Most Popular Chemistry Paper for March 2012

Like January 2012, the most accessed paper for March 2012 on ChemFeeds was a small feature in Angewandte highlighting winners receiving recognition for their work, in this case the ACS 2012 National award. The winners in no particular order were David O'Hagan, Arnold L. Rheingold, Philip P. Power, Jonathan A. Ellman, Christopher A. Reed, Stephen Hanessian, Mitsuo Kira, Enrique Iglesia (not to be confused with the famous singer), and Raymond E. Schaak.

However, the honor of being the most highly accessed original science article was shared by two different JACS papers:

From Sarah Reisman's Group: Enantioselective Synthesis of Tryptophan Derivatives by a Tandem Friedel–Crafts Conjugate Addition/Asymmetric Protonation Reaction
From Aiwen Lei's Group: Silver-Mediated Oxidative C–H/C–H Functionalization: A Strategy To Construct Polysubstituted Furans

The paper with the most eye-catching graphical abstract goes to Young-Jae Oh and Ki-Hun Jeong for their Advanced Materials paper titled, "Glass Nanopillar Arrays with Nanogap-Rich Silver Nanoislands for Highly Intense Surface Enhanced Raman Scattering".

Mitch
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Most Popular Chemistry Article for February 2012

I forget that ChemFeeds allows me a very unique window into the popularity of various chemistry articles across chemistry publishers (e.g., ACS, RSC, Nature). For February, the most popular article was an editorial penned by Roald Hoffmann critiquing the chemistry community's response to the 2011 chemistry Nobel prize.

What, Another Nobel Prize in Chemistry to a Nonchemist?

For those that need to be reassured that it is okay for molecular biologists to receive chemistry Nobel prizes then I encourage you to read it.

On a side note, the most popular paper of January 2012 was "New Academicians of the Chinese Academy of Sciences" also in Angewandte. It is not a particular interesting article, but as 10% of ChemFeeds users are based in China it is not surprising.

Mitch

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Organic Chemistry Extra Credit You Tube Parody Videos

Last spring, a few of my students made me an awesome parody video of Rebecca Black's Friday, "It's Lab Day."

This semester, nearly half my class turned in lots of great parody videos.  Not all of them wanted to be shared publicly, but here are most of the videos my class made me!
 

Sunglasses in Lab

Two notes about this one: the guy singing a) is part of our university's a Capella group (no AutoTune here), and b) actually does wear tinted safety glasses in lab

Last Ochem Class

It's true that our department is broke and can't afford sep funnels, so we do extractions in measuring cups.

Organic Chemistry

A nice sampling of three songs while daydreaming in class: one I don't recognize, Billionaire, and Party Rock Anthem

OChem Rock Anthem

Keeping with the LMFAO theme.

Round Bottom Flask

Parody of Toby Keith's Red Solo Cup.  Nice shout out to James over at Master Organic Chemistry in this one.

Organic Chemistry Tips

Like Kramer's Peterman Reality Tour, I never thought someone could recreate the experience of actually being in my class, but this is pretty close.

An OChem Christmas

The students turned these in at the end of fall semester, so several had Christmas themes.  The first one has a pretty low volume, be warned, but awesome hair decorations.  Followed by The 12 Days of OChem, and O' Chemistry.

Enjoy!

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IYC2011: My 3 Things List

The goals of IYC2011 are to increase the public appreciation of chemistry in meeting world needs, to encourage interest in chemistry among young people, and to generate enthusiasm for the creative future of chemistry.

This quote from the chemistry2011.org About IYC page gives us chemists a charge: Embrace the concept that 'Science is for Everyone' and help make science in general (and chemistry in particular) more accessible to a wider audience.

This is an awesome charge.  The message of the chemist can sometimes be misinterpreted or abused for a number of reasons.  One one end of the spectrum, chemistry can be derided as witchcraft of magic by those without a general understanding of the basics of chemistry.  On the other hand, chemistry can be proclaimed as an Absolute Truth for political purposes by those without a general understanding of the nuances of chemistry.  In the middle are misinterpretations and misunderstandings of the vagueness and imprecision of our esteemed field.

So as IYC2011 draws to a rapid close, what are the 3 things you would hope the general public would see as the take-home message about chemistry?  Here's my 3 Things list:

1. "Chemical" is not a pejorative.
2. Chemicals are everywhere.  In everything.  At all times.  There is no such thing as "chemical free."
3. For the most part, chemists are not vindictive, manipulative, political, or nefarious.  They're trying to make other people's lives better everyday.  Better Living through Chemistry is not just a slogan.

So what makes your 3 Things list?  Post your list in the comments, or on your own blog.  If you blog about it yourself, let me know and I'll compile a list of everyone's 3 Things lists as updates to this post.

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Neat-o Curved Arrows in Chemdraw

UPDATE: New Catalytic Cycle video below!

James (of Master Organic Chemistry and the Reagents App/Guide fame) and I had some off-line conversations about curved arrows in ChemDraw. I don't particularly like the suite of arrows ChemDraw gives us in the Arrow Tools menu. Yeah, they give you 4 arc angles, but you have to guess if you need the clockwise or counterclockwise arrow... and I just don't like them. They look, i dunno, amateur or less professional or something.  Nothing against people who use the standard arrows, I just don't like them.

So over the years I've become quite adept at using the Edit Curve function in ChemDraw.  It allows me to make my arrows look however I want them to.  I have a couple of arrow shapes I particularly enjoy, and I use them a lot.

James (@jamesashchem) gave me a hat tip on Twitter for showing him the new arrows, at which point Mark Peczuh (@mwpeczuh) requested a public YouTube video.

So I made one.  Here it is.  If you already know how to use the Edit Curve function then cool.  If not, hope it helps

12/12/11:

Thanks to everyone who left kind comments about the curved arrow video.  Stephen Davey (@stephengdavey) asked if the Edit Curve function could make curly q arrows.  I'd never tried to make one like that before, so I took a crack at it.  Turns out, this arrow doesn't work so well with the Edit Curve function (unless some actual graphic designer knows more about making paths than I do.  If so, please let me know!!).  I ended up combining an arc, an arrow, and a circle and the effect looked ok.  Here are my failed attempts, plus the final output (click for larger):

Later, Bal (@gnak_lab) asked about an easy way to draw catalytic cycles.  I think the question was referring to the "circle of arrows" like in this mechanism for the Heck reaction.  I've done catalytic cycles before, but was never really pleased with the result either.  Then I had an idea.  You can add curvature to straight arrows... so I though if I started with a circle as a template, added the arrows, then deleted the circle, that might just work.  So without practicing first, I shot a video on me making the catalytic cycle for the Sonogashira reaction (I just recreated the mechanism from that site).  The video for that is below.  It's not a polished mechanism, I'd go back and tweak a few things, but for a first try, I think it turned out pretty well

(video at 2x speed for brevity)

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Product Review: The Reagents App

James Ashenhurst over at Master Organic Chemistry has developed an awesome new app called Reagents.  The app is perfect for students taking undergraduate organic chemistry - but anyone working with organic reagents will benefit from this app.  It's available from the iTunes App Store.

via MasterOrganicChemistry.com

The app is a list of all of the most common reagents encountered in undergraduate organic chemistry.  Selecting a link takes you to a page which gives you a short narrative overview of the reagent, an image of the structure of the reagent, and several examples of prototypical reactions using the reagent.  You can 'save' a reagent to your favorites list so you don't have to scroll through the whole list if you don't want.

This is really a heroic effort.  James and his coauthor Richard Apodaca have given organic students everywhere the handy, mobile reagent guide they all should make for themselves... but never do.  The interface is clean, readily obvious, operationally simple, and does exactly what it needs to do.  It's a slimmed down version of the full Organic Chemistry Reagent Guide James rolled out a while ago (which is also spectacular, btw). I've been playing with it for a little while now, and it's great.

The Reagents app is currently free, but that is a limited time offer and will expire soon.  Tell all your organic chemistry professor friends so they can tell their students.  It's currently only available for Apple mobile products, but according to the Reddit conversation, there may be an Android version in the works.

And thanks, James, for giving me one more reason to make sure cell phones are safely stowed during my exams.

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Tweeting to Twitter Twerps

Just letting everyone formally know that I'll be pushing new blog posts out via twitter.  You can follow me @azmanam.

Carry on.

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Organic Chemistry Reactions Mind Map

Well... this oughta cover it.

I was reading comments to my reddit submission of the many oxidation states of carbon, and Aa1979 asked if the functional groups could be arranged logically according to actual chemical transformations.  I replied that would be too reaction dependent... alcohols can be turned into a great many things (chlorides, alkenes, ketones, acids, aldehydes...), then aldehydes themselves could be turned into a great many things (alcohols, alkenes, acids, imine/enamine, acetal...).  I pointed the commenter to a post by James over at Master Organic Chemistry where he has a picture of a whiteboard-mind map of most of the reactions in a standard undergrad text.  Very impressive.

Feeling crazy, and deciding to put of lab work I should be doinghaving nothing to do, I expanded on James' mind map and tried to get as many reactions as I could on one map.  It took about a full day's work using Compendium, and here's the result (click for larger):

These are just about all the reactions you'd encounter in your standard, two semester undergraduate organic chemistry course.  Sure I probably missed a few, or maybe your institution covers reactions a bit differently, but this is fairly comprehensive.  Enjoy.

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A Classroom full of NanoKids: Pt. 3: Nanimals & Friends

To see other creative NanoKids, click here

Last installment today.  Read background about this extra-credit project in my organic chemistry class here.

Thanks for playing along.  If you have creative NanoKids you want to share, feel free to email me.

*Note: My last name starts with Az and is pronounced like Oz, hence the Wizard of "Az" theme

(Note: some captions have been edited to remove class/school specific references)
(Click images to enlarge)

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A Classroom Full of NanoKids: Pt 2: NanoPeople Doing NanoThings

To see more creative NanoKids, click here

Here's part 2 in the 3-part series on NanoKids the students in my organic chemistry class made as extra credit.  Full background here, but basically the only rule was they couldn't violate an atom's valence (had to obey the octet rule).

Next week: Nanimals and NanObjects!

Enjoy!

(Note: some captions have been edited to remove class/school specific references)
(Click images to enlarge)

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A Classroom Full of NanoKids: Pt 1: NanoSports & Nano'Tainment

To see more creative NanoKids, click here

As part of IYC2011, every week I'd discuss something cool about chemistry with my organic chemistry class. After the radical chapter, we talked about the arrow-pushing mechanism of ozone/oxygen natural interconversion and the mechanism of CFC-catalyzed ozone degradation. We talked about the funnel model of the drug discovery pipeline and how long it takes and how expensive it is and what a gamble it is to bring one new drug to market. One Friday in April we had a Breaking News version where we talked about the dangers of - and ubiquitous use of - DHMO. Things like that.

During the nanotechnology week, I showed my students some of James Tour's anthropomorphized nanoPutians.  I also showed them some of the interesting creations often highlighted/voted on over at CBC (1, 2, 3, and 4).  So I offered them some extra credit if they made me some novel and creative NanoKids of their own.  I encouraged them to be as unique as possible - but the only rule is the structures must obey the octet rule.  Naturally, I was inundated with NanoKids (I limited the submissions to 5 per student).  Over the next post of two, I wanted to share my students' creations.  This week's installment is subtitled NanoSports and Nano'Tainment.  The Nano'Tainment category is NanoKids featured in movies, TV, or video games.

Next week: NanoPeople Doing NanoThings!

(Note: some captions have been edited to remove class/school specific references)
(Click images to enlarge)

This isn't even half of them. Stay tuned for more awesome Nanokids

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A Companion Reagent Table Widget

A while ago I introduced my Reagent Table widget (and desktop gadget) I created using the widget builder on Wolfram|Alpha.  I've found the widget to be quite handy for quickly accessing physical properties of reagents from my computer.  I've embedded the widget on my personal homepage, so it's really quite straightforward to locate key physical properties as I set up a new reaction.

That's all well and good... but finding the data is only half the time-consuming problem.  The other time taker is calculating out the rest of the values in the reagent table.  If my previous posts haven't made it clear, I really like letting technology help me save valuable time.

So I made a companion widget to augment the capabilities of the first Reagent Table Widget.  This one allows you to enter an amount (either in grams, mmol or mL) of a substance and it will calculate out the rest of the values you would normally calculate: grams, mmol and/or mL.  Scroll down, and the same basic properties are listed (MW, d, BP, etc), allowing you to fill in the rest of the needed values.  Unfortunately, I cannot seem to have the CAS number included in the output.  The other widget has your CAS number information.

The coolest addition to this widget is the ability to scale your amount by, oh... say, the number of equivalents you're using.  If you've calculated that you're using 2.37 mmol of your starting material, and you need to use 1.5 equivalents of the next reagent, you can type in 1.5 * 2.37, select mmol, type in the molecule, and it will calculate your values based on 3.555 mmol!

The widget is below.  Again, feel free to embed it wherever you need it to be - blog, iGoogle, personal home page, wherever . Hover over the plus sign in the bottom right corner and click 'embed this widget.'

I'm unable to create desktop gadget versions of this one. It seems the problems mentioned with the previous desktop widgets are exacerbated when there's more than one input field. The submit functionality is totally broken. I've submitted a bug report and if it gets fixed, I'll post the desktop gadgets.

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