Tag: chemistry

“Familiar, this evaporation:
Water boils from stovetop causation.  
As molecules ready,
The temp’rature’s steady:
Much action in steaming stagnation.”

The 19 April 2022 Twitter limerick described the chemistry behind the action of boiling water.  (With respect to the title, a “heating curve” is a specific type of graph often used in chemistry and other STEM disciplines, but it always seems an appropriate turn of phrase when using circular stove burners and cookware in the kitchen, as well.)  

“Familiar, this evaporation: /
Water boils from stovetop causation…”

Boiling water in a pan on the stove is an example of vaporization, a phase change between the liquid and gaseous phases of a substance when the appropriate conditions are achieved.  For water at atmospheric pressure (1 atm), the boiling point temperature would be 100 ℃, 212 ℉, or 373 K, depending on the scale used.    

(“Evaporation” is not fully synonymous with “vaporization“– which would have also scanned well– but the former is generally the more familiar word.)  

“As molecules ready, /
The temp’rature’s steady: /
Much action in steaming stagnation.”

We can imagine heating water on the stove and measuring its temperature as a function of the heat added.  We would see a steady increase from the water’s initial temperature up to the boiling point.  Then, the graph would flatten out briefly: the temperature would be steady for some time, depending on the amount of water being heated.  A certain amount of heat energy would be necessary to accomplish the phase transition itself (converting the water molecules from the liquid phase to the gas phase), before the temperature could keep rising.    

The “steaming stagnation” of the phase transition, an alliterative summary of the phase shift from liquid water to gaseous water, would involve significant molecular action.  

(As with the use of “evaporation” in the first line, I quibble somewhat with my 2022 poem as I expand it here.  I initially used “seeming stagnation,” but the rhyme it immediately brought to mind with “steaming” was too perfect not to adopt.  However, the change admittedly renders the meaning less precise, since steam is itself the gas phase of the sample of interest.)   

“The nature of light defined, namely:
A difficult task at hand, plainly;
A defining question
Throughout STEM progression.  
Now: wave and a particle, samely.”

The 17 April 2022 Twitter limerick provided a massively abridged overview of the scientific study of light.    

“The nature of light defined, namely:
A difficult task at hand, plainly…”

Light has been a phenomenon of keen interest for observers throughout history.  Encyclopedia entries provide sweeping overviews of investigations from around the world, through millennia of history.    

“A defining question /
Throughout STEM progression.”

The past few centuries of scientific history (“STEM progression”) include several famous experiments that have been used to explore the nature of light. Some experiments have supported the concept of light’s wave behavior; others, light’s particle behavior.      

“Now: wave and a particle, samely.”

At the turn of the 20th century, multiple scientists’ discoveries ultimately led to the theory of wave-particle duality for the nature of light.  In 1905, Albert Einstein proposed the existence of the “light quantum” (ultimately termed “photon”): the tiniest particle of light allowed, which could also be observed to act as a wave.  

Wave-particle duality is the name of the theory used today to describe light’s nature.  Light is best understood via the models of quantum mechanics, which also means its behavior is impossible to fully assess with classical-mechanical metaphors and vocabulary (i.e., those models in which a particle OR a wave would be the better choice).  

Einstein eloquently wrote: “It seems as though we must use sometimes the one theory and sometimes the other, while at times we may use either. We are faced with a new kind of difficulty. We have two contradictory pictures of reality; separately neither of them fully explains the phenomena of light, but together they do.” 

Thus, the two viewpoints (wave AND particle) are considered “samely,” and the mathematical treatment chosen to model light’s behavior in a given situation is whichever will better fit.

“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.    

Since Atkins was skilled at drawing and illustrating, she had particular insight into the value that a photographic technique could provide with scientific samples that defied hand-drawn record-keeping: in her words, such species were often “so minute that accurate drawings of them [were] very difficult to make.”  She used the cyanotype technique to precisely record aspects of several natural specimens.   

“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.

“Gifts polymathic,
Achievements emphatic;
In classrooms, skilled tactics, as
One of the greats…
Department-leading;
In STEM fields, succeeding;
Through lab work, proceeding:
Prof. Josephine Yates.” 

The 13 April 2022 Twitter poem was a pseudo-double-dactyl celebrating chemistry professor Josephine Silone Yates.  Records differ as to the date of her birth (listed as either 1852 or 1859), and she lived until 1912.     

Gifts polymathic, /
Achievements emphatic; /
In classrooms, skilled tactics, as /
One of the greats…   

Josephine Yates graduated with honors from Rhode Island State Normal School in 1879, ultimately earning her master’s degree from the National University of Illinois.  She taught a wide variety of courses at the Lincoln Institute in Missouri and was the first woman to be named full professor there. 

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. 

Professor Yates is perhaps most famous for being the first Black woman to chair a natural sciences department, thus “leading [and] succeeding” in multiple scientific fields, as well as directing both lecture and lab curricula.   

She was also a renowned poet and journalist.  Yates once wrote, regarding her teaching work: “The aim of all true education is to give to body and soul all the beauty, strength, and perfection of which they are capable, to fit the individual for complete living.” 

“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!)     

“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.  

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!

“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.