Efficient enantioselective transformation of lemons to lemonade: a reflection

December 24, 2009

What kind of blogger would I be if I didn’t include some nod to the end of the year? The kind that asks rhetorical questions, I suppose…

But I feel I may as well contribute my 2 cents on 2009 – mostly reflecting on myself, and maybe a little on chemistry as a whole.

With respect to myself, I feel like I’ve learned so much over the past year, and in particular, the past semester. Efforts included an attempt at the C8-C12 fragment of callystatin A for my synthesis class, and synthesizing a small library of heterocycles for the research lab! And to think, back at the dawn of 2009, I was only starting orgo II…

As mentioned before, the synthesis class hit a brick wall when the use of a chiral auxiliary simply failed to work. Infact, out of the three people with my project, I think I was the only one to actually isolate 6 (nevertheless, in complete shit yield – a mere 2%). However, as the morale of my compatriots began to sink toward the end of the semester, I remained vigilant; the more problems I encountered, the deeper my desire to “beat” the reaction. Although I didn’t quite make it to the C8-C12 fragment, I went out swinging. During the final lab period, I was left with 9 mg of crude 7, a promising, yet narrowly RF’d TLC, no time, and no prep-TLC plates. [1]

Results from the research lab were much more promising. Through out the semester, I was a little skeptical of the idea of a library synthesis. I had signed up for research well before I was romanced by the idea of total synthesis, and I quickly grew restless doing the same few reactions over, and over, and over, as I began to yearn for target-oriented hot pursuit. Almost the entirety of the semester was spent testing/generalizing reaction conditions, and prepping starting materials for a final parallel combinatorial synthesis, and right when it was high time for parallel synthesizing, I got that nasty flu. What could have taken place during the last week of actual class had been pushed back into the study period/final exam period. The pressure of time running low sparked something, and I started to view the chemistry as something I couldn’t let beat me, and seeing the work of the entire semester come together gave me hope. In a final sprint to the finish, I cranked everything out in time, and submitted samples for biological screening, reaching the established goals for the semester. Then I did a happy little dance, and took a well deserved nap.

Finishing off the year: my fledgling attempts at real scientific writing. For both my synthesis lab, and research/independent study, I had to write up a full research paper detailing the semesters work. Gone are the days of “lab reports” with slightly differing formats from class to class, having to show monotonous calculations (remember back in the day when you to include the actual calculations for percent yield? yeah…), and trying to “discuss” painfully straightforward reactions.  Full papers just feel right, putting the skill sets developed from lab reports to practical and purposeful work.

On the opposite end of things, actually writing the papers was a gruelingly tedious endeavor. I had thought I kept pretty good notebooks, and don’t get me wrong, I had all the necessary information when it came to writing, but I could have organized things a little better. Multiple iterations of the same step got pretty confusing, pretty fast, and I’m going to have to develop/adopt a much better means of databasing intermediates, reaction steps, etc etc. Also, when it came time to input data/crunch numbers, fuckall, especially for the library synth. For the parallel synth, I input the raw data into an excel spreadsheet, and did the calculations that way. However, I need to bone up on my word-excel tips and tricks, because manually transferring all the data into word was a major pain.

Back in the day, our orgo II professor was testing out the use of electronic notebooks in the academic lab. Then, it seemed highly unnecessary – the user interface isn’t intuitive, we don’t need results from single experiments beyond the week that we do them, and the chemical library is limited enough that it’s usually just faster to do everything in a pen/paper notebook anyway. However, for lengthy projects, I’m beginning to see the benefits of it, and am seriously considering what stage of my project I’d like to be inconvenienced.

Ultimately, for even a single semester’s worth of struggle and success, compiling everything into a single polished entity was, and still is, incredibly rewarding. If this is the kind of “runners high” and agony/elation one gets from thesis writing (and eventually finishing the damn thing), count me in! I live for this kind of suck.

With respect to the chemistry community at large (and mostly, as comment/response to excimers latest post on CBC), the year as a whole did suck a bit. The economy is shit, H1N1 will kill us all, and I firmly believe that western civilization is headed for some kind of zombie apocalypse. Oh yeah, and a fair share of scientific skulduggery went down, too.

But, maybe we’re looking at the suck-age in the wrong light… Unfortunately, the amount of lies, falsifications, hoaxes, and half-truths, is highly open to speculation. Maybe the amount is increasing or decreasing over time, staying constant, or dependent upon phases of the moon, tides, and rate/magnitude of recent celebrity deaths. Maybe it’s straight up random….

At the end of the day (year), it’s a shame that any kind of ‘bad science’ happens in the first place, and it’s a damn shame that it does make its way into good/reputable journals from time to time;  because there’s no way gauge the amount of bad science that goes unchallenged compared to bad science that gets what it deserves, it’s an overall triumph that bad science got called out, period. At least, that’s the approach I’m taking…

So happy holidays. Eat, drink, enjoy friends and family, and be merry while your at it, even if its for all the wrong reasons (like chemistry). Hell, maybe even get a gift for your biologist friend acquaintance. To balance out the starry eyed nature of this post, I might have something delightfully cynical coming up soon. But maybe I’ll save that for early January when everyone starts dropping their new years resolutions…

[1] Sorry the .gif looks a little grody. Even the tried and true Tot. Syn method produced weird lookin’ results… Just give it a click, I promise it looks better. At least, a little better.


Under the weather

December 14, 2009

As part of the “mission statement” of this blog, one of the top rules/ideologies is definitely “don’t blog about how I haven’t blogged.” However, for now, I’ll bend that rule, as it’s partially chemistry related. And, well, I do like keeping things somewhat fresh around here.

Aside from the fact that it’s the end of the semester and shit needs to get done, I’ve also managed to come down with a nasty cold/flu that’s been haunting me for the better part of a week. Although I’ve had no lasting fever or seriously serious symptoms, I’ve had some seriously annoying ones, and they’ve brought their A-game.

I’ve had a very constant headache, my nose is either overly runny, or overly dry, I’ve been super tired, and the urge to sneeze is unrelenting. It’s not fun…

Additionally, since I’ve been sick, I haven’t made it to a proper pharmacy during normal business hours, and stores on campus don’t stock anything that contains the good stuff… The replacement, phenylephrine, is in served up in lower doses, and apparently suffers from reduced bioavailability, and limited overall effectiveness¹, at least, compared to its pseudoephedrine predecessor. Rabble rabble rabble, I’m sick and grumpy, rabble rabble.

Real posts are on the way soon, though.

[1]Here‘s the actual article if you’re interested.