Born to Pun

Opinions vary, but I really enjoy the wordplay from ACIE. Regardless of how lame the puns are, they’re at least trying, occasionally they make me smile a bit, and truth be told, I’ve checked out a papers before based solely on the quality and cleverness of the pun.

But then this popped up in my RSS reader… for shame. And right on the heels of the some of their best work, too…

Don’t Look Directly At It

Yesterday was round one of P-Chem lab. I have nothing to report other than pictures of glowing green amazingness. If you’re curious, these are from Raman spectroscopy of liquids.

Here’s our old-school Raman spectrometer. What it lacks in brute force and technological advancement, it makes up for in charm and sheer awesomeness: particularly, the key operated master laser switch. I was hoping that a large red button with flip cover would appear after the key was turned, but that’s only a feature on newer models…

And here’s the other end of the thing.

A normal liquid sample. This one is carbon tetrachloride, I believe.

More impressively, this was spectra collection of liquid nitrogen.

Closer.

Even closer, with the lights off.

In conclusion, lasers are cool, as is liquid nitrogen.

Extraordinary Measures

The ladyfriend and I went to go see the movie Extraordinary Measures this weekend. Considering she’s a film major, and chemistry’s my bag, it was an obvious match up on our to-do lists, and allowed us both to thoroughly geek out over the finer details regarding our craft. Furthermore, considering many of the reviews I’ve seen of the movie ragged on it for being too technical, I’d like to take the time to review the movie as a scientist, for other scientists.

To get everyone up to speed, and without ruining anything, the (based on a true story) movie focuses on John and Aileen Crowley’s (Brendan Frasier and Keri Russel) search for a cure for Pompe Disease, which afflicts two of their young children. They team up with researcher John Stonehill (Harrison Ford), start a biotech company, and against all odds, hop on the fast-track to saving some little kids. Considering the movie is based on a true story, I wouldn’t say the plot is a big secret or anything. However, if you’re going to be all scientific about it and see it without preconceived notions, then you might want to stop here. If you’re curious and don’t mind a few minor factual spoilers, read on!

Hot Sweet Isoquinolinones!

I’m shifting gears this semester, and now it looks like I’ll be cooking up a library of isoquinolinones. Something along the lines of these bad-lads: 

Not exactly the kind of hardcore total synthesis I was looking for, but the steps for this are looking a little more appetizing. Purification is looking stupid-easy, and it’s projected that the only columns that will be necessary will be for the purification of final product. (On the bright side, I’m sure most total synthesis projects around here would be column heavy and rather draining) And if that doesn’t make you giddy with excitement (or at least jealous), then maybe this will: considering I’m just cooking up a library of these things, I’ll most likely get to use an automated prep-HPLC system to take care of the dirty work!

I’m overjoyed.

Welcome to the Future!

Happy 2010, everybody! Everything’s new and exciting and, well, ok: pretty much same. But it’s nice to try to think of it like it’s new and shiny!

Anyway, finally – back at school where I belong! Being home for a month was… odd. On the one hand, the break from science was extremely necessary, however the whole month was a little overkill; toward the end I was getting a little antsy to get back to a lab. Furthermore, the southside/suburbs of Chicago are, in my opinion, an pit of intellectual despair*. So being anywhere where I can thoroughly geek out over stuff is incredibly comforting. And finally, the Midwest just doesn’t understand tasty beer.

So, now that it’s 2010, maybe some chemistry related resolutions are in order:

• learn more about cross-coupling reactions: despite the enthralling synthesis class last semester, we didn’t even scratch the surface of cross-coupling reactions. And when it comes to making stuff, I’ve heard they’re kinda important…
• get into some serious synthesis: I mentioned before that the library synthesis wasn’t exactly doing it for me, but was starting to grow on me. Well, if I’m lucky I may get to have the best of both worlds: continuing work on the library project, and maybe picking up a more complex molecule synthesis or fragment of a total synthesis! Depending on an upcoming meeting/discussion with my adviser, this might be possible. So I’ve got my fingers crossed.
• learn to cook: I know, I can “do chemistry”, but I can’t cook? What kind of chemist does that make me? Well, I’ll tell ya, the phrase “medium-high heat”: totally not quantitative. Certainly not journal-worthy¹. But truth be told, I could stand to learn a bit more about cooking. And considering how much I love food, particularly the delicious and gourmet, it’d be a worthwhile investment. Now, time to get some proper gear to outfit my otherwise spartan kitchen… and one of those wall-knife-magnet things. They’re so cool.

  and finally

• post more! yeah yeah, typical blog resolution. But, I will not rest until I’m posting with the diligence and impact of Derek Lowe. Or, until they develop a blogging platform that will transcribe my ongoing chemical-based stream of consciousness. Both would be acceptably awesome.

To a happy, healthy, and productive 2010.

*A bit harsh, I know, but that’s just my opinion. Although I’m not stoked about the southside, I fell in love with the city as a whole again while being home. If you’re from the Chicago area and want to wax poetic about neighborhoods of the city, discuss real deep dish pizza, or argue about Sox vs. Cubs, let me know.

[1] Ok, maybe Tet. Lett…²

[2] I’ll be here all week. Don’t forget to tip your waitresses.

Efficient enantioselective transformation of lemons to lemonade: a reflection

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

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.

ANTC

Finally! Back home where I have a wifi connection… Thanksgiving with the ladyfriend was lovely, except her grandparents house did not have wireless. It’s weird how a (broadband) internet connection is a completely integral part of modern day computing. It’s a brave new world we’re living in… Anyway, hope you had a lovely Thanksgiving, too. If you don’t live in the US and don’t do the whole Thanksgiving thing,well, I hope you had a lovely November 26th.

Regardless, Thanksgiving in suburbia, and away from the internet led to a fair amount of TV watching, which in turn, led to this. Because we have reality shows for Ev-ry-thi-ng, and I have yet to see the idea elsewhere, I call dibs on the idea: Chemistry Reality Show. America’s Next Top Chemist? Iron Chemist? Real Chemists of Boston/Chicago/Berkeley/San Diego/etc? Whatever you call it, I’m sure it will eventually make its way to the airwaves, and when it does, I expect royalty checks to start rolling in.

There’d be the obligatory challenges: the severly time limited challenge, best use of a reagent challenge, the limited equipment challenge, discipline specific challenges, chromatograpy deul. Historical challenges – recreating classic experiments with classic reagents/apparatus. It’d be great! Kyle Finchsigmate and Dylan Stiles would totally be called in to guest judge.

And if that doesn’t wet your whistle, I’m also proposing MTV: Labs. Similar to Cribs, a member of the lab would welcome the camera at the door, give the full tour, include a little bit of product placement and mandatory “inside the fridge” shot (maybe inside the hood?), show off any ghetto-fabulous or fabulously ghetto equipment and instruments, and finally kick the camera crew out when the tour is over. If you and any co-workers are the right kind of geeky, and have a little spare time and a video camera, I invite you to give it a try, and to post your results!

Feel Good Hit of the Summer

Remember that song by Queens of the Stone Age? You know… the one that goes “nicotine, Valium, Vicodin, marijuana, ecstasy, and alcohol. c-c-c-c-c-cocaine.”

Man, that song takes me back. No, there was never a time when I was a totally drug addled mess, it just reminds me of when I first heard the album “Rated R” by them. Also, it gives me a lovely idea for a series of posts… Why? Because everybody likes learning about drugs! So, I’ll be detailing some of the unique chemistry/science behind the drugs, and perhaps any experiences I’m willing to share…

For starters, we have nicotine: a stimulant naturally produced in the nightshade family of plants! Right off the bat, we can see that there’s a single chiral center. This naturally occurring S-enantiomer is responsible for all of the physiological effects associated with nicotine. But, if for whatever you ingest a genetic oddball plant or a synthetic racemate, don’t worry, because the R-enantiomer is still biologically active, but only about half as potent.

If you’re getting your fix from nicotine, you’re most likely getting it by smoking tobacco, but there are a few alternatives: dip, snuff, snus, or chewing tobacco. All of which are inherently gross, albeit enjoyable, because ultimately, all of these routes of ingestion can lead to some form of cancer. It’s not the nicotine that’s the problem, but it’s the other carcinogens present in tobacco and tobacco smoke that’ll do you in. Considering that smoking is the most common method of nicotine ingestion, this is doubly upsetting due to the inefficient nicotine delivery method of smoking.

The flashpoint of nicotine is a low 95 C, and the point of autoignition is right around the point of vaporization^1,2. So, if you smoke, you actually ingest much less nicotine than is present in the leaves. Therefore, you’re also ingesting more combusted plant material, naturally occurring carcinogens, etc, than optimal. I don’t mind that people smoke, but I’m dumbfounded that we haven’t developed a more efficient method of nicotine intake, that would still pair well with reading a newspaper, drinking coffee, or going out to a bar/party.

Once nicotine is ingested, it’s carried through the bloodstream to the brain, zips through the blood-brain barrier, and gets to work as an acetylcholine receptor agonist³, which boosts the levels of a few neurotransmitters, including dopamine, serotonin, and norepinephrine, resulting in that “nicotine buzz.” In addition, tobacco leaves contain a few natural monoamine oxidase inhibitors⁴ (MAOIs). MAOs do a whole bunch in your body, in particular, they can metabolize certain neurotransmitters such as (surprise, surprise…) dopamine, norepinephrine, and serotonin. In addition to helping you keep that nicotine buzz going a bit longer, whatever evolutionary advantage the nightshade family gained by producing nicotine or other metabolites, it also developed a method to increase certain metabolites’ effectiveness in mammals! Call it evolution, call it ‘design’, call it whatever, but it’s brilliant engineering of some kind, and I think that’s pretty fucking cool.

With regard to more recent developments in nicotine enjoyments, there’s menthol. It will give your cigarettes or dip a minty refreshingness, and will also prolong the time it takes for your body to metabolize nicotine to cotinine.⁵ Cool, right? (No pun intended…) However, the cooling sensation apparently makes it easier to smoke more with each drag, and ingest more nicotine, thus eventually making it harder to quit.⁶ I’m going to posit that the combination of more nicotine and a longer half-life isn’t exactly helping the addiction situation, either. Also, maybe some of you have heard that if you smoke menthol cigarettes, the menthol will “crystallize your lungs”? I’ve so far been unable to find any definite scientific data regarding it, but according to the most legit source I found, it’s all just a myth. And a hokey one at that…

Once you’ve had your way with nicotine, cytochrome p450 enzymes get to work metabolizing it into cotinine, and a bunch of other goodies:⁷

Next up on the hit-list (pun intended), Valium!

Because it’s not chemistry, supporting anecdotes info is included below, along with references.

Scheme Early, Scheme Often

The upcoming ACS conference is just over a mere 4 months away! Who’s excited?!

OK, It’s a little early to be geeking out over the conference, seeing as how it hasn’t even been that long since the last conference. Nevertheless, I’ve begun to think about it. Particularly, seeing as how I’d love to attend. Seems normal in the “chemistry rights of passage”:

1. Start research
2. Start a blog
3. Go to conference, and report on conference
4. Get published
5. Become professor
6. Become world famous chemist
7. Become some sort of superhero/james bond type figure, with your science-side as your regular identity, and your “super powers” drawing heavily from your scientific background, not unlike Tony Stark/Iron Man…

Well, clearly the error compounds a little with each step, but generally, that’s my plan.

Anyway, I was wondering, what is the protocol (if any) for asking a PI to fund an odyssey to a conference? I’ve seen plenty of conference reports ’round the blogosphere, but most (if any?) don’t mention how the trip was acquired in the first place. Ideally, your professor will offer you an all-expenses-paid vacation from chemistry to chemistry, but then again, ideally your yields will always be better than or equal to those published, and your ΔRfs will always be >1. If you’re an undergrad and happen to live in the conference city, then maybe conference attendance won’t break the bank, but if you’re further up the food chain, or farther away from the city, the combined costs of attendance, travel, and lodging start to add up.

What with the economy, these days, and, well… ever: if you’re a student, there’s a fair chance you’re dirt poor. If you’re not a student, judging by the Registration Rates, it looks like the ACS thinks you’re going to get a hand, anyway. So, any funding one can squeeze out of their respective institution, the better. But how? Furthermore, if you’re like me (undergrad scum), or perhaps a fresh grad student, you probably don’t have the chops for your PI to straight up offer to send you, but you still want to go. Is there a diplomatic way to ask to go, or will you invariably look like a n00b¹.

Of course, for myself, the likelihood that I’ll make it all the way to SF looks slim to nil. Truth be told, it’s probably not “worth it” to send me off to such a conference armed with little more than a youthful exuberance for chemistry, and I certainly don’t have the bankroll to fund the entire trip myself… but, at the same time, if I could possibly manage to swing such an endeavor from my university, I’m sure as shit going to take the opportunity! Also, if I can manage to score a freebie Fisher “Caffeine Mug,” that would make the entire cost of attendance totally worth it! (So what if they can be purchased for sub $3 at the ThermoFisher gift shop! While all swag is free, “earning” such a mug by finagling it from the Fisher people would be priceless.)

[1] Completely unrelated, but bravo for a masterfully comprehensive account of a “noob.” If there were an award for best user-generated knowledge articles (wiki, urbandictionary, etc), this guy might take the cake.