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.

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.)

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.)

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."

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.

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.

cobalt is cheap

Since the Ir has been going so awfully terrible I've been looking into other metals. For those of you familiar with the periodic table you'll notice that iridium metal is in group 9 of the d-block, along with Rh and Co. These are typically metals of similar reactivity (Ir and Rh closer to each other than Co) so its common to look at the same molecules with a different metal. Reason being, Ir is the sort of thing in which the global production is measured in ounces, whereas Co is measured in metric tonnes.

The more interesting part to me, since I don't personally pay for the metals I'm using, is that Co chemistry produces some of the deepest blue and green complexes that you'll come across. Look up Cobalt Blue in wikipedia and think, prettier than that. I made my first green complex ever, which completes my personal chemical spectrum. My better half does seem to believe me, so perhaps I'll have to document that in the blog. I'm pretty sure the only one I wouldn't be able to get my hands on immediately is red. Green is one of the less common colors in the lab though.

I digress. True to the title of the blog, I made the new Co complex and got crystals on the first try. High fives were distributed throughout the lab on the way down to the crystallographer, and it seems that the crystals are well behaved (not twinned) and diffract well. Sweet.

Neon yellow/green needle-like X-ray quality crystals were grown from a solution of pentane chilled to a temperature of -40 C overnight.

crystals and purity, waiting for number 3

My previously mentioned crystals came through for me and gave a nice structure with a decent R factor. 5.9, which is fair, for small molecule work the goal is really less than 5, but 5.9 is fine with me. I might try to solve the structure myself just to see if I can't get it down a little farther. I'm guessing that the staff crystallographer just punched the "solve" button and went with the computer answer, so I could probably shave a few more thenths off the R factor with some careful work. Don't hold your breath though.

The next success dates back to something I've been trying to do since the first week I arrived here. In the very first post I made I referred to a compound I was attempting to sublime in an effort to purify it. Purification of this product has been an absolute pain in the tuckus. Crystallization (via layering, slow cooling, slow evaporation, crashing) sublimation, chromatography, and chemically protecting/deprotecting have not worked at all. What did work was just decreasing the amount of material that I was trying to make at once. There's no reasonable explanation for why this would work, but its tough for me to worry too much about something that worked out well for me. The NMR shows better than 99% purity. Awesome.

So if good things come in threes that means I should have something else good coming my way. Today I'll be working on the Ir recycling by flipping the switch on the muffle furnace and letting that sucker plug away all day. I've been having trouble determining what the right temperature is that the iridium oxide needs to be at in order to decompose to the metallic iridium. I haven't really found any reliable numbers for this, but Wikipedia suggests that 1100 C is just about where I need to be. Please note that Wikipedia is not a credible source. Not that's its wrong, but its like writing a book report and citing Cliff's Notes. The muffle furnace I'll be using maxes out at 1100 C, but we'll see just how far I can push it. 1200 C would be nice, just to make sure that the job gets done.

steady progress

I did get my line back from the glassblower and in fine condition. I reset all the clamps and got the pump oil warmed back up. All the pins are greased, the inert gas manifold now has an inlet and an outlet at the opposite end (as it should) and a shiny new Hg bubbler/monometer vented (through a sulfur trap of course) up into the hood. Proffesor Heller was not particularly pleased about the Hg, and pointed out (rather after the fact) that we had some stop-flow valves in the lab for that purpose, but I don't have a port for a pressure gauge, nor do I really want one, so the Hg monometer still serves some purpose. Enjoy this picture of my hood, and notice that this is as clean as its ever going to be for the rest of existance. The line is repaired, the inside is clean from when the sash was fixed. (Those stains are happy accidents of years gone by.) A fix on the fridge is in the works and soon my chemistry might even start to work again. Keep your fingers crossed.

some crystals

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

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

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

Sublimation mixed results

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