Ivan's weblog

My readers have been complaining that I don’t write here anymore. I’ve run out of inspiration, but here are some interesting science news:

Nature News reports that injecting the aminoacid leucine into rats’ brains makes them eat less and gain less weight. So don’t be surprised if books start to appear with titles such as “Loose 50 pounds in 24 hours with the Leucine™ diet!".

As pointed out by an anonymous reader, more retractions are shaking the chemistry world. These are for papers by Prof. Sames at Columbia about Ru-catalyzed C-H activation. Check out these blogs for more details:

blog.tenderbutton.com
paulbracher.com

Note added on March 16: Now it’s also in the New York Times

As reported in La Jornada, two Mexican scientists retracted three articles published in Journal of Organic Chemistry, Tetrahedron, and Tetrahedron Letters after finding that the results were irreproducible. The principal investigator is Prof. Eusebio Juaristi, a very well-respected chemist. It should be pointed out that this is being reported over a year after the initial retraction, so one can’t say that the scientists didn’t admit that there was something wrong with the results in a timely fashion. Making this the main front-page story in a national newspaper is an exaggeration in my opinion, especially giving it a conspiracy-theory title, but we all know that some newspapers like to dramatize things a bit…

Today I saw a fire extinguisher that had the equivalent of this NFPA diamond:

This is a standard code to tell firefighters about the risks of specific substances. The areas covered are health hazards, flammability, and reactivity.

Now, what is ironic is that, when fighting a fire, the last thing I would worry about is the hazardous (?) substances contained in the fire extinguiser itself (and I would certainly not expect them to be flammable!). But don’t worry, the 1/0/0 diamond above means “may cause irritation", and is the same as the one assigned to substances such as sodium chloride. So, in the end, this is almost like looking at the nutritional information label on a water bottle…

Disclaimer: fire extinguishers can be hardazous if misused–always use the appropriate fire extinguiser according to the fire source and conditions! (And while we are at it, don’t try this at home, eat fruits and vegetables, and talk to your doctor.)

It is often said that general chemistry students tend to have trouble with the proper use of significant figures. However, it turns out that they are in good company–quantum chemists have been doing the same mistake for years (and yes, I’m one of them!).

This article discusses the problem:

Uncertainties in Scaling Factors for ab Initio Vibrational Frequencies
Karl K. Irikura, Russell D. Johnson III, and Raghu N. Kacker
J. Phys. Chem. A; 2005; 109 pp 8430 - 8437;

http://dx.doi.org/10.1021/jp052793n

As you may know (if you do quantum chemistry), the vibrational frequencies from ab initio calculations are systematically wrong, so they are often fudged by multiplying them by a “scaling factor". This factor is usually reported with four figures (something like 0.8982).

The authors of this article estimated the uncertainty of the scaling factor itself, and concluded:

The uncertainties presented in Table 1 reveal that the scaling factors are accurate to only two significant figures. The common practice of reporting four significant figures overstates the precision of vibrational scaling factors.

Figure 2 is especially revealing. It also shows that the basis set hardly affects the scaling factor, once the error bars are taken into consideration.

So, if this article is right, it turns out that generations of quantum chemists are sometimes no better than undergrads when it comes to reporting their results with “honest” precision!

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus
Ivan Tubert-Brohman, Cristiano Ruch Werneck Guimarães, and William L. Jorgensen
J. Chem. Theory Comput.; 2005; ASAP Web Release Date: 25-Jun-2005; (Article)
doi:10.1021/ct0500287

Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate

Cristiano Ruch Werneck Guimarães, Marina Udier-Blagovic, Ivan Tubert-Brohman, and William L. Jorgensen

J. Chem. Theory Comput.; 2005; ASAP Web Release Date: 04-Jun-2005; (Article) DOI: 10.1021/ct0500803

While flipping through the new edition of Essentials of Computational Chemistry, I was pleasantly surprised to see that my article about semiempirical molecular orbital calculations of halogen-containing molecules is mentioned at the end of the relevant chapter (section 5.7.5).

I forgot to post about it, but my second paper in the Jorgensen lab was submitted last week:

Tubert-Brohman, I.; Guimarães, C. R. W.; Jorgensen, W. L. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus. Journal of Chemical Theory and Computation, submitted.

Let’s see how it does…

It seems that my friend Alán is graduating in a finite amount of time! He has 2 out of 3 signatures already.

Now I have to start working on my dissertation…

Of course, part of the reason for linking to his blog entry is that I’m new to blogs and want to test if the pingback feature really works. ;-)