Sometimes you just need a push

HEY GUYS!!! Our ride to group meeting just got here.

My laboratory is a “lazy Susan” of responsibilities. Care for the GPC, solvent stills, hi-vac line, etc. etc. etc. changes hands every year or so. That way everyone learns to care for several different instruments and no one gets stuck with a real pain for too long. This also means that the lazy good for nothing student (LaGooNS) that inhabits every lab finds a new way to slow your project to a crawl every year or so.

My LaGooNS is currently in charge of our group’s elemental analysis machine. Initially, I was glad that I didn’t have to run it. It takes forever to run a sample and I really didn’t need it very often, as I was mostly repeating other peoples work. But two months ago I reported a new chain-transfer compound and my advisor said those 4 little words, “pure by elemental analysis,” that might as well have been the sound of my project running into a brick wall. You see, my LaGooNS doesn’t really like running the EA. I gave him an unknown compound 7 weeks ago and he hasn’t even moved the vial. He took a year to run a sample our PI gave him, and that was only after she emasculated him in public.

To make matters worst, he openly admits that he “has no shame”; that he really doesn’t feel bad after being dunce capped by our adviser. He feels no guilt or remorse for being a giant douche, so I can’t really appeal to his common decency.  Now I am faced with a conundrum. Do I a) throw him under the bus, tattle and get my results or b) patiently wait for my project to vitrofy and die? I can’t really tattle on him, I’d lose face with my peers and possibly with my boss, but I can’t really sit on my hands either. I’m left with threatening him, “run my samples or I’ll fucking kill you,”  hoping my adviser takes note of his sloth and gives him a kick in the pants, or volunteering to take over the EA … sigh. I guess I’ll start reading the manual.

Back on the Chain Transfer Gang

 

Rock out! Do a chain-transfer study!

Chrissie Hynde wants to know why no one does chain transfer studies anymore? This gripe excludes anything to do with RAFT, which is the only thing that comes up when you search for “chain-transfer constant” on SciFinder or Google Scholar. Every time someone reports a novel monomer or initiator they should report its chain transfer constant just like they report NMR, mass spec or elemental analysis data. It’s an important piece of data, not just an inconvenience, and frankly it isn’t that difficult to observe. Chain transfer may be inconsequential at low molecular weight or conversion, but ramp up your molecular weight and chain-transfer can wreak havoc! Really, even at low molecular weight, a chain-transfer study will give you insight into why your PDI is 2.3!

I think the lack of chain-transfer data is due to organic chemists moonlighting as polymer chemists, but complaining about non-polymer chemists is a gripe for another day.

For those of you who don’t know, chain-transfer occurs when a kinetic chain-end is terminated and another initiating species is generated. In radical polymerization this frequently occurs by hydrogen or halogen abstraction.

Chain transfer to carbon tetrachloride.

Chain-transfer has the effect of decreasing the molecular weight and increasing the PDI, but not changing the conversion. It renders otherwise controlled polymerizations unruly and pushes high molecular weights out of reach, so obviously it is worthy of our concern.

Perhaps I am just bitter because I have to determine chain-transfer constants for 9 or 10 comonomers. Or maybe I’m mad because there is very little data on chain-transfer to azide or alkyne containing moieties despite all of the hype about “macromolecular engineering through click chemistry.”

A cursory search of Google Scholar for articles with the words “Chain Transfer Constant” since 2005, excluding anything involving RAFT, generates only 242 results!!! That is absolutely ridiculous.

For a much better explanation of the finer points of chain-transfer, please have a look at George Odian’s book Principles of Polymerization.

I looked into his eyes and I saw pure evil

If only Paul were alive today.

I’ve heard a lot of people talk about what jerks famous scientists can be. For example, this guy seems to think Reza Ghadiri is a little insensitive. However, I’ve never really believed them. Professors are intelligent, evolved elders who may seem harsh but always have our best interests in mind, or at least aren’t malevolent. Furthermore, hearing tales of temper tantrums or the persecution of an unlucky student or junior faculty member is one thing, but actually seeing it is a whole other ball of wax. Some of these folks are just assholes.

This morning I attended a pretty good, though 15 minutes too long, guest lecture by a very famous Harvard scientist about biomechanics stuff. Afterwords a foolish/over-eager first year graduate student thrust his hand into the air and asked something to the effect of, “You made a bunch of simplifications/assumptions in your model which deals with microscopic phenomena. How do you think your model and its assumptions would work with the added complexity of macroscopic systems?”

Please bear in mind that I am paraphrasing. Without skipping a beat, the professor responded, “That question isn’t worth asking.” It doesn’t really matter how it will scale and furthermore that was a “poorly formed question.”

The venom with which this man responded to a stupid question from a stupid graduate student stunned me. I was simultaneously filled with schadenfreude and disgust that a MacArthur fellow could be so rude.

You’ve got a lot of growing up to do

I swear that the internet can read my mind. After reading Paul at ChemBark talk about dangerous and inconsiderate lab mates and how to deal with them, I couldn’t help but think that while dangerous lab mates blow themselves up only every once in a while, dirty lab mates piss me off everyday. Low and behold, Chemjobber “scooped” me on complaining about, or at least acknowledging, dirty lab mates and their detrimental effect on laboratory productivity and safety.

I have not one, but two disgustingly dirty lab mates. They refuse to store products in vials with labels, and instead insist on keeping them in flasks on their benchtops – or worse in the fridge- with only cryptic Sharpie hieroglyphs to identify their contents. I suppose that this is their business.  That is, up to the point where they start to eat into the stock of round bottom flasks, which has long since passed. But when one is in the practice of never cleaning their glassware, it accumulates and eventually intrudes onto the bench/fridge space of others. What do you do when this happens? You can either be a grown-up and tell them to move/clean their crap, or you can be passive-aggressive and slowly push their stuff back a little everyday until it is confined behind an imaginary line that you drew down the middle of the bench and then pretend that nothings happened, see below.

A month ago there was no "AGAM Bench Space" in this picture

I obviously chose the second option. This may be the weenie way out, but sometimes the intense argucussion that would precipitate from telling an 8th year graduate student (yes you read that right) that they need to clean up after themselves just isn’t worth the time and frustration. The combination of having the most seniority and being the most pathetic makes you a little touchy about upstart kids telling you how to do things. I’m hoping that this person will finish, or just stop showing up so that I can just clean their bench for them. I’m such a weenie

I don’t know, we just didn’t “click.”

Barry Sharpless tells us how he really feels.

 

While trying to work off campus I have been totally paralyzed by my campuses IT department. I cannot access SciFinder, Web of Knowledge or Science of Synthesis. I am at my wits end here. What’s the point of Web 2.0 if I can’t even access my resources remotely? I guess it forces me to post something.

The copper catalyzed azide-alkyne cycloaddition (CuCAAC) or “click” reaction, the once megapopular tour de force of macromolecular engineering, is slowly being left by the wayside like a high school quarterback who didn’t get a scholarship. The idea is still quite popular, who doesn’t love simple, quantitative reactions with easy work ups and functional group tolerance, but the CuCAAC is yesterdays news. There are a dozen “click” reactions and most of them don’t leave copper laying around.

Like slap bracelets and pogs I was late to the “click” party. At my first undergraduate “research” position I was puzzling out how to functionalize an ε-caprolactone ring and my adviser suggested I use a “click” reaction, without any other explanation. Being back in the days before wikipedia and web 2.0, I asked my graduate student labmates who explained that “click” wasn’t a reaction but an ethos, neglecting to inform me that there was a single reaction, the CuCAAC, which I am sure my adviser had in mind.

Fast-forward a couple years and I am looking for a modular way to make high molecular weight block copolymer, >100kDa per block. Finally, I have a chance to “click” with the cool kids, but after looking through the literature it doesn’t appear that anyone has made a “click” copolymer with anything other than oligomers*. To fight the entropy loss required to couple the chain ends of 1000 repeat unit long macromolecules I’ll need a bigger hammer than CuCAAC. Furthermore, I have sever concerns about chain transfer due to alkyne or azide chain ends and chain end fidelity with ATRP. Who’s going to save me? Why RAFT-HDA “click” conjugation of course! Not only does it alleviate my fears about chain-end fidelity, but it’s been proven to work with high molecular weight polymers.

My only problem now is going home smelling like RAFT agents and convincing my adviser, a through and through Matyjaszewski disciple, to use RAFT.

EDIT: Turns out CuCAAC isn’t as orthogonal as advertised. Perrier described a side reaction between azide and electron deficient olefins, i.e. monomers, that makes its use for coupling high molecular weight polymers unattractive.

*Funny how 10kDa is a polymer when I make it, but an oligomer when anyone else does.

Holy Best Practices Batman! It’s the “Dirty Dozen”

It seems like all of my favorite blogs, Chemjobber, ChemBark and Everyday Scientist, are all talking about chemical safety and dangerous labmates as a result of the screwball at Texas Tech who blew himself up in January. I thumbed through their commentary shaking my head and muttering about “what an idiot” he was, then patting myself on the back for being such a superior researcher.

Eventually, I was lead to an online copy of “Prudent Practices in the Laboratory: Handling and Disposal of Chemicals,” which is free online and which I highly recommend having a look at, where while browsing I discovered that organic and inorganic azides are “explosion hazards, especially with ground glass joints” and are “notorious shock-sensitive explosives.”

WHAWHAWHAT? I frequently prepare azido pendant functional polyesters and small molecules and no one’s ever mentioned this to me. I mean I read the MSDS for sodium azide and it said don’t eat it, don’t pour it down the drain and don’t mix it with metals. OK CHECK, I didn’t do any of those things, but at no point did anyone pull me aside and say “don’t use a metal spatula with your polymer it might detonate.” In fact my trusty undergrad was the only one who mentioned that I might not want to perform extractions of my sodium azide reaction mixture with methylene chloride for fear of creating explosive diazides.

Now I know that this is squarely my responsibility, so I’m not trying to blame my PI or older students in my laboratory. Well maybe I blame them a little. I just thought that it was A.) funny that even on the internet, land of self-important delusions, I can feel insecure in my knowledge of chemistry and B.) worth mentioning that before isolating your organic azides fetch a plastic spatula and your undergrad.

Productivity or Lack Thereof

Deep into the late summer doldrums I noticed that not only have I not bothered to post in several weeks, but neither has anyone else that I read. This can be excused as it is hot, humid, disgusting weather and most everyone I know is on or is about to go on vacation. My PI is included in the list of people hitting the beach this month, which means that despite my best efforts, I can’t seem to stay past 5:15PM. Furthermore, silly side project like reanimating the “ancient GC” and finding someone to simulate something on Spartan keep coming up and seeming like great butterflies to chase. To help curb this non-productivity I have started doing a couple things that I think are worth sharing.

1. Pomodoro Technique: If your unfamiliar with the “tomato technique” take a look at the Wikipedia page. I have found it incredibly useful for desk work. Work time is broken up into 25 minute periods with short rest periods in between. A specific task is picked for each period and I have to stick to this task until it is done or the period is over. For me this has had the effect of disciplining my mind and forcing me to pick a specific task as opposed to “working.” It takes a sea of work with no land in sight and reduces it to a small pond that I can swim across.
2. Organize Projects: If you are going to do something dumb like resurrect a GC of similar vintage to Nirvana, don’t just work on it. Isolate specific things that you need to do to get it going, i.e. find a new computer, hook up gas cylinders, replace the capillary column. If I don’t do this it is incredibly difficult for me to look at that pile of wires and tubing and not feel overwhelmed.
3. Stop Being so Ambitious: Let’s be honest with ourselves: grad students, at least initially, are all overambitious. They could be making way more money, working way less, if they had just gotten a real job, but they’ve got something to prove. They like being “smart” and showing everyone how great they are, but eventually this comes back to punish you. It’s your adviser’s job to get as much out of you as they can and if you don’t push back they’ll let you drown in your own work load. This can be as discrete as just not being the first person to volunteer for some side project that has nothing to do with your thesis. However, never forget that you are your own worst enemy. You are the one that thinks up something and just has to try it. Try it on the weekend, write it in your idea book, just don’t start working on it right now while you ought to be working on “real” work. Exploring your ideas is one of the perks of this job, but most of them aren’t going to work anyway, so don’t make the cohesiveness of your thesis suffer for your lack of discipline.
4. (Added 2-11-11) Anti-social is a Mac only, read awesome, program that keeps you from visiting social networking, dating, news and blogging sites while its running. The best part is that after you turn it on for a prescribed amount of time you can’t turn it off prematurely without restarting your computer. It isn’t a terrible inconvenience, but it reminds you that you’re doing something that you shouldn’t and most of the time if forces me back to work. I use it to keep me off of Facebook (no one does/says anything interesting anyway) and OKCupid (I’m looking for someone who likes Hi-vacuum and slow dancing). If you haven’t tried out this fantastic program I hope that the AGAM seal of approval convinces you to give it a shot.

It seems like we’re just going in circles

I guess this why I set up a Google reader account in the first place. Yet another macrocycle article has come down the pipes, this time from Wolfgang Binder at Martin-Luther University Halle-Wittenberg. I feel a little silly for mentioning this as it is nearly a month old, but it dovetails nicely with my previous posts on macrocycles.

Binder and coworkers prepared macrocyclic polystyrene via a cyclic NMP initiator. Seems pretty clever, though it didn’t seem to work that well, PDI>2 and multimodal molecular weight distributions. If they could suppress “radical ring-crossover” (RRC) reactions, which they identify as the reaction competing with addition, and increase the control of this reaction they may really have something here. I strained myself to think of ways to suppress RRC reactions, but all I could come up with is use more monomer and use less initiator, make it a little hard for the macrocycles to find each other, and only go to low conversion. However, this eliminates one of the advantages of a controlled polymerization, namely getting to control your molecular weight. A better idea would be to use a less substituted, see less active, NMP initiator to shorten the lifetime of the propagating radical. I am sure they’ve thought of these things.

Journal of Polymer Science Part A: Polymer Chemistry 2010, 48, 3402-3416.

DOI: 10.1002/pola.24126

GAMePoG

The great and malevolent polyester God (GAMePoG) must be listening, or reading this blog, for he has sent me a great gift. While browsing my Google reader this afternoon I stumbled upon this excellent review of cyclic polyesters by Scott Grayson at Tulane. They mentioned my much beloved N-heterocyclic carbene ring expansion polymerization, but ultimately decide that how they’re preparing cyclic polyester is much better (may the GAMePoG blight their reactions). I’d be shooting an email off to Scott this evening asking if he’s looking for a Post-Doc if it weren’t for those gigantic Louisiana cockroaches. My girlfriend has vetoed a Post-Doc anywhere south of the 30th parallel north for this very reason.

expanding your mind

Yesterday John over at “The Rheo Thing” reposted from “All Things Metathesis” about the wonders of ring expanding metathesis polymerization, REMP. This stuff’s pretty cool, but it seems sort of limited in it’s applications, at least as mentioned. You can make cyclic polyoctenemer and you can hydrogenate that to make cyclic polyethylene. Yey!!! you reduced the viscosity of your polyethylene!!! The much more interesting application exists in making functional polymers as Grubbs and company published last year1. They say this chemistry has applications in “drug delivery and nano technology,” which are my favorite  applications, because it means their research is too cool and they are too famous to care if it has any application.

Unique topology is cool, and as you will find out it is what I hang my hat on too. I think that the work done by Hedrick and Waymouth using N-heterocyclic carbenes for the ring expansion of lactide is also worth a look if you’re into this sort of thing. Expanding upon this chemistry Philippe Dubois reported using N-heterocyclic carbenes for the preparation of “jellyfish” polymers earlier this year5. Utilizing orthogonal* polymerization chemistries, Dubois prepared lactide macromers which were then ring expanded to make jellyfish. I can’t put my finger on it, but this chemistry just seems more versatile than REMP.

*Orthogonal is the new “click”

1 JACS, 131, 2009, p5388

2 Angew. Chem., Int. Ed. 2007, 46, 2627–2630.

3 J. Am. Chem. Soc. 2009, 131, 4884–4891.

4 J. Am. Chem. Soc.2007, 129, 8414–8415.

5 Macromolecules 2010, 43, 575–579