Field of Science

One ring to bind them all: things you might not know about benzene

Space filling model.  c. Michelle Francl
UPDATE:  The Sceptical Chemist has a quiz up on benzene structural formulae based on the article in Nature Chemistry.  

Next year is the 150th anniversary of Kekulé's paper proposing the cyclic nature of the benzene 'nucleus.' and the 190th anniversary of Michael Faraday's paper on bi-carburet of hydrogen, more familiarly known as benzene.  In Berlin in 1890, on the 25th anniversary, German chemists threw the Benzolfest in honor of Kekulé.

I wrote a short 'fest' for Nature Chemistry, which appears in the January issue($).  I learned much about organic chemistry's iconic molecule, and herewith are 10 pieces of trivia that did not make it into the final piece.

1. There are 217 skeletal isomers of benzene, including the iconic hexagon, more than 300 if you count stereoisomers. [Patrick W. Fowler, MATCH Commun. Math. Comput. Chem. 63 (2010) 333-346].

 2. Benzene tastes sweet, with a hint of almond, and can be tasted in water starting at about 0.5 ppm, or roughly 1 drop in 40 gallons.

 3. An alternate synthesis (circa 1850) claims to passes benzoic acid through a “red hot gun” barrel packed with pumice. There's no evidence that it actually works.

 4. There is a tie knot that is hexagonal, perfect for tie-wearing chemistry conference attendees.  It was discovered by mathematicians, but you can still wear it.

 5. Dewar never suggested benzene's preferred structure was bicyclic. He used the structure, along with the more conventional structure, to demonstrate the potential of his brass molecular models. ["On the oxidation of phenyl alcohol, and a mechanical arrangement adapted to illustrate structure in the non-saturated hydrocarbons," Proceedings of the Royal Society of Edinburgh 6: 82–86 (1867), you can find it on Google Books]

6. The extraction of flowers of benzoin - benzoic acid - was first reported by Michel de Nostredame, otherwise known as Nostradamus, in the 16th century.

7  Kekulé actually didn't didn't present his revolutionary theory in January of 1865, his colleague Adolphe Wurtz read the paper in his absence.

8.  As late as the 1920s, major figures in organic chemistry did not think benzene or its derivatives were planar.  Sixty four years after Kekulé's paper was submitted (almost to the day), crystallographer Kathleen Lonsdale submitted her paper showing unequivocally that hexamethyl benzene, and presumably therefore benzene, was planar. "Thus the 'diamond' [puckered] type of benzene ring is shown to be wholly inadmissible." (Emphasis is Lonsdale's.) [K. Lonsdale, Proc. Roy. Soc. A, 494-515, 1929.]


9. In the days before ChemDraw, there were stamps.

10.  Hexagons were not the only proposed structural formula for benzene.  Loschmidt suggested the representation at the right.



If you would like a reprint of the essay, send me an email.

Tea transitions

Tea bag is paper. Vapor is from phase
transition of water
Introductory chemistry at my college has a broad audience.  My students are not just potential chemistry major and pre-meds, but I teach geologists, art historians, psychologists and even students who simply want to know more about how the hidden world of atoms and molecules works.

I tell them my job is to help them transition from being science students to scientists -- or rather into people who can critically assess and use the science information they encounter.  Can they filter the junk from the reality?

Enter the Food Babe, whose stirs up real science with fake science and then peppers it with a healthy dose of panic to produce posts that are at a perfect level for my students to read and try to tease out fact from fiction.1  I couldn't do a better job if I made them up.

This example is about my favorite beverage:  tea.  Are plastic tea bag safe, wonders the Food Babe?

To quote:
"Another temperature consumers need to worry about in tea is the “glass transition” temperature. Here’s the science behind the glass transition temperature or, Tg, and why it becomes dangerous according to The Atlantic: 
“That is the temperature at which the molecule in certain materials such as polymers begin to break down. As a rule, the Tg of a material is always lower than the melting point. In the case of PET and food grade nylon (either nylon 6 or nylon 6-6), all have a Tg lower than the temperature of boiling water. For example, while the melting point of PET is 482 degrees Fahrenheit, the Tg is about 169 degrees. Both nylons have a lower glass transition temperature than PET. (Remember that water boils at 212 degrees.) This means the molecules that make up these plastic tea bags begin to break down in hot water.” (Emphasis is the Food Babe's.)

Since we just finished looking at ways to display information about the phases of materials, this is a great piece to dissect.

Phase diagrams are a compact way to show not only the state a material might be in under a given set of pressure and temperature conditions, but the astute reader can pull some information out about the energies required to get a material to change state, and even something about the forces that hold a material together.

The iconic phase diagram in general chemistry is the one at the right for carbon dioxide.  The diagrams are not difficult to read.  The solid lines indicate conditions where two phases are present, in equilibrium.  So at normal atmospheric pressure (1 atm) and -78.5oC, solid CO2 ("dry ice") and gaseous CO2 are in equilibrium with each other.  At normal pressure, if you heat solid CO2 above  -78.5oC, it will change from a solid directly into a gas without melting, it's icy cold, but doesn't produce a liquid when it warms.  It's a "dry" ice.

When a material changes phase, it's important to understand that the core identity of the molecule doesn't change. That is, the structure of the individual molecules does not change, molecules do not 'break down' during a phase change. The CO2 molecules in the solid are just like the CO2 molecules in the gas.  What changes in a phase transition is the arrangement of the molecules, their relationships to each other.  In the gas phase, the molecules are widely separated and moving randomly, while in the solid they are arranged in a crystalline symmetrical array, and don't move much.

There are more possible phases for a material than the familiar solid, gas or liquid.  Many materials have several different ways for the molecules to pack themselves into a solid.  (Water has more than a dozen different types of ice, with different densities and other macroscopic properties.)  Some solid forms are crystalline, with all the molecules neatly arrayed.  Others show less order on the molecular level. These forms we call amorphous solids.  Some amorphous solids are called glasses.  At the glass transition temperature, a nice crystalline solid can change into a less ordered glass form.  For a polymer like the PET, the glass transition temperature is when (on the molecular level) the molecules become less rigidly ordered.  On the level we can observe, it means the polymer becomes less brittle, more malleable.  Softer.

It does not mean that the (presumably dangerous) molecules break down and leach into your tea water.  If there is a danger lurking in your fancy PET tea bag (and there might be) - this isn't it.


1.  The classic example is about airplane travel and gases, where she tries to get people incensed about the 'fact' that the cabin air contains nitrogen because the airlines are too cheap to use pure oxygen, and about pressurized cabins.  It's not only wacky fake science, but a bit scary because she suggests medication doses and timing will have to be adjusted due to the nitrogen content.  (Do not take medical advice from the Food Babe.  She doesn't even know what is in the air she breathes.)

You can't find the airplane air post on her blog anymore, like her infamous microwave post ("For the experiment pictured above, microwaved water produced a similar physical structure to when the words “satan” and “hitler” were repeatedly exposed to the water.") it's been taken down. She's blocked caching, but you can read it here.

Weird words of science: prilled iodine

"Sample of iodine" by LHcheM.
Licensed under Creative Commons
Attribution-Share Alike 3.0 via Wikimedia Commons
I was browsing the paper version C&E News on the train yesterday afternoon, and noticed two back to back advertisements for halogens, one for bromine reclamation, the other for iodine.  Prilled iodine to be precise.  Prilled?  I had a vision of lacy violets frills.

Prills are tiny balls of a substance, formed by letting droplets of the liquid fall from a height (in a prilling tower.) Surface tension has its way and the droplets become spheres, which then solidify.  Many bulk industrial chemicals, particularly fertilizers and detergents, are prilled for easier handling.

Prilling has its roots in 18th century copper mining, referring to beads of high purity copper.

While I rarely buy chemicals, I have purchased iodine flakes for a teaching lab.  The catalog does offer me the choice of "iodine, beads" — prills by another name.





Fire Burn and Caldron Bubble: A chemistry set for the iPad

From BlueCadet's design for the app
Round about the cauldron go;
In the poison'd entrails throw.
Toad, that under cold stone
Days and nights has thirty-one
Swelter'd venom sleeping got,
Boil thou first i' the charmed pot.

Double, double toil and trouble;
Fire burn, and cauldron bubble.
                            Macbeth, IV.i

Perhaps not surprisingly for the daughter of two chemists, this scene from Macbeth was my introduction to Shakespeare. I loved to hear my father recite the charm the three witches crafted 'round the cauldron.  It was so evocative of visits to my Dad's lab, where vapor from bubbling pots rose to collapse back into liquid form, dripping steadily into flasks.  The sweet-sharp scent of acetone swirled around like mist.   Worrying whether the tomato soup heating in a beaker on a Bunsen burner was safe to eat — poison'd I grasped (entrails were frankly a mystery when I was six, despite my kindergarten teacher's attempt to broaden her small town Midwest children's palates beyond chicken and mashed potatoes).

Though a confirmed theorist (the only things extracted in my lab are coffee and tea), I still love the idea that you can pull a chemical reaction off the paper and, by boiling and bubbling (along with much swelter'ng and perhaps even a dash of dragon's scale), transform the known into the new and very different.  The Chemical Heritage Foundation, where I was a fellow in 2012, has one of the world's largest collection of vintage chemistry sets.

The CHF teamed up with developer BlueCadet to develop an app, ChemCrafter, for the iPad that recreates some of the fun of these classic sets, right down to the bubbling beakers, explosions and fires.  I played a small part in the development, researching some of the more obscure reactions to be sure of the details of what happened.  Among the more fascinating things I learned was that when sodium metal reacts with liquid bromine, there is no reaction until the beaker is tapped (the source I consulted actually gave a minimum required force), then the reaction is explosive.  I'm trying to imagine (1) how someone discovered this and (2) what the experiments to determine the force must have looked like!

We worked hard to be sure the chemistry was as accurate as it could be (bubbles? fire? color?), down to the thermochemistry (yes, you can have fun with Hess' law and yes, the enthalpies of reaction and the points you earn thereby are extensive properties).

ChemCrafter (after the classic Chemcraft chemistry sets) is free and you can download it for the iPad at the iTunes store.


Watch Rosie Cook talk about the Chemical Heritage Foundation's chemistry sets and learn more about the collection here.


Nitrogen in the snow

We are expecting another round of wintry weather tomorrow, and an article in the local paper noted that the snow and bitingly cold weather we have had recently are good for farmers.  The cold reduces the population of some pests, particularly the species making their way north.  The article also noted that snow contains nitrogen from the atmosphere, providing a little extra boost for lawns come spring.

The atmosphere is roughly 80% nitrogen, in the form of N2.  The form matters.  Nitrogen gas is very unreactive, so much so that it many "air sensitive" materials are packed under pure nitrogen.  (The part of the air that is reactive is molecular oxygen, O2.)  Snow certainly contains dissolved nitrogen gas.  Henry's law predicts the solubility of a gas in a solvent, water in this case, as a function of temperature.  It might seem at first glance counter intuitive, but gases are more soluble in cold solvents than in water (the opposite is true of most solids, as anyone who has tried to dissolve sugar in cold ice tea knows).  An inch of snow contains about 7 milligrams of nitrogen gas per square foot, or about 1/3 of a kilogram in an acre of snow.  Given that fertilizers are spread onto fields at a field of roughly 300 kilograms per acre, it's not much.

The trouble is actually that this nitrogen isn't in a form that easily accessible to plants.  Nitrogen in the atmosphere must first be "fixed" or changed into a more reactive form, typically tetravalent nitrogen (ammonium) which is then converted to the nitrate ions that plants can use.  So where does the useful sort of nitrogen come from?

Industrially, nitrogen is fixed in the Haber process.  Since nitrogen is so unreactive, this requires pressures hundreds of times those of earth's atmosphere and temperatures more likely to be found on the surface of Venus (over 700oF).  Nitrogen is fixed in the biosphere by microbes, which undertake an elaborate enzymatic dance to do this at low temperatures and pressures (and yes, scientists are on the job of trying to figure out how to get the enzymatic processes to work at industrial scales.)

Lightening strikes also convert minuscule amounts of N2 in the atmosphere to nitrogen oxides, and industrial pollution has also injected nitrogen oxides into the atmosphere. Industrial pollutants are by far the biggest contributors. The nitrogen oxides become nitrate ions. These are the nitrogen sources that turn a blanket of snow into a gentle fertilizer.

To put it into perspective, snow and rain probably deposit about 5 kilograms total per acre over a year. It's not much, it's not quite all natural (the rates were much lower in pre-industrial days), but it's something.

Isotope and the hidden women of science

It was a century ago today that the word isotope first appeared in print, in a letter to Nature from Frederick Soddy, who would go on to win the Nobel prize in 1921.  Nature Chemistry has a Thesis column by Brett F. Thornton and Shawn C. Burdette ($) to commemorate the occasion, as well as a post up at the Sceptical Chymist.  The post is illustrated with a photo of a plaque which reads "At a dinner party held in this house in 1913 Frederick Soddy (1877-1956) introduced the concept of 'ISOTOPES'..."  Thornton and Burdette also point to the dinner party as the moment when the term isotope was coined.

But Soddy did not coin the word.  The woman who did coin the term, Dr. Margaret Todd, has been gently set aside and one is left to assume that the word came to Soddy out of thin air. Margaret Todd was a physician and novelist, one of the first women to enroll in medical school in Edinburgh after the exams set by the Scottish Royal Society of Physicians and Surgeons were opened to women.  She was gay.  She wrote a popular novel under a male psuedonym, but it's the single word she handed Soddy that is her most enduring authorial legacy.  You need a good Greek term, she told him.  Try this one.

Sweet Hearts and Frogs



Last week I was at a workshop on teaching in British Columbia where I learned to make a string from a stick (if you're talking about teaching, it's really useful to be put in a situation where you have to learn something entirely new). We used obsidian points to scrape the outer layer of bark from dried stalks of dogs bane (Apocynum cannabinum), then pulled free the fibrous layer at the surface.  The instructor warned us about handling the plant before it was dried, noting that the sap could disrupt your cardiac rhythm. The ethnobotanist and two chemists in the group immediately murmured, "digoxin?" As you might imagine, an activity that features obsidian points, bone knives and an open fire doesn't lend itself to a quick search of the literature, so we were left to wonder for the evening.

cymarine
The sap of apocynum plants, such as dogs bane, contains cymarine, which is a potent cardiac glycoside, like digoxin.  The term glycoside indicates these are structures that contain a sugar chemically bound to the rest of the molecule.  The sugary parts of each molecule are the hexagons with the O's in them on the left side.  Cymarine has one such hexose; digoxin has three.  At first glance the molecules might seem very different, but clip the sugars off and the remaining parts of the structures are very similar.

Cardiac glycosides are produced mostly by plants (foxglove, dogs bane, oleander), but toads also secrete them (check out this paper in Heart about someone who took a purported aphrodisiac that contained dried toad venom and died a few hours later from what looked like digoxin poisoning).  So don't kiss any toads, it's not sweet for your heart.
digoxin

Update: Read the Naked Scientists on why people might lick toads: Tripping over psychogenic toads.

Oversharing and zero point energy wands: pseudoscience in the NY Times

While poking around the other day for some general reading material on the zero point energy, I discovered zero point energy wands (which claim to access not my favorite flavor of zero point energy —molecular vibrational — but the zero point energy field of the universe).  A few hours later someone sent me a link to this piece in the NY Times about spiritual cleansing of living spaces (and quotes one of the practitioners on how quantum physics explains it all, see page 2).  I suspect it is time to add another section to my quantum mechanics course. No, no, not instruction on proper wanding technique...you can find that here....but perhaps a brief conversation about how to get a handle on unpacking pseudoscience that has been cloaked in quantum physics jargon and responding to it is in order.

I suspect that when confronted with examples of psuedoscience, most chemists are like me, we jump into lecture mode.  Partly because we think the way the world works is so fascinating, we can't wait to share.  Partly because we think that if we share what we know (and so much of science is about sharing everything from space to materials to results) then people will see the universe works the way we see it works.  Face it, we overshare.

So how to respond, and more to the point, how do I help my students respond?  I wrote a piece recently offering some practical advice on combatting chemophobia for chemists (Nature Chemistry 5439–440 (2013), $).  The short version is watch your language, this is not the moment to play the "I call salt sodium chloride" card (even if you do have a jar labeled NaCl(s) on your kitchen counter) and to listen, to try to suss out whether this is a conversation that at its root is about politics or parenting where the science is secondary, this may not be a teachable moment.

But what about language when the jargon is flying the other way?  The book on wanding (which despite enormous temptation, I did not download onto my iPad) throws around words like "scalar" and "phase-locked" and "zero point energy" with abandon, but the meanings have shifted.  Sometime subtly, sometimes they are utterly scrambled.  How can you have a conversation where the words are the same, but the languages incompatible?


Some thoughts from ChemBark about combatting chemophobia on a broad level.
Sciencegeist hosts a festival unpacking the mysteries of toxic (and not) chemicals
Science Online 2013 takes on chemophobia
And finally, an non-science article from the NY Times that gets the science right: the venerable Harold McGee on wine wands (no zero point energy invoked!)

Quantum quivering



One thing that still stuns me about quantum mechanics is the notion that all molecular motion does not cease at zero degrees Kelvin (despite what you might read in your intro chemistry book).  Quantum mechanics tells us that when molecules vibrate, they can only do so at certain frequencies -- or energies.  Fascinatingly, the ground state vibrational energies (the lowest vibrational energy state a molecule can be) are not zero.  The molecules continue to vibrate, not matter how cold you get the system, you can never freeze out that vibrational energy.  Nor is the so-called "zero-point energy" of a molecule negligible.  The zero point energy of water is about 7 times as large as the thermal (translational) energy at room temperature).   I imagine all these water molecules arrayed in the solid, gently breathing, no matter how much energy you suck out of the system, they keep on vibrating.

Fine, fine, atoms are quantum mechanical objects and I'm willing to believe that the rules are a bit different in this realm, but surely such things are not true of macroscopic object?  Physicists Amir Safavi-Naeini and Oskar Painter have shown that objects far larger than atoms exhibit this quantum effect.  Watch the video to see how they did it!


While looking for a basic reference on zero point energy to link to, I discovered zero point energy wands...but that's a tale for another day!

A small sip of oxidane

My better half pulled a pitcher out of the refrigerator last night and poured a glass, thinking it was what we usually stock, lemonade. "Um, what is this?" The vibrant green color bordered on neon. "Either margarita or appletini. Given the color, I'd hazard appletini." The face he made was priceless.

As it turns out, the stuff tastes perfectly acceptable, once you get past the name and color. But names definitely matter. If offered a sip of oxidane, would you (should you) drink it?