Categories

## 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.”

Categories

## 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!)

Categories

## 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.

Categories

## 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

Categories

## Electron Configurations

“Use noble gas configurations
As a shorthand for core information.
How the atom arrays
Its electrons: display
This arrangement in compact notation.”

The periodic table arranges elements according to their physical and chemical behaviors… but why are those behaviors different from one another in the first place? The electronic structure of an atom (that is, how the electrons in that atom are arranged) of each element is unique and governs each element’s behaviors. The 12 April 2019 limerick introduces the skill of representing these arrangements in a compact form: writing “noble gas” configurations.

“Use noble gas configurations/ As a shorthand for core information.
Electron configurations represent the number of electrons in an element and their probable locations, which are called orbitals. (Why are orbitals “probable” instead of “definite” locations? This is due to the unusual rules of quantum mechanics.)

Sodium (Na), for instance, has eleven electrons. These are distributed into orbitals of increasingly higher energy, as represented by the following full electron configuration: 1s22s22p63s1
The 1s orbital is lowest in energy, followed by 2s, followed by the three orbitals in the 2p subshell, followed by the 3s orbital. (The s and p labels come from abbreviations for “sharp” and “principal,” which are historical descriptions related to these concepts.) The superscripts denote how many electrons populate a given orbital or subshell. By adding up the superscripts, we confirm that we’ve accounted for all eleven electrons.

Commonly, chemists use “noble gas” notation, where the symbol of the nearest noble gas to the element in question is placed in brackets to replace part of the electron configuration. The nearest noble gas for sodium is neon (Ne), which contains ten electrons, so we can also write: [Ne]3s1
Here, the ten innermost electrons (1s22s22p6) are accounted for by comparison to neon’s configuration; the eleventh, outermost electron is notated separately.  These inner electrons are called core electrons (we often refer to “the noble gas core”); the outer electron is called a valence electron.

“How the atom arrays/ Its electrons: display/
This arrangement in compact notation.”
Compared to a full electron configuration, a noble gas configuration is a more efficient notation for arranging electron configuration information, as seen above. This compactness becomes quite dramatic with atoms containing large numbers of electrons.

Categories

## 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.”

Categories

## Potential Energy Surfaces

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

“Endo/exoergicity/
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.

Categories

## Gas Laws

“The gas laws according to Boyle,
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,/
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!

Categories

## Organic Chemistry

“ The topics in classrooms organic
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/
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!

Categories

## 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.