably someday help others.

As with so many things, it is daunting to try, but more daunting to consider not-trying! So: to be continued.