rejection

Paper got rejected. Amusing since the reviewers gave it two thumbs up out of three. The third guy didn't leave his thumb in an up or down position at all, which means that whatever we wrote just happened to rub the editor the wrong way. To boot, the boat has kind of sailed on the relevance of the paper. It looks like my primary authorship is going to be shelved for now, and probably buried in some sort of collaboration as an afterthought. Maybe it won't even make it into the text, it will just be supplementary info. Goody goody.

The astute reader will notice that I have added a new label for this post, "research defeat". Hopefully this label won't get much use.

Research is stalled until the NMR facility gets their act together and drops a probe into a magnet that can look at something other than 13C and 1H. These are the times I regret not booking my Christmas flight way earlier.

mixed bag

New paper has been first drafted. Heller recently tore it apart (from abroad even!) and sent it back, notifying me that he prefers separated Results and Discussion sections. I personally enjoy discussing my results as they come up, it leads to less confusion for the reader who might not want to read the whole paper (most readers are of this type.) Doesn't matter much, what does is that several of the claims in the paper were found to be untrue while Heller was in Europe. This will result in frantic synthesis of materials and copious amounts of low temperature high field heteronuclear NMR. On the upside is better to have something you thought didn't work turn out to work. Much better than having someone else contradict you in the literature. A good catch, and perhaps another try at a new crystal structure. It seems as though this new product is temperature sensitive, although not terribly so (stable in an ice/water bath.) This could lead to some interesting antics with the crystallographer.

Harry Potter

Towards the end of the semester is notebook check time for those lucky TA's who happen to be teaching organic chemistry. Labmate Mark is one such lucky duck. I held the door open for him as he walked in with a stack of about 30 notebooks of various sizes and shapes. One notebook in particular caught my eye, as it had gold edging on it. After Mark set the notebooks down on his desk, I picked up the gold-edged notebook to have a better look. It was a Hogwarts School notebook replete with all the appropriate Harry Potter insignia and crazy little fake medieval pictrograms. This particular notebook was from the Gryffindor house. At this point I was impressed with this students dedication to her fantasy niche, but the icing on the cake came when I flipped to the front of the book to see the name. I'm omitting the actual name to spare further embarrassment if this person ever grows up.

Jane Doe, aspiring wizard
Gryffindor House, 2nd Year
Potions Class, section AC

After all this snickering I do have to admit that this girls notebook was immaculate, probably the best kept notebook in the section. If you need to pretend that you're a student wizard to maintain your interest in organic chemistry, then I guess that's just fine with me.

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.

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....

Ir recycling step 4

The crucible of concentrated nastiness has removed most of the volatiles, which will prevent a huge flame ball from forming in this step. Here, we are simply heating off any of the volatile salts and burning solid organics down to ash. The iridium/ash may be good enough to carry on, however, the recycling will be much easier after heating to higher temperatures. The setup is shown below: a crucible with the iridium residues being fired by a Meker burner with the air mixer on low, gas on low. Lots of smoke (fairly toxic) is given off in this step. Although the picture is taken with the sash up, it was down for the duration of the burn-off, save for the picture.

Ir recycling step 3

Many of the higher boiling solvents and other nasties (mineral acids, oils, phospines, etc.) are still present and the waste residue currently has the consistency of chunky fondue. Unfortunately the smell doesn't resemble fondue in the least. Many of the bad smelling, high boiling residues left are removed by extensive heating in a crucible to 300 - 350 C using a heating mantle and sand bath. This was also a good time to throw in the tissue papers I used to clean up a few spills. No worries, as all of the organics are being decomposed in the hot acid and will be fired off in the next step.

Ir recycling step 2

The next step is to strip all of the volatile materials from the waste, employing a Rotovap. This is merely a contraption which heats the solvent in one pot while cooling the vapors so that they drip into another pot (the solvent trap.) This step happened mostly without incident, save but one batch of waste which was not properly neutralized. Of course, if you take dilute acid and strip the solvents off, what you end up with is concentrated acid. This hazard is inherent, since most of the volatiles are benign, anything which is particularly nasty is going to be concentrated and become nastier. As my labmate says, usually to make himself feel better while pouring waste down the drain with the water on, "The solution to pollution is dilution!" I have discovered the opposite is also true "If you want to make nasty waste even worse, concentrate it!" Its not as catchy, but equally relevant to the task at hand.

This nastiness will all be remedied in the next step.

Ir recycling step 1

The first thing to do is collect the waste. As you can see in the photo, there is a good bit of it from the various labs in the department. Some of it has been evaporated already, so its pretty dense. Most of it, however, is a lot of solvent for not a lot of metal. This picture shows the bulk of what I collected initially. In the present form of whatever it was collected in I would estimate the volume to be 4 to 5 liters.

precious metal recycling

I just had one of the first years make a boat load of the starting material he and I will both be using for our projects over the summer. He scaled up enough to use all of the remaining iridium (Ir) which was in the department, meaning that if we ever need to make this material again, we will have to buy more Ir. Iridium is pretty expensive, at the current market prices it costs just a tad under the price of gold, but that doesn't reflect the actual obtainable price because there are a lot more people out in the world dealing gold than iridium. Strem will sell the hexachloroiridate salt for 50$ per gram.

I've embarked upon recycling the iridium waste in the division for both practical reasons as well as pure interest in the brute force methods required to recover iridium residues back into usable materials. The procedure is basically this:
1. collect the waste
2. evaporate the low boiling solvents (<100 degrees C with partial vacuum)
3. evaporate the high boiling materials (heating mantle at about 300 degrees C)
4. fire the residues to ash (Bunsen burner with the air mixer open pretty far)
5. crush the ash and fire to redness (Meker burner with the air mixer open as far as possible.)
That gets to the raw metal, which is where I'll leave it for now. I think this whole process is pretty interesting, so I'll keep the individual steps updated on the blog. The method isn't proprietary and can be found in "The Journal of Less Common Metals", a tome of which I have never seen nor heard of until I starting this process.

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.

pyridine

The ligand that I've been working on (the A+B = C+D thing in a previous post) has been one tough cookie to crumble. The main reason for this is (I think) that the solubility of the starting material is pretty poor in THF, which is the solvent of choice for analogues of the target compound. The smart move here is to switch to a better solvent. After testing solubility of the starting material in a number of different solvents (THF, fluorobenzene, nitromethane, glyme, pyridine, DMSO, and methylene chloride) it turns out that this stuff is soluble only in pyridine and DMSO. DMSO is a great solvent if you never want to isolate your product again. Everything is soluble in DMSO. I'm soluble in DMSO. It boils somewhere up around 180C which doesn't really make it strippable. This leaves pyridine, which is what I've been using, but I can't say I'm terribly excited about this either. It stinks(if you can smell it, you're not working carefully enough), its tough to dry, tough to vacuum transfer and is particular bad for gentlemen such as myself, if you know what I mean. (For those that don't know, pyridine could be used as a very effective male sterilizer, so long as you don't mind not having lungs, a liver, or several other major organs as well.) The upshot of all this is that when I get frustrated trying to get the pyridine to pump over in time for me to get down to my NMR time, I can't throw the bomb to the floor in frustration for consideration of my future kin.

in the opposite direction

I've spent the last two weeks working on new compounds, one is a variation on a ligand we've been using here, and the other is a new metal complex. After a considerable amount of effort I have made (I think) both of them, but they are so unstable they fall apart into starting material. That is to say, there is more than one way to make these things. Say I can get complex P (the desired product) either starting with A + B or C + D. What I have essentially done is found a way to fleetingly make P from A + B but ultimately what I have done is to make C and D from A + B in a really fantastically expensive and time consuming way. Not that this is uncommon, but to have it occur to two different projects at the same time is extraordinarily frustrating.

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.

wrong

Things have not improved. Our chemical storage refrigerator stopped working over the weekend. There are two reasons to keep chemicals in a cold storage refrigerator: it will decompose to something else or it has a very low boiling point and could generate enough pressure in a closed container to explode at room temperature. This means that you need to have an explosion-proof fridge, just in case. And we did, (luckily nothing blew up) but it also makes repair or replacement a much more expensive proposition for the lab.

In better news I should get my line back tomorrow.

sash troubles

The cable which supports the counter weight for the sash on my fume hood snapped yesterday. This is a minor inconvenience compared to the other myriad of poor fortune which has befallen the lab in the last week. My Schlenk line is going to the glassblower on Tuesday (hopefully it will be in tip top condition upon its return.) To boot, Jake's line got completely wrecked and Derrik's sash had a crack in the safety glass, which the fellow's who came to fix my sash insisted also needed to be taken care of by ES&H regulations, so his line is down as well. For those of you keeping score, that leave two functional Schlenk lines - one of which is only half functional - for 8 lab members. Oh - and the facilities manager who came to check up on the sash progress noticed that some of the clamps we were using to hold the Schlenk lines up were wrapped in asbestos tape, so they were confiscated. Goody goody. Things can only improve from here.

crystals and dissapointment

Well, a picture of the crystals just to show you how big they were. Unfortunately the camera I was using does not take very good close-up shots. There are two whole crystals shown in the J. Young tube, with a penny for size comparison. These were blocky, and I could actually tell you the space group just by looking at the facets on the crystals if I were to take the time to look them up. Unfortunately careful 11B and 13C NMR analysis indicates almost certainly that these are not what I thought they were, and to boot, they are pretty common and easy to obtain, which explains why I got such huge crystals.

some crystals

Finally a break. The liquid pearl mentioned in the previous blog was painstakingly filtered (4 hours on a Buechner) and a quick 13C NMR said the prize was in the filtrate. Weird because the pearly part stayed on the filter, but I think there was just a wee bit of pearl in a bulk of dull white crap. Cooling the filtrate overnight in the fridge gave some nice flakey crystals, clear but with a significant iridescence, kind of like mica. While this is well and good, they aren't really X-ray quality crystals because they are just thin plates, nor are they worth getting a structure of anyway.

And in better news, a vial that's been in the box freezer for almost a month now (haven't looked at it in a few weeks) has yielded big fat blocks of clear crystals. Theres one thats nearly 3 mm square, almost neutron diffractable. Almost. More to the point, these are definitely X-ray quality, and they're of an unreported complex, so they might be worth collecting data on. I doubt it though, but we'll see what Prof. Heller thinks.

X-ray quality crystals were grown from a solution of THF over several weeks in a -40 C freezer.

Liquid pearl

For reasons I may explain later (or not, it doesn't matter) I was converting some phloroglucinol to 3,5-dihydroxybenzenesulfonate. The prep calls for diluting the aqueous solution with ethanol in order for the product to crystallize overnight. Whatever, this didn't happen. After a few other attempts I evaporated all of the solvent and then tried to dissolve it into a minimum of water, which didn't work at all for some unknown reason (it was soluble in water to start out with - maybe a pH issue). It did give a suspension which looked remarkably like liquid pearl. Pretty as it is, this stuff turns out to be nearly impossible to filter because the particles are so fine. These particles are however, soluble in neat ethanol, and hopefully some crystals can be coaxed out of solution this way.

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.

THF solvent bomb

After improperly refilling the tetrahydrofuran solvent bomb, the color of the sodium benzophenone ketal was no longer dark purple, not even bright blue or even green, it was yellow, indicating a total loss of the flask's integrity. I emptied the bomb and quenched the remaining sodium. In the process of vacuum transferring new THF into the freshly made bomb flask, the convection in the condensed THF was so strong that it created a little fountain in the center of the bomb, with a well about 1 cm deep and spray that came up and spattered the sides of the flask. I called over Jake and Derrik to look at it but they were not as impressed with it as I was. Regardless, its a very pretty blue color.

a promising reaction

Finally, a promising reaction. The salt metathesis reaction I ran last week appears to have worked, although the NMR spectra indicate ~ 85% purity, and a pretty unassignable mess of chemical shifts. Nonetheless, I think crystallization might succeed, and if I can get some good single crystals then it will be up to Warren, the staff crystallographer, to do the rest. The first attempt will be slow evaporation of the reaction mixture.

stir plate repair

We don't have enough working stir plates. I attempted to repair one by stripping it down and washing the moving parts with hexane. No dice. I regreased it with some Loctite N-5000 (the packaging proudly proclaims "Nickel-based anti-seize lubricant for the Nuclear Power Industry") but still, no dice. I began removing parts I thought looked extraneous. This worked somewhat, and as it turns out the piece that was obstructing the bar magnet was the cooling fan. When I say it worked "somewhat" I mean that it worked until the motor overheated and seized, in spite of the newly applied Ni-based nuclear power grease. At the very least this is now a valid state of disrepair to warrant tossing the old plate and ordering a new one. A view of the carnage...


The pieces in the foreground are some of the amputated bits. The washer and lock washer appeared to have no purpose whatsoever. The shiny bits are what remains of the cooling fan after being torn out of the middle of the stir plate.

Student Grades

Well, grades are in for the class I'm a TA for. As you can see from the neatly constructed histogram, there are some winners and there are some losers in this bunch.
I don't know if it's luck of the draw, or actual TA influence, but the three high grades are from my section, and the three low grades are not. I'd like to think I personally had something to do with it, but I fear that the sample size isn't large enough to get too snobby. I'll wait to see what the TA evaluations look like before making any more presumptuous claims.

March Madness

It's tough to convince a bunch of chemistry grad students that a NCAA bracket is a good idea, even for a small amount of money. Are grad students a bunch of squares? Well, there is one bracket racket going on in the department, but the buy in is a six pack of beer, and really, who wants to win 40 six-packs of low quality beer? Someone who wants to throw a low quality party, that's who. And although I'm not so out of touch with normal society as to not want to participate, there is also enough square in me to not want to play for what is essentially the right to host a drunken frat party with all of my not so square friends.

Exam proctoring

The class for which I TA had their exam today. I helped Prof. Heller out by going over the exam questions ahead of time, just to make sure that the poor little babies weren't overly challenged. (We wouldn't want to hurt their confidence going into exam week, now would we?)

For one of the questions, Heller wanted to use some data that was actually obtained by one of the students in the class. I dug it up for him but it wasn't exactly to his liking. "Do you think you could find a spectrum which has minor impurity peaks in it?" I told him I couldn't, but I said I would have no problem inventing the data in excel and producing a fake spectrum which was indistinguishable from the real thing. This is apparently not something your PhD adviser likes to hear, although he wasn't so appalled as to not use the spectrum. It was a little frightening how easy it was to make a plausible looking spectrum from completely falsified data. A test for the reader....three of the following spectra are real, the fourth is invented. Can you tell the difference? (click on the image to enlarge it)

Drinking

Yesterday, Labmate Jake, with nothing but grading to do for the rest of the day, decides to have an afternoon beer at his desk. Soon after, three beers have been consumed and the severity of his red pen has become decidedly more docile. This will come into play later in the evening.

Our dear friend in another lab has completed his post-doc position and will be returning to his home in Europe on Thursday. In his honor, our lab as well as Prof. Heller (our fearless adviser) go out for a few beers after work at the University Inn Pub. Several snippets:

Krista: (pulls out pouch of tobacco and rolling papers, begins to roll a cigarette)
Prof. Heller: Wow, I haven't seen anyone roll their own cigarettes since I lived with my parents.
Derrik: Your father rolled his own, did he?
Prof. Heller: No, my mother was a truck driver in the army. She could roll 'em with one hand while the other was still on the wheel.
(Slight pause as the group forms their own mental pictures of Heller's mother in a truck rolling a cigarette one-handed, meanwhile Heller finishes half his beer in one pull.)

later on...

Jake: (finishes beer, sets empty glass on table)
Prof. Heller: Looks like you're empty (grabs pitcher, begins to pour Jake another beer)
Jake: (a little slurred) Oh, that's OK, I've probably had enough.
Prof. Heller: What? (continues to pour beer)
Jake: Um, maybe just half.
Prof. Heller: Nonsense (finishes pouring Jake's beer)
Jake: Hmmm (picks up beer, almost misses his mouth with it.)
Prof. Heller: (signals to waitress, holds up empty pitcher) Miss, we seem to've gone dry, could we get another?

Sublimation mixed results

After taking care of the details such as fixing thermometers and getting dry NMR solvent, the results of the purification are in. A partial success! The final material is more pure in that there are fewer products present (3 as opposed to 7) however only about 50% product, down from about 75%. Looks like I'll have to make a new batch from scratch.

wet NMR solvents

The deuterated benzene bomb in the lab is dried using CaH2, which should be a pretty effective drying agent. I prefer it to NaK alloy, mostly because you don't have to worry about the flask exploding after you finish transferring all of the solvent off. The downside is that you miss the pleasure of the deep purple color of the NaK benzophenone ketyl which tells you definitively that your solvent is indeed H2O free. After several crappy NMR spectra using the C6D6 over CaH2, a blank spectrum confirmed that my solvent was wet. I made a new bomb and then quenched the leftovers. (No fizz, of course.) The new bomb has a much whiter color to it than the wet bomb, which only brings to my attention three other solvent bombs in the lab sporting a depressingly dark grey color. SEP? you betcha. Maybe now I'll be able to tell if the sublimation worked or not.

Hg Thermometer Repair

Of course the sublimation won't work unless I have a thermometer with which to monitor the sand bath temperature. Most of our thermometers in the lab have broken threads, meaning there are gaps in the column of mercury. Argonne National Labs suggests dropping the thermometer from a short height. After a couple hundred drops with about four variations on height and padding thickness and I was ready to kick things up a notch.

I looked at the centrifuge for a couple minutes trying to figure out how I was going to counterbalance the thermometer and spin it up without breaking the top off. I settled on creating a bucket on a string, similar to the grade school experiment where you have a kid swing a bucket of water over his/her head. Except water isn't mercury. Long story short, the thermometer didn't break but the thread was still broken. On the bright side, I didn't have to bust out the mercury spill kit. After I left work frustrated, my labmate apparently put a heat gun on the bulb for about 4 minutes and viola! thermometer fixed (sort of, it's still miscalibrated by 3 C).

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.