Nature Chemistry

The Nature Publishing Group, which puts out such high quality journals as Nature and Nature Chemical Biology, has just published the first issue of their new journal: Nature Chemistry. The goal of this new journal is to be sort of like JACS without all of the shit. At least that's what I thought until I stumbled on this steaming pile.

P.S. Don't ask me what happens to the pyran double bond. They screwed it up.

incredible awesomeness

In my experience it's pretty unusual to have a reaction that not only works well, it actually provides a more pure product than the starting material. I stumbled onto just one of those this week. I have several steps that have been worked out in the route I use and several others I've improved. This little beauty is one of the ones worked out for me, and it seems to be a doozy. I had never put material into the reaction that wasn't clean until last week. I had some residue from crystallizing the starting material that was mostly sm, but had several other spots. I submitted it to the reaction and came out with product that was almost as clean as the ones with clean sm!

To push the reaction a bit, and to try to maximized my amounts of material, I put a really dirty mixture of compounds in. Lane 1 is mother liquor from an 80 run of the prior rxn, lane 2 is similarly from a 40 g run, and has very little sm left in it, and lane 3 is them combined. Probably less than half starting material, but amounts to a wet weight of almost 100 g. I boiled it in acid overnight, and lane 4 shows the results of taking a drop and working it up. Not the most pristine thing, but pretty damned awesome nonetheless.

unadulterated sweetness

some people just can't count

I have a huge sodium hydride reaction going today, almost 100g of 60% NaH, so I've been trapped in front of the hood babysitting all afternoon. It's really boring to stare at that reaction and make sure it doesn't vomit fort it's hateful contents, but is exceedingly preferable to the alternative.

While killing time in between additions I was catching up on some journals and saw this beauty:

Org. Lett., 2008, 10 (21), 4739-4742

I'm impressed by any significant amount of work that can be done in two steps, especially since they seem to add two distinct groups and deprotect in those two short steps. I flipped through the article to find the schemes with the method and its application and came to this:


Scheme 2 shows the appending of the steroid moiety and deprotection in 3 steps. I thought that was odd since they weren't doing as much as they supposedly would in the end, and had already exceeded the alloted steps. I read on and they show the application in scheme 3, and it took 4 steps to get it done. I flipped to the last page only to find out that was it. No more schemes, or discussion. The two step synthesis was completen in a paltry four steps. They were even kind enough to point out in the conclusion that they did indeed perform only two steps (highlighted in yellow), in direct conflict with the scheme. Apparently researchers in California can count vessels as steps. I wonder why they didn't go all the way and call it a domino or multi component reaction?

I also wonder how this made it past review.

yet more journals

I posted about my pile of reading a while ago, and it has somehow gotten away from my pretty badly. I've tried to get on top of it, and even had gotten the pile to a somewhat diminished state versus its prior grandeur, but any ground I had advanced upon has been lost and then some.



Oddly none of them are that old. Some are several months old, but I don't think any are from before early fall (unlike my pile of C&EN in the shitter at home), and none have been on my desk for more than a month or two. It seems that I've gotten to the point where I can wade through a pile of dead trees this size every month or two now, but the people providing the pile have similarly advanced in their abilities.

I guess this is part of why I seem to have gotten so neurotic about keeping up with the ASAPs of the journals I actually care about. I'm afraid to get behind in yet another huge pile of reading.

fun with credit cards

I got a new card recently mostly because of the 0% for the first year. A few days ago I got an email saying I could choose, or make, the image for the front of my card. My mind was awash with the possibilities of crude and insulting things I might use, but I figured it was too good to be true. I waded through the basic process until I got to the upload your own image part, which had "guidelines". As an aside it had choices of canned images to use and it automatically presented the most popular ones. It seems pretty stupid to me to want a "custom" image and pick one from a most popular list. Sort of like getting something labeled custom off the shelf at Target. The list of limitations cheerily described as guidelines removed all of my areas of interest rather rapidly, not unsurprisingly, but also has an interesting laundry list of shit that's seemingly unacceptable. No sex, violence, or copyrighted material, sure, but no Olympics? Two of my favorites are no competitive marks/names, and any photo that might result in non-acceptance or other problems at point of sale.

JACS Finally Redeemed Itself

JACS sucks and I have commented on this before. This is how I usually read JACS: I scan through the abstract graphics and look for organic structures. If there are pretty nanotubes or clouds or lightning bolts or puzzle pieces, etc., then I skip it. That is until I stumble on an abstract graphic with a sperm cartoon.


So I read further. And these guys actually made this thing above so that they could release progesterone using light. You hit the compound with a laser and it releases progesterone. And you ask "Why is that useful and what is the deal with the sperm?" They used this technique to measure changes in the swimming pattern of human sperm in the presence of progesterone. That got me curious. Then this sentence at the end of the paper got me really curious.

"Supporting Information Available: Full experimental details, UV, 1H, and 13C NMR spectra, full characterization of all new compounds described herein, full experimental details of the
photochemical studies, sperm preparation, and biological measurements." Emphasis mine.

Yep. Sperm preparation. So I had to go to the supplemental info file. And here is how they "prepare" the sperm:

"Sperm Preparation: Human semen samples were obtained from healthy volunteers. Fresh ejaculates were allowed to liquefy at room temperature for 30–60 min. Sperm were purified by a “swim-up” procedure. About 2 ml liquefied semen was layered at the bottom of a 50 mL falcon tube, which contained ~ 4 mL of human tubal fluid (HTF). HTF comprised (in mM): 97.8 NaCl, 4.69 KCl, 0.2 MgSO4, 0.37 KH2PO4, 2.04 CaCl2, 0.33 sodium pyruvate, 21.4 sodium lactate, 2.78 glucose and 21 HEPES, adjusted to pH 7.3-7.4 with NaOH. Motile sperm were allowed to swim up in HTF at 37 oC for 60–90 min. “Swim-up” sperm were pooled and washed 3 times (900×g, 15 min, RT). Number of sperm was determined in a Neubauer cell counter. Washed sperm were resuspended in HTF containing 4 mM NaHCO3 and 3 mg mL-1 human serum albumin (HSA) (Irvine Scientific, USA) (HTF++) at a density of 2 × 107 mL-1 This sperm suspension was incubated for 2-3 h at 37 oC and then used for further experiments."

You think organic chemistry sucks. Imagine having to purify some "healthy volunteer's" sperm. And since when is a fresh ejaculate not "liquified" at room temp?

perhaps the best shirt ever made

I went to Boston this weekend for Chi-Li's wedding, which was pretty awesome. Of course during the ceremony, after the usual boilerplate, when the preacher turned to Chi-Li and said "Chi-Li ..." he was immediately cut off by Chi-Li's "I do!". Everyone laughed, I wished I had been filming it instead of just taking snapshots, the preacher played it off well, with an "OK!", and then continued on with the more proper sequence of incantations. It was a very Chi-Li moment.

After the reception, which was also awesome, a bunch of us took off for the real reason people go to their friend's weddings, drinking with your buddies. Among the many people in attendance was Rich whom I hadn't seen since the fall ACS last year. He surprised me with a shirt he had bought at a concert quite a while ago. The shirt was so awesome, he had gotten one for himself and another for me, and waited all this time to surprise me with it. To say the least it's absolutely incredible. Words hardly do it justice.

Breaking Bad

If you haven't seen Breaking Bad, you must put this on your netflix queue immediately. The first season just came out on DVD, and I watched all seven episodes in two days. The next season just started, and this is perhaps the only reason I would consider getting cable.



If you are not familiar with the show, it is about a mild mannered high school chemistry teacher/chemistry badass who finds out that he has terminal cancer and decides to cook meth to leave his family with a means to support themselves when he dies. He quickly generates a buzz, since his chemistry skills enable the manufacture of an extremely pure product. There are a number of sweet chemistry references in the show, and I won't mention them here because I don't want to spoil it for any of my three readers.


The show is based in "scientist 1's" hometown of Albuquerque, New Mexico, which provides for a stunning landscape in which to cook meth. Enjoy!

nitpicky bullshit

I didn't make it all the way through my ISI alerts on Friday, so I'm trying to finish them up now and I actually found one that was worth keeping and had some good references. In general I only read chemistry journals, except when a good article is presented to me from a non-chem source like this. Most chemical journals follow similar formats of footnote/end note so I'm not too familiar with other styles, but I do realize they exist. On days like today, however, when I get exposed to other formats, I wonder why.

Here is, I can only assume, a successful and popular format I stumbled onto today from an Elsevier journal Toxicology. Early on it the paper I found some refs that looked like they might be worth fetching and saving:



Handily linked, but the link only takes you to the endnote. Wow, way to use technology to the utmost. Anyway, I went to the end of the article a little surprised there was no number, but knew that some people like to have no reference numbers. I can't guess as to why that would be a good thing, but I don't publish in those journals, so it's really not my problem or concern. I get to the end of the article, and the 4 references I want are in 4 different places on 2 pages:



Now THAT'S convenience! It appears that they are in alphabetical order, which makes sense, but they're still all over the place. I had to flip back and forth from the front to the back every time I looked up the new paper due to my weak memory and inability to remember the names for any length of time. Luckily only one guy was referenced more than once, and the papers were in two different years. I had wondered why the body references had no reference number, but did have a year. I still am not sure what would happen if you had to reference some sort of super stud who published in your field many, many times per year every year. I think the reader would be forced to just get every reference listed and see which was important. Obviously much better than having them individually numbered.

The actual end notes themselves are rather poorly constructed as well:



I went to look up J. Pharmacol. and after not finding it (actually saving me quite a bit of time) re-examined the ref to find that it was actually Br. J. Pharmacol. The incredibly clean lines of the formatting free text had slid right over my brain like a chamois leaving nary a residue. Once I had the journal correct, I glanced back to find the year and had to re-read the whole thing again to realize the year is buried with the authors, before the title. How nice. To make the footnotes somewhat discernible from each other so you can find them in the document's jumbled entrails, they moved the year away from it's surrounding info.

All of this to get the lovely benefits of "Singhal et al., 1999; Boronat et al., 2001; Hatsukari et al., 2003; Kapasi et al., 2004" vs "⁵".