Archive for December, 2010

Mechanochemistry II

Mosey has a nice follow-up study on the origin of Woodward-Hoffman forbidden ring opening of cyclobutene under mechanical stress.1 (See this blog post discussing the earlier work of Martinez.2) Pulling on cis substituents of a cyclobutene causes the ring to open in a disrotatory fashion. Normally, the WH forbidden pathway is accessed by photolysis which creates a new electronic state. Mosey asks if this same mechanism is occurring during mechanical stress.

On the face of things, this seems unlikely; how can a mechanical force lead to a new electronic state? CASSCF computations with either no applied external force or with varying sized external forces and IRC computations help answer this question. Without an external force, a diradical (or at least a species with high diradical character – and this could be the transition state) is found along the disrotatory pathway. This same diradical is found regardless of the size of the externally applied mechanical force. What does change is the position of the TS along the pathway: as the force increases, the TS becomes earlier, and the reaction barrier diminishes. No change in the electronic state is affected by the applied mechanical stress.


(1) Kochhar, G. S.; Bailey, A.; Mosey, N. J., "Competition between Orbitals and Stress in Mechanochemistry," Angew. Chem. Int. Ed., 2010, 49, 7452-7455, DOI: 10.1002/anie.201003978

(2) Ong, M. T.; Leiding, J.; Tao, H.; Virshup, A. M.; Martinez, T. J., "First Principles Dynamics and Minimum Energy Pathways for Mechanochemical Ring Opening of Cyclobutene," J. Am. Chem. Soc., 2009, 131, 6377-6379, DOI: 10.1021/ja8095834

electrocyclization Steven Bachrach 20 Dec 2010 1 Comment

Catalyzing the keto-enol tautomerization

Proton and hydrogen transfers can be catalyzed by many things. Da Silva shows that carboxylic acids can catalyze the hydrogen shift that converts an enol into a carbonyl species.1 The specific example is the ethenol to acetaldehyde tautomerization. This reaction has a barrier of 56.6 kcal mol-1 (computed using the composite method G3SX).

With formic acid as the catalyst, the reactant is the hydrogen-bonded complex of ethanol with formic acid and the product is the complex of acetaldehyde with formic acid. The transition state is shown in Figure 1. The barrier is only 5.6 kcal mol-1, a significant reduction. da Silva discusses how carboxylic acids might be catalyzing the enol-keto tautomerization in the troposphere and also in combustion reactions.

Figure 1. B3LYP/6-31G(2df,p) optimized TS of the formic acid catalyzed enol-keto tautomerization of acetaldehyde.


(1) da Silva, G., "Carboxylic Acid Catalyzed Keto-Enol Tautomerizations in the Gas Phase," Angew. Chem. Int. Ed., 2010, 49, 7523-7525, DOI: 10.1002/anie.201003530

Keto-enol tautomerization Steven Bachrach 08 Dec 2010 6 Comments

AIM analysis and molecular structure

Bader has been advocating for his topological electron density method (also called AIM for “atoms in molecules”) as the answer to most fundamental chemical issues for a couple of decades now. He summarizes his position regarding molecular structure in a recent paper.1 Here he argues that physics (meaning quantum mechanics) provides a way to uniquely and non-arbitrarily define molecular structure. The atom is defined by the volume enclosed by zero-flux surfaces around a nucleus. The bond path indicates which atoms bind together.

He is careful to indicate that the chemical bond, used in a sort of intuitive way by most chemists, is ill-defined, beyond or outside of physics. His “bond” (or “binding”) is simply the bond path – indicating a pair of interacting atoms.

Bader really wants the union of the bond paths to correspond with the general notion of a bonded molecular structure. He suggests that for all cases, the chemical bonds in a molecule are always observed as bond paths within the electron density. This may be true so far – but certainly we have not examined (computationally nor experimentally) the electron density of all compounds! Equally bothersome is that bond paths occur between atoms for which most chemists would consider to be non-bonded – like between the ortho hydrogens of biphenyl or between hydrogens across the bay region of phenanthrene (see this post). He argues that the barrier for biphenyl rotation arises from the stretching of the C-C bond when the rings become co-planar, but why does this bond stretch in the first place?

While Bader is certainly allowed to call the bond path a “bond”; the question remains whether this definition offers improvements or advantages concerning how we think about and understand molecules, their properties and reactions. To me, this remains an open question.


(1) Bader, R. F. W., "Definition of Molecular Structure: By Choice or by Appeal to Observation?," J. Phys. Chem. A 2010, 114, 7431-7444, DOI: 10.1021/jp102748b

Uncategorized Steven Bachrach 03 Dec 2010 3 Comments