pleochroism

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?

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!

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

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

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

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

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.

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

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

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

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

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

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.

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

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

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

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

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

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

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

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...