Author: chemphasis

Categories
Science Poetry

Grammar of Elements

“Unerring, preparing is 
James Andrew Harris: 
T’ward isotopes heavy, his
Labwork maintains.  
Methods intrepid for 
Element 104
Find rutherfordium,
Now to be named.”  

The 12 April 2022 post was a Twitter biography poem noting some of the accomplishments of James Andrew Harris (1932-2000), whose research was integral to the discovery of multiple new elements.  Harris was a Black chemist who faced discrimination in his own career before his significant achievements at what is now Lawrence Berkeley National Laboratory.  Throughout his career, he supported many African-American students in their pursuit of STEM coursework and research.    

“Unerring, preparing is /
James Andrew Harris: / 
T’ward isotopes heavy, his /
Labwork maintains…”  

James Andrew Harris was an outstanding nuclear scientist who led the Heavy Isotopes Production Group in the Lawrence Radiation Laboratory at UC Berkeley during the 1960s.  This lab group worked on synthesizing precursor species necessary for the bombardment experiments that would yield new elements.  Careful, meticulous preparation (i.e., “preparing” that was “unerring”) of the heavy-isotope precursors was necessary for the success of subsequent steps.  

“Methods intrepid for / 
Element 104 /
Find rutherfordium, /
Now to be named.”

This work ultimately led to the identification of two new elements, through the intrepid preparation methods of Harris’s team, followed by subsequent experiments and analyses by the research team led by Albert Ghiorso.  The elements in question had the atomic numbers 104 and 105 (meaning an element with 104 protons and an element with 105 protons, respectively).  Near the same period of time, a research team at the Joint Institute for Nuclear Research (JINR) in Russia also identified these two elements in the lab.  

Each lab group used their own names with each of the two elements, and it took many years for the International Union of Pure and Applied Chemistry (IUPAC) to resolve this naming controversy.  The IUPAC is the worldwide authority for chemists in terms of standardized nomenclature and communication.  As recounted in the poem, the IUPAC decided that Element 104 would be known as rutherfordium, after Ernest Rutherford; further, that Element 105 would be known as dubnium, after the town of Dubna, which is where the JINR is located. 

(This detailed discussion process yielded new, consistent reference points for chemists… and a title for this post!)     

Categories
Science Poetry

Flat Confirmation

“Cogitate, calculate: 
Dame Kathleen Lonsdale,
Through X-ray spectroscopy,
Compound discerns.
Insight incipient: 
Hex-methyl-ation will 
Benzene’s geometry 
Flatly confirm.“

As a new year and new semester are now officially underway, I will return to the weekly routine of these posts.  The 11 April 2022 poem began the 2022 week of “Twitter biographies.”  The first was a pseudo-double-dactyl poem summarizing a key experimental insight in chemistry from Kathleen Lonsdale, who lived from 1903-1971.  

“Cogitate, calculate: /
Dame Kathleen Lonsdale, /
Through X-ray spectroscopy, /
Compound discerns…”

Dame Kathleen Lonsdale was the first woman elected as president of the International Union of Crystallography, in addition to many, many other honors.  

X-ray crystallography is a technique in which, by sending high-energy X-rays at a sample of a compound, a chemist can examine how those X-rays are scattered: a useful analogy might be inferring the shape of an object from the shadow it casts, although X-ray crystallography techniques are far more involved and exacting.  Many compounds’ structures have been discerned through this technique, generalized in the poem as “X-ray spectroscopy” (again, a less precise characterization than is ideal, this time for the sake of the meter).          

“Insight incipient: /
Hex-methyl-ation will / 
Benzene’s geometry /
Flatly confirm.”

The specific experiment commemorated in this poem was Lonsdale’s use of X-ray crystallography to determine the geometry of benzene, a compound which had interested chemists for many years.  Before this insight, it was known that a benzene molecule contained six carbon atoms and six hydrogen atoms and arranged these atoms cyclically, in a ring.  However, scientists had still disagreed for decades as to its planarity: was the ring flat?  (Did it have all of its carbon atoms in the same plane?)    

Lonsdale determined an answer to this question by analyzing a derivative of benzene called hexamethylbenzene, which has a methyl group (-CH3) attached to each carbon in the benzene ring.  She noted that the central benzene ring had to be flat to account for the results seen via her X-ray crystallography experiment.  Thus, the geometry was “flatly confirm[ed]”: benzene was shown to be planar, via significant and convincing evidence.  

Categories
Science Poetry

Winter Break

Semester autumnal concluding
With Finals Week tasks, grade-computing…
Pause pathway reactive 
For routine refractive 
In spring-academic-preluding.  

This is a non-Twitter limerick written specifically to wrap up the Fall 2022 semester and look ahead to the Spring 2023 term.  

Semester autumnal concluding /
With Finals Week tasks, grade-computing…

This is Finals Week on campus, which means the number of assessments to evaluate skyrockets, as the number of class meetings dwindles.  “Grade-computing” is the order of most days, as assignments and exams accumulate.  

Pause pathway reactive /
For routine refractive…

The image of a reaction coordinate diagram— which chemists use to map out the energetics of a reaction— comes to mind often during the peaks and valleys of an autumn semester, which can combine to provide the sense of an academic roller coaster.  The “Finals Week tasks” mentioned in the previous lines can build into a fearsome metaphorical maximum, and at winter break, the “pathway reactive” can find a brief energetic minimum, even if the academic year is not fully complete.   

 A “routine refractive” is one that changes direction slightly, via some significant poetic license.  (In a STEM context, refraction is a term describing the bending of light rays.)  For a few weeks, the academic-year routine is briefly interrupted, and focus shifts elsewhere.  

In spring-academic-preluding.  

Part of that refractive routine involves turning attention towards the new semester and its new classes.  Class preparation is always a significant part of winter break, in the “spring-academic-preluding,” but it will be helpful to rest at least briefly before that begins.  I will likewise pause these posts for a few weeks!

Categories
Science Poetry

Matter of Degrees

“A molecule’s turning rotations;
Its stretching and bending vibrations—
To calculate, heed them:
The degrees of freedom.
(Forget not three types of translation!)”

The 10 April 2022 limerick addressed a concept related to molecular motions and energetics.  The main idea here is that a molecule can undergo 3N types of motion, where N is the number of atoms in a molecule.  The types of motion are more precisely termed “degrees of freedom” in chemistry analyses.  

“A molecule’s turning rotations; /
Its stretching and bending vibrations…”

We can consider water as a sample molecule.  Water, with its V-shape, has the formula H2O: thus, three atoms and nine (3N) degrees of freedom.  

We can think of the ways that a water molecule could move.  It could “translate” (move in space) in three dimensions: the x, y, and z axes in a Cartesian system.  As we look at a water molecule, we see that it could also “rotate” in three ways: first, so that the H atoms spin to the “left and right” around the O atom; second, in the direction perpendicular to the first direction (so the H atoms spin “over and under” relative to the O atom); third, within the plane of the screen itself.  

The possible “vibrations” correspond to the remaining number of degrees of freedom possible for water as a non-linear molecule.  These can be calculated via the equation 3N-6 (since six degrees of freedom are already occupied: three translations and three rotations).

From that equation, we can confirm that water has three vibrational modes: a symmetric stretch, in which both O-H bonds stretch and compress at once; an asymmetric stretch, in which the O-H bonds alternate their motion; and a bending mode, in which the molecule’s H-O-H bond angle changes.  

“To calculate, heed them: /
The degrees of freedom. /
(Forget not three types of translation!)”

The concept of degrees of freedom facilitates many calculations in chemistry, such as those related to infrared spectroscopy. 

Interestingly, this essay is slightly misaligned with the poem: the “three types of translations” provide the poetic punchline, but it doesn’t work to omit that prose-based explanation until the end.  

Categories
Science Poetry

Solution Composition

“A solute plus solvent: solution.  
We quantify its constitution:
Numeric relation;
Expressed concentration,
Decreasing upon its dilution.”

The 9 April 2022 Twitter limerick returned to far less dense material than the mechanistic deciphering of the last few verses and posts!  As the title suggests, this post (composition) translates a poem related to solution chemistry.

“A solute plus solvent: solution…”

A solution is a homogeneous (uniform) mixture of two substances: the substance present in the lesser amount is the solute, and the substance present in the greater amount is the solvent.  

If we take one gram of table salt (sodium chloride, NaCl) and dissolve it in enough water to form exactly 150 mL of the solution, we generate an aqueous solution of sodium chloride: the salt is the solute and the water is the solvent.  

“We quantify its constitution: /
Numeric relation; /
Expressed concentration…”

Chemists have several ways to quantify the constitution of a solution (to answer the question of how much solute and how much solvent will be present in the solution) and find its concentration.  Concentrations are calculated through “numeric relations,” or equations. The most common concentration expression is molarity: moles of solute divided by liters of solution (M = mol / L).  

In the solution described above, 1.00 g of sodium chloride (NaCl) is equal to 0.0171 moles of NaCl, due to its molar mass of 58.4 g/mol. By taking 0.0171 mol NaCl divided by 0.150 L of solution, we obtain a molarity of 0.114 M here.  

“Decreasing upon its dilution.”

If a solution is diluted, more solvent is added, while the amount of the solute stays the same.  

For instance, in our example, if enough water is subsequently added to generate exactly 300 mL total, then the solution’s volume is doubled, and the molarity becomes half what it was: the solution’s concentration “decrease[s] upon its dilution.”  

Some analogy likely applies here about how the clarity of this simpler post, compared to the last few, benefits from its succinctness (its “smaller volume”)!

Categories
STEM Education Poetry

Process(es) of Elimination

“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 (SN1 and SN2).  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 (SN1, SN2, 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 SN1 or SN2 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 SN2, SN1, 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 SN1 and SN2.

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.

Categories
STEM Education Poetry

Scenic Route

“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!  

Categories
STEM Education Poetry

It Takes Two (Steps)

“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 SN1. 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 SN2 process: an incoming nucleophile (Nuc) replaces a leaving group (LG) on a molecule. However, SN1 is a stepwise process that requires two distinct steps, rather than the concerted single step of SN2.  (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 SN1 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 SN2 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 SN2 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 SN1 and SN2 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 SN2 mechanism’s single step, the SN1 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 SN1 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.” 

Categories
STEM Education Poetry

All Fresco

“A creative process, wall-stationed,
With paintings long-lasting, emblazoned;
The technique, pervasive
On surface abrasive,
Forms fresco through carbonatation.” 

The second mechanism poem from NaPoWriMo2022 was the most general of the verses from that week, posted on 5 April 2022.  It concerns the chemistry behind frescoes, an artistic medium seen widely throughout history and cultures, thus justifying to a reasonable extent (I hope) the pun in the post title.    

The topic of fresco chemistry involves much fascinating science, art, and history.  As with last week’s entry, the chemical reactions of interest here deserve some preliminary framing and additional words.  Unlike the SN2 mechanism and others that will be described in future posts, this is a process reflecting general inorganic chemistry steps, rather than the specific electron pushing of organic molecule depictions. However, it still seemed to fit reasonably well in this week.  Here, the abbreviations in parentheses denote the phases of the chemicals of interest: (s) for solid; (l) for liquid; (g) for gas; and (aq) for aqueous solution.   

Step One: CaCO3 (s) → CaO (s) + CO2 (g) 
Step Two: CaO (s) + H2O (l) → Ca(OH)2 (aq) 
Step Three: Ca(OH)2 (aq) + CO2 (g) → CaCO3 (s)

The fresco cycle shown here is a three-step process.  The first two steps prepare an artist’s materials for this artistic medium.  The first is called calcination: calcium carbonate (CaCO3) is heated to yield calcium oxide (CaO) and carbon dioxide (CO2).  The second is called slaking: calcium oxide is mixed with water (H2O) to form calcium hydroxide [Ca(OH)2], known to fresco artists as lime plaster.  

The third step is the chemistry behind the fresco formation itself and the focus of the poem.     

“A creative process, wall-stationed, /
With paintings long-lasting, emblazoned…”

Frescoes consist of two layers of lime plaster used to coat a wall and create a painting surface (“wall-stationed”).  In the rougher layer, the arriccio, plaster is mixed with coarse sand and applied directly to the wall.  The intonaco layer (lime plaster and fine sand) is then applied over the arriccio layer to become the actual painting surface. 

In fresco chemistry, pigments are painted directly on a surface consisting of calcium hydroxide [Ca(OH)2].  As the fresco dries, the calcium hydroxide reacts with the carbon dioxide (CO2) in the air and forms the stable and long-lived compound calcium carbonate (CaCO3): trapping the pigments, leading to an image that will be “long-lasting [and] emblazoned” on the wall.  

A fresco artist ideally applies an intonaco layer only to an amount of wall feasible to finish before the plaster dries.  The corresponding term is giornata, for “a day’s work.”  

“The technique, pervasive /
On surface abrasive…”

The technique is “pervasive”: seen in many eras and locations throughout history.  Calcium hydroxide is a basic compound, bases are caustic; lime plaster is a “surface abrasive.” 

“…Forms fresco through carbonatation.” 

The last reaction in the sequence shown is called carbonatation, as it forms calcium carbonate.  It is sometimes called carbonation, but the first term is less ambiguous (multiple processes are denoted as carbonation)… and scans more readily in this limerick!

This reaction is key to the buon fresco (“good fresco”) technique, in which the artist is painting on fresh lime plaster, aiming to cover their giornata.  A related technique is called fresco a secco (“dry fresco”), in which the artist uses paints on an already-dried surface.

Categories
STEM Education Poetry

Concerted Actions

“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 SN2 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 SN1 and SN2: two types of nucleophilic substitution (abbreviated as SN) that were both celebrated during NaPoWriMo2022. Both involve a nucleophilic attack, or “incursion.”  SN1 reactions occur via a two-step process; SN2 reactions occur via a single, concerted step.  (This non-intuitive naming is because one species is involved in the rate-determining step of an SN1 mechanism, whereas two species are involved in the rate-determining step of an SN2 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).  SN2 reactions are favored by polar aprotic solvents (polar solvents that lack a proton; acetone is a common choice), while SN1 reactions are favored by polar protic solvents (such as water).  “Polar aprotic submersion” denotes that the reaction occurs in polar aprotic solvent, hinting at SN2. 

“With leaving group egress /
As synchronous process…”

As shown above, in an SN2 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 SN2 (Walden inversion).”  

The closing line reveals the SN2 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).