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.


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  1. That the emission wavelength does not change with increasing pi conjugation.


    Thanks Sam. What a silly paper. Anyone (who is more on the organicy side of things) interested in this idea of fluorescence vs. conjugation length might want to look at this paper first.

    Comment by excimer — September 29, 2008 #

  2. Yeah, assumption #2 made me giggle as well.
    Man, those plots are hideous.

    Comment by psi*psi — September 29, 2008 #

  3. does the image after the third paragraph show up for everybody? i’m trying to be “legal” by not uploading the image.

    Comment by sam — September 29, 2008 #

  4. Yup, the image shows up fine. How could anyone look at that graph and not be immediately suspicious?

    Comment by Steven N. Severinghaus — September 30, 2008 #

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