Chemical Musings (v. 2.0)

You know, I like to write (when I can) about various things that are in some way, shape or form important to me. Hopefully these topics somehow relate to organic chemistry. Regardless of their focus, every post I write initially comes from a thought, notion or experience that is important to me.

But for all the things in my humble little life that take center stage, I have to say, they seem so trivial compared to the devastation that is being faced in Burma. I have no idea what it is like to be in a situation like those folks are. The sheer loss of life, property and dignity is simply unimaginable to me.

Kinda puts things in perspective. 

I was musing this morning, while drinking a cup of coffee, on whether chemistry graduate students (doctoral) might have to pay tuition someday. Can you imagine that!?! For years, chemistry graduate students have been able to get paid to get a Ph.D. Regardless, they are paid to get a degree. Or in other words, the degree does not cost them anything (well… maybe a soul or two). 

Nowadays, everything is paid for: tuition, chemicals, overhead, instrument time… all paid for out of the PI’s grants or start-up funds. Just imagine if we were like..shudder… the history graduate students! We would have to….ugh… teach to get paid in order to pay our tuition. Now, we teach to get paid, sure. But we know that just around the corner is Research Assistant land, where one gets paid to do research (and not teach). And we all know we went to the Great White Tower to do research, not teach!

Face it, the river of funding is not flowing so freely these days. Universities are raising tuition and fees at sinful rates. Raw materials are getting more expensive to ship. 

Could the free ride come to an end someday?

Just a thought.

Today I have the privilege of hosting a small article by Heather Johnson. Please be nice, as this is her first contribution to Milomuses.com.

10 Online Scientific Journals for Your Organic Chemistry Research

Thanks to the Internet, we no longer need to spend so much time inside a library gathering published scientific research. With almost every leading journal now offering online access, research has become something you can do from the comfort of your laptop. Below are 10 commonly used online resources for research in organic chemistry.

• The Journal of Organic Chemistry (JOC) – This popular journal is published by the American Chemical Society. Since 1936, JOC has been an important resource for chemists and students alike.
• Organic Letters – A fairly new publication, this peer-reviewed journal has been specializing in organic chemistry news since 1999. It is a popular resource and is also published by the American Chemical Society.
• Organic and Biomolecular Chemistry (OBC) – This peer-reviewed journal is published every two weeks by the Royal Society of Chemistry. It was founded in 2003 and has since grown to become one of the most influential organic chemistry journals in the world.
• Archive for Organic Chemistry (Arkivoc) – Established in 2000, Arkivoc is a free online journal that is published by a non-profit organization. It was created so that organic chemistry research could be conducted without restrictions and membership fees.
• Beilstein Journal of Organic Chemistry – This peer-reviewed, open access journal is made available to the public by Beilstein-Institut, a non-profit organization that is dedicated to the advancement of chemistry.
• European Journal of Organic Chemistry – This peer-reviewed journal was first published in 1998 after the following journals merged into one: Gazzetta Chimica Italiana, Bulletin de la Société Chimique de France, Bulletin des Sociétés Chimiques Belges and Liebigs Annalen/Recueil.
• Methods in Organic Synthesis (MOS) – This searchable database of articles brings attention to the latest developments in organic synthesis. Online articles date back to the year 2000.
• Accounts of Chemical Research – Another popular journal from the American Chemical Society, this publication covers all areas of chemistry and biochemistry.
• Carbohydrate Research – This leading journal on carbohydrate chemistry and biochemistry has been in circulation since 1965. Organic chemists with a specific interest in sugars and their derivatives should consult this publication for research.
• Journal of Sulfur Chemistry - This international journal is quickly expanding and is currently accepting research papers that deal with the study of sulfur science.

Although the above list is hardly exhaustive, these resources offer an abundance of online information. Some are open access journals that are completely free to the public, while others require a subscription fee to access archived information. However, many researchers feel that occasional fees are nominal when compared to the convenience of online research.

By-line:

This post was contributed by Heather Johnson, who is an industry critic on the subject of becoming a pediatric nurse. She invites your feedback at heatherjohnson2323@gmail.com.

I happened across a new blog this morning whilst cruisin’ the internets. C&EN, the weekly rag of the ACS (and a source for many of my posts), has a “permanent” blog set up (”News, notes, and musings from C&EN”). All in all, I have to say that the content is rather reasonable. I am not expecting a lot of hard-hitting penis and feces references, ala Kyle, but so far I think it is rather good. I hope it works.

Of course, having multiple authors is a great way to keep the content flowin’… cough….cough…ahem…

This is what happens when you have a society that does not take science seriously:

In my opinion, NMR has to be, by far, the greatest tool ever created for the organic chemist. Any of my readers who have had even a cursory exposure to organic synthesis should be able to appreciate the infinite coolness of this non-destructive technique.

When I was a wee lad in grad school. I was trying to make a large, awful, polypyridine based ligand. Part of the synthesis required the installation of a diethylacetal group.

Now, making diethylacetals is a snap, but interpreting the NMR, for me (at the time), was not so easy. Here is the diethyl acetal portion:

At first I thought all was good. I had successfully located Ha (~1.3 ppm) and Hd (~5.7 ppm), they integrated properly etc… But Hb/c… round about 3.8 ppm, confounded me. This was the first time I had ever seen this. And I was stumped.

So, what did I, the daring and clever grad student do? Did I run to Silverstein to learn about diastereotopic protons? Nope. Did I ask the NMR wizard of the department? Nope. I ran to the computer to “simulate” the spectra.

Spectra simulation is used when you have a spin system that is so complicated that simple first-order analysis will not help (or is too difficult to be useful). In the above case, a tree-diagram would have worked just fine, but I was a noobie graduate student. So, I fired up my handy copy of Mestre-c (which, sadly, is not really free anymore…) and set about simulating the spectra.

By trial and error (who reads manuals anyway), I was able to determine that what I was looking at, experimentally, was two doublets of quartets (dq) with the chemical shift of one being 3.92 ppm and the chemicals shift of the other proton being 3.77 ppm. J_Hb-Hc = 9.5 Hz and J_Hb/c-Ha = 7.1 Hz.

Here is the resultant simulation:

Not bad, eh?

I have run into diastereotopic protons many times. These guys are easily identified if you remember that they cannot be interchanged via symmetry operations (reflections etc…). Now, I do not need to simulate the spectra, the tree-diagram works just fine.

Amazing how experience works like that…

Now that I think about it, I once had a 2,6- substituted pyridine compound where, oddly enough, the protons off carbons 3,4 and 5 all showed up as one big singlet (integrated to 3H). That confounds me to this day….