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.

dioxane and pyridine

Dioxane and pyridine are two of my least favorite solvents. Their usefulness arises when you need something polar (like water) but need to keep water away because it will destroy your chemistry. On the other hand, dioxane and pyridine (unlike water) are very unpleasant to come in contact with. In fact, in the grand scheme of polarity, more polar compounds tend to be way more toxic the more polar you get (like DMSO), until you get to water, where the toxicity drops off to nothing. Aside from this minor unpleasantness, pyridine smells terrible. (Of course, smelling it would indicate ingestion anyway.) As one of the less couth of my labmates likes to say after he lets out a ripe bank of flatulence, "There is no escape, if you can smell it, its already inside of you." A pleasant thought to be sure.

What do I have to gain from these unpleasantries? Really cool looking cobalt compounds.

Maybe.

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.

cobalt is cheap

Since the Ir has been going so awfully terrible I've been looking into other metals. For those of you familiar with the periodic table you'll notice that iridium metal is in group 9 of the d-block, along with Rh and Co. These are typically metals of similar reactivity (Ir and Rh closer to each other than Co) so its common to look at the same molecules with a different metal. Reason being, Ir is the sort of thing in which the global production is measured in ounces, whereas Co is measured in metric tonnes.

The more interesting part to me, since I don't personally pay for the metals I'm using, is that Co chemistry produces some of the deepest blue and green complexes that you'll come across. Look up Cobalt Blue in wikipedia and think, prettier than that. I made my first green complex ever, which completes my personal chemical spectrum. My better half does seem to believe me, so perhaps I'll have to document that in the blog. I'm pretty sure the only one I wouldn't be able to get my hands on immediately is red. Green is one of the less common colors in the lab though.

I digress. True to the title of the blog, I made the new Co complex and got crystals on the first try. High fives were distributed throughout the lab on the way down to the crystallographer, and it seems that the crystals are well behaved (not twinned) and diffract well. Sweet.

Neon yellow/green needle-like X-ray quality crystals were grown from a solution of pentane chilled to a temperature of -40 C overnight.

Ir recycling step 5.2

I have become seriously delinquent in the updates. That's what happens when you get busy with real work I guess.

The muffle furnace was a disaster. I was able to fire the IrO hot enough, but since I let it go for so long, the salt vaporized and formed a glaze on the inside of the furnace. Jason explained to me (rather after the fact) that he wasn't surprised in the least that this had happened, and it was actually a pretty common problem they had to deal with when he was taking a ceramics class as an undergraduate. Basically what happened was this... There was a crack in one of the shelves in the furnace, and one of the three crucibles was set directly over the crack. This allowed a hot spot for form and the crucible broke, leaking molten salt onto the ceramic. The hot salt fused with the ceramic and lowered the melt temp just enough to make the crucible, shelf, iridium residue, and heating element meld together into one big block of solid meteorite like material. I'm really just about done with this whole process. I'm going to take on what I've got for the iridium and call it good enough. Pictures soon of the muffle furnace disaster. I'm really really busy with real chemistry.

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."

crystals and purity, waiting for number 3

My previously mentioned crystals came through for me and gave a nice structure with a decent R factor. 5.9, which is fair, for small molecule work the goal is really less than 5, but 5.9 is fine with me. I might try to solve the structure myself just to see if I can't get it down a little farther. I'm guessing that the staff crystallographer just punched the "solve" button and went with the computer answer, so I could probably shave a few more thenths off the R factor with some careful work. Don't hold your breath though.

The next success dates back to something I've been trying to do since the first week I arrived here. In the very first post I made I referred to a compound I was attempting to sublime in an effort to purify it. Purification of this product has been an absolute pain in the tuckus. Crystallization (via layering, slow cooling, slow evaporation, crashing) sublimation, chromatography, and chemically protecting/deprotecting have not worked at all. What did work was just decreasing the amount of material that I was trying to make at once. There's no reasonable explanation for why this would work, but its tough for me to worry too much about something that worked out well for me. The NMR shows better than 99% purity. Awesome.

So if good things come in threes that means I should have something else good coming my way. Today I'll be working on the Ir recycling by flipping the switch on the muffle furnace and letting that sucker plug away all day. I've been having trouble determining what the right temperature is that the iridium oxide needs to be at in order to decompose to the metallic iridium. I haven't really found any reliable numbers for this, but Wikipedia suggests that 1100 C is just about where I need to be. Please note that Wikipedia is not a credible source. Not that's its wrong, but its like writing a book report and citing Cliff's Notes. The muffle furnace I'll be using maxes out at 1100 C, but we'll see just how far I can push it. 1200 C would be nice, just to make sure that the job gets done.

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.

guarded optimism

The crystals I sent the X-ray lab seem to have held up in the mounting oil and diffracted well enough. The strong scattering (shown in the picture) and unit cell dimensions indicate some sort of monomer with one heavy atom (the metal atom) per unit cell. I don't have the solved structure in hand yet, but I'm ready to declare victory as far as getting a quality crystal. I've seen better, these were pale orange needles. Not too shabby though.

X-ray quality crystals were grown from a standing cooled solution in heptane over several weeks at a temperature of -35 C.

a break from recycling, and some crystals

Finally, some good news. But first an update on the frustrations of the Ir recycle project. The setup for chlorination was tested, but due to operator error, some adjustments may have to be made. I'm suspicious that the dedicated gas regulator for the Cl2 gas tank is corroded to the point of uselessness, however this is no excuse for ineptitude, at least not yet. In better news, I have located a muffle furnace, so perhaps this is an end to the current destruction of crucibles from around the department. More on that later.

CRYSTALS! A vial left in the freezer has yielded some needly orange crystals. Perhaps not the best for crystallographic analysis, but the crystallographer here thought they would be just fine. Currently I'm awaiting time on the diffractometer, so we'll wait before I declare total success. I'm still counting it as a triumph to get crystals at all, though.

Ir recycling step 5.1

The thermal shock on the crucibles has proved to be too much. Recall that the Meker burner did not generate enough heat to reduce the ash mixture to elemental material and salts, but it did come close. The solution then, or so I thought, was to use more Meker burners set up in a tripodal fasion. This (I patted myself on the back a few times for this) would allow greater control over slow heating as well as provide more actual area on on the crucible which was being heated so as to not develop "hot spots" on the crucible itself (slow heating is ineffective if the thermal shock is due to one area of the crucible expanding while another cool area does not.)

I set up (painstakingly) a couple of stands with Meker burners perfectly in place for the tripod along with the crucible at the optimal height and then started up all the Meker burners at the lowest possible gas flow. I increased the gas flow slowly on each of the burners over the course of about twenty mintues, carefully monitoring all of the surroundings to make sure they were not overheating.

Long story short the heat load was too much for the dry powder fire extinguisher which comes standard on all of the hoods in the lab. The heat triggered nozzle fired fine yellowish powder all over myself, the setup I was so proud of and half of the lab. A picture (of course) of the misery will follow shortly after I get it off of Krista's camera.

Ir recycling step 5

This is a note of contention as to whether or not this step is necessary. Professor Heller suggested that the black Ir/ash was good enough to carry on, while I thought this step would yield better results. As such, I'll do some of the batch both ways and see if the result is the same.

I've used a glassblowing torch in order mix some O2 in with the natural gas. This increases the temperature of the flame considerably, enough so that the bottom of the crucible glows like a light bulb. After a fews tens of minutes of heating, the black Ir/ash has melted into a glowing red lava-like goo. There were two separate layers evident, what I can only guess is metalic iridium made up the glowing red material in the bottom of the crucible, covered by a clearish liquid layer which I'm guessing is molten salts. This step gave off some pretty intense radiant heat, making me wonder if the fire extinguishers in the top of the hood would be triggered, happily this did not occur.


Several attempts were made to get this process to work correctly. I was successful once, shown in the picture, but subsequent attempts led to the crucibles breaking due to thermal shock and uneven heating. I tried to remedy this by using a Meker burner on full blast for hours, but the temperatures achieved was not enough to convert the ash to salts and the (presumably) iridium oxides to metallic iridium. I tried to spread the flame of the glass blowing torch out by loosely affixing the Meker burner grating to the top of the torch, but the O2 content was too high in the cavity in between, leading to a lot of backfiring and me almost crapping my pants. Clearly, a safe, more controlled heating method is needed, either by furnace or adapting the current setup to prevent thermal shock to the crucible and promote even heating. More on this soon....