X-ray quality crystals were grown from...

more crystals!!!

2009-04-15T09:56:00.001-07:00

Like I said, with the ligand on the metal the rest of the chemistry will follow fast. I've got 4 different crystal attempts going on several derivatives. Derivative number 1 was accomplished in no time at all. I chilled a hexane solution in the argon box over the weekend and got tiny blocks of crystals. The crystallographer swooned about these crystals. They looked a little small to me, but he seemed to think they were of the perfect size. In the picture these crystals look black, however if you break them up the fractured crystals look deep purple. The solution of these crystals is also a deep intense purple; I'll try to get a decent picture of the color later. The diffraction pattern is weak, but lets hope a structure can be coaxed out of the data.

xtls

2009-04-10T21:51:00.000-07:00

The crystals were exceptional. Observe the sweet diffraction...

I got the structure back at 6% R factor, which the crystallographer claims is of "better than average quality". I tend to think that the average is 5%, so this would be slightly worse than average quality, but I suppose the crystallographer should know better than I do.

This is the product I have been seeking for so long via the magnesium ligand activation. As mentioned in a previous post I had given up on the magnesium and switched to lithium. This worked like a charm and now that the ligand and metal have come together the fun of derivatizing can begin.

X-ray quality crystals were grown from a slowly evaporated methylene chloride solution.

xtls in the beam

2009-03-26T10:37:00.000-07:00

Its always a good day when there are crystals in the beam. These are an olive green color. Waiting to see if they diffract...

end of teaching

2009-03-23T10:09:00.000-07:00

Another successful quarter of teaching has come to an end. Usually I go on about the miseries of teaching and how disappointing the students were, etc. etc. Instead I'll focus on the positive; again this quarter, my students have outperformed the other TA's sections. This has happened often enough that I should no longer consider it a fluke. The difference is small, my students' average bested the other two sections by 30 pts and 10 pts respectively, where the classes' individual standard deviation was 140 points (all graded out of 1000 total points). I'm not a statistician, but I think consistently beating the other sections for 6 out of 6 quarters, even by small margins, means something.

The secret? Not coddling the little snots: tough love and high expectations along with a bit of attentiveness. This is college, not the 4th grade. I tell the stupid ones they're stupid and the smart ones that they're not trying hard enough. At the end of the quarter I get glowing TA reviews from them. The public loves me, and sometimes, I might even say that I'm proud of them.

Grignard in the sonicator

2009-02-18T16:22:00.001-08:00

One last trick for this *%$&ing Grignard reaction. Sonication is sometimes used to activate the magnesium surface. Ultra-high frequency sound waves are pulsed in a small pool of water. The reaction vessel is submerged in the water and the sound waves cause small bubbles on the surface of the magnesium. These bubles collapse with considerable localized force, and in an ideal situation, activate the surface of the metal. I'll cut to the chase and mention that this did not work either, frustrating me to no end. I am done with Victor Grignard and his ways.

Just because I am giving up on the Grignard reaction and Rieke magnesium does not mean I am admitting defeat here. The magnesium complex was never an object of attainment, merely a means to an end. The object is to get cobalt on the ligand in a high-yielding manner under reasonable reaction conditions; I simply need to try new means to achieve my end. Next up? We run kitty-corner on the periodic table and pound the ligand with a little lithium.

Teflon tape to seal joints

2009-02-11T21:40:00.000-08:00

I wanted to find a way to reflux under inert conditions without drawing silicon grease into the reaction flask. I tried using some Teflon tape in between the joints. This sort of worked, but sort of didn't. When I tested the the seal it held better vacuum than ground glass on ground glass, but unfortunately it was not as good as a greased joint. I tried to make a better seal with a little more pressure. With enough pressure the tape in the joint became translucent, looking as thought it almost would form a perfect seal. With a little more pressure I cracked the glass into millions of little pieces, cutting my hand in several places and making a mess of tiny glass shards in my hood. I do not recommend this method.

sodium sculpture

2009-02-06T08:01:00.000-08:00

These are two pictures of the same solvent pot. The opening of the bomb flask is very small, so only skinny things can fit through, such as the stir bar (the black pill shaped object). To fit the sodium (drying agent) through the hole it was rolled between two fingers in the dry box for form a long skinny cylinder of metal. After stirring for prolonged periods of time, the ends of the soft sodium metal are warped from banging into the sides of the flask to give the unusual shape shown in the pictures above.

kosher fake butter

2009-02-02T12:36:00.000-08:00

One of the labmates got a rather large shipment of chemical the other day. On the side of this very large bottle was a stamp proclaiming this chemical as kosher.

Interesting, we thought. Most of our chemicals are explicit in stating that these chemicals are for research use only and not to be used for food or drugs. This got the lab chatting a little bit about what was inside. Acetoin (and the very similar diacetyl) are used to give things like margarine their butter-like flavor and smell. It's most recognizable as the smell of microwave popcorn. I considered this for a moment before cautiously sniffing around the outside of the container. I couldn't smell anything so I cracked the lid and made a rookie chemist mistake; I sniffed right in the mouth of the jar. A seasoned chemist would advise not sniffing at all, but when smelling the chemical is absolutely necessary you are supposed to waft the scent towards you. Well, the freshly opened acetoin nearly knocked me flat on my ass. It smelled awful, and only after about five minutes later, when my sense of smell started to clear up, did it start to smell anything like butter.

Some additional trivia... Less than a gram of this compound was needed, but the smallest quantity available is 1 kilogram. Rabbi Gershon Segal certified this particular fake butter flavoring as kosher; thanks, Rabbi.

Reike Cobalt

2009-01-28T22:16:00.001-08:00

Co is apparently ferromagnetic. Who knew? Not me, until I talked to one of the students from the lab downstairs. Dunno why it was so surprising, on the surface I was thinking that iron was the only ferromagnetic material. I knew this wasn't true already though, because I've used gadolinium before and we also have a number of neodymium magnets in the lab. Silly silly silly.

This came about while trying to make finely divided cobalt powder in the same manner that Rieke Mg is synthesized. Whether this actually produced Reike Co or not is not certain, but it certainly didn't work for what I wanted it to. I did not spend a whole lot of time sorting out the rubble, but I did notice the Co particles lining up on the magnetic field lines of the stir bar. Weird.

schlenk line pt 2

2009-01-21T08:14:00.000-08:00

A good working space is tantamount to good productivity. Schlenk lines are generally mounted on some sort of support, most typically a metal cage. (VWR lists these as "lattices" or "lab frames".) The cage serves not only as a support for the Schlenk line, but also as space to connect reaction vessels using clamps while they are being used. Most everything in the hood is held together with fasteners. The cage itself and other permanent fixtures are attached using smaller 90 degree frame connectors which are tightened down using small Allen wrench. Other items such as reaction vessels are attached on a temporary basis using thumb screws. When I first arrived at the Heller lab the hood assigned to me had a cage made of stainless steel and aluminum rods, fixed directly to the back of the hood. When I moved my work space the new hood was a mish-mash of rusty steel, corroded aluminum, and about half constructed with fiberglass rods. Totally unacceptable. This was totally disassembled and a new cage was constructed using only metal rods. No individual pictures exist of only the cage, but the reader should take note of the underlying structure in future pictures.

Reike Magnesium (Mg*)

2009-01-20T09:50:00.000-08:00

In order to get my Grignard reactions to work even a little bit, I've been heating them considerably. This was fine when I was working in THF, as I would usually heat them to 70 C or so. The bomb flasks I'm using can handle the extra pressure (THF boils at 65 C). Now I'm using diethyl ether as a solvent to prevent activation of the alpha hydrogen in THF; unfortunately this means I'm restricted to lower temperatures. I tried to calculate the pressure I would build up in the flask while heating the ether to 70 C. I didn't get the number exactly, but suffice to say it's more than I'm comfortable with having in my hood. So the next great idea is to lower the required temperature by using "highly activated magnesium powder" also known as Reike Magnesium. (The abbreviation commonly used is Mg*.) This is made simply by reducing Mg-dihalide to elemental magnesium using a strong reductant, usually an alkali metal. The easiest way I can see to make this is to stir up the MgCl2 with potassium metal in THF while refluxing. Potassium melts at a slightly lower temperature than THF boils, so the molten potassium reacts quite easily with the MgCl2.

Rieke Magnesium is called such because Ruben D. Rieke has championed this form of magnesium as a route to generally inaccessable Grignard reactions. He has also commercialized this process, you can see his outfit here if you like. I browsed the website myself, and noticed a little grammatical mistake that I'll now make light of.

Often times my students, and occasionally even my well learned labmates, will do what is called "verbification". (This word actually shows up in several on line dictionaries now, very depressing) That is, they take a noun and use it as a verb to imply action of the noun on a subject in an obvious manner. One of the most common nouns which is subjected to verbification in the lab is "cannula", a long metal tube used to transfer liquids between reactions vessels while excluding the outside atmosphere. Often the transfer process is reffered to by the slur "cannulate". This appears in Rieke's website...

No need for a drybox or a solvent still. Simply cannulate Rieke® Metals in THF into a reaction flask under an atmosphere of argon or nitrogen.

I have been telling my students (and labmates) that "cannulate" is not a word, although you can in fact transfer something using a cannula. I was amused to see this grammatical miscue on a commercial website. Upon further investigation it turns out "cannulate" is actually a word, but it refers to the act of puncturing with a cannula, not transfering a vessel's contents. A near-miss for the author's of Ruben's website, but a miss for sure. As I tell my students quite often while they struggle to pronounce words like meridional, molybdenum, mesitylene; part of being educated is sounding educated.

Grignard Reaction

2009-01-19T10:18:00.001-08:00

François Auguste Victor Grignard enjoyed his heyday in the late 19th and early 20th centuries. In his spare time, when he and Franz Haber weren't trying to figure out how to kill each other with phosgene, he played around with Mg and halogenated reagents. The ubiquitity of this reaction is attested to in the quote "...every chemist has carried out the Grignard reaction at least once in his lifetime..." by M. S. Kharasch and O. Reinmuth in Grignard reactions of Non-Metallic Substances (Prentice-Hall, New York, 1954). It was true in the '50s and is still true today. Although the Grignard reagent is a very useful synthetic tool for organic chemistry, it is actually most chemistry student's first attempt at becoming an organometallic chemist. Things usually go poorly, in part because the TA's are organic chemists themselves, ill trained at how to handle the air and moisture sensitive reagents, but mostly because the organic chemistry laboratory is ill-equip to handle such sensitive manipulations. These experiments, often set up for failure, are the last of many student's attempts to become interested in organometallic chemistry. This is unfair, due mostly to the great amount of voodoo required to get a desirable reaction in the first place.

I have spent a considerable amount of time recently trying to make my ligand into a Grignard reagent so as to assist in metallating with cobalt. Things have not been going well. This reaction has been attempted at least 10 times now with varying levels of success. The two most successful attempts have occurred January 6th and previously on December 8th. Suspiciously, these days coincided with a moon phase of waxing gibbous. I am not proposing that the phase of the moon determines the outcome of this reaction, but I am not willing it rule it out yet either.

The typical reason for a Grignard reaction to not proceed as desired is a lack of "activity" of the Mg. This is usually directly related to the amount of exposed surface area of Mg in the zero oxidation state. The same principle is true of making contacts in electronics; anyone who has torn a flashlight apart can see the contact where the circuit of the battery is completed. If the contact is dirty (black copper oxide or green copper carbonate) one need simply rub it with some sand paper to expose the copper metal in order to make a good contact. Several tricks for activating Mg turnings have been tried in the work I'm currently attempting.

Pre-treat the Mg: The Mg turnings which exist in our storage cabinet turned out to be pretty awful and disgusting. I wish I had noticed this before I started to use them, but hopefully you can learn from my mistakes. Not really knowing what pure, uncorroded elemental magnesium should look like, I thought the Mg was clean enough, and nothing a crystal of I2 couldn't take care of (see below). Simply looking at a metal to judge the level of corrosion is like having perfect pitch. Some people think they can sing a C note on demand but few people actually can. The safe bet is that any metal which has been sitting around has some tarnish or corrosion to it. I washed a portion of the Mg with 1 M hydrochloric acid to shine it up. This is an exothermic reaction which gets pretty warm (and also evolves H2 gas) so I had a bucket of ice water nearby just in case. After that I gave it a few thorough rinses with deionized water and then anhydrous diethyl ether. Just to be sure this stuff was dry before I took it into the Ar box I left it under vacuum in a sand bath at 130 C overnight. The difference is pretty clear. On the left are the Mg chips as they were in the store room. On the right are the same chips after washing. Like I said, I'm embarrassed to admit I even tried using the unwashed chips. At the time I thought this hadn't worked. More on that later.

I2 crystals: The typical activation reagent used in Grignard reagents is to add a small crystal of iodine. Iodine is used because it is a solid at room temperature, so it is easier to use than bromine or chlorine, although these would presumably have the same effect. The iodine reacts easily with the surface of the magnesium, and after the small amount of I2 is consumed, fresh Mg surface is left exposed to react with your halogenated reagent. Small amounts of preformed Grignard reagent are sometimes used in this same manner, although I did not attempt them myself with this reaction. After using I2 I was still isolating protonated reagent at the end of the reaction, which at the time made me think I was getting some water into the reaction somewhere. I was also having reactivity problems. As I followed the reaction by NMR I noticed that the Grignard product was slow to form, and soon after it did I would see the protonated product.

Heat: In order to speed things along I was heating the reaction and using THF as a solvent so that I could use higher temperatures. (Diethyl ether is the typical reagent, but THF boils about 30 C higher.) Heating a Grignard is not usually advised, as the formation of Grignard reagents is usually exothermic, and therefor performed at room temperature or sometimes in an ice bath.

Drying/Activating Mg: Frustrated with the prospect of water somehow getting into the reaction, I decided to use a qualitative indicator to ensure everything I was adding to the pot was dry. I made up a soluton of sodium naphthalenide. (Simply 1:1 Na metal and naphthalene in THF, about 0.1 M.) After stirring for a few hours all the water will have reacted with the Na and the solution will be dark green. I slowly added the dark green solution to Mg chips stirring in THF until the reaction solution remained pale green, indicating that the Mg was activated and no water existed in the pot. This still gave me slow reactions, and after heating protonated product was still apparent.

At this point I am running out of tricks, but there is one more, to be discussed in another post. As it turns out the Grignard reagent that was forming had the Mg stabilized by a THF when it was isolated, and in solution it was no doubt solvated. Most Grignard reagents are only stable in solution, but probably what happened was the Grignard was activating the alpha proton on THF either at high temperatures or while being isolated. I tried all of the above with diethyl ether as well, but no luck... the reaction does not get hot enough to go to product at the temperatures accessable using ether. The next trick? Rieke Magnesium.

Building a Schlenk Line pt 1

2009-01-14T18:04:00.000-08:00

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.

sublimation apparatus

2009-01-13T08:35:00.000-08:00

I've used the sublimation apparatus before and had it work, but never like this. Labmate Krista was purifying some starting material (I think it was some type of imidazole) and got some real gemstones. This first picture shows you basic air-free sublimation device.The Teflon pin and black hose on the top left of the device connect it to the Schlenk line so that the atmosphere inside the sublimator can be cleared of air and either inert gas (argon for us) or vaccuum can be maintained. Doing a sublimation under vaccuum lowers the temperature at which the sublimation has to take place. The heating mantle on the bottom, although rusty and corroded, heats the oil bath (the opaque mess in the beaker which ought to be clear and colorless) which keeps the impure imidazole hot. Under vaccuum the imidazole is below the triple point, so as it is heated it vaporizes into the atmosphere of the sublimator. The vapors are cooled on the cold finger (peice of glass sticking down into the middle of the sublimator) which is kept cold by cold water flowing through it (through the two hoses on top). Upon very close inspection the astute observer will notice that the water is flowing backwards in this particular setup. Since the crystals Krista was growing were so spectacular, I asked if this was on purpose. Normally you would want the water to be coldest at the very bottom of the sublimator and have it warm up as it exited. Krista assured me that this wasn't skill, merely a silly little mistake. It is absolutely amazing that these crystals came out as well as they did given that the setup appears to be thrown together in someones basement using spare parts and grease someone cleaned out of their griddle. But there you have it. For those of you who are looking at the scale of these crystals, unimpressed, it is true that when most people think of crystals they are thinking of quartz crystals in their local curiosity shoppe. Well rubbish, those cyrstals took thousands of years to make, and Krista had these nailed out in less than a day; much more impressive.

Neglect, and Building a Schlenk Line

2009-01-07T14:20:00.000-08:00

Once again, the blog has fallen by the wayside. Upon signing in after a long hiatus I found a comment asking about building a Schlenk line. I started talking about this then stopped, long before the conclusion of Schlenk line building was completed. This seems as good as any reason to resume this disscussion, which I'll start again from the beginning. later....

In other fantastic news, I recieved a new digital camera from my in-laws. This camera has a fantastic macro function and should provide some pretty stellar photos for the blog.

pleochroism

2008-10-05T11:29:00.000-07:00

Pleochroism occurs when a crystal absorbs light differently along different orientations within the crystal. Meaning, when looking down one axis of the crystal, light enters randomly polarized (there is no preference for the direction that the amplitudes of the waves are travelling). As the light passes through the crystal, only light which is in a particular orientation is absorbed, allowing other light to pass through. When this occurs for a particular band of visible light, you get crystals that are differently colored when viewed along different directions. This is all very confusing. The best explanation I could find on the web after a brief search is still a bit confusing, but much more elegantly worded with a touch of bad grammar. They're Spanish, so I will give them a free pass. I cut some tiny pieces of the crystal with a razor and tried to line them up so you can see the two different colors. These two crystal fragments (right) were cut from the same single crystal (largest crystal from the left picture). These are technically dichroic because they display only two colors, although pleochroism would only be used for crystals which displayed three different colors, but this is never called "trichroic" for some reason.

red or green?

2008-10-04T22:32:00.001-07:00

The crystals diffract. It has been really difficult figuring out just what color these crystals are. The compound is paramagnetic, so the color is very deep. It looks like a reddish purple color when it is in solution, but the crystals came out almost with a green color when looked at the right way. I took them to the crystallographer who informed me that the crystals are dichroic, and this explains the confusion in the colors. For now, a crummy picture of the crystals and one of the diffraction slices... later, hopefully, pictures showing the dichroism and little more discussion on just what dichroism is and how it works. A resounding success by any measure. X-ray quality crystals were grown from a slowly cooled n-hexane solution.

Soxhlet success!

2008-10-04T21:49:00.000-07:00

The extractor did wonderfully. The green substance from a couple posts ago was much less pure than I had hoped, consisting mostly of a blue substance (identity yet unknown, but not starting material.) There are three pretty distinct colors here, the yellow substance in the top sample tube is the desired product. The bottom tube is the mystery blue compound. I feel like I should spend a little time figuring out what this is so that I can avoid making it in the future. The middle tube is the original sample from the crude mix, composed of both compounds. I forget whether or not I had claimed the green compound in my color checklist, but if I did, it was unwarranted. Instead, I have made a yellow compound (which I can claim) and a blue compound (which I am not claiming yet as it is not properly identified.)

crystals

2008-09-26T15:44:00.001-07:00

Some pretty sweet dark red/purple (or dark green!) crystals have come my way. More on these later as I procure a better camera. The camera on the cell phone does these beauties no justice.

Soxhlet Extractor

2008-09-25T07:56:00.000-07:00

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!

green

2008-08-22T21:25:00.000-07:00

The camera is OK. Nothing spectacular but I think it will do just fine for the blog.

I'm working with some cobalt compounds being ligated with a Grignard pro-ligand. The CoCl2 is pretty typical starting material, and is pure blue when totally anhydrous. When it's wet the color becomes a pink/purple color. The ligand starts with a halide which is reacted with Mg to form the Grignard reagent, all of which are colorless. When the cobalt dichloride and Grignard are mixed the color of the solution turns from blue to deep green in minutes. The final product is pale green color, almost yellow, so there's probably still a lot of impurity in the solution. The first picture is of the solids after stripping the solvent. It looks pretty gooey, but after a bit of scraping its powdery in the bottom of the bomb flask. This material will have to be extracted in order to remove the magnesium salts and unreacted CoCl2. More to come of this in a bit.

problem solved

2008-08-21T10:50:00.000-07:00

Procrastination comes through once again. While feverishly losing bids on ebay for a crummy but not too crummy digital camera, I've allowed my cell phone plan to run its course. For simply agreeing to pay a monthly fee for another two years, Verizon will graciously throw in a new phone. Who could pass this up? The little bonus is that the new phone comes with a 1.3 MP camera, more than enough for my blogging needs. We'll try this phone camera out for a while and see if it really is cut out for the job.

2008-08-16T12:12:00.001-07:00

It's also come to my attention that I had a series of posts going on both iridium recycling and on building a Schlenk line from scratch, both of which have been neglected. I'll get back around to these soon.

colors and technological needs

2008-08-16T12:05:00.001-07:00

My chemistry has turned away from iridium towards cobalt. This means cheaper starting materials and harder characterizations, but it also means a whole new spectrum of colors. I've been getting some really nice blues and greens, some of which are even new products. I made a pretty wierd two coordinate cobalt bis-amide complex which was initially a dark black mess. A little sublimation however, cleaned that right up to a bright green color.

Usually I would have a photo here so that you could enjoy this coloration with me, but I haven't been able to fanagle the camera from home. I think I could benifit greatly from a cheap used camera bought off ebay which I could keep in the lab. Unfortunately I haven't been able to locate a camera as cheaply as I'd like which will still take decent quality pictures.

I guess for now you'll just have to trust me that the colors are as nice as I say they are.

motivated

2008-07-10T10:01:00.000-07:00

While reading up on a few of my friends blogs I remembered that I too have a blog which has been ruefully neglected. I logged in for the first time since February and found this stashed in my edits pile:

"...Scientists themselves, as well as the nonscientific public, tend to lose sight of the fact that science is a human enterprise. The results are supposed to have objective validity, but they are obtained by very human activities which are not without their own interest and importance."
A quote from F. A. Cotton, in "Fluxionality in Organometallics and Metal Carbonyls," Journal of Organometallic Chemistry (1975) vol. 100 pp. 29-41.

Forget for now that Cotton was a bit crusty, what he says has some truth. This blog does mean something, to someone. Even if that someone is just me, that should be enough.

I will start posting again.

Later.

dealing with English

2008-02-29T08:57:00.001-08:00

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.)

glassy toluene

2008-02-10T20:42:00.000-08:00

Well, the blue crystals didn't diffract. That's not the current problem though.

I'm trying to do low temperature NMR with deuterium enriched samples. This requires adding and removing H2, HD, or D2 gas from a sample in an NMR tube in succession by doing repetitions of degassing. Essentially you remove gas dissolved in a liquid sample by removing the gas in the headspace of the sample, which draws out gas in solution into the headspace. To prevent the solvent from evaporating you need to have it frozen.

The solvent is toluene, which freezes at about -90 C. To degass it you need to freeze it in liquid nitrogen (temperature about -200 C). The quirk is that toluene forms a glass initially when forming a solid and then "cracks" as it cools further. As it cools the solid shrinks, forming a good amount of pressure on the inside, which isn't as cold as the outside closer to the liquid nitrogen. This pressure comes to a head with a loud crack that sounds like breaking glass. Since the toluene is in a glass tube, this makes for some scary moments as your degassing. The toluene in my tube cracked several times, but I was doing a lot of cycles, so I got complacent, and I was just getting to the end of the deuteration, the toluene crack shocked the glass too much and that was the end of that.

That mistake sent me back about four days. I supposed I needed to make some new starting material anyway, but I was hoping to bang out that one last good result.

Blue

2008-01-25T10:04:00.001-08:00

On the previous picture showing the yellow crystals you can notice that there are specs of blue crystals mixed in. These blue crystals are a huge thorn in my side. They grow out of solution under the same conditions that the yellow crystals due. The new picture is more representative of the ratio I get, making purification a huge problem. These products are paramagnetic, making NMR analysis a tad more difficult, and as of yet I don't know what the blue crystals are exactly. The crystallographer reports that they are diffractable (actually better than the yellow crystals, surprisingly since they seem a bit smaller) and thus, he will collect on them and see what they are.

This is just about the most expensive way to go about characterizing an unknown compound. No other characterization methods have been successful, and I'm a bit worried that I'm going to find out these blue crystals are nothing but starting material with some bit coordinated to it. Nevertheless, X-ray quality crystals were grown from a slow cooled solution of heptane. And I'm not counting these as "Blue" on my color checklist until I find out what they are.

Structure! and pretty pretty pictures.

2008-01-23T15:05:00.000-08:00

Bingo! The crystals worked. I got a full structure with excellent probability ellipsoids. There is a little disorder in one of the tert-butyl groups, but that's almost to be expected, and certainly won't keep this from being a publishable structure. Fantastic!

In other good news I was reading up on how to take pictures of crystals with a regular camera on the internet. The only thing that I found was that people would focus one ocular of the microscope, shine a really really bright light on the crystals and then take the picture just by holding the lens of the camera up to the lens of the microscope. I was exteremly skeptical that this would produce anything worthwhile, but for lack of better ideas (and a little spare time on my hands in between reactions) thought I would give it a try. Eureka! It works! I used my labmates xenon bulb mega flashlight for the light source (it hurts your eyes to look at what the flashlight is shining on at close range, but works well under the microscope) and the crappy lab microscope with a regular digital camera. The crystals shown are the same batch I just got the crystal structure of.

I'm also including this on my colors checklist. Yellow. Check. These crystals are of a cobalt complex, which is were the color comes from.

consecutive good news

2008-01-22T08:23:00.000-08:00

Well more crystals to the X-ray lab yesterday. The crystallographer was rather optomistic in spite of what I thought were pretty poor crystals. Apparently he found one that he liked out of the bunch that I brought him. Perhaps it'll actually turn out. The diffraction pattern for one position is below. I also thought I would include the photo (black, white, grainy as it is) from the alignment camera. You can barely make out the mounting filament in the bottom of the picture. To give an idea about scale, the mounting filament is about the size of a human hair.

In other good news, Professor Heller found a taker for the remnants of the paper that was rejected. This means I'll get buried on the author list somewhere, but if I get some more work done on it, perhaps I won't get buried too far. The rest of the work is pretty straightforward so hopefully I'll be able to wrap it up quickly.

The caveat here is that nothing is really straightforward. Heller enjoys reminding us "if it were all that easy someone else would have done it already."

The Chelate Effect

2008-01-21T08:44:00.000-08:00

Teaching can be a disappointing enterprise. The other TA's and I worked fairly hard on updating a lab procedure to eliminate a lot of the systematic error that was persistent in the lab. I taught this same course last year in this same semester, so I was pretty familiar with what went wrong. The procedure is pretty simple: you make up some electrochemical copper cells and then measure the voltages at various temperatures. Plot the data and you can get delH, del S, Keq, del G and all this fantastic information. Although that last comment carries a whiff of sarcasm, this lab is pretty instructional if you don't screw it up. In spite of our best efforts to idiot-proof the lab, a substantial amount of idiotic data remains. As you can see from the plot below, the AB and BC data points are quite similar to what a grouping might look like for an epileptic firing a shotgun. (What we're looking for is more like the grouping of an epileptic firing an Uzi, preferably in one big spasm.) The R^2 value is supposed to indicate roughly the goodness of fit for the data. An R^2 of 1 is the gold standard, but 0.90 or up is good for this lab. As you can see, we have missed by an order of magnitude. Idiots.

those effing xtls

2008-01-21T08:40:00.000-08:00

Of all the bogus crap I have to put up with in the lab. I grew more "crystals" from the same solution that didn't diffract well enough. Instead of taking them right over to the crystallographer, I had enough to take and NMR and then, if pure, enough to send off for elemental analysis. So I took the NMR. Starting material. Effing A, D.

Nothing is more frustrating than spending large amounts of time and effort on purifying starting materials that were apparently only dirtied with extraneous reagent.

bogus crystals

2008-01-16T14:17:00.000-08:00

Well, the crystals didn't diffract well enough to even get the space group. The crystallographer suspected that they crystals were twinned. Very dissapointing, as this was going to be a good solid page in the paper I was writing. All hope is not lost however, as there are still several crystallization methods that are still under consideration and the distinct possibility that the original mess could give me a non-twinned cyrstal. It would help if the argon-box freezer would stay cold for more than a day at a time.

crystals

2008-01-14T11:25:00.000-08:00

Its always a good day when you have crystals on the diffractometer. These are dark orange needles. I was messing with the microscope we have in lab, trying to figure out a way to take a picture of the crystals, but all I can get at the moment is a blurry mess. The X-ray lab had such a camera, but I feel kind of silly asking to use it. For now, we'll have to settle for the diffraction slice. As you can see its not as good as the last one I put up, but that doesn't mean I'm any less optimistic about it.

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

color

2008-01-10T09:41:00.000-08:00

As promised in an earlier post. Steps are being taken to document the pretty colors. What we have here is a basic iridium starting material. Iridium will be the metal atom of choice for most of the non-blue or green colors, which will be filled in with cobalt probably.

Coincidentally, my mother-in-law has towels that are this exact same color. Is this orange or yellow? Perhaps it shouldn't count for either. If I were going to be particularly rigorous about this I would take a UV-Vis spectrum, but lets not get hasty.

In other research news, I have a new compound which has been characterized by NMR. The next step is to try to get some crystals. Two initial attempts, one by reacting in THF and slowly evaporating the solution, the other by reacting in a concentrated heptane solution and cooling in the box freezer. Hopefully good news soon to follow.

Start

2008-01-08T16:47:00.000-08:00

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...

rejection

2007-12-20T10:00:00.000-08:00

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

2007-12-16T11:48:00.000-08:00

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

2007-12-05T13:20:00.001-08:00

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

2007-12-03T11:17:00.000-08:00

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

2007-11-14T09:37:00.000-08:00

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

2007-11-08T17:02:00.001-08:00

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

2007-10-24T16:03:00.000-07:00

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

2007-10-12T13:08:00.000-07:00

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

2007-10-12T13:05:00.000-07:00

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

2007-10-05T10:29:00.000-07:00

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

2007-08-13T08:32:00.000-07:00

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

2007-08-09T08:41:00.000-07:00

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

2007-08-08T22:48:00.000-07:00

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

2007-08-07T13:48:00.000-07:00

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

2007-08-01T14:13:00.000-07:00

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

2007-07-10T15:02:00.001-07:00

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

2007-07-09T16:58:00.000-07:00

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

2007-07-03T18:49:00.001-07:00

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

2007-07-03T18:42:00.001-07:00

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

2007-07-03T18:39:00.000-07:00

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

2007-06-23T17:55:00.000-07:00

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

2007-06-21T13:54:00.001-07:00

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

2007-06-15T07:50:00.001-07:00

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

2007-06-01T09:28:00.000-07:00

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

2007-05-25T12:58:00.000-07:00

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

2007-05-18T07:47:00.000-07:00

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

2007-05-11T07:24:00.000-07:00

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

2007-05-08T09:20:00.000-07:00

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

2007-05-03T21:53:00.000-07:00

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

2007-04-30T08:17:00.000-07:00

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

2007-04-26T21:07:00.000-07:00

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

2007-04-25T10:03:00.000-07:00

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

2007-04-20T08:09:00.000-07:00

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

2007-03-22T11:11:00.000-07:00

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

2007-03-20T08:27:00.000-07:00

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

2007-03-19T13:21:00.000-07:00

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

2007-03-15T12:19:00.000-07:00

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

2007-03-14T09:07:00.000-07:00

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

2007-03-08T10:47:00.000-08:00

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

2007-03-07T09:03:00.000-08:00

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

2007-03-05T12:50:00.000-08:00

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

2007-03-04T15:49:00.000-08:00

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

2007-03-01T11:36:00.000-08:00

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

2007-02-27T21:36:00.000-08:00

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.