What Got Me Hooked on Organic Chemistry

I’ve had an interest in all aspects of science as long as I can remember. Chemistry has always been one of those interests. Organic chemistry began to hold a particular fascination for me due to a pair of related synthetic experiments in my high school organic chemistry class. It’s one thing to discuss theoretical, paper chemistry in a class. It’s another to actually make stuff. That’s when my interest was permanently captured.

The experiments were simple ones, of course. Each began with the same starting material, salicylic acid. Both reactions were esterifications, via different conditions.

The first experiment was an acetylation of the phenolic hydroxyl group of salicylic acid with acetic anhydride to give acetylsalicylic acid (aspirin) as its product. I had known for many years at that time what the chemical name for aspirin was — but I didn’t really have an understanding of what it meant. This changed that.

The second was a Fischer esterification (although I don’t recall referring to name reactions in high school) of the same salicylic acid starting material in methanol, to produce methyl salicylate, or oil of wintergreen. The smell of every reaction I would ever again run went downhill after that. (And, of course, you should not deliberately smell the contents of your reaction flask.)

It fascinated me at the time that the same starting material could give products with vastly different properties and uses via a single functional group conversion. To me, this is still one of the cooler parts of organic synthesis — made even cooler when you’re making and characterizing compounds yet unpublished in the scientific literature.

No, I don’t recall what yields I achieved running these reactions. For the sake of argument, we’ll just say it was quantitative. Or a “Swiss yield.” (Bad chemistry joke alert: A Swiss yield is when you leave in the stirbar when weighing your product. I think I first heard that one during a Rick Danheiser seminar. Chemistry humor — not an oxymoron. Believe it!)

Now that I’ve spilled…what aspect of chemistry, or any other science, had you “at hello?”

The Dose Makes the Poison

In my house, we’ve recently had a bit of a mouse problem. Or, rather, a mice problem. We’ve known of their presence in the garage for a while. We often let the cats (we have three) out there periodically to roam around, investigate and basically do cat stuff. Well, a few days ago one of the cats left a well-gnawed and barely recognizable mouse-shaped present at the bottom of the steps leading into the garage. That cat earned her keep, I guess, but – ICK!

It gets better. That same day, I walked past one of our other cats, who was lazily sprawled across the kitchen floor. I reached down to pet his head, and there, between his paws was yet another mouse. This one was more intact, but equally dead. More importantly, it was in the kitchen. So, we’re on the lookout for more, and a bit wary. But, like I said, we have three cats – hopefully they’ll quickly address the problem for us.

What’s the chemistry connection? Well, these events brought back a memory of when I was a chemistry grad student. My wife and I were dating back then, and she and her roommate had a similar mouse problem in their apartment. Sadly, however, they had not one cat. What was their solution? First they tried traps – no luck. The little bugger evaded the jaws of death, and still roamed freely through their kitchen cabinets. It kept nibbling its way into boxes of food, and left its tiny mousepoop everywhere in a seemingly unending act of defiance. The stakes were high, and they decided the best strategy would be to poison their cute, yet disgusting, houseguest. Clearly, these two young women were not to be trifled with. (Did I learn a lesson there? You betcha.)

They purchased a couple of d-CON Mouse-Prufe Bait Wedges, and set them in strategic hidden places. (I should point out that back then, live traps were not readily available, so it wasn’t really an option to capture and possibly rehabilitate the mouse) A few days later, the effectiveness of this product became clearly evident as the smell of a dead and rapidly decaying mouse filled the apartment. I seem to remember it took a day or so for the two of them to finally locate the mouse, tucked away behind the bottom drawer of a kitchen cabinet. As neither of them wanted to touch the mouse-corpse, I was called over. I picked up the dead mouse with a newspaper and took it outside to dispose of it. I returned inside where accolades were showered upon me for the manliness of my achievement. Okay, maybe not so much.

Essay Competition at Nature Chemistry!

Last week, The Sceptical Chymist posted about an essay competition being conducted by Nature Chemistry in celebration of the International Year of Chemistry. The essay is to be written in the style of the “In Your Element” feature, which profiles a single chemical element, appearing at the end of each issue. Entries will be accepted through August 1, 2011. Details and instructions for entering the contest can be found here.

Due to contest rules, the world will just have to wait for my seminal essay on Yttrium -- all in iambic pentameter. Photo courtesy of Wikipedia user Alchemist-hp

Sadly, I cannot enter the competition, as I don’t quite fit the demographic. The instructions stipulate that it shall not be more than five years since the final training appointment (e.g., Ph.D. or postdoctoral position) of any competing author. Also, the essay must cover one of seven elements: helium, nitrogen, sodium, copper, bromine, indium or plutonium. If you have a burning desire to write about any of these elements, now’s your chance!

Hi, I’m your neighbor, and I’m a chemist. Sorry.

I’ve noticed that the neighbors I’ve had over the years seem to have had professions that were disturbingly — useful. They’ve run the gamut of professions and trades — plumbers, carpenters, electricians, lawyers, accountants, teachers, nurses. These are the sorts of neighbors with skills one could conceivably want to tap into if the need arose, and you had a reasonably friendly relationship with them.

I can think of one specific example where a former neighbor, an electrician, gave me advice on how to drill a hole through my foundation, dig a trench, and run some cable out to our backyard pond to hook up a receptacle to power the pond pump. I followed his suggestions (all up to code, of course), and it still works great to this day. See? Neighbor = useful resource.

Yes, those are lab coats. Dont be afraid...

But, a chemist? Heck, the minute you tell your neighbor you’re a chemist, there’s usually an awkward pause, and if they follow up with anything at all, it’s “So, um, what do you do?” So you assess the expertise level of your audience and begin to explain what you do, the goal of your research, and how it possibly might fit in to something that could affect them at some point.

Three or four sentences in, however, it’s clear that they didn’t really want an explanation at all, on any level. Their eyes glaze over a bit, then they avoid eye contact and perhaps fidget. If you’re quick enough to pick up on these social cues, you can try to recover with something like, “Hey, how about that local sports team?”

No chemistry experiments happening here, folks. Please move along.

Being a chemist means being met with suspicion. What am I up to, you ask? Do you suspect, say, that I’m doing experiments? Trust me, pal, without a fume hood, I’m not synthesizing anything, legal or otherwise, that involves the use of organic solvents. The catboxes smell bad enough.

And as far as being asked for my help with something, I’m not holding my breath (with or without a hood). I can’t recall one instance where a neighbor has come over and said, “Hey, you’re a chemist. Do you have a minute? I need some help with…this…um…thing.”

So, to all my past and current neighbors…I’m sorry. I apologize that my chosen field is one not ideally suited for home use. Please forgive me for my seeming inability to share your alarm in discovering that a food product you love contains chemicals. I am truly sorry.

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12 Things I Love About Chemistry

Okay, I’m late to the party, but here are my contributions. This might be a fitting (and easy) way for me to get in the game.

1. Submitting pure target compound to an assay for testing
2. Purifying crude material by trituration and avoiding a tedious chromatography
3. Finding an inexpensive, reliable vendor for a critical intermediate as an alternative to Aldrich
4. That moment when a crystallization begins to bloom
5. Elucidating the structure of an impurity that gives you insight to optimizing reaction conditions
6. Using a synthetic step from the literature that’s really old (i.e., older than me)
7. When pure product crashes out of a reaction mixture
8. Spot-to-spot conversion by TLC
9. When a colleague is excited about an experimental result
10. That “A-ha” moment in data analysis
11. Tension-free project meetings
12. Learning early on that being serious about science wasn’t the same as being solemn