Articles by: orgopete

Peer review and the new media

I attended a Macintosh Users Group recently. (Yes, I am a Mac user.) This meeting was unusual. Natali Del Conte, a tech writer for CNet and CBS, was the featured speaker. She talked about being authentic, social networking, and how technology has changed how we get information. She argued that gone are the days that information is simply pushed to us and that Walter Cronkite is the most trusted name in news.

A detail I have come to think more about is what we know. I remember that stomach acid was thought to cause ulcers, but Marshall and Warren have received a Nobel prize for their discovery of the role of Heliobacter pylori and its role in peptic ulcers.

Mitch (Feb 08) and azmanam (Feb 02) have posted on congressional misunderstanding of science and false or poor science reporting, respectively, but I don’t think chemists are as cognizant of the accuracy or correctness of textbooks or peer reviewed papers. There have been a few cases in which errors have entered the chemistry world.

I wrote the the archivist at the Oregon State University Library inquiring about whether there was any correspondence regarding a paper Pauling published (there wasn’t). I wondered what the referees may have said.  Now, I have been thinking how this is like the comments to a blog post. One of the really interesting things about the new media, is errors can be pointed out. They can be argued and open to everyone.

I have been thinking about how our ideas of atomic theory have evolved. In doing so, I have been reading a fascinating series of transcripts from recordings deposited at the Center for History of Physics of the American Institute of Physics.

It was interesting that some people thought Niels Bohr had confused the literature with his papers. However, overall, what I liked was how these transcripts contained the personalities of the scientists, their interests, and in some cases their ideas (or biases) about topics being discussed. I felt these transcripts from leading scientists were like our modern internet (although generally without the details of the science).

Our modern internet has no rules. It can be difficult to sort out the wheat from the chaff. We need to learn who to follow and who to ignore. Peer reviewed journals only give the filtered result. The referees reports are confidential. Comments are not published except in blogs. Now that science is moving toward electronic publication, would a new model for scientific publication improve the scientific world?

Just to note that this is not unusual in chemistry. Organic Synthesis has long provided a kind of review for a select set of procedures. I don’t foresee H.C. Brown’s papers becoming ignored, but independent reports could prove useful. Similarly, critical steps to improving yields  would be helpful. You can find examples of this in the Organic Chemistry Forums.

Should online journals allow comments? Would it be useful? How could it be done? Would it be science?

By February 25, 2010 13 comments opinion

How Water Freezes Lower on a Negatively Charged Surface

I first heard this on National Public Radio and then I searched for it. In short, David Ehre, Etay Lavert, Meir Lahav, and Igor Lubomirsky report in Science, (Water Freezes Differently on Positively and Negatively Charged Surfaces of Pyroelectric Materials) water freezes at a lower temperature (-18°C) on the negatively charged side of a lithium tantalate plate with a strontium titanate film than on the positive side (-7°C, and -12°C uncharged).

Is this unique or is this a manifestation of something in our standard introductory organic chemistry textbooks? I thought it was the latter. Let me explain how.

For the purpose of thinking about this problem, let us assume the metal surface is simply a flat charged surface, without contour. If the surface has a negative charge, then the water should be attracted like a flagpole. One hydrogen should be anchored to the surface of the metal at right angles and the other hydrogen could spin about that axis with the flag hydrogen at 105°. It should not be surprising that this configuration should not be as good of a surface as one with greater rigidity.

If we compare with the positively charged surface, then both pairs of non-bonded electrons should be anchored to the surface and locking the hydrogens in a fixed position. This should limit the degrees of freedom and enable crystal growth.

For those that may be wondering where this is found in your textbook, it may not be there. The negatively charged surface is the one that seemingly will have the most important stereochemical constraints and information in a textbook. The analogy I was comparing is the stereochemical restrictions of proton transfer reactions. In that context, the angle between a proton and donor-acceptor electron pairs in a hydrogen bond is usually 180°. One can find smaller bond angles in intramolecular proton transfer reactions, such as the decarboxylation of a beta-ketoacid or a Cope elimination reaction of an amine-oxide as six and five-membered ring examples.

You may also encounter a … transition state which transfers a proton via a four-membered ring. While this mechanism is present in some textbooks, I am troubled by a lack of precedent for this proton transfer. In a normal hydrogen bond, the preferred bond angle is 180°. Variations from 180° are commonly found in six and five-membered rings …

While the four-membered ring is expedient and avoids a zwitterionic intermediate, I am skeptical sufficient experimental data exists to support it. In the normal hydrogen bond, the electron-electron repulsion forces the nuclei to be linear.  While smaller angles are present in six and five-membered rings, a continued decrease in bond angle increases the electron-electron repulsion exponentially as predicted by Coulomb’s Law. This could be compensated for with a large nucleus…. A larger nucleus can attract electrons and mitigate their repulsion. However, I have resisted writing any examples of proton transfers via four-membered ring intermediates. [A Handbook of Organic Chemistry Mechanisms, p 65]

I could have drawn a model with two attachments points for water. That would probably look better if a plane charged surface is present rather than several pairs of electrons. If a two point model were to be present, then another model for the melting point difference is needed.

P.S. this is my first post here. As I often seem to think of something bleeding edge, not obvious, heretical, or downright wrong, I hope if there were any comments, this is just an idea. I may change my mind tomorrow.

By February 10, 2010 3 comments science news