ANTC

November 30, 2009

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

November 23, 2009

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 vaporization1,2. 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. Read the rest of this entry »


Scheme Early, Scheme Often

November 18, 2009

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.


The Little Rotovap That Could, But Probably Shouldn’t

November 17, 2009

I suppose the category “In the Lab” is slightly inappropriate. This isn’t from either the labs I’m associated with (research or teaching), merely the lab two friends of mine work in. But I don’t have an “In a Lab” category, nor do I particularly wish to incorporate one, so… deal with it. Semantics aside:

This is ‘ol vappy. At least, that’s what I named it. I think it might be one of the saddest rotovaps around.

'Ol Vappy

It’s the resident of one of the labs here, a lab that is unfortunately strapped for cash. I can’t say how old it is, but I can say for sure that it is, indeed, old. Let’s have a closer look at the little guy…

Jack-Stand

Here is what supports the whole beast. Once upon a time, before the advent of the fancy motorized rotovap, they apparently supported and adjusted the positioning with these things. With respect to ‘ol vappy, this stand doesn’t work. I mean, it works, in that it does support the damn thing, but it is no longer adjustable. I was instructed to not even attempt to adjust the base, lest the universe collapse upon itself.

Over the Shoulder

Here we can also see that there is no attached water bath. Instead, an oil bath atop a rather dubious looking hotplate/stirrer has been substituted. For some reason, it has a superfluous septa attached – reasons nobody could explain to me, yet everyone suggested I leave on, just in case… Furthermore, there is no knob, so you have to utilize that awkward “nipple-pinch” technique to turn it on or off.

Dubious Indeed

Speaking of dubious hotplates, this one has even been maimed by some reaction or scalding oil spill…

It’s apparent that he’s been physically abused by his current owners, and is in need of a new, loving home. If you wish to adopt or sponsor ‘ol vappy, please let me know.

Kidding aside, I don’t know how to feel about this. On one hand, it’s unfortunate that this thing is fairly decrepit, and should have been put out to pasture by now¹. Doubly so that there are research labs anywhere that don’t have the cash to upgrade when necessary. However, on the other hand, it’s very “triumph of the human spirit” that the damn thing (barely) works at all….

[1] Speaking of “out to pasture,” I’ve seen where rotovaps go when they die! While walking to the NMR one day, I spotted a door in the basement I’d rarely seen open. In front of the door was a cart filled with half-dismantled rotovaps, and when I peered in as I walked by, I saw walls filled with all kinds of used/broken/half taken apart rotovap pieces, and other mangled labware. Tending to this room was a very Doc Brown looking fellow who was sitting at the workbench inside. The whole experience was very surreal, and if I didn’t have NMRs to run, I would have asked to play/tinker with things and perhaps attempt to come up with some sort of Rotovapenstein. (Rotofrankenvator? Rotovrankenstein? Semantics….)


Try, try again. And again. And again. And again…

November 16, 2009

Well, my project for my synthesis class is, apparently, hopelessly doomed. My compatriots and I working on the chiral auxiliary project have hit the same wall as students last year did (confirmed by our TA), the attachment and removal of the auxiliary. I coincidentally happen to be up to my eyeballs in pseudoephedrine, which, (for any over eager readers) is not as fun as it sounds: rather than reduce the stuff and sell it on the streets, it’s already been earmarked (condemned) to reactions with propionic anhydride. That reaction’s just fine, but it’s the propionamide’s fate in the Sysiphus-like auxiliary attachment/detachment that’s causing problems…

Anyway, apparently the conditions achievable through our methods are simply not stringent enough for the reaction to work in an efficient and repeatable manner. Therefore, given that there’s no clear end in sight and we’ll never get off this stupid island so there’s no use trying, lab periods have become less and less about the destination, and more and more about trying to forge new paths to get there. None of them have worked so far, but it’s all about the learning experience, right?

Now, everything’s kind of turned into a contest for “style points” and lab is less of a “lab” period, and more a “chemistry jam session.” Who has the best ghetto-rigged solutions for specific apparatus? Who has the best looking columns/best way of “automating” a manual column? Who’s got the prettiest lookin’ NMRs and best tricks to get it that way?¹ For the steps that we’ve obtained good (‘publishable’ for final paper) results, we’ve begun to divide and conquer epic scale-ups so that we can have ammunition readily available to conquer the next step.

For the latest step, and/or extra steps, we’re starting to try new methods – not necessarily to get results, more to get exposed to new techniques. A little while back I spent the better part of a lab period attempting to vacuum distill the propionic anhydride to hopefully boost the yields on the pseudoephedrine reaction. It was completely unnecessary within the scope of the project, but still worth a shot. Did it work? Nope. At some point during each attempt, a disgusting bump occurred, shooting impure garbage (and disgusting, blackened phosphorous pentoxide drying agent) through the short-path, causing an epic re-start. Worse than that, the yields went up and matched published yields as soon as I scaled up the reaction, anyway. But it’s cool – I wouldn’t have encountered a vacuum distillation otherwise during the course. And, aside from using iffy drying agents that turn my solution weird colors, I’m pretty confident I could properly pull off a proper vacuum distillation on my own, without having to look up a procedure of any sort. (So, it’s not rocket science, but for extra pure stuff, I would have had no idea to flame dry the glassware.) While the grizzled/jaded vets out there can attest, its nothing to throw a party about, I still think it’s pretty cool that I picked up something that nobody else has really encountered in lab yet, and even if peers are doing actual research, depending on the research environment, it’s still something they might not come across for a while.

Ultimately, I’m not blazing any trails that fellow chemists haven’t been walking for some time now. However, it feels amazing to ‘play’/explore, something that’s not really encouraged in the research lab, and something that teaching labs haven’t let us do so far.

Perhaps you’re not a chemist, or if you are, maybe you’ve lost the feeling of when something like running a vacuum distillation was fun, new, or exciting. So, best I can liken the overall experience to is taking a vacation to a city you don’t know, and learning how to navigate it while you’re there. At first, you probably know where your hotel is, and little else. You start to explore, learn where a few major streets are, and start to forge deeper and deeper into uncharted (to you) territory. Wrong turns aren’t necessarily bad; they’re usually fun, and still give you insight to the city that you previously didn’t have. Depending on the layout of the city, and if you’re good/lucky, you might even start to navigate instinctively, based on where things should naturally be with respect to your mental ‘working model’ of the city. It’s like that.

That doesn’t sound like a vacation to you? Then you’re just no fun…

[1]Speaking of NMR tricks, I shared the No-D NMR technique, and got looks of “your crazy… so crazy it just might work.” Thus far, we haven’t needed to titrate butyllithium, but I think I might, just to blow their minds.


Signs from a higher power.

November 15, 2009

And that power is Google.

About halfway through last week, my TI-89 went on the fritz¹, so instead of doing quick lab calculations on my 89, I’ve been using Google. Yep, that’s right. If you didn’t know, you can input plenty of mathematical operations into the Google search bar, and it’ll spit out an answer. In addition to the math calculation, it’ll also spit out whatever it interprets as it’s actual search.

So, when mindlessly inputting values to determine masses in my scintillation vials (and because years of advanced math courses have robbed me of basic math skills), such as “13.0946-13.0266″, google will interpret it as math, but also as coordinates on the earth. And, given the quantities of stuff I’ve been working with lately, and the mass of the empty scintillation vials, I keep getting coordinate hits in Senegal, which is close enough to Dakar.

This got me to thinking. I’m totally using lab data/google hits to plan some kind of epic vacation/geohashing. Maybe I’m not going to Dakar just yet, but as soon I get a hit for Hawaii, I’m taking it as a very strong sign from a higher power that I’ll need to take a pilgrimage to Hawaii. Or, if down the line I ever freak out and have some sort of mid-grad-school-life-crisis, I’m taking this as a sign to enter the Dakar Rally. (Although as of now, it no longer goes to Dakar) If ever I straight up drop chemistry, or need to take an immediate and unexpected break from it, the Dakar would be a TOTALLY bad-ass way of doing so.

So, next time you happen to punch in a quick calculation to google, keep an eye out for any “hidden message.” You never know where it may lead you, or your procrastination…

PS, for those keeping score at home: stop it, that’s kinda weird. But if you’re interested, definitely keep an eye out during the coming week. I’ve been slaving away over a hot keyboard the past few days and have a few fresh posts raring to go. One of which is relatively serious and heartfelt, and I hope you’ll fully appreciate. The other two, well, less so, but I hope you enjoy them for what they are.

[1] All better now! And I learned how to force a reset if a program freezes, or you give it a calculation that takes WAY too long…


Scientific Accuracy

November 12, 2009

I’m going to hazard a guess that the things I lay awake and think about at night are far different than whatever keeps you up at night.

Take, for example, the new Jameson Whiskey commercial…

I suppose, in a world where a man can dive in after his beloved cargo, fend off a giant octopus, weather a storm, and make it to shore, then anything goes, but what I’m really curious about: would a barrel of whiskey even sink?

Whiskey is marginally lighter than water¹, and most woods seem to be lighter than water², so I suppose it would come down to the amount of cast iron used to bind the barrel together…

Granted, for 99.99%³ of people, you’re drinking whiskey because you enjoy the smooth, mellow taste, or because it gets you drunk. Or both. But, damnit, I’m a proud member of that .01% that also enjoys a stiff glass of fact-checking with their drink, too. I also enjoy drinks that pour shots for you. Seriously, so helpful.

Good to know that if chemistry doesn’t work out, I can apply to be a Mythbusters intern.

[1] I <3 WolframAlpha

[2] Wood Facts While less definitive than WolframAlpha, and considering I’m no expert on the deciduous trees of Ireland, the wood choice might play a considerable difference. However, I’m going to assume they weren’t using fine hardwoods for barrel construction, either…

[3] Stat’s are approximate. However, if you can give me any other reasons to drink whiskey, please let me know. I’ll write a thesis on it….


A salt and battery

November 10, 2009

Apparently sand in my lab is a treasured commodity, to be traded equally with ground unicorn horn, so instead of topping our columns off with sand, we’ve been known to use sodium sulfate, instead, usually with no problems…

Today, however, as I sprinkled sodium sulfate onto the top of my column, a little chunk of congealed sodium sulfate made its way down, and embedded itself deep below the delicate line of silica, requiring me to repack my column, and mucking up my otherwise well oiled machine of column –> quick snack –> math discussion –> back to the lab…

Watch it, sodium sulfate! I’m putting you on notice. [1] Falter with me again, and you will rue the day.

PS, A belated “Happy No-Shave November” to all. I’m disgusting, how are you?

[1]

OnNotice


It’s quiet. Too quiet…

November 7, 2009

Normally, my synthesis class is pretty great. 8 hours of lab a week, Wednesday and Friday, 5-9 pm. The Friday session usually isn’t as grueling as you’d think. As I’ve said before, I don’t mind late hours in lab, and as for any Friday night festivities, 9pm is still early enough to not miss anything good. Given that its the late session, and it includes a Friday night, most people stray from it, and it’s a much less hectic lab experience than the other options. Usually makes for a good time…

Last night, however, was by far the most draining lab experience ever, as there was NOBODY there. Of the 2 people I really talk to in lab, one guy was out sick, one girl left after about 40 minutes into the lab period (she didn’t really feel like being there last night, and she was on the cusp of having finished all her previous work, but not having enough time to successfully start the next step, so I don’t blame her.) Of everyone else in the lab, there’s the two Asians who only really talk to each other, and my TA. My TA is good for casual conversation, but that’s not always logistically possible if he’s taking care of things on the opposite side of lab.

After 3 hours of listening to nothing but the low rumble of the fume hoods I wanted to gouge my eyes out, and considered personally testing my products for biological activity. I thoroughly sympathize with any readers who have non-talkative labmates AND can’t even listen to music. Perhaps we can form a support group? If you do happen to work in an environment with NO sound, please tell me if/how you’ve avoided complete insanity. Thanks.

In related news, last night marked a lovely milestone for me: using ALL of the product from my latest step for a carbon NMR in a decently timely manner. The sample still had to be submitted in the night queue, so now the fate of my project rests in spinner 45 of the autosampler. I’ve held a vigil to honor the NMR gods, praying that the sample runs as expected, the tube doesn’t crack in the machine, and the autosampler spinners aren’t randomly cleaned out. I’m also pouring a bottle of CDCl3 in the waste container for my samples that couldn’t be here, just in case.

 


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