Most Popular Chemistry Papers 2010 (1/3)

There are finally enough people visiting ChemFeeds (~150/day) that metrics like most accessed chemistry paper might actually be statistically significant information. So below I present the top two most clicked on abstracts from ChemFeeds for the first third of 2010.

First Place: Emil Knoevenagel and the Roots of Aminocatalysis
by Benjamin List in Angewandte Chemie International Edition
(DOI: 10.1002/anie.200906900)

2nd Place: Total Synthesis of the N,C-Coupled Naphthylisoquinoline Alkaloids Ancistrocladinium A and B and Related Analogues
by Gerhard Bringmann, Tanja Gulder†, Barbara Hertlein, Yasmin Hemberger and Frank Meyer in Journal of American Chemical Society
(DOI: 10.1021/ja9097687)

Some Notes on the metrics. This information probably says more about the people visiting ChemFeeds than the quality of the papers. It would appear ChemFeeds visitors skewer heavily towards the organic synthetics. Perhaps with the recent addition of being able to click on category feeds like all materials and all physical feeds it’ll balance out.

Mitch

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Is Chemistry Incompatible with Web 2.0?

(This post is in response to the April 19 editorial in C&E News.  For the response to the May 10 editorial, click here)

A recent ChemJobber post notes that C&E News Editor-in-Chief Rudy Baum‘s editorials sometimes have a tendency to approach the controversial – and sometimes the purely political.  I wanted to discuss this weeks editorial which threatens to call into question much of my online existence (sorry, Mitch.  If Rudy’s right, I think you’re about to spontaneously e-implode).

In this week’s editorial, “The Limits of Web 2.0,” Baum decries the cliché “information wants to be free” for both its out-of-context usage (the full quote says information wants to be expensive because it is valuable and free because the cost of information dissemination is shrinking almost hourly – thus a struggle) and for its lunacy (information can’t wish for anything – it’s inanimate).  Rather, Baum says that it’s people who wish that information would be free.  I’d amend Baum’s correction slightly.  People really want information to be free and readily accessible.  I’d argue public libraries have long made most information “free,” if you were willing to do the legwork to get it.

But the bulk of Baum’s editorial promotes Jaron Lanier’s book You are Not a Gadget: A Manefesto, and summarizes Lanier’s main points, namely that the wisdom of crowds can be dangerous and science should be loath to adopt web 2.0 ideals.  Lanier points out that around the turn of century, a “torrent (a word hijacked by the web 2.0 crowd -ed.) of petty designs sometimes called web 2.0″ flooded the web.  And through the use of web 2.0, we apparently are losing sight of the trees for the forest, er, the taggers for the cloud.

Baum writes in his editorial (cross-posted for free on the web 2.0 CENtral Science blog, natch), “The essence of what Lanier is saying is that individuals are important and that we’re losing sight of that at our own peril in elevating the wisdom of the crowd to a higher plane than the creativity of a single person.”  That is, we are valuing the cloud more than the individuals, when the cloud can’t exist – and has no meaning - without the existence of the individuals.  Lanier notes that collective intelligence can be used well, but only when guided by individuals who can direct the course of the hive mind and help steer clear of common groupthink pitfalls.

But the most interesting quote comes near then end, when Baum quotes Lanier as saying that scientific communities “achieve quality through a cooperative process that includes checks and balances, and ultimately rests on a foundation of goodwill and ‘blind’ elitism.”  I’m not really sure what that means…

But to Lanier’s thesis that science ought to be wary of embracing web 2.0 and its ideals, I find it interesting that Baum writes his editorial at C&E News, the magazine of the ACS, whose flagship publication, the Journal of the American Chemical Society, has featured a JACSβ page for some time now.  The same C&E News whose blog has become so popular that it had to split off into several child blogs.  Where each post for each ACS article has links to share the article on one of several social networking sites.  Where scientists can now browse their favorite article on their iphones with ACSMobile.  While perhaps late to the party in some areas, the American Chemical Society has certainly ‘logged on’ to web 2.0 as a way to export content to the web-savvy scientist.

Plus, we have our own Mitch, a one man walking encapsulation of web 2.0.  His most successful application is, in my opinion, the chemical forums, which typically sees between 8,000 and 11,000 visitors per day.  This blog seems to be a big hit, and his ChemFeeds is a one-stop source for your aggregated list of your favorite journals’ graphical abstracts.  All this innovation on Mitch’s part earned him an interview with David Bradley (of ScienceBase) in his chemistry WebMagazine, Reactive Reports.

There’s also the Chemistry Reddit as another outlet of chemistry news and notes.

In the inaugural issue of Nature Chemistry, the Nature Publishing Group recounted how they have completely bought into web 2.0 as a means of science communication – each issue of Nature Chemistry even features a roundup of their favorite posts from the chemical blogosphere (which reminds me, to the left, Mitch has also created an aggregated rss feed of several popular chemistry blogs).

And, of course, web 2.0 in the sciences has been discussed in the blogs several times over the years.  We have over 3 pages of posts categorized Web 2.0, mostly Mitch’s posts on new web 2.0 platforms he’s developed.  Jean-Claude Bradley writes about web 2.0 in response to a very interesting post at Nascent, a blog from the folks at Nature.

So, all of these prove that web 2.0 has been talked about many times in the context of science.  Has it worked?  With the exception of blogs, sadly I’m inclined to say no.  At least not yet.  And even with blogs (with the possible exception of All Things Metathesis, and In the Pipeline, though Derek isn’t allowed to talk about his work b/c of intellectual property issues), not a lot of academic or industry leaders are prone to blogging.  It’s not like we’re reading Phil Baran’s blog and getting inside his head on a daily basis.

Sure, there is a subculture of people who are active on the web 2.0 scene, but it surely hasn’t taken off as a medium for all chemists to enjoy.  It theoretically should.  Chemists are always benefited from communal sharing of results and information.  But there are still (and probably always will be) people who seem reluctant to join the new technological paradigm.  I like the way Timo Hannay words it in his post on Nascent,

“But it’s not up to the doubters to ‘get it’, it is up to those of us who support these developments to demonstrate their value. And if we can’t then they don’t deserve to be adopted and we don’t deserve to be heard.”

Especially if there are people at the position of Editor-in-Chief for arguably the top chemistry magazine denouncing the web 2.0 movement, clearly it has a ways to go before it will be appreciated by all to the point where web 2.0 is ‘taken for granted,’ where we don’t even realize what we’re doing when we post results and opinions via web 2.0 technologies.

Let’s get moving!

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This Message Will Self-Heal in 3, 2, 1…

Cassandra Fraser

Recently, Cassandra Fraser’s group reported on a very cool property, reversible mechanochromic luminescence, observed in an easy to make material.^[JACS] The molecule of interest is the difluoroboron complex of avobenzone (BF₂AVB), that UV absorbing molecule in your sunscreen minus the boron and fluorines.

In broad general language, mechanochromic luminescence describes the ability of some materials to change colors after scratching under UV light. The image below shows BF₂AVB coated on weighing paper (A), a cotton swab is used to write “Light” (B), the surface is hit with a heat-gun (C), the surface is ready to be written on again with a cotton swab (D).

The image brings up all kinds of creative ways to write secret messages, especially as the letters will fade over time even without using a heat gun. But before the CIA intelligence wonks in the audience get ahead of themselves the material doesn’t seem to be completely reversible at room temperature without annealing.

…even a small mechanical perturbation, such as a slight touch with the tip of a cotton swab, changed the green-blue BF2AVB film emission to yellow. The yellow emission gradually reverted back to green again at room temperature, with much faster recovery at elevated temperature. The written regions were no longer readable after annealing.

The field has, in short order, gotten tantalizingly close to a 100% reversible mechanochromic luminescent material at room temperature. Congrats!

Link to article: Polymorphism and Reversible Mechanochromic Luminescence for Solid-State Difluoroboron Avobenzone

Sam covered one of the first entrants to reversible mechanochromic luminescence a year ago: reversible mechanochromic luminescence is cool

Mitch

Update and Correction: Cassandra Fraser has corrected me, apparently the wording of the paper was just awkward to my ear, the material is fully reversible at room temperature!

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NanoPropulsion

Stephen J. Ebbens

Jonathan Howse

The current state of the art in nanopropulsion devices was recently reviewed by Ebbens and Howse in an article last Friday.^[SoftMatter] A short summary of the nano- systems is presented below with video action shots when I could find them.

The Whitesides

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble propulsion
Terrain: Aqueous meniscus
Max Speed: 2 cm/s
Mitch’s Name: The Karl Benz (since it was the first)
Article: Autonomous Movement and Self-Assembly

The Sen-Mallouk-Crespi

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Self electrophoresis/Interfacial tension
Terrain: Settled near boundary in aqueous solution
Max Speed: 6.6 um/s
Mitch’s Names: The Ford Mustang of nanopropulsion. (It is a hot rod, get it?)
Article: Catalytic Nanomotors: Autonomous Movement of Striped Nanorods

The Jones-Golestanian

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Pure self diffusiophoresis
Terrain: Free aqueous solution
Max Speed: 3um/s
Mitch’s Name: The Volkswagen Beetle
Article: Self-Motile Colloidal Particles: From Directed Propulsion to Random Walk

The Mano-Heller

Catalyst: Glucose oxidase and Biliruben oxidase
Fuel: Glucose
Propulsion: Self electrophoresis
Terrain: Aqueous meniscus
Max Speed: 1 cm/s
Mitch’s Name: The Komatsu Truck (because it is huge)
Article: Bioelectrochemical Propulsion

The Feringa

Catalyst: Synthetic catalse
Fuel: H₂O₂
Propulsion: Bubble/interfacial
Terrain: Acetonitrile solution
Max Speed: 35 um/s
Mitch’s Name: The F150 (has some exhaust issues)
Article: Catalytic molecular motors: fuelling autonomous movement by a surface bound synthetic manganese catalase

The Sen-Mallouk

Catalyst: Pt (CNT) (+cathodic reactions at Au)
Fuel: H2O2/N2H4
Propulsion: Self electrophoresis
Terrain: Settled near boundary in aqueous solution
Max Speed: 200 um/s
Mitch’s Names: The Ford Mustang GT (has more kick than the regular version)
Article: Bipolar Electrochemical Mechanism for the Propulsion of Catalytic Nanomotors in Hydrogen Peroxide Solutions

The Feringa v2

Catalyst: Glucose oxidase and catalse
Fuel: Glucose
Propulsion: Local oxygen bubble formation
Terrain: Free aqueous buffer solution
Max Speed: 0.2–0.8 um/s
Mitch’s Name: The Chevrolet Nova (more hot rod action)
Article: Autonomous propulsion of carbon nanotubes powered by a multienzyme ensemble

The Gibbs-Zhao

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble release mechanism
Terrain: Aqueous solution
Max Speed: 6 um/s
Mitch’s Name: The Rover
Article: Autonomously motile catalytic nanomotors by bubble propulsion

The Bibette

Engine: External magnetic field
Propulsion: Flagella
Terrain: Aqueous solution
Max Speed: unknown
Mitch’s name: The BMW Mini E (because there is no such thing as a magnetic car)
Article: Microscopic artificial swimmers

The Sagués

Engine: External magnetic field
Propulsion: Doublet rotation coupling with boundary interactions
Terrain: Settled near boundary in aqueous solution
Max Speed: 3.2 um/s
Mitch’s Name: The Smart ED
Article: Magnetically Actuated Colloidal Microswimmers

The Fischer

Engine: External magnetic field
Propulsion: Propeller drive
Terrain: Aqueous solution
Max Speed: 40 um/s
Mitch’s Name:
Article: Controlled Propulsion of Artificial Magnetic Nanostructured Propellers

The Najafi-Golestanian

Engine: Conformation changes in linking units
Propulsion: Time irreversible translations
Terrain: Free solution
Max Speed: ?
Mitch’s Name: The Eternal Concept Car
Article: Propulsion at low Reynolds number

Some devices that were not included by the authors of the review article, but should definitely be included in any list like this are below:

The Gracias

Engine: External magnetic field
Propulsion: Brute Force
Terrain: Aqueous solution
Max Speed: ?
Mitch’s Name: The Truck Cranes
Article: Tetherless thermobiochemically actuated microgrippers

Tetherless Microgrippers Grabs Tissue Sample – Watch today’s top amazing videos here

The Nelson

Engine: External electromagnetic fields
Propulsion: Flagella
Terrain: ?
Max Speed: 18 um/s
Mitch’s Name: The Tesla Roadster (simply awesome)
Article: Characterizing the Swimming Properties of Artificial Bacterial Flagella

Artificial Sperm – Watch more funny videos here

Link to Review Article: In pursuit of propulsion at the nanoscale

Mitch

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Crystals from IR Lasers

I was perusing Chem Feeds when this paper caught my eye with its snazzy abstract (right). The authors, Alexander et al., report crystallizing a supersatuated solution of KCl in agarose gel by using an IR laser. They are capable of crystallizing any pattern of interest by using a mask. The nice thing about using an IR laser is it won’t cause your solute to have side photochemical reactions from this process.

Although the highlight of the paper is its potential use as a 2d or 3d method of controlled crystallization, I wonder how well the general method of nonphotochemical laser induced nucleation (NPLIN) is at crystallizing stubborn molecules that normally are a pain to crystallize at the bench. Any new tricks that will decrease the time it takes to make nice crystals would be appreciated by myself and I’m sure others…

Amazon

Link to Alexander et al.’s JACS paper: Spatial Control of Crystal Nucleation in Agarose Gel

Update (August 6th): Aaron Rowe covers this in C&EN — Lasers Spark Crystal Growth

Mitch

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Magnetic Levitation: Because TLC Plates are so 20th Century

Mirica et al. had an awesome JACS communication out last week. They use magnets to track the progress of reactions. A schematic is shown below.

By using a paramagnetic solution (GdCl₃) and polymeric beads as their solid support, they monitor the progress of reactions as a function of their beads’ height. The setup is very sensitive to the density (g/ml) of the beads, thus as the beads are chemically modified the height changes. The beads cluster together when they are mostly all starting material or product. They spread out as different beads take different amounts of time to become fully reacted. Some images from their paper and supporting information really highlight this effect.

Reprinted with permission from the American Chemical Society: Journal of the American Chemical Society (Dec. 2008).

What else can we use magnets in the lab for, ideas anyone?

Link to article: Using Magnetic Levitation To Distinguish Atomic-Level Differences in Chemical Composition of Polymers, and To Monitor Chemical Reactions on Solid Supports

Mitch

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32-electron chemistry

We all remember learning about octets and valence electrons in school. We may also remember the first time we saw an 18-electron transition metal complex. This week Dognon et al. discuss the possibility of 32-electron organometallic complexes.^[JACS] In order to reach 32-electrons, f-orbital participation is essential. Below is a picture of a hypothetical organometallic complex with 28 carbons in a cage around an actinide element.

Although these systems are not new, as the Smalley group made U@C₂₈ in the gas-phase in ’92,^[Science] Dognon et al. examine a series of these systems for different actinides. The major conclusion is that the plutonium system is theoretically predicted to have the largest bonding energy for its Pu⁴⁺@C₂₈ complex. Since fullerenes and the intercalation of metals often only need heat to be synthesized, I wouldn’t be surprised if these complexes have already been made but missed as impurities and byproducts.

Link to paper: A Predicted Organometallic Series Following a 32-Electron Principle: An@C28 (An = Th, Pa+, U2+, Pu4+)

Update 1: Jyllian Kemsley also covered it at C&EN — Stable Caged Actinides Proposed(subscription)

Mitch

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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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Problems with Aryl Enediyne Cyclizations?

Enediynes are lovely functional groups that are famous for undergoing Bergman cyclizations as shown below.

Scheme 1. Bergman cyclization.

Vavilala et al. have found an alternate reaction pathway for thermal enediyne cyclizations when bulky aryl groups are attached to the terminal ends; they observed indene formation.

Scheme 2. Pascal cyclization anyone?

Making indenes from enediynes is an old trick, either by photochemical or some exotic initiator, the caveat with this work is it runs under thermal conditions. The reaction they ran is shown below.

Scheme 3. Thermolysis (TCP = 2,4,6-trichlorophenyl)

No Bergman cyclization products were observed. The idea being, the distance of the terminal carbons (C¹-C⁶) is crucial in determining which type of cyclization will occur. An interesting part of the paper is Matzger gets mentioned by name as a referee and as holding a different opinion of the authors, he basically argues the results are due to transfer hydrogenations from bergman cyclization intermediates. Definately an interesting read if you have time.

Link to paper: Thermal C¹-C⁵ Diradical Cyclization of Enediynes

Mitch

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