Category: STEM Education Poetry

“Rivaling SN, 
An elimination will 
Lead to formation of 
Newfound alkene.
(E2 results from build 
Anticoplanar;
Abstraction and leaving,
Coincident, seen.)”

This post is from 8 April 2022 and marks the last of the mechanism-themed poems from NaPoWriMo2022.  These verses were fun to write but, as with both the kinetics and enthalpy “series” in previous months, the resulting essays deal with themes that can seem remarkably abstract!  Next week marks a return to some less involved topics, for the remainder of the semester.      

This last poem addresses two new types of reaction mechanisms that often compete with the nucleophilic substitution reactions seen in previous posts (S_N1 and S_N2).  These two new types of reaction pathways are called eliminations, wherein a base reacts with (often) an alkyl halide to “eliminate” a hydrogen atom and the leaving group, ultimately yielding the formation of an alkene, a compound with a double bond.  As with the nucleophilic substitutions, eliminations (represented generally as E) can occur via a two-step process (E1, for unimolecular elimination) or a single-step, concerted process (E2, for bimolecular elimination).  Both are shown in the diagram below, using conventions of electron-pushing mechanisms.  

Via E1, the bond to the leaving group breaks first, yielding a carbocation as the bromide ion leaves.  As shown here, a neutral base with a lone electron pair then abstracts (removes) a proton, so that the electrons originally in that C-H bond form a new pi bond between two carbon atoms.  Besides the bromide ion, which departed in Step 1, the other side product is the now-protonated generic base, from Step 2.  

Via E2, the negatively-charged bulky base doesn’t have enough room to attack the alkyl halide as a nucleophile.  Instead, it abstracts a proton, and the subsequent formation of a pi bond then causes the departure of the bromide ion as the leaving group, all in one reaction step. The leftover side products here are the now neutral tert-butanol and the bromide ion, both from the single reaction step.     

As with the other poems from this month, before launching into the essay, it’s worth acknowledging the motivation: the “why do we care about this in the first place?” aspect of such complicated topics.  These four reaction patterns (S_N1, S_N2, E1, and E2) are evident in a tremendous number of settings.  Chemistry students traditionally begin their extensive training in chemical and biochemical mechanisms by learning these four options and learning how to predict which of the four is likely to predominate given a set of reaction conditions.  The reactions have massive implications for organic synthesis, biochemistry, and many other branches of chemistry.  However, trying to learn them in the first place can be imposing.  This poem takes several aspects of the elimination mechanisms and presents them in a rhymed format, which ideally might be memorable for students learning the material.     

“Rivaling SN, /
An elimination will / 
Lead to formation of / 
Newfound alkene…”

Nucleophilic substitution reactions and elimination reactions “rival” one another: they involve comparable reactants that can accomplish multiple mechanistic steps, competing for the most likely pathway in a given situation.  The reactant molecules in the reactions shown here could also theoretically undergo S_N1 or S_N2 reactions, respectively.    

Why is this?  Both bases and nucleophiles use electron pairs to achieve mechanistic ends: many molecules act as one or the other interchangeably.  How a negatively charged species will act comes down to its own bulkiness and other reaction conditions.  Does it have enough room to attack as a nucleophile, or is the organic molecule crowded (sterically hindered), so that abstraction of a proton is more feasible?  Is it neutral or negatively charged?  Many such questions help students make the “call” of whether S_N2, S_N1, E2, or E1 is occurring in a given scenario.

An elimination pathway yields a “newfound alkene”: a molecule containing a double bond.      

“(E2 results from build /
Anticoplanar; /
Abstraction and leaving, /
Coincident, seen.)”

Discerning between E1 and E2 mechanisms means considering characteristics of the reactant molecules, the base, the solvent, and other factors, in processes reminiscent of discerning between S_N1 and S_N2.

The new consideration for eliminations is that E2 has a geometric constraint (required 3-D arrangement) in the organic substrate.  The proton that is abstracted from the alkyl halide and the leaving group must be “anticoplanar” to one another: in the same plane, on opposite sides of the molecule.  “Abstraction and leaving [are] coincident”: these two steps happen in a concerted fashion, via E2.

“Diene and a dienophile
In movement, concerted, beguile.  
Diels-Alder reaction
Results in compaction:
Route cyclohexenic in style.”  

The penultimate mechanism-themed poem of NaPoWriMo 2022 was posted on 7 April 2022 and celebrated the Diels-Alder reaction, a well-known process in which two molecules combine to yield a single product. 

Just as chemists are often keenly interested in reaction pathways via which molecules can alter their stereochemistry (the 3-D arrangement of atoms), they also celebrate processes by which new carbon-carbon bonds can be formed, and the latter occurs here.  The Diels-Alder reaction also forms a particularly stable molecular shape, a six-membered ring.  Both aspects are particularly useful in the key objectives of organic synthesis: making new molecules.  

Thus, this particular reaction is another early one from the curriculum of Organic Chemistry.  As with the past three posts, this post is intended to help summarize some of the most pertinent material for students learning the reaction.  Likewise, as with the other organic mechanisms cited in this series, it is probably useful to include a diagram.  

This drawing uses the convention of the skeletal structure for simplicity’s sake: that is, only the “carbon skeletons” of the molecules are shown.  Each vertex or terminus represents a carbon atom bonded to a number of hydrogen atoms appropriate to achieve its desired number of four bonds total (so it can obey the octet rule).  For instance, the “dienophile” above, ethene in this case, is depicted as a short set of parallel lines.  In a chemist’s reading, this translates instantly to H₂C=CH₂.  Each of the two carbon atoms must be bonded to two hydrogen atoms, along with participating in the double bond.  Moreover, electron movement in the reactants (left-hand side of the reaction arrow) is depicted via red curved arrows.  The new bonds formed by these electron movements are shown in red in the product (right-hand side of the reaction arrow). 

Covalent bonds in organic molecules are represented with lines; a single line represents a single bond (also known as a sigma bond), and a double line represents a double bond, consisting of one sigma bond and one pi bond.  As the diagram shows, the two reactants that participate in a Diels-Alder reaction are classified as a diene (a molecule with two double bonds) and a dienophile (a molecule that wants to react with a diene).  Here, the simplest diene is 1,3-butadiene, and the simplest dienophile is ethene; they yield the simplest Diels-Alder product of cyclohexene.

As with the last few weeks, we have much build-up and context here, given all of the shorthand and jargon inherent in a chemical mechanism.  Ideally, this background will help the next 280 words or so make more sense.       

“Diene and a dienophile /
In movement, concerted, beguile…”

The Diels-Alder reaction involves the interaction of a diene and a dienophile.  The mechanism is generally postulated to occur all at once (“movement concerted”), as shown with three red arrows of electron movement in the single reaction step.  The electrons in each of the pi bonds here (a pi bond is often thought of as the “second” bond in a double bond) participate in what is called a cycloaddition.  This means that two new bonds form between the diene and dienophile to yield a six-membered ring, as the single product takes on a hexagonal shape.  Additionally, the electrons from a third pi bond shift their location.  

“Diels-Alder reaction /
Results in compaction…” 

The reaction is named for Otto Diels and Kurt Alder, who published their findings in 1928 and received the Nobel Prize in Chemistry in 1950.  The reaction results in the “compaction” of the molecular geometry of interest: it is smaller, since two reactant molecules have reacted to form a single product molecule.  

“Route cyclohexenic in style.”

The reaction shown above, with the simplest possible dienophile and diene, yields a molecule named cyclohexene.  The name gives us several clues about its structure: “cyclo” (the molecule is cyclic; it is a ring); “hex” (six carbon atoms are involved); and “ene” (the structure includes a double bond). 

This closing line was my favorite from the mechanism poems, as I appreciated the wordplay possible with “scenic route” and “cyclohexenic route.”  I also find the “scenic route” title fitting for this post, given the extensive background, since that phrase is often a euphemistic shorthand used to explain that something will take much more time!  

“Lesson on SN1: 
Two-step-long journey
Begins with the leaving group’s breaking away.  
Nucleophilic attack racemizes. 
(Activity, optical: lost in the fray.)”

The third mechanism poem from NaPoWriMo2022 was posted on 6 April 2022 and looks specifically at the process of unimolecular nucleophilic substitution, which is abbreviated as S_N1. This is again a step-by-step depiction in which electron movement is represented by curved arrows; the poem again seeks primarily to communicate several attributes of the mechanism to an audience trying to learn them.  

Here, the same net effect occurs as in the previous discussion of the S_N2 process: an incoming nucleophile (Nuc) replaces a leaving group (LG) on a molecule. However, S_N1 is a stepwise process that requires two distinct steps, rather than the concerted single step of S_N2.  (To reiterate from a few weeks ago: you’re not wrong.  It’s confusing that the two-step process has the number one in its abbreviation! This is because the rate-determining step in an S_N1 mechanism is the first step, which only involves one species.) 

Shown above is a generalized depiction of this molecular process.  Because this poem will discuss the three-dimensional structures of the molecules a bit more, the scene is much busier than for the S_N2 poem/essay.  The gist of this mechanism is as follows: 

Step One) Reactant loses leaving group to form Intermediate.
Step Two) Intermediate reacts with Nucleophile to form Products.      

Before I launch into the discussion of the poem itself, it is worth remembering that several shibboleths accompany the vocabulary of organic chemistry, and a few will be cited here.  A chemist pronounces the word “carbocation” as “car-bo-cat-ion”; a non-chemist would likely pronounce it as rhyming with “vacation.”  “Racemization” is likewise pronounced in a non-intuitive way. Those are the two main terms seen in this entry (but as I think about it, the general topic might make for many more interesting poems for the next NaPoWriMo).

And finally, a theme of both the S_N2 poem and this one is the change in the optical activity or chirality caused by the reaction. Chemists care about chirality (“handedness”) of molecules for many reasons; one is that it is a property that can have major implications in biological settings. More generally, such properties are aligned with the stereochemistry of atoms in a molecule: their three-dimensional arrangement in space. A fundamental theme of chemistry is the idea that the structure (3-D shape) of a molecule is linked to its function; the S_N1 and S_N2 reactions are the first illustrations of stereochemical concepts that most students encounter.

With all this buildup, the poem itself might well seem anticlimactic… but I will resolutely start the official 280-word count here.

“Lesson on SN1: / 
Two-step-long journey /
Begins with the leaving group’s breaking away…”

In contrast to the S_N2 mechanism’s single step, the S_N1 mechanism is a two-step process.  In Step 1, the reactant forms an intermediate, also called a carbocation: the bond between the leaving group and the rest of the molecule is broken, yielding the positively charged intermediate.  

“Nucleophilic attack racemizes. /
(Activity, optical: lost in the fray.)”

In Step 2, the carbocation intermediate reacts with an incoming nucleophile.  Depending on the structure of the reacting molecule, a property called “optical activity” can sometimes be monitored during the S_N1 process.      

Above, the “Reactant” depicted (where X, Y, and Z all represent distinct substituents) is optically active.  When placed into an instrument called a polarimeter, the “Reactant” would rotate the polarimeter’s light in a certain direction: dextrorotatory (d) for right; or levorotatory (l) for left, a behavior which is quantified as the sample’s “optical activity.”  (Other notations for structural differences are often used, as well; rationalizing those would take this poem-explanation over its word limit!)    

In Step 2, as shown, the nucleophile reacts with the “Intermediate” to form the “Products.”  Why are there two?  When the incoming nucleophile attacks, it can do so from the front or the back, relative to the planar (flat) intermediate.  Each option happens 50% of the time, leading to what is called a racemate or racemic mixture: “[n]ucleophilic attack racemizes.”  The final product mixture would NOT rotate the polarimeter’s plane-polarized light anymore: the optical activity has been lost.

Many aspects of mechanisms are framed in bellicose vocabulary (e.g., “nucleophilic attack”), as highlighted here by the closing descriptor for the optical activity: “lost in the fray.” 

“A nucleophilic incursion
In polar aprotic submersion,
With leaving group egress
As synchronous process:
It’s SN2 (Walden inversion).”  

The 4 April 2022 limerick was the first in a week of posts that summarized specific organic chemistry mechanisms: step-by-step depictions of how molecules transform over the course of a given reaction.  

I remember my introduction to chemical mechanisms as involving a tremendous amount of specialized vocabulary: with exams perpetually on the near horizon, it seemed like I needed to memorize several complicated terms long before I could process what each of them truly meant.  This poem and the ones that follow are intended to put some of the key trends and words together in a memorable way for someone trying to learn the basics.

In a first for these essays, I think it will be useful to have a small illustration for a few of these, over the next five weeks. Some additional introductory words are likely useful here, too, since one of the few things I suspect of being even more off-putting than unexpected chemistry jargon would be an unexpected chemistry diagram! 

In these diagrams, curved arrows show electron flow, which is the underlying impetus for all of these processes.  The curved arrow starts where the excess electrons are and points to where they end up, in a given reaction step; electrons typically move in pairs (two at a time).  Lines represent covalent bonds.  Dash-wedge notation shows three-dimensional (3-D) arrangements of these bonds.  A “wedged” triangle shows that the bond is coming towards the viewer, and a “dashed” triangle shows that the bond is behind the screen.  

(This illustration is brought to you courtesy of the whiteboard setup still present in my kitchen, which has never quite recovered from being a Spring 2020 classroom.)

Finally, to turn back to today’s mechanism and limerick: one of the simplest mechanisms of interest in Organic Chemistry is the S_N2 process, depicted above.  Overall, it is a depiction of how Molecule A turns into Molecule B: how a negatively charged nucleophile (abbreviated generically as Nuc above) replaces the bromine atom in the original molecule; as part of the same process, the bromine atom “leaves” the original molecule, becoming a negatively charged bromide ion, also characterized as the leaving group.      

“A nucleophilic incursion /
In polar aprotic submersion…”

Two mechanisms commonly taught to organic chemistry students are S_N1 and S_N2: two types of nucleophilic substitution (abbreviated as S_N) that were both celebrated during NaPoWriMo2022. Both involve a nucleophilic attack, or “incursion.”  S_N1 reactions occur via a two-step process; S_N2 reactions occur via a single, concerted step.  (This non-intuitive naming is because one species is involved in the rate-determining step of an S_N1 mechanism, whereas two species are involved in the rate-determining step of an S_N2 mechanism… since its single step is the only one!)  

A perennial, early challenge for students is discerning via which mechanism a nucleophilic substitution occurs.  One clue is the solvent (the reaction medium).  S_N2 reactions are favored by polar aprotic solvents (polar solvents that lack a proton; acetone is a common choice), while S_N1 reactions are favored by polar protic solvents (such as water).  “Polar aprotic submersion” denotes that the reaction occurs in polar aprotic solvent, hinting at S_N2. 

“With leaving group egress /
As synchronous process…”

As shown above, in an S_N2 process, the nucleophile attacks simultaneously with the departure of the leaving group (“leaving group egress”), since everything happens at once (a “synchronous process”).   

“It’s S_N2 (Walden inversion).”  

The closing line reveals the S_N2 label and a corresponding inversion of stereochemistry: the 3-D arrangement of the atoms. The inversion is named for Paul Walden, the chemist who studied the process in 1896, and can be detected when the reaction occurs at a chiral center (which is not the case shown above).

“The product in flask: data, quotes, looks;
The time that each task, new or rote, took;
Stoich calcs and dilutions;
Key findings; conclusions; 
Next questions to ask… all in notebook.”

The 11 April 2021 limerick returned to one of my favorite themes, the chemistry lab notebook, which I’ve explored a few times in this space before!    

“The product in flask: data, quotes, looks; /
The time that each task, new or rote, took…”

In this particular poem, it was fun to build towards “notebook” as the final rhyme, then shape the remainder of the limerick around it.  This required some stretching of vocabulary, at times, but within reason, as is ideally clear by taking one line at a time.  

A chemist would record information about “the product in flask: data, quotes, looks.”  What is the product’s mass? Its melting point?  What statements would the chemist wish to record about the experiment?  What does the product look like?       

Another common record included in the notebook would be “the time that each task, new or rote, took.”  Each step in an experimental procedure is either a new attempt or a repeated (“rote”) one; further, it’s useful to know how long certain steps (heating under reflux, stirring, etc.) can take.  

“Stoich calcs and dilutions; /
Key findings; conclusions…” 

The “A” rhymes in this limerick (with its AABBA form) all build on “notebook,” while the “B” rhymes are a bit less forced.  The phrase “stoich calcs and dilutions” refers to the lab-focused mathematics completed in a lab notebook (theoretical yield and other stoichiometric calculations, M₁V₁ = M₂V₂, etc.).  Perhaps the most obvious things to highlight in a lab notebook are the “key findings [and] conclusions” from a given procedure.    

“Next questions to ask… all in notebook.”

The final line of the poem highlights the self-perpetuating nature of scientific research: what “next questions” do the conclusions of a given experiment invite?  Those creative reflections are also an important part of a procedural record.  

“To isolate via filtration,
Consider the process notation:
Whether vacuum or gravity 
Will the product compatibly 
Obtain, through work-up situation.”

The 10 April 2021 limerick discussed two additional work-up techniques useful in the organic chemistry laboratory: vacuum filtration and gravity filtration. Each is accomplished via the use of a specific type of set-up requiring a specific type of funnel, a fact which provides this essay’s title.    

“To isolate via filtration, /
Consider the process notation…”

This poem notes the distinction between two different techniques with confusingly similar names (both involving filtration).  To complete an organic chemistry work-up and isolate a target compound, one must first decide which type of filtration is most useful, or “[c]onsider the process notation.”    

“Whether vacuum or gravity /
Will the product compatibly /
Obtain, through work-up situation.”

Often in organic chemistry lab, a chemist seeks to separate a liquid from a solid via some kind of filtration, a relatively simple task accomplished by using glassware and filter paper.  

If the target compound (the compound that the chemist wants to further analyze or use) is the solid, vacuum filtration is the work-up technique of interest.  By using (typically) a Büchner funnel covered with filter paper and creating a vacuum, the solid is isolated and thoroughly dried on that paper.  If the target compound is in the liquid phase, instead, then gravity filtration is used, with a glass stem funnel.  Here, the filter paper catches any unwanted solid byproducts, and the liquid that passes through the paper and funnel continues into the next step of analysis or synthesis.

The goal with either type of filtration is to “compatibly / [o]btain” the target product while avoiding any additional impurities: to remove as much “extra” material as possible.  If the product is a solid, then the vacuum set-up ensures that as much liquid as possible is removed.  If the product is a liquid, then the slower gravity filtration ensures that no extra solid material is accidentally carried along.  Common objectives in the lab involve learning both techniques and discerning between their optimal uses.   

“Assembling set-up, distillation,
Can lead to a bit of frustration.
Be sure to securely 
Clamp glassware so surely
Experiment defies ruination!”  

The 9 April 2021 Twitter limerick highlighted distillation, a lab technique used in organic chemistry laboratories to purify liquid samples.  The poem highlights one of the ways in which such a lab technique might go awry… and encourages students to avoid it!  

“Assembling set-up, distillation, /
Can lead to a bit of frustration…” 

The first semester of organic chemistry lab introduces techniques and tools one at a time, building to increasingly complex experiments in which their uses can be combined.  One such technique is distillation: separating a liquid mixture into its component parts, based on differences in their boiling points.

A “simple distillation” is typically one wherein two components of a liquid mixture have boiling points distinct from one another.  This mixture is placed in a round-bottomed flask, which is connected to a condenser, which is connected to a receiving flask.   The mixture is heated until it reaches the boiling point of the first component; at this point, the first component vaporizes, travels as a gas into the condenser, and is condensed into the first receiving flask.  (The condenser circulates cooling water through an outer jacket: within the complex set-up of the laboratory fume hood, one condenser tube connects to a faucet and the other to a drain.)  Once this first component is separated out, a second receiving flask is used to collect the second component, as its own boiling point is reached.    

Typically, these steps are all new for students; although they will become well-practiced with the distillation set-up, assembling it can be frustrating initially.   

“Be sure to securely /
Clamp glassware so surely /
Experiment defies ruination!”  

This set-up is often one of the first to involve multiple pieces of glassware– including, most notably, the condenser. To avoid “ruination” (the watery collapse of the endeavor!), it is important to clamp the pieces of glassware together and, further, to clamp everything securely within the hood itself. 

“Exacting; extracting… 
A sep funnel’s function:
To isolate layers and
Compound obtain.
(Avoid a moment most 
Melodramatical:
Ere product’s sure, 
From waste’s discard, 
Refrain!)”

The 8 April 2021 Twitter poem addressed another laboratory technique: using a separatory funnel, a specialized piece of glassware that allows a chemist to separate different components of a given reaction mixture (the environment in which the reaction has been taking place).  

“Exacting; extracting… /
A sep funnel’s function: /
To isolate layers and /
Compound obtain.”

Each step of an organic synthesis depends on two key parts: the reaction itself, which converts reactant to product, and the work-up, in which the product compound is isolated (identified and purified), while excess solvents and side materials are discarded.  

The separatory funnel (“sep funnel”), as its name suggests, is particularly useful in separating liquid layers from one another, based on their different densities.  Often, the layers of interest are “water” versus “non-halogenated organic solvents,” where the latter layer would be less dense than the former.  In the case of “water” versus “halogenated organic solvents,” through, the latter layer is more dense than the former.  (Chemists typically use “aqueous” and “organic” as efficient shorthand for the layers.)

Either way, depending on which layer the target product occupies, the chemist will use the sep funnel, to “compound obtain.”  

“(Avoid a moment most /
Melodramatical: /
Ere product’s sure, /
From waste’s discard, /
Refrain!)”

I suspect that anyone reading the discussion of different densities above, whether or not they are a chemist, might quickly note the most challenging hazard of using a sep funnel: being absolutely sure which layer is which (and which layer thus contains the product) before proceeding.  A best practice is to wait to discard the other layer until subsequent steps are completed, to be sure the target product hasn’t been accidentally lost: “Ere product’s sure, / From waste’s discard, / Refrain!”

When a student is learning the technique, though, this lesson can sometimes be hard-won.  This is unfortunately clear from the occasional “moment most / [m]elodramatical”… directly after the moment when someone’s synthesized product is inadvertently lost to the waste container.

“Consider lab drawer’s Bunsen burner…
Providing new role for chem learner
(Through method, flame-testing,
Steps towards metal-guessing):
Of cation’s ID, discerner.”  

The 7 April 2021 limerick summarized a qualitative analysis technique often used in introductory chemistry, which employs one of its most memorably named instruments, the Bunsen burner.  

“Consider lab drawer’s Bunsen burner… /
Providing new role for chem learner…”

Combustion can occur completely or incompletely.  Complete (stoichiometric) combustion is what is taught in the textbooks: a hydrocarbon fuel reacts with oxygen and is converted fully to carbon dioxide and water.  The path from start to finish actually occurs via a wide network of complex reactions involving radicals, which are species with unpaired electrons; these can cause all sorts of side reactions and products.  When the combustion is incomplete, these side reactions include the formation of soot.  Soot has many detrimental effects, and Robert Bunsen (1811-1899) was interested in developing a burner that could produce a particularly clean flame, avoiding these effects.  His burner has been widely adopted for use in introductory chemistry laboratories (by “chem learner[s]”).     

“(Through method, flame-testing, /
Steps towards metal-guessing): /
Of cation’s ID, discerner.”

A traditional and interesting use of the Bunsen burner is the flame test, or “method, flame-testing.”  A wire is placed into a solution made from an ionic compound, which includes a cation derived from a metal of interest.  The wire is then placed into the flame, and as the ionic solution evaporates, the flame will turn a certain color based on the emission characteristics of the metal ion in question.  For instance, copper would turn the flame a bluish-green, and potassium would turn the flame violet.  

If a student is given an unknown compound and asked to determine the cation in this compound, they could use the flame test behavior as a step towards identifying the unknown; their role as “chem learner” could then also include being “of cation’s ID, [a] discerner.”