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 bondsDash-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).

Categories
Science Poetry

Taking Shape

“A simplified rhyming summation:
Chem concept of hybridization.  
Geometry-fixing 
From orbitals’ mixing;
Molecular bonding formation.”

The 3 April 2022 Twitter limerick addressed some key topics related to molecular geometries: the shapes molecules adopt, which impact their reactivities.  Molecular geometries are explained by chemists via several different theories and concepts, depending on which lens is most useful for the situation at hand.    

“A simplified rhyming summation: / 
Chem concept of hybridization.” 

The first two lines state that this poem will summarize the chemical concept called hybridization, acknowledging that this will be a simplification!  

“Geometry-fixing /
From orbitals’ mixing: / 
Molecular bonding formation.” 

VSEPR Theory is the simplest explanation of three-dimensional molecular geometries, via concepts of “valence-shell electron-pair repulsion.”  Via VSEPR Theory, a methane molecule (CH4) would be predicted to have its geometry (shape) because of four regions of electron density (the four C-H bonds) around the central carbon; this shape would be called tetrahedral

However, that geometry does not make sense with carbon’s electron configuration: the way in which a carbon atom has its electrons distributed among its orbitals, via its subshells and shells.  Carbon’s electron configuration as an individual neutral atom is represented as [He] 2s2 2p2 (an arrangement suggesting that carbon will form only two bonds).    

The concept of orbital hybridization is introduced via a different approach called valence bond (VB) theory.  Via hybridization, orbitals mix together to generate what are called “hybrid orbitals,” capable of forming bonds of equal energy.  Methane’s orbitals undergo “sp3 hybridization,” which means the one s orbital and the three p orbitals in the n=2 shell are averaged together to yield four sp3 orbitals of equivalent energy, rationalizing why methane can form the four equivalent bonds necessary for the tetrahedral shape.  

This can be summarized poetically as “geometry-fixing from orbitals’ mixing,” resulting in “molecular bonding formation.”  The last lines can be read in two reasonable ways: either as “a given geometry (formation) is rationalized via hybridization” or as “hybridization results in the formation of several molecular bonding interactions” (i.e., the chemical bonds of interest).  

Categories
Science Poetry

Trend Fashions

“To rank-classify chem collections,
Note elements’ relative directions;
Sort kaleidoscopic
With chart Periodic.
(Beware, though, of trending exceptions!)”

The 2 April 2022 Twitter limerick described the concept of periodic trends, or periodic properties: qualitative information that can be inferred from the relative location of elements on the Periodic Table of Elements (PTE).

“To rank-classify chem collections, /
Note elements’ relative directions
…”

The first two lines provide an overview of some ways in which the Periodic Table of Elements (PTE) provides an enormous amount of information. Collectively, sets of elements can be “rank-classif[ied]” with respect to many of their properties: for instance, it can be discerned which of a given pair of elements has the larger atomic radius (atomic size) or first ionization energy, based on their relative placement (“relative directions”) on the PTE. Similar analyses can be completed for many other periodic properties; the practice of doing so is called analyzing periodic trends.

For instance, iodine (I) is lower than bromine (Br) in the column for the halogens (Group 7A) on the PTE. Without looking up any specific data, we can predict from our knowledge of periodic trends that an atom of iodine is larger than an atom of bromine and that iodine has a lower first ionization energy (a lower energetic cost for forming a singly-positively-charged ion) than bromine.

Sort kaleidoscopic /
With chart Periodic. /
(Beware, though, of trending exceptions!)

One of the most amazing aspects of the PTE (the “chart Periodic”) is the way that it allows chemists to arrange a wide array of chemical information in a meaningful way: to “sort [the data] kaleidoscopic,” in this limerick’s phrasing.

However, not every trend described is a perfectly linear one, as nuances in elements’ electron configurations can lead to exceptions from the trends in question. Often, the question I ask of my General Chemistry class is not to “predict this trend” but rather to “rationalize the exception to this trend.” This can be a complex topic to encounter, meriting an accentuating “beware”!

Categories
Science Poetry

Fourth Dimensions

“To month of light verses, returning;
Fourth year of this fourth month’s discerning. 
Attempt quaternary:
Chem rhymes ancillary,
With goal of supporting STEM learning.”  

This post returns to the more familiar routine of translating past Twitter chemistry poems.  This particular limerick was posted on 1 April 2022 and marked the beginning of National Poetry Writing Month (NaPoWriMo) 2022.  

“To month of light verses, returning; /
Fourth year of this fourth month’s discerning.” 

April 2022 was the fourth NaPoWriMo for me (which is difficult to believe).  My first year of April poems fell in 2019 during the overlap of National Poetry Writing Month and the International Year of the Periodic Table.  The subsequent April routines have marked various stages of progress through the COVID-19 pandemic and thus provided stability during some strange times.

The combination of the fourth attempt at this routine and the theme of passing time (with time as the fourth dimension) together gave rise to this post’s title.  In these poems, I use the forms of light verse as structures through which to communicate chemistry concepts; most commonly, these forms are limericks or double dactyls.  This April routine provides a “fourth month’s discerning”: a way to practice understanding and communicating chemistry concepts in a different way. 

“Attempt quaternary: /
Chem rhymes ancillary, /
With goal of supporting STEM learning.”  

This month was my fourth attempt (“attempt quaternary”) at this routine, in which “chem rhymes ancillary” were a useful addition to my academic routine.  As can be seen throughout this website, my goal is to use this approach to scientific content to “support STEM learning.”  

I suspect I’m primarily writing to the student I once was: interested in the unusual vocabulary and etymologies of chemistry… to a sometimes-distracting extent! However, I hope these essays might be more generally interesting to others as well. 

Categories
Science Poetry

Act of Learning

Astronomer, learnéd… expounding
Through proofs, figures: dense and confounding.  
The student, receptive
To nature’s perspective,
Will exit the lecture resounding.  

This week’s poem is a non-Twitter one; I had initially drafted it during the summer, when I was focused on a series of posts inspired from lines from works of literature, as a limerick-framed restatement of some of the images and themes of Walt Whitman’s “When I Heard the Learn’d Astronomer.”  However, as this poem is primarily a paraphrase, it did not seem to fit as well with the others, which used direct quotes or allusions to initiate the new verses and essays, so I tabled it for a few weeks.

Astronomer, learnéd… expounding
Through proofs, figures: dense and confounding.  

Walt Whitman’s “When I Heard the Learn’d Astronomer” famously describes a speaker’s encounter with a lecture from a renowned scientist.  The speaker first notes the overwhelming amount of data presented in the auditorium: “When the proofs, the figures, were ranged in columns before me, / When I was shown the charts and diagrams, to add, divide, and measure them…

I teach many content-heavy chemistry courses.  I appreciate their roles in various disciplinary curricula, but I am also aware that the first presentations undoubtedly seem “dense and confounding” to new students.    

The student, receptive
To nature’s perspective,
Will exit the lecture resounding.  

Whitman’s poem concludes with lines describing how the speaker seeks refuge from the information-dense presentation in a primary encounter with astronomical observation: “[R]ising and gliding out I wander’d off by myself, / In the mystical moist night-air, and from time to time, / Look’d up in perfect silence at the stars.”  

The student is clearly open to appreciating the subject matter at hand (in the limerick phrasing: “receptive / [t]o nature’s perspective”), but via a direct, self-initiated study: the truest example of active learning

I expect that the limerick form might seem trivializing here, but I had intended this verse as a tribute.  Whitman’s poem is one I remember when teaching, where my goal is primarily that students progress toward becoming independent life-long learners, regardless of their responses to the chemistry content presented.  In reading, I find the effect of the speaker’s shift from the passive voice (“When I was shown”) to the active observation (“I… [l]ook’d up in perfect silence at the stars”) to be unfailingly moving.   

Categories
Science Poetry

Isolation Incident

“A simplified Chem situation,
Analysis by isolation:
One species in excess 
So rate law is expressed 
In pseudo-nth-order notation.”

The 22 October 2021 Twitter limerick was the last in the poetic series for National Chemistry Week 2021.  It summarized a technique called the isolation method, which (as with other approaches highlighted in the last few poems) is a technique used by chemists to simplify a complicated rate law.  

“A simplified Chem situation, /
Analysis by isolation…”

The first two lines note that this is another simplifying scenario in the discipline of chemistry, pertaining to kinetics.  

Isolation method” is a phrase that came to mind often in 2020’s early days of the pandemic, as the terms “social distancing” and “isolation guidelines” suddenly were added to everyone’s lexicon.  In the chemistry setting, though, the approach allows an investigator to examine the kinetic role of one reactant at a time as it affects a rate law.

“One species in excess /
So rate law is expressed /
In pseudo-nth-order notation.”

The last three lines summarize a typical example.  One experiment I cite often in class involves the fading of a pink-colored solution over time, where the solution takes on a vibrant color because excess base is present (a case of “one species in excess”) with a chemical indicator (phenolphthalein).  By monitoring the fading of the pink color, students determine information about how the reaction depends specifically on the presence of the phenolphthalein.  

Rate laws are typically classified as first-order, second-order, etc. with respect to a given reactant.  When the isolation method is used, the phrasing changes to pseudo-first-order, etc., acknowledging that this is a finding that has yet to be fully clarified to explore the role of the excess reactant.  “Pseudo-nth-order” means the value of n is under investigation (and is a phrase that fits neatly into a metric rhythm!).

In the case of the experiment described above, the experimental finding is that the rate law is pseudo-first-order with respect to phenolphthalein.  When the entire rate law is determined, it is first-order with respect to both phenolphthalein and the base, so second-order overall. 

Categories
Science Poetry

Coordinating Events

“Reactant and product, by
Way of transition state…
Progress reactive in
Graph summarized:  
Ornate coordinate,
Diagrammatical;
Relative energies,
Here analyzed.”  

To my chagrin, I realized last week that I had accidentally set two essays to post at the exact same time!  That means that I am suddenly a bit less ahead of the writing process here than I like to be.  However, I also cannot help but find it fitting that this misstep happened in the midst of a set of poems devoted to kinetics, given how concepts of timing and (at the molecular level!) collisions are so pertinent to this theme.   

In any event, the next Twitter poem was posted on 21 October 2021, and it described the concept of a reaction energy diagram; this is an efficient way for chemists to communicate information related to both the thermodynamics and kinetics of a chemical reaction of interest.      

“Reactant and product, by /
Way of transition state… /
Progress reactive in /
Graph summarized…”

A reaction energy diagram is a graphical depiction of the relative energies of the distinct species involved in a chemical mechanism.  I’ve highlighted such chemical communication here before, noting another common title of potential energy surface (when such a PES is considered in two dimensions).  

The reaction energy diagram described here cites “reactant and product, by way of transition state.”  This essentially will look like a hill, with the transition state at the peak in the middle.  The height of the hill is called the activation energy, or activation barrier, of the chemical reaction: the higher it is, the greater the barrier that must be overcome, and the longer this process takes.  These concepts are related through the Arrhenius equation, which states:

k  = A * e [-Ea/(RT)]

The rate constant (k) depends on a “pre-exponential factor” (A), which can be dissected into information about the mechanism, multiplied by an exponential term in which the activation energy (represented here as Ea), the gas constant (R), and the temperature (T) are all involved.  

Equations can look complex, but again, the two big ideas communicated here are that: first, the greater the activation energy is, the longer the reaction will take; second, the lower the temperature is, the longer the reaction will take.  The former concept is discussed by this poem.                

“Ornate coordinate, /
Diagrammatical; /
Relative energies, /
Here analyzed.”  

The last lines acknowledge that a reaction energy diagram is sometimes called a reaction coordinate.  This “ornate coordinate” is a diagram that provides an efficient analysis of the relative energies of the reactant, transition state, and product of a chemical reaction.   

Categories
Science Poetry

Steadying Influence

“Ready?  State steady-state
Approximation (the
Famous, eponymous 
Calc step involved):
Key intermediate’s
Change over time shows a 
Negligibility;
Rate law resolves.”

The 20 October 2021 Twitter poem was another posted in National Chemistry Week 2021.  This poem highlighted another simplifying technique commonly used in chemical kinetic analyses, called the steady-state approximation, and it did so via a pseudo-double-dactyl structure.  

“Ready?  State steady-state /
Approximation (the /
Famous, eponymous / 
Calc step involved)…”

The biggest challenge with this week of poems was identifying potential rhymes related to these often-math-centric concepts!  The first line here grew out of considering the phrase “steady state.”  The steady-state approximation takes its name from the “eponymous calc step involved”: a mathematical simplification relying on the idea that the concentration of a given reaction mechanism’s intermediate remains relatively consistent (steady).     

“Key intermediate’s /
Change over time shows a /
Negligibility; /
Rate law resolves.”

In this simplified mechanism, a reactant forms an intermediate, which forms a product:  

Reactant → Intermediate → Product

To monitor this reaction’s rate, we consider the appearance of the product over time. Without going too equation-heavily into the details, we can look at the big ideas. 

The intermediate is typically in what is called a steady state: once the reactant forms an intermediate, that intermediate forms the product.  The intermediate’s concentration stays relatively steady: relatively constant.  Stepping briefly into calculus, the derivative of a mathematical function represents the change of that function over time.  For a constant function, the derivative is zero.  

Thus, the steady-state approximation is that the change in concentration of this intermediate over time is roughly equal to zero.  Chemists use this approach and the steps that ensue to derive a rate law, finding the rate of the appearance of the product over time.  The change in concentration of the intermediate over time is approximated as zero (it “shows a negligibility”), so the rate law is more easily calculated.     

(This poem and essay obviously approximate several mathematical steps of their own; however, ideally, they provide an introduction to another kinetic concept useful to chemists.)