Gronert vs protobranching

21 May 2009 - Thermochemistry

In the universe of simple hydrocarbons, branches are stabilizers: isobutane is more stable than n-butane and neopentane is more stable than isopentane. As to the reason why, there is not exactly agreement. Classic explanations point to stabilizing C-C-C, H-C-C and H-C-H 1,3 interactions based on hyperconjugation. In 2006 Scott Gronert turned things upside down and proposed a group additivity model in which these interactions are in fact described as destabilizing with other factors more stabilizing than previously thought and preserving the balance (DOI). In his view this 1,3 repulsion is simply a case of steric hindrance and can only be destabilizing.

In 2007 a group around Schleyer introduced a novel concept called protobranching, defined as the net stabilizing 1,3-alkyl-alkyl interactions existing in normal, branched, and most cycloalkanes (methane and ethane excluded) that they used to reassess several important energy contributions to thermodynamical stability such as resonance energy (DOI). This concept of course is a direct assault on the Gronert model and in a recent article called The Folly of Protobranching - generously sprinkled with exclamation marks - the man himself counters (DOI).

In the Schleyer model, propane has one protobranch, two protobranches can be found in n-pentane, three in isobutane and 6 in neopentane. Its energy content can be calculated from the simple hypothetical reaction of neopentane with methane to give ethane. In this isodesmic reaction (without any real life significance) the type of bonds in the participating molecules do not change but in the reaction product all protobranches are removed. The enthalpy change that can be calculated from the heat of formation - you do not have to own a lab for this kind of research , a pocket calculator suffices - can therefore be entirely attributed to the effect of protobranching, arriving at an enthalpy per protobranch of 2.28 kcal/mol.

According to Schleyer, the protobranching model has some serious consequences for several commonly held stability beliefs. Take for instance cyclopropane whose strain energy of 27 kcal/mol can be calculated from the isodesmic reaction of cyclopropane with 3 eq. of ethane to form 4 eq. of propane. Problem is that in this reaction the reaction product is burdened with protobranches and therefore this strain energy is overestimated by 10 kcal/mol. Likewise the resonance energy found for benzene (36 kcal/mol) is actually twice as high when correcting for perturbing effects not only of protobranching but also that of regular conjugation and hyperconjugation.

Enter Gronert. He argues that additivity schemes involving heats of formation are a a data-fitter's dream. He also recalls that in simple alkenes CCC angles are expanded at the expense of HCH and HCC angles, clearly establishing that 1,3-interactions are repulsive. An attractive force would require the the invention of a heretofore-unknown intramolecular interaction. Gronert also wonders why protobranching is nonexistent in intermolecular interactions or in alkenes where it is replaced by hyperconjugation. Protobranching is also sending out confusing messages: ''Do the similar stabilization energies of the C7 species norbornane (13.8 kcal/ mol) and n-heptane (14.1 kcal/mol) imply that they have approximately the same level of strain?".

This debate is no doubt going to be continued and feels similar to the phenanthrene hydrogen bonds debate. It certainly belongs in the unsolved problems in chemistry category.


Making it move

12 May 2009 - autonomous movement

Converting chemical energy into motion can be done on a molecular level with synthetic molecular motors and on a larger scale regular molecular motors facilitate the motion of proteins and cells. In the macroscopic world the mercury beating heart and the tears of wine demonstrate how certain chemical phenomena can also drive motion.

The so-called camphor boat (Nakata et al. 2006 DOI) is an example of current research into autonomous motion. It consists of a small disk (3 mm diameter) of camphor or camphanic acid mixed with KBr (think IR spectroscopy) which is placed on water in a petry dish. It cannot be avoided that the disk is slightly asymmetric and as the acid slowly dissolves in water, a camphanic acid layer that forms around the disk is also asymmetric. The disk will then move in the direction of the water with lower concentration of camphanic acid due to the higher surface tension (see the Marangoni effect for the physics involved) and hey presto, autonomous motion!. Added surfactants can make the motion stop and resume again reminiscent of a chemical clock.

Another self-propelled system, demonstrated by the Whitesides group, consists of placing a small disk of platinum in a hydrogen peroxide solution filled tub. As the metal is oxidized by the peroxide, bubbles of hydrogen gas escape from its underside providing the propulsion (Ismagilov et al. 2002 DOI). The Pt disk is coated with PDMS with one side made hydrophilic by plasma oxidation and this enables two disks to attract each other creating a form of self-assembly. Multiple chiral disks (adjusting PDMS shape and position platinum "eye") can mimic swarming behaviour of animals.

What is still missing in these exploits is of course directed motion. In a peculiar segmented platinum/nickel/gold/nickel/gold nanorod (length 1.5 micrometer) / hydrogen peroxide system, the Pt segment as before provides the locomotion (explanation is slightly different: dissolved oxygen causing a surface tension gradient) and an applied magnetic field align the rods through the nickel segments (Kline et al. 2005 DOI). The scientists responsible were able to coerce the nanorods into spelling their university's call sign and there are worse ways to spend your Sunday afternoon.

A most recent contribution from the Jean Fréchet group goes to show that you can even use light to directly and controllable propel objects floating on a liquid. Well known manifestations of converting light to work are the Crookes radiometer and the solar sail. The novelty approach (Okawa et al. 2009 DOI) consists of a small block of PDMS (millimeter scale) covered on one side with a so-called carbon nanotube forest material. This is the blackest known material and any incident light is effectively converted to heat which in turn heats up the liquid surface which in turn creates a surface tension gradient and ultimately motion. With a modest speed of 8 cm/s this device still outperforms the other contestants but the race is far from over.

Nanotubes unzipped

03 May 2009 - Nanotechnology

Two back-to-back articles in the April 16 issue of Nature report on how to get nanoribbon from nanotubes. Nanotubes are the cylinders of chicken-wire hexagons of carbon and nanoribbons are the graphene strips so making one using the other makes sense. Graphene nanoribbons have been produced before by lithographic patterning of graphene sheets, by chemical vapor deposition and by sonification of graphite.

A group around James M. Tour (of nanocar fame) has successfully cut open a multiwalled nanotube lengthwise in a sulfuric acid / potassium permanganate solution in water (Kosynkin et al. DOI). The permangate oxidizes the double bonds in the nanotube just as in regular alkenes and the newly formed nanoribbons have the edges all oxygenated by ketone groups. Reduction was accomplished with hydrazine and ammonium hydroxide and a surfactant. The nanoribbons (yield > 90%) are difficult to work with, they easily fold on to itself (like adhesive tape) and tend to aggregate. It is was not possible to distinguish between zigzag edges or so-called armchair edges.

In the second article, Jiao et al. (DOI) take another approach and simply etch away the top from a nanotube by argon plasma etching. They do this in several steps: deposition of MWCNT material on silicon, spin-coating a layer of PMMA on top of it (partially submerging and protecting the tubes), peeling away the film thus obtained and apply the plasma. The top half is basically destroyed, reducing the yield to 20%.

These are two successful methods for the unzipping of nanotubes but should also be applicable to fullerenes. Some effort has already been spent in opening up fullerenes for example see Endohedral hydrogen fullerene.

The Bargellini reaction

02 May 2009 - Named reactions

Name: Bargellini reaction - Bargellini, G. Gazz. Chim. Ital. 1906, 36, 329
What: multicomponent reaction of a phenol, a ketone, chloroform and potassium hydroxide forming a sterically hindered alpha-phenoxy-isobutyric acid:


Recent sightings: the reagent chloretone is the ketone and chloroform rolled in one for example (Cvetovich et al. DOI):

The reaction is also found to work with aniline derivatives (Butcher et al. DOI):