SitNews - Stories in the News - Ketchikan, Alaska

Chemical Eye on Cage Compounds
by Preston MacDougall


December 05, 2006
Tuesday PM

Habeas corpus is Latin for "You should have the body". As an avid NPR listener, I recall hearing Nina Totenburg use this phrase umpteen times - even before September 11, 2001. To be perfectly honest, I had no clue what it meant. The laws of chemistry were much more important to me - that is until October 17 of this year.

If you're curious about what happened on October 17, or still in the dark (ages) about this "body business", or both, I highly recommend Jeffrey Toobin's commentary in the December 4th issue of The New Yorker. Reformatting "Killing Habeas Corpus" as a game of Clue, one possible murder scenario would be "Arlen Specter did it in the Senate Chamber with a squash racket."

That would not be the winning answer however, because C-SPAN showed President Bush doing it in the East Room with a pen.

The Bush Administration earnestly argued that the rights embodied in the "writ of habeas corpus", as well as some "quaint" Geneva Conventions, were obstacles to protecting the American people from Al Qaeda terrorists. After much deliberation, particularly in the Senate, the Military Commissions Act of 2006 was signed by the President on October 17. Judging by subsequent Op-Ed titles, this law has generated passionate interest in arcane Latin phrases, even among chemists.

Before I get to the chemistry connection, I will let Supreme Court Justice John Paul Stevens explain this "body business". The following comes from his opinion on the case (Rasul v. Bush) of suspected Al Qaeda terrorists who were trying to force the government to legally justify their incarcerations: "Executive imprisonment has been considered oppressive and lawless since John, at Runnymede (where he was forced to sign the Magna Carta in 1215), pledged that no free man should be imprisoned, dispossessed, outlawed, or exiled save by the judgment of his peers or by the law of the land. The judges of England developed the writ of habeas corpus largely to preserve these immunities from executive restraint."

In other words, when judges say to a prosecutor "You should have the body", they mean that the prisoner should be present (in body) to hear and challenge the evidence. I find both history and chemistry to be infinitely fascinating. So I was inevitably captivated by a debate that combines the Magna Carta with the right to challenge evidence - an activity that is common to courts and labs.

With hundreds of presumed "enemy combatants" imprisoned there, Guantánamo Bay reminds me of a novel class of so-called cage compounds.

Cage compounds are common in chemistry, coming in all sizes, shapes, and compositions. Some smell nice, such as the sandalwood oil component <-santalol, others are quite odious. Zeolites are minerals that can be envisioned as three-dimensional labyrinths of pores connected by tunnels. The pores can be many cubic nanometers in volume, allowing chemical reactions to occur inside, but the tunnel sizes can restrict which molecular products ever see the light of day.

Molecular size is easily estimated by adding up the average sizes of the constituent atoms. These values come in two sets: bonded radii and so-called van der Waals (nonbonded) radii. For a given atom, the former are smaller than the latter because when atoms bond to one another they get much closer than they would if they were just colliding.

Coincidentally, both sets of radii originate in California; Linus Pauling was a chemistry professor at Cal Tech when he published his classic text "The Nature of the Chemical Bond" in 1939, and Arnold Bondi was a research chemist with the Shell Development Company when he published his "van der Waals Volumes and Radii" in 1964. Even today, both are frequently used and cited as evidence in chemical research. We can call these the California Conventions.

Pauling gave no bonded radii for the noble gas elements (helium, neon, argon, krypton and xenon) because there were no known compounds of these elements. Then, in the 1960's, fluorinated compounds of xenon were made and isolated. X-ray measurements of the lengths of the bonds between the fluorine and xenon atoms confirmed that the atoms were much closer than the sum of their nonbonded radii. In other words they were bonded and these were bona fide chemical compounds.

The same thing happened with krypton, and there is tentative structural evidence of compounds of argon. Some chemists point to recent evidence of helium and neon atoms trapped inside all-carbon cage molecules as evidence of compound formation of even these inert elements. This would violate one of the long-standing "laws of chemistry".

Upon examining the evidence, the average distances between the trapped atoms and the caging atoms is much larger than the sum of their nonbonded radii.

Habeas corpus is an integral part of our legal heritage. As a nation built on the rule of law, it doesn't seem wise to yank out one of the cornerstones.

When it comes to the synthesis and understanding of chemical compounds, we have a chemical heritage as well. Part of that jurisprudence should be habeas coniunctionem, which is Latin for "You should have bonding."

On the Web:

More Chemical Eye On... by Preston MacDougall


Preston MacDougall is a chemistry professor at Middle Tennessee State University. His "Chemical Eye" commentaries are featured in the Arts and Public Affairs portion of the Nashville/Murfreesboro NPR station WMOT (

Publish A Letter on SitNews
        Read Letters/Opinions
Submit A Letter to the Editor

Stories In The News
Ketchikan, Alaska