glowing bananas

October 13, 2008 at 2:58 pm | | crazy figure contest, literature

Great paper in Angew. from Nick Turro and others: Blue Luminescence of Ripening BananasAngew. Chem. Int. Ed. 2008, 47, 1-5.

The figures are deliciously entertaining!

no figures!

October 10, 2008 at 1:14 pm | | crazy figure contest, literature

This Science paper has no figures. Surprising, with words like “Illusory Pattern” in the title. But I truly appreciate that, if they didn’t need one, the authors decided not to waste space with a superfluous image.

i guess this is how you comment on a JACS comm

September 29, 2008 at 11:15 am | | crazy figure contest, EDSELs, literature, science community, scientific integrity

So I guess there’s not really an official way to get a comment published in JACS. So I’ll be a jerk and complain to everyone on the AEthernet. I saw a paper in JACS which really caught my eye, an interesting title for me, who designs fluorophores:

Yamaguchi, Y.; Matsubara, Y.; Ochi, T.; Wakamiya, T.;  Yoshida, Z.-I. How the pi Conjugation Length Affects the Fluorescence Emission Efficiency. J. Am. Chem. Soc. 2008 (ASAP).

And, of course this amazing fit to data in the TOC image (scroll down to see what this plot should look like):

My first thought was, Whoa! Then I immediately thought, Wait, why do all the points fall exactly on the theory line? That’s unusual. Still, I read the paper with much interest. By the time I got to the end, I earnestly thought it might be an April Fools edition JACS.

I followed the basic theory (Marcus-Hush theory) and the mathematical manipulations. Their result was fascinating: the length of the pi conjugation should directly influence the deexcitation rates: , where Aπ is the length of the conjugation, Β is a constant (approximately 1 Å-1), c is the speed of light, ν is the emission frequency, h is Planck’s constant, and kr and knr are the radiative and nonradiative deexcitation rates, respectively. This is interesting, because fluorescence quantum yield (Φf) is defined by those same rates: . So inserting an equation that depends on conjugation length should be a simple and interesting result.

But, for some reason, the authors normalize out the leading factor. I didn’t really understand why. Anyway, the final result is a little different than I would have figured: . Now, somehow Aπ can be negative, and the authors justify that with the fact that it had become a logarithm in their mathematical gymnastics. I won’t really argue that that’s wrong, because I don’t understand why they did it in the first place.

And here comes the central problem with the paper. In order to confirm this theoretical relationship between quantum yield and pi length, they plot the theoretical equation along with data they have measured (plot above). But they never measure Aπ, they calculate it from the measured rates listed in the table; those same rates were calculated from the measured quantum yield. This is circular logic. So there’s no “correlation between absolute fluorescence quantum yield (Φf) and magnitude (Aπ) of π conjugation length,” as they claim. Instead, they simply plot the ratio of rates versus a different ratio of those same rates. The real axes of the plot are  on the ordinate and  on the abscissa. That’s totally unfair and misleading!

They claim that other independent measures of pi length also work, and that is shown in (of course) the Supporting Information. There, they do give some analysis using Δν1/2a3/2 as a value for Aπ, where Δν is the Stokes shift in a given solvent, and a is the Onsager radius of the molecule in a continuous dielectric medium (taking the relevant factors of the Lippert-Mataga equation). The authors chose not to plot this analysis—they offer only a table—so I’ll plot the real results for you:

That’s sad. Note also that the calculated values cannot be less than 0.5, because size is always positive and even zero for this Lippert-Mataga value of Aπ means that the exponential goes to 1 and the denominator of the new theoretical quantum-yield equation goes to 2.

How does Aπ scale with the Onsager radius or the Lippert-Mataga measure of size?

Well, there is a trend. Not a great trend, but a trend nonetheless. This paper would have been a lot better if they had explored these relationships more, finding a better measure or estimator of size or Aπ. Instead, the authors decided to deceive us with their beautiful plot.

Assumptions in this paper:

  1. That all the nonradiative pathways come from intramolecular charge transfer.
  2. That the emission wavelength does not change with increasing pi conjugation.
  3. For the independent test, that the charge transfer in all cases is unity, so that the change in dipole moment from ground to excited state equals the distance over which the charge transfer occurs.

Assumption 1 is fair, but not entirely applicable in the real world. Assumption 2 is patently false, which they even demonstrate in one of their figures; however, that may not be this paper’s fatal flaw. Assumption 3 is, well, fine … whatever. The real problem is that the authors do not independently test the theoretical prediction, and use circular logic to make a dazzling plot (dazzling to the reviewers, at least).

The biggest disappointment is that the approach and the concept is really interesting, but the authors fail to follow through. I think this could have been an great paper (or at an least acceptable one) if they had been able to demonstrate that the deexcitation rates (and thus the quantum yield) did depend on the size of the pi conjugation. For instance, if the authors had been able to accurately predict pi-conjugation length using the experimental deexcitation rates, then they could have then flipped that and predicted quanum yield from the size. Instead, there’s just a stupid plot that doesn’t make any sense.

So this paper wins an EDSEL Award for the worst paper I’ve read in JACS. I have no idea how that even got past the editors, saying nothing of the reviewers! That said, I am willing to admit my ability to be totally wrong. If so, I apologize to everyone. Please let me know if I made any mistakes.

metabolic pathways made easy

September 25, 2008 at 8:05 am | | crazy figure contest, great finds

Nick was kind enough to send our lab this helpful chart of metabolism pathways (from Sigma Aldrich):

I think Nick put it best: “This really helps to put different aspects of metabolism into perspective.  Sort of.”

what is the SPF of hair?

September 23, 2008 at 5:28 pm | | crazy figure contest, literature, science@home

Hair provides about SPF 10 UV protection to the head. At least according to this recent paper: Parisi, et alSolar Ultraviolet Protection Provided by Human Head Hair. Photochem. Photobiol. 2008. The intersting thing is that long hair provide about the same or even less UV protection than short hair. The authors posit that this could be because long hair is more likely to part and expose the scalp.

Oh, that’s how they did it.

Squeezed Light

February 17, 2008 at 3:25 pm | | crazy figure contest, literature

A figure from “Manipulating the Vacuum: Squeezed States of Light (Eur. J. Phys 9 (1988) 257).


While the figure was cute, I was more impressed with how it was directly referenced in the text:

The uncertainties in E and B are non-zero even in the vacuum state (where no photons are present). Squeezed light (see figure 1) has the property of a lower level of uncertainty in either E or B than the vacuum state.

conference registration

February 10, 2008 at 10:27 pm | | conferences, crazy figure contest, literature, science community


I always register for a conference the second I receive the annoying email two years in advance. But not everyone does, apparently. Someone wrote a letter to Nature Physics, analyzing the time distribution of registrations to a few conferences. The bottom line: people universally wait till the last minute. No kidding?

“The distribution of registrations … up to the main deadline for abstract submission (T*)…. The inset shows the distribution in time of payment of the conference fee (credit-card payments only): the distribution is more peaked towards the deadline because, although registration is reversible, payment is irreversible.”

(Via Metadatta.)

what a happy lightbulb!

January 10, 2008 at 6:56 pm | | crazy figure contest, literature

Another one for the silly-figure contest:


This is the table-of-contents image for a recent JACS paper: “Solid-State Photodecarbonylation of Diphenylcyclopropenone: A Quantum Chain Process Made Possible by Ultrafast Energy Transfer“.

I suppose that this silly image is germane to the subject of the paper (especially the “chain process”). But, really?!? How old are we? Some people have fun with TOC images, I suppose.

In fact, is that the little MS guy that helps me figure out things in Excel? Microsoft should sue for copyright infringement.

what’s wrong with this picture?

January 1, 2008 at 9:35 pm | | crazy figure contest

Sorry, my site has been down for a few days. Here’s a treat for the eye:


What’s wrong with this picture?

bad chemicals

October 24, 2007 at 8:58 am | | crazy figure contest, literature, nerd

OK, I know this is old news (Paul already blogged about it), but I just received my very own hard copy in my mailbox, so I have to post it:

I just love this! I want to use it next time I teach gen chem. I know chemistry can be hard. Look, even OUP and ACS get it wrong sometimes. And I mean really wrong.

What I don’t understand is how did they do this?!? Which chemical-drawing program let’s you make a hydrogen join the ring of benzene? Or have oxygen form four bonds? Or… They must have had little red squares all over their screen!

what a silly figure!

September 2, 2007 at 10:02 am | | crazy figure contest, literature

Here’s a great figure. Very informative. Just look how happy people will be to walk through this scanner!


Strange. This is from a real paper: Applied Optics, 46 (25), 6232-6236, 2007.

Thanks to Spectroscope for this one!

Laugh it up, Fuzzball

July 18, 2007 at 9:16 am | | crazy figure contest

The figure is from an economics editorial from the Wall Street Journal. Since nothing I could say can do a better job than Dr. Chu-Carroll, I’ll let him do the discussing. I guess us crazy chemists aren’t the only ones that can fit a 10th order polynomial to 2 points.

Fun with lines

July 11, 2007 at 2:40 pm | | crazy figure contest, literature

Found this figure on the JACS online front-end graphic in this month’s edition.

They drew a line through 2 points, and missed one of the points in the process. Having never actually collected data to publish, I’m a little mystified by these graphics, since they aren’t from the paper. I’m sure in some context it would make sense, but I’m going to go ahead and just assume they haven’t pulled out the ol’ bore sighter for their fitting software in a while.

While we’re on the subject, do you submit these graphics in addition to your manuscript? I recall one graphic that looked like it was drawn on a piece of notebook paper a while ago.

Science Fair

June 17, 2007 at 3:06 pm | | crazy figure contest, science and the public, science@home

Last weekend I had the pleasure of judging middle school science fair projects. It’s always refreshing to see the kids interested (or at least pretending to be interested) in science. There were a lot of great projects. It was also nice to have a coordinator that wanted us to find a winner, instead of the “everyone’s a winner” approach I’ve encountered judging at some other schools. In honour of their efforts, I’ve put together my own science fair project.

How do glasses relax? This is important because glasses are important for people with bad site to see good.

I think glasses will relax. I think this because if glasses didn’t relax, then we wouldn’t be able to see through them. But I’ve seen through a glass before, so it must have relaxed.

1) Paper
2) Pencil
3) Regeneratively amplified femtosecond Ti:Sapphire oscillator
4) Stopwatch
5) Notebook
6) Something to make things cold

1) I ask 5 friends, David, Melissa, Lindsay, Billy, and Rainbow if they thought glasses relax.
2) I wrote down what they said, and averaged the results.
3) Make a liquid supercold.
4) Shine a lazer through it, and see what comes out.
5) Analyze your results.

My independent variable was the number of people I asked. My dependent variable was if the glass relaxed.

These were my results.

As your can see, David, Melissa, and Rainbow all said that glasses relax, while Billy and Lindsay said glasses cannot relax. This confirms my hypothesis that glasses can relax, because more people think glasses can relax than glasses cannot relax.

My hypothesis was correct. If I could do this experiment again, I would see if playing different types of music would make the glasses relax faster. This experiment was important because it shows science works.

100 Great Science Fair Thesis Projects

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