Introducing ChemFeeds your Graphical Abstracts Portal

Decided to make a new website, ChemFeeds, where you can view pretty graphical chemical abstracts from various sources like JACS, Angewandte, JOCS, OrgLett, and a whole host of others. It even has the Angewandte puns^CBC, vis-à-vis OCB.

Feel free to roam around at the website, link is here:
http://www.chemfeeds.com/

Feedback and suggestions on how to make the website better and more useful for you, would be great.

Update 1: Permanent link can now be found in the top right header of this website. Which is an extension of the concept and scripts introduced here: Full Frontal JACS

Mitch

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Full Frontal JACS

The Journal of the American Chemical Society (JACS) has flirted with web 2.0 with it’s recent JACS β initiative. It has been warmly received around the blogosphere [CSB, TCB, CBC]. Although, I don’t have any complaints about the website, what I really wanted was less hand-holding and more of a shotgun approach to navigating through JACS online.

The nicest thing about thumbing through the print edition of JACS, is reading all the various chemistry that is outside your research tunnel-vision but still interesting.  If you go to the JACS homepage, here, you’ll see a list of 20 of the most recent articles, but not all of them! For example, 31 papers were added to ASAP today and only the last 20 are shown on their website, hardly a dire circumstance, but the fact is you miss some by using that setup. JACS also offers a nifty RSS feed of their articles, but I’ve never come across an RSS reader that’ll nicely format an active feed, 30+ submissions a day, in a format that will ever make me want to read it.

So how does one go about designing a more attractive JACS online browsing environment? Below is my attempt, it is as busy and attractive as a conference poster, but it lets you see a huge list of the most recently added papers to JACS ASAP.

The website parses through the JACS RSS feed. I was a bit worried about incorporating the graphical abstracts, but since they are included in the RSS feed, I’m going to claim fair use. The site isn’t pretty, but it gets the job done.

Here is a link for your viewing pleasure, Full Frontal JACS: http://www.chemfeeds.com/

Comments are always welcomed, but obviously this format is not for everyone.

Edit: A link to the site has been included in the links section to the right, towards the bottom under websites, titled Full Frontal JACS.

Update 1: Improved ACIE RSS feed

Update 2: Links edited to point to ChemFeeds instead of the simple script.

Mitch

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ACS Day2: Graphene Ribbons

Dresselhaus of MIT did a review of her many years in carbon nanostructures. She also presented some of her recent work with different types of graphene ribbons. Specifically, for the zigzag case shown below the electronic structure will be highly metallic while the armchair graphene will have a more traditional semiconductor electronic structure.

From graphene to nanotubes to graphene again and now nano ribbons what’s next for the nanostructure field? Gold nanotubes anyone…

More Info: Crystalline Graphene Nanoribbons (thanks to Excimer)

Mitch

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Molecular Strain: Make me, I dare you

Roald Hoffmann and Henning Hopf have a great new paper out in Angewandte titled Learning from Molecules in Distress. The paper is a romp through the field of “unhappy” hydrocarbon chemistry. It starts with a rationalization of the field of highly strained molecules, but quickly goes to the psychology of sadomasochism and vexing contemporary philosophical dilemmas as the Trolley problem and the Swampman.

On an aside, the Swampman thought experiment is thus,

“Suppose lightning strikes a dead tree in a swamp; I am standing nearby.My body is reduced to its elements, while entirely by coincidence (and out of different molecules) the tree is turned into my physical replica. My replica, The Swampman, moves exactly as I did; according to its nature it departs the swamp, encounters and seems to recognize my friends. It moves into my house and seems to write articles on radical interpretation. No one can tell the difference.“

As many of the elements in your brain get replaced within a month or so from the food you eat, this really shouldn’t be such a dire philosophical dilemma, than a common curiosity of everyday life. But I understand lightning is more theatrically appealing than a sandwich.

This is all within the context of explaining the glamorous life of the investigative synthetic experimentalist. Mission accomplished, if that was an intended goal. The paper also does discuss chemistry, and special attention was given to cyclic ozone 1, dicarbon dioxide 2, hexaazabenzene 3, and hexaprismane 4.

The masochistic chemist has 2 problems with the synthesis of these types of molecules. The first is near and dear to my heart, stability. Although, these molecules lie in a potential minimum and thus are thermodynamically “stable”, they can be quite reactive with itself or other molecules within the atmosphere or the medium it finds itself in. Plus, even thermodynamic stability have qualifiers, the size of the potential well may be so shallow to never see these peculiars at room temperature, which is likely the case for hexaazabenzene.

The second problem for molecules in distress is the inability of a clear synthetic strategy to the target; these molecules are unknown for a reason. Thus, the ever enterprising physical organic chemist needs to utilize chemistry outside a pure organic chemistry approach and may have to chase these molecules down within the complexation with metals, or in low temperature inert matrixes, or even perhaps atom by atom in an STM. In any case this paper is a fun read and should definitely be shared.

Mitch

Note 1: The Hoffmann & Hopf paper: Learning from Molecules in Distress
Note 2: Paper originally covered by CBC: kinky!
Note 3: RajaLab Weblog has covered some interesting sulfur helicene chemistry: Carbon-Sulfur [11]Helicenes: Syntheses, Structures and Properties
Note 4: Also covered by selenized: the value of making things

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Diaza[12]annulene: Would You have Known Better?

The recent retraction of two papers regarding diaza[12]annulenes by Yamaguchi et al. and Shi et al. from separate groups have strengthened the argument for stronger peer review and more thorough literature review by authors. http://dx.doi.org/10.1002/anie.200704704

But anyone can be an armchair synthetic chemist and point fingers at what should have been done after the fact. The easiest finger to point, is presumably between 7 coauthors, 4 reviewers, 2 editors no one ran the appropriate literature searches to find that these reactions are known and yield products with exactly 1/2 the mass as those reported in the papers. But, now we come to the bitter truth in modern chemical research, we simply do not perform the thorough literature searches of yester’year. Some will say this is a problem, but assuming those 13 scientists are typical of scientists of today then it simply isn’t a fair commentary to make. So, I thought it would be more beneficial to reread the papers and see if I would have come to the same conclusions given the same series of data, as I’m oblivious to heterocyclic chemistry in general and the Zincke reaction in particular, and have a typically topical background like most chemistry graduate students (I’m a Nuclear Chemist after all).

First up the Yamaguchi paper: http://dx.doi.org/10.1021/ol061585q
The title is the One-Pot Synthesis of N-Substituted Diaza[12]annulenes. Just looking at the title, we should be expecting ¹H,¹³C-NMR, definitely MS data, and likely a crystal structure since the molecule would have two cationic-like centers. Picture shown below.

As can be seen in the structure this monstrosity should have some serious pi-pi stacking possibilities, and isolating crystals shouldn’t have been too problematic, but none are isolated. An image of their NMR data for the structure above is below.

It would be at this point that the little voice in my head would be like, “hmm…. why do I have aromatic proton peaks? I should probably count those pesky buggers again. Yup, 12 delocalized electrons.” If one is postulating that this is antiaromatic, then one hallmark of antiaromatic hydrogens, located on the outside ring, are that they shift upfield (lower ppm) and lie to the right of 8 ppm and likely 7ppm. So, it would have been at that point where the paper would of confused me.

Second up the Shi paper: http://dx.doi.org/10.1002/anie.200702140
The title is the [12]Annulene Gemini Surfactants: Structure and Self-Assembly. So, we should be expecting yucky yellow oils, and with the word structure, perhaps even a crystal structure. The molecules examined are shown below.

Independently, they confirm the odd aromatic protons of Yamaguchi and they obtained a yellow powder, not necessarily an oil, but well within reasonable expectations. They did some calculations with Gaussian and discovered the results below.

The expected distorted structure is seen in II but lied 1.7 kcal/mol higher in energy than I. This is just odd, for a cyclic antiaromatic system we should expect to see 2^nd order Jahn-Teller distortions shift the molecule away from planarity and this was not seen by calculations. This is where the authors and reviewers can be faulted, at that point some one should have suggested an experiment to see whether the NMR peaks would move upfield as a function of temperature. As scientists, we love making graphs, and that would have been a neat confirmation of both the structural predictions from calculations, and an easily verifiable hypothesis.

In summary, I don’t feel it is fair to fault the authors, reviewers, editors for not knowing every obscure heterocyclic named reaction. However, it is prudent upon all of us to ask the right questions about our research, to put-off deadlines if necessary, and to apply our full intellect and diligence to our experiments.

Some Armchair commentary here:

• Pipeline: Neat wish it were true, kids these days, Exciting Nonsense Wins Another One
• Coronene: Cornies 2007: Molecule of the Year

Mitch

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The NanoArt 2007 Competition Begins

The chemical blogosphere has had their little pretty picture tangos in the past: CF, CBC, TCB, H.D

But, now you can put your SEM where your mouth is. Cris Orfescu proclaimed scientist-artist hybrid is hosting a NanoArt competition, details found here: http://www.nanoart21.org/html/nanoart_2007.html

The competition is truly open to anyone, since he offers 3 images to color if you don’t actually get to take cool nano pictures yourself. The seed photos are shown below.

So if you know how to use photoshop, you’ll be set. Good luck!

Mitch

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Chemical Graphics

A lot of recent discussions in the chemical blogosphere have centered around making Chemistry visually more stunning: TheChemBlog, Carbon, Kutti. I present my own work below. The molecule is an acetylacetate complex of Rutherfordium.

If your going to be showing off your beautifying molecule skills, bring your A⁺ game.

Note 1: Oddly enough, I believe that is the correct geometry of the complex.

Mitch

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