“To isolate state of transition, Note how E relies on position: The resulting stratagem Seeks energy’s maximum In calc’s geometric submission.”
The 16 April 2022 Twitter limerick returned to more conceptual material, summarizing a specific type of chemistry calculation called a transition-state optimization.
“To isolate state of transition, / Note how E relies on position…”
A transition-state optimization calculates the energy of a molecule (or chemical entity, more broadly) as a function of its molecular geometry; molecular geometry is a shorthand communicating the position of all the atoms in a given molecule. The overall shape of most reaction coordinates resembles a hill; it represents an energetic barrier, which must be overcome for the reaction to occur and the products to be formed. The transition state is at the top of this “hill.”
To figure out the energy that a reaction needs to proceed, it is necessary to determine the height of the peak that must be scaled: to find the transition state (to “isolate state of transition”). To achieve this, a chemist generates a drawing or a set of data representing a molecule and submits it to a computational software package. The ensuing calculations determine energy (E) as a function of the position-related data: aiming to see how the energy changes as positions of the atoms change.
“The resulting stratagem / Seeks energy’s maximum / In calc’s geometric submission.”
The verses in this site have summarized an energy minimization before: how to identify a reaction’s reactants and products, by looking for the lowest-possible energy arrangement of a molecule: the minimized molecular shapes on either side of the reaction barrier.
A transition-state optimization is the opposite; this “strategem” seeks to find the greatest-possible energy arrangement for the species of interest. In other words, this is an energy maximization process, aiming to identify the species at the top of the energetic barrier, “climbing the mountain,” in the famously melodic words of this post’s title.
“Artist and scientist, Anna C. Atkins, With nature’s cyanotypes, Technique refines. Photos botanical Yield tome expansible: Blueprints for future work Here intertwine.”
The final “Twitter biography” poem from NaPoWriMo 2022 was posted on 15 April 2022 and noted some of the many accomplishments of botanist and photographer Anna Atkins (1799-1871).
“Artist and scientist, / Anna C. Atkins, / With nature’s cyanotypes, / Technique refines…”
Anna Christian Atkins was an English artist and scientist; she explored multiple interdisciplinary overlaps of scientific investigations and illustrations. She learned the cyanotype technique from its inventor, a friend of her family: Sir John Herschel. Cyanotyping is a photochemical process that takes advantage of the light-sensitivity of certain iron-containing compounds to generate images on a deep blue (cyan) background.
“Photos botanical / Yield tome expansible: / Blueprints for future work / Here intertwine.”
Atkins used the cyanotype technique to develop a “tome expansible,” a book that is generally accepted to be the first compilation of photographic images: Photographs of British Algae: Cyanotype Impressions. With some poetic license, this collection became “photos botanical” in the verse. Pages from this book can be seen at the link and provide clear images of the intertwining, delicate samples of interest.
Atkins’s book was an important historical document in its own right and also set the stage for the use of photography in scientific research for years to come. The last few lines note this metaphorically and highlight the fact that the cyanotype process is the same chemistry behind the blueprint process.
“Writer, physician, and Doctor Graham Travers: Last role, pseudonymic, for Margaret G. Todd. Term ‘isotopic,’ her Etymologic endeavor, Will clarify masses at odds.”
The 14 April 2022 Twitter biography poem alluded to some of the many STEM-related achievements of physician Margaret Todd (1859-1918), including a contribution to the disciplinary vocabulary of chemistry.
“Writer, physician, and / Doctor Graham Travers: / Last role, pseudonymic, for / Margaret G. Todd…”
Margaret Georgina Todd was a Scottish writer and doctor. The first two lines seem somewhat redundant in describing her career (“physician and doctor”), but as the third and fourth lines note, “Graham Travers” was the pseudonym under which she wrote her most famous book: Mona Maclean, Medical Student.
“Term ‘isotopic,’ her Etymologic endeavor, Will clarify masses at odds.”
In the field of chemistry, Todd is known for proposing the term “isotope,” in a conversation with radiochemist Frederick Soddy.
Soddy had been studying elemental forms that corresponded to the same entry on the Periodic Table of the Elements (PTE). These species shared the same atomic number (number of protons) but were seen to behave chemically differently in some scenarios, which could be ultimately attributed due to their different mass numbers (number of protons plus number of neutrons). Via collaborations with Ernest Rutherford, Soddy developed the concepts of nuclear reactions and radioactivity, proposing processes by which some of these intriguingly different chemical entities could decay into one another.
Learning about this research, Todd suggested a new term (“etymologic endeavor”) with which to describe these interesting species. She proposed the word “isotope,” from the Greek for same (“iso”) and place (“topos”), since isotopes are located at the “same place” on the PTE: they are instances of the same element.
At the macroscopic level, the behavior of isotopes explains why atomic weights (average atomic masses, represented by the numbers underneath the chemical symbols on the PTE) are not whole numbers: different isotopes are present on Earth in different “abundances,” ultimately resulting in fractional values for these average quantities.
Her teaching responsibilities included courses in both the sciences (chemistry, botany, physiology) and the humanities (English literature). Such multidisciplinary skills, or “gifts polymathic,” constitute considerable achievements for an outstanding teacher.
Department-leading; / In STEM fields, succeeding; / Through lab work, proceeding: / Prof. Josephine Yates.
“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.
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).
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.
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.
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!
“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.
“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”)!
“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.
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