goodbye, chemcrack

I’ve been giving this a lot of thought, and sadly I will be releasing chemcrack to the flotsam and jetsam of the internet, and shutting down this blog. This is for two reasons:

First, it seems as though I will not be able to expand the site through to create tabs for categories and unlock other helpful organizing features — without cracking my wallet.

Second, the topics on this site get about as controversial as “how to measure the wavelength of a microwave using cheese.” But in the future, I’d also like to write about being a female in STEM and topics more political in flavor. When I do, I would prefer to be an anonymous blogger without my identity associated with the blog as I do with chemcrack.

I will not be giving up the blogosphere but am only moving to a new website. Maybe some of my older posts can be discovered there, in bits and pieces.


So, I’m pretty behind on these posts. These past few months, I’ve been channeling all of my writing mojo into graduate applications.

HOWEVER! You can look forward to the following posts in the coming months:

“How do fish breathe underwater?”

“What do cats and aromatic molecules have in common?”

“MOFs, COFs, ZIFs, and onomatopoeia!”

P.S. To my undergraduate compatriots applying for graduate school: Are you suffering from writers block? Need tips? A laugh? Another shot of espresso? Well, this post by femalescienceprofessor should give you at least one of those things (guesswhichthings) at the link

“It is that which at this instant, issuing out of a labyrinthine tangle of yeses and nos, makes my hand run along a certain path on the paper, mark it with these volutes that are signs: a double snap, up and down, between two levels of energy, guides this hand of mine to impress on the paper this dot, here, this one.”

Primo Levi

At the end of The Periodic Table

Today I almost set my dorm on fire…

Here’s the story:


I was making oatmeal in my microwave. [Classic “this-will-have-to-do” college meal.]

First, I poured into a ceramic bowl what I esteemed the optimal oat-flakes to water ratio. Sometimes I add too much water and as I heat the oatmeal, hot sludge bubbles out of the bowl and is reconstituted as a sticky crud on the microwave’s glass plate. Not today, said I, snatching a folded piece of paper from my desk and inserting it between the ceramic bowl and microwave plate. I start the microwave and busy myself with watering the cacti in my window.

Pop-pop-pop! go the contents of the microwave.

I rush over in time to see tiny bursts of flame erupt within the microwave. My oatmeal crud-catcher is on fire!! I fling the microwave open and dash out the flames, which had barely begun to eat away at the paper.

The paper now sports three interesting burn-holes of curious geometry. When I unfolded the paper, here is what I found: half a math proof and some scribbles–the largest of which had been obliterated by fire. These drawings were done with a graphite pencil.


Let’s review why:

GraphiteGraphite consists of sheets of carbon atoms locked together into a tight network. We do not typically consider carbon a conductive material (think about the conductivity of coal, or perhaps an oil, or a fatty acid), however the type of bonding network which forms between these atoms is special and allows for electrons to zip through the bonds between atoms and transmit with relative ease across the sheet. This property bumps graphite into the class of conductors, with free-flowing electrons.

When I place a conductor in the microwave, the radiation generated by the device sloshes the conductor’s free electrons back and forth inside the material, generating heat. Inside the graphite sheets, electrons go shooting across the tracks laid down by my scribbles and heat the lattice as they go screaming and crashing through the graphite network..The heat from this process was sufficient to ignite the paper the graphite was rubbed onto, and presto, we have a fire.



At least one of these experiments is worth trying at home (with a fire extinguisher nearby–safety first, guys).

Graphite animation source: “Graphite” by Saumitra R Mehrotra & Gerhard Klimeck – Crystal Viewer Tool on Link: Licensed under CC BY 3.0 via Commons –

metaphors in chem

Metaphors in chemistry: some silly, some useful!


“we cannot do without [metaphor], even at the level of one specialist speaking to another. This is true in many areas of science, but in chemistry more than most. Molecules are anthropomorphized mercilessly, and there need be no apology for that”

Stories of the Invisible: A Guided Tour of Molecules

Philip Ball

Oxford University Press


[1] Boat conformation:

[2] Maxwell’s demon:

[3] Hydrogen bonding in water: Stories of the Invisible: A Guided Tour of Molecules, Philip Ball, Oxford University Press 2001.

Moody liquid crystals

I think most of us figured out when we were children that mood rings do about as good a job at predicting moods as conspiracy groups do at predicting the end of the world. Maybe you also suspected that the ring was temperature rather than temperament-responsive, and performed some experiments to test your hypothesis. At room temperature, the ring was amber. You put it on your finger and it turned blue. You set it in the sun and watched it turned green.

So how do they really work?

A mood ring consists of a thermotropic liquid crystal encased in glass or quartz. Color changes in the liquid crystal respond to changes in temperature. Typically, the colors in the liquid crystals are “calibrated” to the average skin temperature of 37 degrees Celsius so that deviations towards higher and lower temperatures produces different colors.

The liquid crystals in mood rings are not unlike those utilized in the liquid crystal display (LCD) monitors in our laptops. These “crystals” consist of long, rod-like molecules which are loosely ordered by intermolecular interactions into a parallel-packing pattern as shown below. However, the molecules maintain some freedom of motion within the lattice. These ordered structures retain the phase behaviors of both crystals and liquids, earning themselves the name liquid crystal.

The liquid crystal phase encompasses a number of possible subphases, each with varying degrees of orderliness. For thermotropic (temperature-sensitive) liquid crystals, the molecules will coil or tilt as the temperature is fluctuated. These changes in structure produce changes in the liquid crystal’s light absorption properties, and thus we see a continuous evolution in color. For mood rings, this color progression generally proceeds from yellow to violet as the temperature is raised.

Picture 1 source:

Picture 2 source:

Information source:

the way things go

Biological processes are complex.

Really. Really. Complex.

These fancy biochemical transformations follow reaction pathways that are the handiwork of selective evolutionary pressures and their cumulative influences over a relative infinity of time…

What is especially striking about these pathways is their intricacy. Often they are guided along a chain of events, a series of indirect actions cascading towards a specific chemical end, the final domino.

Here’s an example:

The body’s chemical response to caffeine

The physiological benefits of caffeine spring into action through an indirect series of chemical responses to the initial absorption of caffeine into the small intestine.

Caffeine competitively inhibits phosphodiesterase, the enzyme that degrades cyclic AMP. This increase of cyclic AMP usually mediates most of the pharmacological actions of caffeine. This is due to caffeine’s structural similarity with adenosine. By blocking the degradation process of cyclic AMP, caffeine indirectly affects regulation of cAMP-dependent protein kinases, which are responsible for the regulation of glycogen, sugars and lipid metabolism. In addition, it stimulates the release of hormones, in particular: epinephrine (adrenaline).  [1]

The Rube Goldberg machine is an irresistible analogy for these chain reactions. I like to think (I do like to think) that the Rube Goldberg machine is a meditation on causal ingenuity. These “machines” link disparate events (such as a piece of paper catching fire and a bucket of water being filled) by physical causation. Anyway, I wanted to share one of my favorite Rube Goldberg set-ups below. Surfactants oozing down a plank! Exploding balloons and wheelbarrows! Fire!

The entire sequence is a thirty-minute feature. Yes, they got it to go for as long as you sit in your evening commute or devote to preparing and consuming a breakfast burrito… You can see the entire video at the Institute of Contemporary Art in Boston (which is where the 250th American Chemical Society meeting is being held, and where I am currently tippity-typing from.)