April 15, 2009

more crystals!!!


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.

April 10, 2009

xtls

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.

March 26, 2009

xtls in the beam

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

March 23, 2009

end of teaching

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.

February 18, 2009

Grignard in the sonicator

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.

February 11, 2009

Teflon tape to seal joints

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.

February 6, 2009

sodium sculpture



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.

February 2, 2009

kosher fake butter

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.

January 28, 2009

Reike Cobalt

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.

January 21, 2009

schlenk line pt 2

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.

January 20, 2009

Reike Magnesium (Mg*)

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.

January 19, 2009

Grignard Reaction

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.