I’ve been AFMing myself blind for the past three weeks or so, and now it’s time to tell you all about how to make the demon box do your bidding.  Instead of devoting a post to tweaking PID settings and finding the setpoint sweet spot, though, I’d rather put something up that you’ll actually read.  Time for group superstition?  You bet!

Feeding the AFM: a simple way to garner favor.  It is a little-known fact that you will get better images if you scan over lunch.  This may not be feasible in many labs…and, of course, it is not recommended to offer the instrument food directly.  Perhaps the instrument feels sorry for you not having a life because you have to babysit and make sure it doesn’t flake out.  It is unknown precisely why this works.

Spending late nights and weekends with your tappy little friend is also useful, but for other reasons: the building is usually quieter then, so there are fewer vibrations to worry about.  (Never mind the vibration isolation table or platform or whatever else you have there.)  And perhaps it is just happy to see you.  It gets lonely sometimes.  Be careful, though–if you are extremely tired, you are likely to break tips.

Serenading the instrument, however, is not recommended.  Singing Lady Gaga and playing the guitar can introduce artifacts to your scans.[1]  Perhaps the AFM just has no taste in music and is irritable.

If things are going terribly wrong, and you have tried all else, I recommend playing the following video while menacingly waving a blunt object:

Even if the AFM is unpersuaded by this apparent (and quite empty) threat, you will enjoy fantasizing about smashing it to bits.  If this last-ditch measure fails, go home.  Some days are just no good for scanning.

In all seriousness, though, the easiest thing you can do to get good images is to use good tips.  For tapping mode (all I can do for the time being, though I suspect this will change), Budget Sensors are well-loved by my group.  Vista Probes, on the other hand, are really only suitable for scanning probe virgins.  (Noobs will learn to tweak and tune and troubleshoot because they will have to do so about every other scan, and you won’t have to worry about them breaking your good tips.  It is possible to get decent images with these, but babysitting is definitely required as they can be quite flaky.)  More experienced users: any favorites?

[1] Not my doing: I lack these talents.  One of my labmates does these things very well, though.

  There’s a cool little paper in ACIE about making iodocarbonates from allylic and propargylic alcohols and iodine under CO₂ atmosphere, iodolactonization style. Well, I thought it was iodolactonization style, but they draw an actual iodine carbonate (IOCOR) as an intermediate, rather than an iodonium. Regardless of the mechanism, I think that any reaction that utilizes as reagents gases more commonly viewed as supplies is pretty cool.[1] Bent alkyne — NOT cool.

  I think you can even run it by simply throwing dry ice and iodine in a THF solution of your alcohol. Don’t worry about the oil, seems like you’ll need chromatography anyway. Simple reaction that provides nicely functionalized, differentially protected compounds. What caught my eye though was their emphasis on chemical fixation of carbon dioxide. Erm… Let’s do the math for scale up.

  We’ll need carbon dioxide (8.4 Gt, 190.9 Tmol — total emissions in 2006), tert-butyl hypochlorite (2 equiv), sodium iodide (57.3 Gt, 1 equiv), THF (1140 km³).
  See what I mean? How can one be serious about industrial scale chemical fixation of carbon dioxide? Even if it’s quicklime? What do you guys think about the whole atmospheric carbon issue?

  On a related carbon-based note, I read up on nanotubes.[2] More carbon-based than carbon dioxide, CNTs have made a quick appearance here at CBC before. Nowadays, it seems like we know how to produce them efficiently and selectively (single-walled over multi-walled, for instance). Here’s an incredibly cool picture from this Science article, which illustrates a striking process of transforming an unappealing black powder into a very unusual material.

[1] The professor from that lab knew a student who came to try to activate nitrogen. Specifically, he intended to revert a Schiemann reaction. He claimed that he had isolated phenyldiazonium tetrafluoroborate in low yield from PhF+BF₃ reaction, run in liquid nitrogen.
[2] NOT an online video sharing website for really tiny internet junkies.

Guys and gals, I would like your input on something. I am giving a laboratory safety seminar to first-year organic chemistry graduate students in about a week. While I already have notes from the prof who used to to this seminar, the powers that be decided that it would be best if a senior graduate student did the talk- someone who still works in the lab and knows the dos and don’ts of modern organic synthesis. And I’m a sucker for an audience. You should know this by now.

So my question to you all is this: what would you want to cover in a hour-long talk on lab safety, given that:

• The audience consists only of first-year organic grad students and the majority of them will be doing organic or organometallic synthesis;
• A majority of them already have research experience either as an undergrad or in industry;
• My part of the talk is geared toward working in the lab as opposed to department and school policies and such, which is covered by someone else. In other words, the current talk has a considerable amount of chemistry in it.

While the slides I have for this talk are pretty good, in some ways they are not terribly up-to-date. In the interest of sheer curiosity for your thoughts, I won’t divulge the current content. The floor is yours.

Holy crap, 2010 is almost upon us. Time for a last-minute 2009 Corny!

Badass AFM? Oh yes. IBM’s Science paper on the high-resolution single-molecule AFM of pentacene was so jaw-droppingly sweet it almost made all the crappy stuff that happened in 2009 seem irrelevant. I covered it already, but to wit:

Mazel tov! Normal blogging (y’know, with Ψ*Ψ and LiqC) will commence next week. Happy New Year!

I’m calling it right now: 2009 sucked major ass. It was an okay year for me, at least: another year down of killin’ bitches and throwin’ em in ditches. [1] But for society as a whole, there’s little to look back on with fondness, especially in science.

Remember how we bitched about the Nobel in Chemistry going to the discovery of the structure of the ribosome? That was silly of us. The science they won it for was, at least, based on facts. Consider the biggest science news stories of the year:

At the top of the shit heap was Climategate, that overly-publicized clusterfuck of epic proportions that forced us to have a dialogue about the nature of science and how it affects policy-making.

And then we find out that 12 highly-cited structures in the PDB were faked. And then this business in Peter Schultz’s lab with two high-profile articles in Science and JACS getting retracted, of which the chemistry blagosphere was privy to quite a while back, leading (perhaps indirectly) to the researcher in question not getting tenure at UT Austin.

And then, just this week, we find out that nearly 50 papers, if not more, in Acta Crystallographica C and E were retracted after it was found that two authors were taking structures and replacing atoms and fudging unit cells![2] I cannot, for the life of me, understand why anyone would want to do this, in Acta Cryst. no less, which is little more than a slightly peer-reviewed repository nowadays. Disgusting.

And with all of this tremendous bullshit, therein lies a insidious trend: as the world becomes more dependent on technology, we need its constituents to become greater champions for science. And in America, the opposite trend is happening. The scientific process allows people to be wrong; the process of gaining knowledge rationally is meant to be self-correcting. Being wrong is one thing. But fraudulent reports such as these not only take longer to correct, it undermines everything science stands for. Science is not about landing yourself a great job, it’s not about showing off your intellect, nor fame, nor glory, nor a means to your personal end. But the scientific establishment nowadays relies on its successes for the sake of its own power structure. And in 2009, that hubris was exposed in no small way.

So, goodbye, 2009. Don’t let the door hit your ass on the way out.

ETA: But hey, there were some high points to the year. For example, a majority of you reading this have survived the year, indicating that celebrities do not, in fact, read our blog. We also found out that you can oxidize alcohols with sodium hydride, not to mention the irony of iron cross-couplings. And that you can continue to publish the synthesis of molecules that kinda look like other things if you’re famous(ly crazy) enough. Hell, if you’re *really* famous, they don’t even have to look like anything. I’d also call 2009 the year of “what the christ is this shit?” but that’s pretty much every year, isn’t it?

[1] Er, by “killin’ bitches” I mean doing a lot of chemistry, and “throwin’ em in ditches” I mean publishing some of it.
[2] List of Acta. Cryst. retracted papers here and here.

The egregious lack of comedic chemistry-themed Twitter accounts has forced me to action. I present to you the Fake IUPAC Gold Book, a Twit in the vein of the incomparable Fake AP Stylebook. (There’s nothing original in the world, so steal what you love.) It’s like a Y2K version of the IUPAC Gold Book, but with far more snark and slightly less potty humor.

More chemistry-related swearing can be found on my Twitter, as well as on Ψ*Ψ’s.

Merry Christkwanzahanudan from everyone here at CBC.

I spent the better part of my day tinkering with our group’s microscope and figuring out how I could connect the output directly to iMovie on my computer. The microscope has a polarizer on it, so I decided to bust out some epic fail crystals[1] I made and make them even the slightest bit useful.

So, for the benefit of our “beloved” “readers,” I put the fruits of my labor on YouTube for everyone to enjoy. Sorry, no audio track, but I put in subtitles. You don’t want to hear me talk, anyway. I sound like some unholy mix of valley girl and my music professor in college.

Enjoy.

[1] Epic fail crystals: the kind of crystals you labor over for days at a time trying to make correctly, finally isolating some of suitable quality, finding out they diffract beautifully, with a structure that is incredibly easy to solve. And then finding out, after all that work, that it wasn’t what you wanted.

  As bioorthogonal as CBC is, we still have some respect to biofolk.[1] See, these people won’t be anywhere without chemistry. The sun of Barry Sharpless shines real close to me and burns me with the hot fire of click chemistry.[2] While the initial message was directed at medchem people as a new way to think about creating diversity, the reliable reactions that work on any scale is something that everyone likes. Even biologists, with their inability to step outside of the Eppendorfs full of hella dilute and sensitive stuff. Especially biologists. This is why our lab looked into what makes The Click Reacion fail on biological substrates, and how to prevent it in ways other than making unhappy compounds resembling the crazy scribble of the neophytes who don’t know any better. Bertozzi’s cyclooctynes are incredibly cool in their own right, their only problem is relatively low reaction rates and lengthy synthesis. The ability to adapt the original click conditions to mid-micromolar concentrations of vulnerable macromolecules is, in my view, quite impressive. You’d better agree.

  Now, you’ll be surprised how easy it is to screw up this great reaction. I couldn’t get it work in a chemical setting myself from the first time. So, we’ll be holding an online help session on clicking things. If you ever had any difficulties with copper-catalyzed azide–alkyne cycloaddition in any setting, please report here. You can write us an e-mail, but for obvious reasons (blogging powers!) I prefer it to be discussed here. It will help us address the problems that other people are facing, and, hopefully, solve some of them right away.

  [1] Right?..
  [2] Try mixing neat phenylacetylene and benzyl azide with copper (I) source if you don’t believe me.

[1] 3D fanatics, rejoice! For there is now a simple way to add 3D representations of molecules to your blagoblag. Co-developed by Markus Sitzmann of NCI/CADD and Mr. Noel O’Blog, they have developed a simple script that you can load from the NCI website and, with a SMILES or InCHI key, allows you to visualize a molecule using Twirlymol, which is basically a no-frills Jmol which loads much, much, much faster. To wit:

EDIT: Changed molecule to show off the 3D-ness.

The code for blogspot is on Noel’s post above; for WordPress use the following template:

<div id="DIVNAME" height="500" width="500"></div>
<script type="text/javascript" src="http://cactus.nci.nih.gov/chemical/structure/MOLECULE/twirl?div_id=DIVNAME"></script>

Use an arbitrary name for the DIVNAME, and the MOLECULE string should be a SMILES or InCHI key; common molecules in NCI’s database such as “aspirin” or “buckminsterfullerene” work too. Converting a structure to SMILES or InCHI is easy with ChemDraw; highlight the structure and go to “Edit-Copy As.” You should convert the SMILES or InCHI key to a web-friendly address using CADD’s Chemical Identifier resolver; that was necessary for me to get the structure to work. Adding styles to the div tag allows you to change the background color and have sexytimes.

I don’t think there’s an easy way to change the color scheme for the atom labels, which are the standard CPK colors.

I apologize if you learned something today; that was not my intention.

[1] This post was written entirely for the Simpsons reference.