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...

rejection

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

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

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

mixed bag

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

Harry Potter

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

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

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