Posts Tagged organic chemistry

The Periodic Kingdom [Book Review]

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. Read the rest of this entry »

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Response letter to an alarmist anti-caffeine organization

Stumbled across caffeineawareness.org by accident… weird site full of bizarre alarmist propaganda against the consumption of Caffeine.

For example: “Consume 5 grams and you’re DEAD, and it’s perfectly legal!” is touted in an ad on the sidebar of the website. The website also claims that caffeine is “highly addictive”, which seems hyperbolic, given how Caffeine actually works.

As I discussed previously, prolonged exposure to a significant (over 200mg) amount of Caffeine will result in an increase in the number of Adenosine receptors in your brain (this is called “upregulation”, and is your brain’s attempt at recovering homeostasis). This results in a “diminished returns” benefit of future Caffeine consumption until the brain is given a break from the chemical, and can downregulate back to normal levels. (this takes roughly 2 weeks for most people — individuals with severe Caffeinism may require longer periods, but you would have to be a serious compulsory consumer of Caffeine, 800mg or more / day, to be that bad)

Moderation is key, of course. If we view coffee as a tool, rather than a necessity, it can be a very beneficial ally. Habitual consumption of ANYTHING is generally a bad idea, and Caffeine is no exception.

Caffeine is nowhere NEAR as addictive as cigarettes, for example, or any harder addictive stimulants (Methamphetamine, Cocaine, Crack-cocaine, etc.). In fact, those harder stimulants don’t even interact with your brain in the same way that caffeine does (meth & coke tend to hammer your Dopaminergic receptors predominantly, whereas Caffeine simply prevents your Adenosine / Purinergic receptors from being used for a short while — there is some dopaminergic side-interactions with Caffeine, but it focuses largely on the Adenosine A1 / A2 receptors because of the homologous chemical structure to Adenosine.)

Here’s my response to them: Read the rest of this entry »

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My last undergraduate term paper EVAR.

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.) Read the rest of this entry »

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Limonene, part 1

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!

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Getting wired, the old fashioned way

So I’ve started drinking coffee.

This may seem a completely mundane statement — akin to saying something like “I am wearing underwear” or “I drove my car to work today” — so perhaps I should provide a little background:

I generally avoid caffeine and other mind-altering substances (always have, and likely always will be, drug-free — provided you don’t count alcohol :P ), and I just could never get into the flavor of coffee. I always felt that if I wanted to drink something that tasted like the inside of a sweaty shoe, I’d just go straight to the source and save myself the $1.95.

That said, I have, in the past, occasionally partaken in various novelty coffee drinks — Lattes, Cappucinos, Mochas, etc. When Charlie’s Coffee Bar & Gallery was open (long ago, in the before-time), I would now and then treat myself to a sweet drink. But as a general rule, I would tell them to “hold the espresso.” Not for any moral or sociological reasons or anything — but just because my body is so damned sensitive to caffeine!

See — this is how I figure it — I drink so little caffeine my brain is uber-intolerant to its effects and so the tiniest amount has a really potent effect on me. Seriously. If I even so much as smell espresso, I’m hyper for 20 minutes. Read the rest of this entry »

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