Tag Archives: chemistry

The Periodic Kingdom [Book Review]

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I’ve actually had this book for a while — I picked it up while back east on holiday with my family. Somehow, it got shuffled away and then rediscovered when planning out this years books.

The Periodic Kingdom is a book that explores the Periodic Table of Elements (ie. chemicals) through the perspective of geography. I was initially attracted (pun not intended) to it partly because I’m a nerd for chemistry, but also because I’ve been sort of working on my own variant-approach to teaching chemistry, and I wanted to see what Atkins has to say.

P.W. Atkins is a professor of Physical Chemistry (the kind that deals with quantum mechanics, as opposed to organic or biochemistry, which deals more with life-based compounds) at the University of Oxford. Throughout the book, he clearly shows that he has both academic prowess and extensive teaching experience; it’s worth noting that simply because I’ve read many books on scientific topics where one or the other is lacking — it’s not often that you find both.

That said, I was a little disappointed with the book. Continue reading →

Contextual Learning

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One of my profs and I occasionally chat about his curriculum. This was his first year teaching at IU East and he’s still fine-tuning his style. The main roadblock he runs into, and I can totally understand, is that a lot of his students have a very nonchalant, sometimes completely ambivalent, attitude towards the course material.

One thing I suggested, for when he teaches Organic Chemistry next year, is to draw in real-world examples to help illustrate and provide context for the material. I call this “contextual learning” (there may be a more official title for it, but I wasn’t an education major, so I’m just going to call it that). Continue reading →

My last undergraduate term paper EVAR.

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Below is a copy of my term paper written for my Cell Biology course. I wrote it in a slightly less-formal style of scientific journalism, but didn’t spare on the technical details. Feedback, good or bad, is appreciated.

The Effects of the Consumption of Methylxanthines on the Adenosine Receptor System

Every year, humans around the world consume an estimated 10 to 20 billion pounds of coffee. (Gale) While some may drink it for the flavor, one can imagine it is probably the psychoactive stimulant, caffeine, that is the puppetmaster, beguiling we Americans to consume 200 mg (approx. 2 cups of coffee), and our northern European counterparts, up to 400 mg, every day. (ibid) For most people, it provides a useful mental edge: sharpening their focus and providing a subtle kick-in-the-pants of chemical motivation. Caffeinating over that sharpened-edge, however, can lead to disorders of sleep, anxiety, and even a jittery anxious quasi-hallucinatory state known as “caffeine intoxication”, all noted by the DSM-IV. (ibid) The other dark side is the silent escalation of tolerance to caffeine’s beneficial effects. Prolonged, regular exposure of caffeine can set up the consumer for an uncomfortable withdrawal period, ripe with headaches, myalgia, fatigue, and anxiety. (Ramkumar et al.) Continue reading →

Napoleon’s Buttons [Book Review]

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This is by far the most interesting book I’ve read this year (and is a definite contender for the “all-time” best, as well!)

The premise of the book is “17 molecules that changed history.” From cotton to caffeine, scopolamine to saponin, this book colorfully lays out both the chemical nature of these significant molecules, explaining how they function and WHY they work the way they do; it also illustrates the historical impact, going into great detail about how the course of history was heavily affected by the molecular properties of the topical substance.

The author explained in her introduction that her publisher had initially balked at the idea of using the actual chemical structures in the text — perhaps it was the intimidating look of an organic stick structure that threw them off; But Le Couteur does a terrific job of demystifying these seeming cryptic diagrams, using arrows, circles, and notations to indicate key differences in otherwise similar structures.

In spite of this, Le Couteur’s main focus in the book is not on the technical chemistry, but rather on the historical relevance.

I find that when I’m learning something, the more connections I can form with an idea, the stronger my memory — this book is a powerhouse in that regard; the knowledge of the structural nature of these compounds (at least the relevant functional groups, anyways) coupled with the historical relevance, creates memorable, almost mnemonic, impressions in my mind.

One of my favorite stories from this book was about Isoeugenol (one of the key chemicals in the common spice “Nutmeg”). Centuries ago, before America declared its independence, the English and the Dutch were top world powers. The Dutch’s East India Trading Company dominated the spice islands, Indonesian region, and pursued Captain Jack Sparrow to the edge of the earth. They also controlled Manhattan island (then called “New Amsterdam”).

The British controlled the isle of Run, a tiny island down n Indonesia, near Australia. It was a fairly non-descript island, save for one particular feature: It contained a LOT of nutmeg. At the time, both the Dutch and the British were dealing with the plague, and Isoeugenol, found in nutmeg was believed (somewhat correctly) to help prevent the spread of that disease.

After some fighting, some discussion, and some agreement, the two nations traded the isle of Run for Manhattan island. The plague passed, and everyone moved on. It is quite likely that Holland would have yielded New Amsterdam eventually anyways, since the British presence in the New World was more prevalent, but who knows how things would have turned out that way!

If you enjoy non-fiction, particularly historical or science-oriented, this book is a must read.

Limonene, part 1

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We’re starting a new lab in O-Chem this week: Extraction of a Volatile Oil from Orange Peels via Steam Distillation.

In layman’s terms: we’re taking the stuff that smells good out of the orange peels by boiling it off. 

The major compound responsible for the orange smell in peels is a volatile oil called “Limonene”, and is also found in lemons. Interestingly, the enantiomer (more on that in a minute) of this compound is not palatable at all (it has an odor similar to Turpentine).

Briefly, an Enantiomer is a mirror-image of a molecule. These 3-d arrangements behave differently (the case study always used is the Thalidomide tragedy) and thus interact differently with the smell receptors in our noses.

d-limonene l-limonene

The enantiomers of limonene, in stick structure form, are pictured to the left. 

They may not look like mirror images, but I just need you to trust me on this. (If you were to make up a MolyMod model of it, you’d see what I mean) You may think that they look identical except for that the left one has a thick black line towards the bottom and the right one has a dashed line. 

In organic stick structures, thick black lines like that indicate a bond whose subsitiuents are coming TOWARDS you, and dashed lines indicate a bond whose substituents are receding into the paper. So the left side one, imagine that the /\\ part at the bottom is coming towards you.

Side note: “d” and “l” indicate which enantiomer is being referred to, and are necessary for drawing the structure correctly. “d” is from the latin “dextrorotatory”, and “l” from the latin “laevorotatory”. [Read more]

If you’ve ever had a citrusy-flavored alcoholic beverage, you may have seen the  bartender “zest” the orange peel into the drink as a garnish. I always used to wonder why they would zest the PEEL instead of just squeezing some juice into it. 

As it turns out, the peel contains the highest concentration of d-Limonene in the orange, so zesting is the easiest / most effective way to get that volatile oil out. 

Also contained in the orange peel are the compounds “Octanol” (like “Octane” found in gasoline, except with a hydroxyl (-OH) group on the end of the chain, making it an alcohol), and “Carvone“, a compound derived from Limonene (via Oxidation).

Carvone is another interesting case like Limonene: its flavor depends on which enantiomer you consume. Fortunately, they are both non-toxic and (in my opinion) tasty. 

The “R” orientation (For the purposes of this blog post, “R” = “d” and “S” = “l” — pardon the confusion) is a major contributor to the flavor of spearmint oil, and the “S” orientation is a “principal constituent” of caraway seeds.

Through oxidation, we can produce Carvone from d-limonene. (If you compare the structures, you’ll notice that the only difference is that extra “O” doublebonded near the top of the molecule.) I suspect that leaving lemon or orange peel out in the open air will cause it to naturally oxidize (via an SN2 reaction), and we could certainly test for this by leaving the peels out and running an FTIR scan on the extract, looking for ketone peaks (that “O” double bond attached to a secondary carbon).

At this point, we are working on developing the procedure. I’m pretty sure that our lab group will be using a distillation apparatus (the big ol’ macro variety) to try and steam off some of the orange oil. The thing I found interesting was that all the sources I consulted (admittedly: all via google) said that orange oil has a boiling point of 176 C — we’re not going to get temperatures that high with our apparatus. I suspect that the heterogeneous mixture (the orange oil is non-polar, and we’ll be mixing it with water, a very polar solvent) may have a decreased boiling point, or that it will piggy back on over or something. We’ll see. 

If it works, we’ll see a thin film on the distillate beaker, if not, we’ll know to look into the short-flask. I’ve got lab again on Thursday afternoon, so we’ll see what happens!

Grad School and Beyond

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I had a meeting today with two Profs from the School of Natural Science & Mathematics; Dale & Errol. Dale is “that Biotech guy” (a gross understatement ;) ), and Errol is a prof in Chemistry (incidentally, he is also my prof in Chem this semester).

Our meeting was the result of a casual chat I had with Errol regarding Grad school, my future career, and what I need to do to make it happen. Quite honestly, I have the desire but am completely blind with respect to what I need to do. Errol suggested I meet with he and Dale to discuss this in more detail.

I suppose I should back up a little bit. Continue reading →