November 30, 2010

Now for the fun, happy, excited post! Over Thanksgiving break, I received a cryptic email from my PI, saying he needed contact info for a patent on the project I was working on. Any news of this had been previously unbeknown to me. So I emailed him my info, and then quickly emailed my grad student. “Hey, this sounds pretty legit. What’s the deal?”

On Thanksgiving day, I got a response back from him saying I’d be listed as second author on one paper, sixth author on another (at that point, do you even still bother counting? Anyway, it was a major collaboration amongst a few institutions, with about 10 names on the paper.) and that I’d also be listed on the patent for work relating to one of them. As far as I know, they’re drafted and pretty much ready for submission.

I’ve pretty much been grinning ear to ear ever since.


it’s not me, it’s you.

November 18, 2010

Alfa Aesar, we need to talk. You haven’t been giving me what I need, so I think it’s time I found somebody else.

My carbon tetrabromide stock fell low, and that’s when you fell into my life. Drawn to you by your fair prices, and impressed by your quick shipping, I would never have thought you to be such a source of aggravation later on.

Two steps after using the carbon tetrabromide, I ran into issues. Reactions not reacting how they should. At first, I thought it was me: impure products, glassware not dried thoroughly enough, bad luck. Back tracking through the reactions, I still couldn’t find the source of the problem, not even thinking about the CBr4, because “Oh, it’s new, it should be fine.” It was not.

The last thing I could have possibly checked in the reaction was your “fresh” CBr4. I… I should have told you before, but I got some from Aldrich instead. It was better. Turns out, your weird CBr4 gave me some kind of dimer. It went undiagnosed for a little bit, hence the cause of my frustration, but you might want to get that checked out. Yeah, so we’re like, over.

Corey-Fuchs-ing someone else
-Chiral Jones

Requiem for a Meme

November 16, 2010

Long, long, long overdue, but I’m finally getting around to that old “Favorite Lab Things” list. For those of you just joining us, the “favorite things” meme was, I believe, started by Chemjobber, and plenty of other chemistry blogs hopped on board. Although I’m quite late to the party, I’m generally quite late to just about everything so don’t take it personally. Here’s my thoughts on my top 10 favorite things in (around) lab.

  1. Clickable Sharpies: This one’s a no-brainer, but for labeling anything, these bad larrys are where it’s at. If you don’t have some, get some. Despite their utility, I think I’m the only one in my lab who swears by them. Apparently everyone else is still fumbling with caps…
  2. The 500 NMR: So nice. Unbelievably nice. Ridiculously nice. Even “crappy” results look good. Furthermore, otherwise “underconcentrated” samples come out with pretty decent resolution, and overconcentration is rarely an issue: I’ve been able to have enough material for a ~5-10 minute carbon, cued up a proton, and a carbon, and with no further parameter tweaking, I get nice looking spectra of each. I only hope to have the need to run a bunch of 2D spectra sometime soon, just to further abuse it’s power.
  3. Grooveshark: Imagine Pandora. Now, imagine Pandora, without the ads, without the limits on how many songs you can skip, and being able to play any song you want, when you want. Because that’s grooveshark. To be honest, the “radio” feature is way less in depth than Pandora’s (you’ll get pretty highly similar stuff, as opposed to the broader range/individual musical aspects that pandora uses to generate a radio station). However, the weak auto-radio aside, you can cue up a playlist to last all day, have the radio fill in the rest, and if you decide you don’t like a song, you never have to decide if it’s really worth it to skip it.
  4. Headphones: When at my desk, and listening to my beloved grooveshark, having headphones is key. That way I can listen to what ‘ere I please, without becoming an nuisance to the girl at the neighboring desk. Besides, she’s new, and I’d like her to think I’m as not weird as possible. My playlist of Lilly Allen, followed by Crystal Castles, followed by Wagner, followed by Manowar doesn’t really support that.
  5. The purple “Cobalt” brand gloves: Best gloves I’ve come across yet. They slide on and off of glove-liners with ease, and don’t get clammy. The exterior is nicely textured for extra grippyness. They don’t rip sometimes, immediately as you put them on. The deep bluish/purple looks totally cool. They’re no more resistant to solvent than normal gloves, but it seems that the quality control is just better over at Cobalt. Best part: they cost the same as the standard, light blue, cheapo quality nitrile gloves. Shame that we just ordered a whole bunch of the cheapie gloves – my own personal stash of cobalt gloves comes at the generosity of a friend whos lab stocks them…
  6. Glove liners: Also a no-brainer. Easily forgotten when they’re there, but quickly noticed when they’re not.
  7. Post It Notes: For the longest time, I didn’t really use post-it notes, up until about two weeks ago. I honestly don’t know what took me so long. They’re nifty and not surprisingly, pretty useful.
  8. Beer.
  9. The burrito place next door: it’s so good, and it’s open til 8. Keeps me fed and happy for hours. Also every 10th burrito is free.
  10. Antics: Chemistry is all well and good, but a lab with zero personality would suck pretty hard. Labmates who are helpful and intelligent are nice. Labmates who are helpful, intelligent, and willing to play dry ice baseball from time to time are nicer. If you find you rarely take part in antics to any extent, you’re probably one of those soul-less people that would make lab suck if it weren’t for such antics. Or, maybe you’re in industry, where I’m sure dry ice baseball is more heavily frowned upon…

honorable mention: Hood-mounted speakers. I haven’t put this into practice, but two labmates have put computer speakers inside their hoods. Seems like a good enough idea, and cheap speakers are easy enough to come by, and disposable enough (there’s probably a pair kicking around your department right now in one of those piles of discarded computer parts)Only definite downside: finding an appropriate music player that I wouldn’t mind leaving in lab/touching with gloved hands…

Maypril Fools!

May 14, 2010

Well, it’s been a while. The past month or so has been an endless blur of school work, lab work, overnights in lab, and thoroughly enjoying being 21.¹ There’s also been a little mischief:

If you’re familiar with the show The Office, you might know of the incident where Dwight’s stuff winds up in jello. Well I, along with a partner in crime, got a chemist friend of ours rather good with a very similar endeavor. Although putting someone’s stuff in jello may be a little passe, the details make it stellar. Well, to a chemist anyway.

The setup: get our friend to think we encased two of his most recent products/intermediates (yellow oil in scintillation vial, and black gook in microwave tube) in jelloy-goodness. However, the danger of catastrophic-jello-leakage was very real, so we pulled a bait and switch, hiding the real products, and replacing them with innocuous stand-ins.

The oil was duplicated with some friend’s product he no longer needed, diluted with DCM to similar appearance.

The microwave tube was my specialty, black gook duplicated by scorching some sugar in a microwave tube.

Both fakes were capped and labeled similarly to the originals, plunked into a beaker with lime green jello, a watch glass to keep everything submerged, and a stirbar for flair.

When all was said and done, everyone kept good spirits, but the victim still insisted he NMR both the real samples, and the fakes; they were that convincing. Of course, my camera was dead the night this was perpetrated, so there are no pics of the results or real/fake comparison pictures, but trust in that it was flawless, as it was hilarious. If you’re still doubtful, you’re cordially invited to try this yourself. (If you bait and switch, it is virtually harmless, after all…)

In other news, the manual 300 has a basic set of instructions next to it, with some very simple rules. Frankly, this was just aching to be done:

Clearly, the next step in project mayhem is to duplicate the instructions word for word, and print that final rule right on the card itself. Oh, and to start the rumor that “snot” is an acceptable NMR solvent alternative to DMSO…

Happy Friday.

[1a] Yeah, I’m running characterization data for a library of compounds, which included running carbon NMRs on everything. Based on the amount of sample I had, I was looking at about 30 min NMR each on the 500. Based on NMR availability and practicality, I chose to bang out the whole lot over the course of two 12 hour overnight timeslots. Yeah, I’m a beast.

[1b] I’m 21! My birthday was April 22 (also, Earth Day), and I’ve since been feeling all too good about slowly going broke. When ACS Boston rolls around, I’ll gladly share a pint with anyone willing. Currently digging: Harpoon UFO Pale Ale

Condenser Party

March 10, 2010

Finally, my laptop and usb cable are in the same place at the same time! Here’s the circus that took place in my hood last week…

To anyone who says that there are no pretty colors in organic chemistry, may I present Figure 1:

Figure 1

Yeah, it’s not exactly the dramatic colors of inorganic chemistry, or even the occasional organic reaction¹, but it’s still magical in its own way. Right? Right…?

For the record, that’s 4 condensers, water lines all hooked up in series, and for most of that glassware, flame-drying was involved. And of course, a fun colored balloon for each. Although getting the entire contraption setup was a highly tedious process, dismantling/purifying everything went like clockwork. Now then, readers, the ball is in your court. If you have stories, or pictures of more ridiculousness, more glassware, even more clamps, and a 5 year old’s birthday party worth of balloons, share them.

1) Bee Tee Dubs, the absolute COOLEST colored reaction I’ve seen was  also last week from my hoodmate: He’s dealing with a slightly large, fairly conjugated molecule (probable chromophore?), and in fact, he’s shooting for a dimer. I’d assume a series of polymers were also generated, because when he ran a column on the stuff, it separated into a rainbow of day-glow colors, and ultimately yielded an absolutely beautiful, vibrant purple solution. Suck on that, inorganic chemistry! I didn’t have a camera that day, but if I ever see that reaction again, I will stop at nothing to get some pictures of it…


March 8, 2010

If you’re going to be a scientist, and you don’t have a Rain Man-like memory, you’re going to have to take notes on what you’re doing from time to time. From here, you’re probably going to fall into one of two camps: pen and paper based lab notebooks, or some kind of electronic lab notebook (ELN). (If there are any other way’s of recording your experiments, I’d love to hear them! Giant Post-It Pads?)

I have an idea that could relatively easily bridge the gap between the two methods. To just check that out, feel free to skip to the end, as this is a fairly lengthy post. If you want to hear a full breakdown, read on.

They have their pros and cons:

For pen and paper based, it’s about as simple as you can get. There’s never any user interface issues, and you can format/enter your data any which way you like. Furthermore, a physical notebook is much safer to handle around chemicals than any electronic counterpart.

However, when it comes to the “brute force” required to manage a physical notebook, it’s evident why people choose to jump ship. There’s a ton of transcribing very similar data back and forth: schemes, reactant tables, and procedures, especially when you have to go back and re-make starting materials. Furthermore, anytime you need to find physical data for a compound, you’ll need to look it up, maybe from an electronic source to begin with. When you do get that data, you’re going to have to get your calculator and quickly punch out masses, millimoles, equivalents, etc. And finally, when you’re all done with your research, you’re going to have to transcribe the whole mess into a digital format. (Unless you want to wrestle with a scanning utility that will scan written work into text, but that’s a whole new can of worms right there)…

For electronic notebooks, there’s the expected equal and opposite tradeoff. From the beginning, all of your work is ready drop into the experimental section of your publication/report/etc (maybe bar some formatting). An ELN is pretty snazzy because you’ll no longer need to whip out your calculator for quick stoichiometric calculations, and most programs offer the ability to save your newly synthesized compounds and their properties, so subsequent experimentals are that much easier! And, of course, you can copy/paste/etc reactions, so rather than write up a completely new notebook page for some minor change, some hot copy-on-paste action, followed by a quick edit to make that change will save you plenty of effort and time in the long run.

With electronic systems, theres also the interface problem. Anytime you want to enter data, you have to stop what you’re doing, de-glove, and enter the data. (Maybe you have a dedicated lab computer, but my lappy comes with me everywhere, and I’d never touch her with a dirty, gloved hand, lest my keyboard get DCMed blank, or I start bringing trace nasty compounds home with me.) If you want anything non-text based, lik a sketch a TLC plate, with pen and paper, you can just sketch the damn thing to scale if you want, and calculate Rf values later if you need to. With an ELN, you either need to calculate Rf values on the spot and enter them as text, or deal with the god-forsaken TLC tool in chemdraw. Over time, you have to deal with potential program upgrades, file incompatibilities, even making the jump to different programs, or worse, hard-drive/server failure.

Although it does have it’s downsides, I’ve really begun to embrace the idea of the electronic notebook. Once you get past the learning curve and learn workarounds to bugs/features you don’t like, things run pretty smoothly. If you simply must have that analog feel in the heat of the moment, jotting down quick notes on the back of your glove or a regular sized post-it can suffice until you have an appreciable amount of data and wish to stop and drop it all into your ELN. Yet still, a surprising majority of my colleagues are still using pen/paper based notebooks…

****THE END****

Anyway, the new idea: Apple has the iPad coming out. (Already, I do know my iPhone can access my web-based ELN, but I’m not using that for in-lab work…)

The iPad is built off the same OS as the phone, and with it’s full size, touchy-feely screen, and hopefully awesome/intuitive Apple engineering, it could be a highly promising platform for ELN development: Want to type things up next to your hood? Sure, there’s no physical keys to get DCMed. Want to draw out a TLC plate or apparatus setup? Physically draw the sucker out! (Who knows, maybe Apple will add a built in camera in the future. Then you can just snap a picture of it!)

I’m a bit concerned about the construction of the iPad – one wrong solvent could eat the screen, or cause the whole thing to bite the dust. (And again, despite the similarity to the iPhone, I’m not volunteering mine to find out.) However, Apple does claim that the enclosures are glass and aluminum, both of which sound decently solvent-proof, which means you can probably use it without fear while gloved up. Furthermore, even if not outright solvent-proof, perhaps it could be retrofitted easily enough.

Bottom line?

As of right now, 500 bucks for a new lab toy seems a little unnecessary¹. All the same, it’s not necessarily the most practical now, but if it does work, it could open up the possibility for far more useful software in the future.

In the meantime, if anybody wants to send me any old, broken, or damaged iPhones or iPod Touches or whatever, I’ll gladly test their resistance to a wide variety of lab solvents/chemicals. Also, I’ll most definitely have to type up a full report and publish it here. If I’m picking up where his research left off, Dylan Styles will certainly be a primary reference. Furthermore, if anyone wants to send me a working iPad to test for their iPad-based ELN development, that would be equally appreciated. (Hopefully, this means you, Artus Labs! Please?)

1) Unless it’s a Kyle Finchsigmate approved MPLC pump

Don’t Look Directly At It

January 26, 2010

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.


Even closer, with the lights off.

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