Building a Schlenk Line pt 1

A good Schlenk line starts with a good plan. In the figure I'm showing the basic sketch of the type of Schlenk lines used in the Heller Lab. This is scheme one of four and shows only the basic outline of the order we put in to the glassblower. There are five pages to the full schematic, one of written instructions and four of figures such as this one detailing the types of tubing, joints, lengths and thicknesses of glass etc. Either you are only a mildly interested reader and don't want to sift through pages of schematics or you are intimately interested and want to make a close copy. If you're the latter you should contact me, I might be willing to give it up (for a price). I will make a couple of suggestions as far as types of joints. The O-ring joints (the three joints in the bottom right of the figure which looks like bulges in the glass tubing) are all Urry-type O-ring joints. What are "Urry" joints, you ask? The glassblower who fabricated this glassware for us didn't know either. "Does that mean, 'eh, I need this in an 'urry'"? Well, no, it means that there is a raised edge running in the middle of the groove. When the clamp is tightened down the ridge presses against the O-ring which makes a better seal. This is particularly helpful when the joint is being removed frequently, as it ought to be if you are emptying the trap out every night. Dirt inevitably gets onto the O-ring and the Urry-joint will make a much better seal with a slightly dirty O-ring than a simple grooved joint will. As it turns out, there's not many glass manufacturers who make a simple groove anymore, but if you happen to get a hold of one save yourself some time and toil; drop it on the floor right now.

There's a design flaw in the sketch above. Its not terrible, but embarassing that it made it all the way through to the final product without getting caught. I'll mention it next time.

Soxhlet Extractor

The Soxhlet extractor is one neat peice of equipment. It is used in conjunction with a solvent in which what you want is slightly soluble, and what you don't want is totally insoluble. The advantage is that you end up using significantly less solvent in the extraction process, and once it is up and running, it can be left unattended for long periods of time. The matter for extraction is the green powder I posted in the previous blog entry. The setup is shown to the right. I'm using n-hexane as a solvent in this extraction, which is collected in the round bottom flask. This was vacuum transferred into the extractor using the Teflon pin you can see in the top left of the photo. The black hose is connected to the Schlenk line. I did not backfill the extractor with inert gas, which means I can operate the extractor at lower energy (longer times between filling the bucket with ice). At the bottom is a stir plate with a heating element. I keep a pretty vigorous stir going to prevent the hexane from bumping. The dish around the round bottom flask is empty in the picture, but I filled it with water and set the temperature on the heating element to be just around 25-30 C. (The hexane will cool as it is evaporated, so you have to put heat back into the system. The bucket is filled with ice water. One hose connects the pump to the cold finger and the other drains back into the bucket. All of the green material from the previous post is inside the paper thimbles you can see in the center of the extractor. The large glass tube on the far left is the vapor transfer tube. "Warm" hexane vapor travels up this tube at about 30 C and condenses on the cold finger, which is at about 0 C (from the ice bath). As the liquid condenses it drips down onto the paper thimbles holding the material. The material I want (light yellow green color) is dissolved. Eventually the level of solvent in the extraction chamber reaches above the bend in the return tube. This is the small squiggly tube in between the vapor transfer tube and the extraction chamber. When this happens the solution in the extraction chamber is siphoned back down the return tube into the round bottom, leaving behind the insoluble materials. This process is repeated a couple hundred times, concentrating the desired material down in the bottom flask. All in all a pretty nifty piece of equipment!

dealing with English

Where has our fearless blogger been off to? At war with the English language.

After a good solid month of struggling with this paper its finally off to the co-authors. All told there is 30 pages of melt-in-your-mouth scientific jargon and nonsensical tables filled with roman numerals, Greek letters, and some special characters that don't even have names. (This is a lie of course, but few people outside chemistry have reasonable cause to know what an angstrom is or what the symbol for it looks like. Many wouldn't know what an ampersand was if not for "Wheel of Fortune")

More to the point, although the paper has not been accepted it is not in danger of being rejected as was the previous paper I wrote. Now it's just a question of where it will be published after its been reviewed etc. etc. Our first try will be to the Journal of the American Chemical Society, which is the most prominent chemistry journal globally. There are those (mostly Europeans) who may contest that Angewandte Chemie should have that title, but most people I know only publish in Angewandte after JACS has rejected their paper.

Actual publication is still a far way off. I suppose I am at the stage that can be considered "2nd draft". There will be a 3rd draft after the co-authors have their say at which point it will be sent to the journal, which will send it out to referees for peer review. After the referees comment on it (assuming it is accepted) there will be a "1st revision" which will be sent back to the journal. The journal typesets the paper at which point it becomes a "Galley Proof" and then publication.

So it would seem that this particular battle with the English language has been won; however, while writing my own paper I have had to spend a lot of unfortunate time reading written reports for the class that I'm TA'ing. This battle has been largely lost I feel, and not solely because of the ESL students. The native speakers have acquired a keen disregard for all things grammatical and pay no mind to spelling or word choice. I try to focus on the English for the written reports because most of the time, their chemistry is even worse. This exercise has been thoroughly demoralizing. I threw away the standard rubric for a much more holistic grading scheme which consisted of "unacceptable" "needs improvement" and "satisfactory". So far only one student in 30 has received a grade of satisfactory.

With all this done I turn my attention to other matters. We have just received shipment of our new belt-drive vacuum pumps, which means that we can begin setting up the new Schlenk lines. Hopefully this will provide some material for the blog (including pictures for those of you who need some breaks from reading.)

Start

Another new year, another new semester. New classes to teach and new students whose names I have to learn. This bunch looks so-so. I haven't given up on them yet. There was a no-show but it was followed with a quick email lamenting some contagious disease. All in all a good first day. No blood, no broken glass, and no health and safety forms to fill out.

I'm going to try to make a better effort for regular posts. Things have been slow lately, and without pictures or some other medium to express my thoughts this blog can get very tedious to read I'm sure.

Prof. Heller has been in kind of a sour mood lately, which prevents retelling stories of his humorous anecdotes. He did happen into the lab during a conversation about biathlons. "The Finns are great at that. They had a lot of practice shooting Russians."

I've been browsing Ebay for a digital camera that I can keep in the lab on a somewhat permanent basis, to aide pictures for the blog. Hopefully that will come to fruition. Until then...

Period Reports

It seems as though I've come to a point in my education when there is an extreme emphasis on writing and not so much on mixing chemical A with B. We've been recently notified that our funding agency is willing to grant us some more money. This is good news. The bad news is that they are holding this money ransom until we turn in our delinquent period report which was due a month ago. Prof. Heller has not told me how much money there is at stake here, but its clear that there is just enough that he's willing to have someone else write the report for him and turn it in, no questions asked. I've written 4 such reports since I've been here (more on the topic of scientific writing later) and it really is a joke. The amount of progress which is actually made on the chemistry is painfully small. The first time I was to write the report I just assumed it was OK to delete the old news and fill in the new results. Not so, I learned, as the funding weinies apparently can notice that the background and strategy sections are the same, so they just assume that you've done no work. Its much more effective to rewrite the entire document even if you provide absolutely no new results with a slightly different word order. The bean counters glance at the document, realize the paragraph sizes have changed, then send off the check. This certainly says something about the capabilities of those who hold the purse strings.

Since I'm not the only one on the budget, these excersices involve compiling the reports of my coworkers. The quality of writing is poor to say the least, partially out of apathy, but mosly out of not being able to effectively communicate. The common public perception of science writing is that it is dry and boring. I categorically agree with this, however, good science writing clearly conveys a message, and boring tediuousness like grammar is essential. It becomes much more tedious when correcting the grammar of others.

I've been request to teach a lab course which carries a writing credit on the undergraduates transcripts for next semester. I'm sure I'll have much more to say on the topic of writing in science after I start to read some of their reports.

A lost muse

I have been trying for weeks to buckle down and write a paper. Its not going well (hence posting to blogger as yet another manifestation of procrastination.) I blame the fact on not being able to find my muse, nevermind that there are no muses for scientific writing. I have settled on trying to locate Clio, muse of history, since I did in fact perform all of these experiments in the past and am now reporting on them. This search for Clio has been starting to wear on Prof. Heller's nerves: a short recent exchange...

The young student approaches the hallowed chambers of the adviser, in an attempt to stay his deadline by feigning misunderstanding of a concept to be discussed in the paper. The point is discussed to exhaustion, and the student makes an unsuccessful break for the door...

Prof. Heller: So... when are you going to have this paper to me?
The Cowardly Procrastinator: Well, its not really in a draft form yet, I need a bit more time for the figures and the introduction is...
Prof. Heller (interupting): Norman Mailer died the other day.
*awkward pause*
TCP: I'm sorry, I don't know who that is exactly.
Prof. Heller: He was a non-fiction novelist. Wrote "The Naked and the Dead". Quite a good author, one of my favorites.
*longer awkward pause*
TCP: I'm not sure what you mean.
Prof. Heller: He was a notoriously slow writer.
TCP: Ok.
*slightl pause*
Prof. Heller: He was very slow, and now he's dead.

The terrified student backs slowly out of the room, not comprehending the exact meaning of the exchange which has just taken place. Safely back at his desk several moments later, two possible meanings come to mind: "Write this paper before you die" or "Write this paper before I kill you" The search for Clio is renewed with vigor.

More crystals, and a picture

As per recent comments... no, the lab does not have a camera. When pictures appear it is only because I happened to have my camera with me what a particularly photo-worthy event was happening in the lab. If I ever continue the saga of the Ir recycling there are more pictures which go with that. I must admit the whole process was so frustrating I'd rather not relive it, but perhaps... someday...

In the meantime... In a previous post I displayed the raw difraction data from a crystal I had grown. It was difficult to tell that this crystal was of poor quality just from the picture, but it was. I have grown the same crystal via another method and this is of much better quality. I'm including the diffraction pattern of this one to show how much better it is than the one previous. (A clue: those big white dots means that the diffraction of the crystal is better.)

X-ray quality crystals were grown from a slow evaporation of a THF solution under Argon.

organization

I walk into Prof. Heller's office to chat about some chemistry that's going on. On the way out I notice that there was a piece of paper with a yellow post-it note lying on the floor. I picked it up and placed it on Prof. Heller's desk. (Or rather, on top of the collection of papers, books, articles, and other things sitting on top of his desk.) An hour later I go in to collect the papers students turned in to him earlier so that I can begin grading them. I notice that the paper I had placed on his desk earlier has fallen off again and is on the floor in front of the door. I pick it up and place it on the desk heap again, this time closer to the center. Several minutes later I walk back into his office to ask a question about the grading scheme I should be using. The paper has again made its way to the floor. I pick it up on my way in and sit down. Prof. Heller looks right at me, picks the paper up off his desk, and throws it to the floor in front of me. I look at him kind of blankly. He explains... "That's a delinquent form that I need to turn in. If I leave it on my desk I'll never remember to do it." He points to the floor in front of the door. "That's the out-box."

salespeople

A short commentary on salespeople.

From time to time in the course of working in a research lab it may become necessary to order some expensive pieces of equipment. I don't relish the experience of talking to sales people but for the most part this is mitigated by the fact that they want to sell stuff to you. Something about commission, I'm sure. What baffles me is that when I need specific information from them, and they get all cagey, like all of a sudden they don't want this sale to continue if it means looking something up or doing a little math. Let me clue in all of the salespeople who I know must read this blog. (*cough*) Price is an object to a graduate student only to a certain extent, after that, the most important things in closing a deal is expediency and minimization of hassle. I don't work in the Purchasing and Acquisions office, I'm a grad student. My patience for paperwork is very thin and if there are two vendors offering nearly the same services, I will take the one that is fast and helps me through my paperwork over the one which is 10% cheaper. Valuable information for anyone trying to sell something to a chemist in my position.

glassblowing and joint sweating

Glassblowing is necessary from time to time in order to fix something you just broke, make a piece of glassware which you need right now, and so forth. Our glassblower arrives biweekly, so if you want something done by him it usually takes a long time, which could be remedied if the physics shop (which houses the glassworks) would just let us use the damn annealing oven.

We needed a piece of tube with a 3/8th inch outer diameter attached to a length of 1 inch tube with a standard taper 24/40 joint. This is nothing more than a tube, attaching one end straight on to the other. I tried for some time to make the first attachment to no avail. I could get as far as blowing out the end of the tube to make an even edge, but I was completely inept at attaching the two pieces. After several poor attempts Professor Heller learned of what I was doing, and although he thought it was admirable, was quick to point out exactly where I was failing.

I was missing a swivel joint used so that you could blow into a tube connected to the end of the glass and spin it at the same time. I distinctly remember that the last time I watched Heller connect two tubes together he did it without the aid of the swivel joint and did just fine. Apparently he was just showing off.

Hand annealing is another issue entirely, as Heller doesn't seem to have the patience to do it properly and as stated earlier, the physics shop doesn't let us use the oven. So even though the piece has been made it still can't be used because its too brittle in the present form.

On a similar note, sweating a joint in copper tubing was also on the day's chore list. I've seen my father and grandfather do it several times. The made it look ridiculously easy, just polish, flux, and sweat. This is a lot easier if you remember that you need the flux, which I forgot about on the first several attempts. I read on line that if you were doing this on household plumbing the best way to keep the water out is to jam a wad of white bread into the pipe before you sweat the joint, then just flush it out after you're done.

Curiously enough chemical stores does not stock white bread.

clean

The lab has been cleaned. This ordeal took two days with 5 diligently working lab mates and a couple of lazy sacks who pretended to care and only took the time to clean up their own personal messes. I try not to cuss a lot in this blog, so I won't comment further on the efforts of the lazy sacks. The lab is now just about as clean as a lab with a clean group would have it when it was dirty, and I think I'll have to settle for that. The real score comes in counting how many incidents there were, in which we scored very well. While cleaning and disposing of over 300 different containers with poor or non-existent labels, there were no occasions of damage to person or property. Broken glass, while amounting to several decently sized boxes, did not result in any cuts or glass dust inhalation. The main source of excitement came while cleaning out a badly degraded bomb flask which used to contain KCp* (a commonly used ligand). The usual routine, starting with an iPrOH quench followed by EtOH followed by MeOH followed by water, failed. The remaining potassium in the flask did not react until the water had been added, causing the entire flask to smoke for a minute or two before catching fire or an additional minute or two (a nice bright yellow flame, quite pretty actually if your not distracted by the fact that the flask could explode momentarily). This prompted detaching the D fire extinguisher from the wall and rushing it over, although its use was never necessary. It did, however, warrant a date change on the wall for "Days since last lab fire" from last August to yesterday.

A note on fire extinguishers: There are three commonly used types, A, B, and C, which are distinguished by their contents: water under pressure, compressed CO2, and a chemical flame retardant. Most people are aware of the difference because they have been told that spraying compressed water on an electrical fire is a poor idea. Just to show why a type D is necessary in this lab, consider that the fire started BECAUSE we put water (a type A extinguisher) on the metal. A type B is CO2 and no, using a type B is not going to cause global warming, but letting your house burn down will. We can't use a type B here because concentrated CO2 is an accelarant for combustible metals.

I don't know why type C doesn't work, but I'm guessing that the chemicals in a type C react similarly with the burning metal. Type D is just powdered NaCl (table salt) with high pressure argon gas. Think of it as the most expensive salt shaker money can buy.

update

After some gentle urging from an adoring fan, a quick update, although not much of interest has happened.

I've been working carefully on two projects, a new ligand synthesis, and isolating some final compounds for what I hope will soon become a complete body of work, ready to be written up and published.

The new ligand synthesis is slow, as stated before its only useful solubility is in pyridine, and once the deprotonation is accomplished it is no longer soluble in this either. After trying to get the arms on the ligand it resolublizes, but only to show in NMR that the deprotonation was not complete, even after overnight sonication. The solution in this case is the cook it good and hard for a couple days. So that is where my NMR tube sits right now, trying to deprotonate the starting material, bathed in 120C oil, bumping away.

The other final synthesis I have been messing with has been postponed until I can completely purify the starting materials. Its this kind of fervid obsession with purity is probably the cause of most OCD which chemists experience outside of the lab. For instance, I am constantly skeptical that the dish washer we have actually gets the dishes clean. This is a manifestation of a fear that my lab mates simply rinse their glassware and place it on the drying rack, which requires me to wash every piece of glassware I use thoroughly before I use it, even if I pull it right out of the drawer.

Some of the booted material has gone from red to deep blue-green, and partially soluble in hexane. I've thrown together some crystallization chambers to see what's really in there after my stuff hits the air. One is a slow evaporation of a saturated hexanes solution, the other is a vapor diffusion of hexanes into a nearly saturated THF solution.

On the positive side of things, the lab has acquired a wiffle bat and some wiffle balls. The good weather and large lawn outside the chemistry hall has drawn us out on several occasions to take our frustrations out on each other in a non-deconstructive manner. I highly recommend this for graduate students everywhere.

steady progress

I did get my line back from the glassblower and in fine condition. I reset all the clamps and got the pump oil warmed back up. All the pins are greased, the inert gas manifold now has an inlet and an outlet at the opposite end (as it should) and a shiny new Hg bubbler/monometer vented (through a sulfur trap of course) up into the hood. Proffesor Heller was not particularly pleased about the Hg, and pointed out (rather after the fact) that we had some stop-flow valves in the lab for that purpose, but I don't have a port for a pressure gauge, nor do I really want one, so the Hg monometer still serves some purpose. Enjoy this picture of my hood, and notice that this is as clean as its ever going to be for the rest of existance. The line is repaired, the inside is clean from when the sash was fixed. (Those stains are happy accidents of years gone by.) A fix on the fridge is in the works and soon my chemistry might even start to work again. Keep your fingers crossed.

Long time, no work

Sorry to disappoint the many many fans who I know attentively watch this blog on a daily basis. The promising reaction I spoke of nearly a month ago now? No crystals, just some gummy crap at the bottom of the vial. Where has our fearless author been this past month? Well, for the first part of it I was feverishly working on a research proposal project as a requirement for staying in the graduate program. The proposal outlines the synthetic plan necessary to synthesize Moebius molecules. I rendered a computer simulation of the molecule for the conclusion, and I've included it here. Obviously its not going to really look red and blue, thats just the coloring used to define the rails and rungs of the Moebius strip. I haven't gotten much feedback on the proposal yet from my committee, but I figure that no news is good news in this particular case. Professor Heller did at least acknowledge it and said he liked the proposal. Good enough for me.

So that covers the first two weeks of my absence, the last two weeks have been spent feverishly preparing for group meeting which I gave yesterday. Mostly this was spent trying to scrape together some results in the wee bit of time I had left in between finishing the proposal and giving the group meeting presentation. All in all I thought it went rather well, and now its time to settle back into some solid, non-feverishly done research.

Introduction

This blog is inspired by one of my friends who has a similar blog. He has two actually, one about general commentary, usually on politics, and one which focuses on his job as a gilded objects restorer. Just about anyone can (and should) comment on politics, but the subject matter is so common that it is difficult for one particular blog to stand out. Gilded objects restoration on the other hand, is a little less common of a profession. Unfortunately he doesn't update this one quite as often, but I'm getting off track.

This blog has an even narrower audience, but I work with equally expensive materials, so why not? The title refers to one of the most satisfying "minor victories" in small molecule investigation: the X-ray crystal structure. I had several such successes at a previous research position, however these molecules turned out to be uninteresting, at least for the time being. So far at my present lab, no crystals have been coaxed out of solution. This is not only disappointing in and of itself, but also makes purification a pain in the ass. Today's task is to purify the starting material, a heavy metal organometallic complex. Since crystallization is out of the question, we're going to give sublimation a hack. This is normally not an option for heavy atom complexes, but previously I've used a heat gun on J. Young tubes and have noticed the compound vanishes off the sides of the tube; very promising.