Category: chemistry

Reaction mechanisms and driving forces of chemical reactions

In the “language” of chemistry molecules can be schematically drawn by using letters and lines – the letters represent the chemical elements and the lines represent chemical bonds. In this picture a reaction can be simply described as a rearrangement of the letters and lines. However, reaction of organic compounds can be quite complex and proceed via multiple steps. While it is easy to schematically depict such a reaction path, it can be close to impossible to actually figure out the intermediate steps experimentally. Nevertheless, these intermediate steps are extremely important – chemical synthesis is a huge industry (about four trillion dollars per year), and the economic and ecologic optimization of fabrication of chemical products requires knowledge of the reaction mechanisms, as well as the microscopic driving forces of the reactions.

Coupling and cyclization ofsformation of enediyne molecules
A chemical reaction represented by drawing chemical wireframe structures.*

Imaging chemical reactions

In our recent work, we were able to stabilize and identify several intermediates of a complex chemical reaction on a silver surface (this surface acts as a catalyst). This was done using atomic force microscopy. Here an atomically sharp tip (usually just a metal wire) is used to scan over a surface. Images are generated by measuring and plotting the forces between the tip and the surface at each point. Some additional tricks are used to enhance the resolution and be able to image the chemical structure of molecules – just like the schematic drawings that you find in the textbooks. Importantly, this imaging is done for individual molecules, that means that a complex reaction mixture (containing reactants, intermediates and products of many competing reaction pathways) can be analyzed molecule by molecule. This is not possible using the spectroscopic techniques that are conventionally used for chemical analysis.

Atomic force microscopy images of chemical structures in a reaction pathway.
Experimental images of the reactants, intermediates, and products of a chemical reaction.*

Microscopic driving forces

To understand why only certain intermediates are stabilized at the surface (i.e. their lifetimes are long enough to catch a significant mount of them at a specific point in the reaction progress), we have conducted theoretical simulations (quantum chemical calculations, as well as numerical simulation of the reaction kinetics). It turns out that that it is not enough to consider the potential energy landscape alone (that is the energies of reactants, intermediates, and products, as well as their transformation barriers). Energy dissipation to the substrate (i.e. transfer of the released chemical energy to the silver surface), as well as molecular entropy changes along the reaction pathway need to be taken into account.

Interestingly, the catalyst (i.e. the silver surface) plays a crucial role for both of these effects: the interaction of the molecule with the surface determines the efficiency of the energy dissipation, and changes in the translational and rotational movement (non-radical molecular species can translate and rotate, while radicals can not) of the molecules across the surface explain the relatively large entropy changes.

In conclusion, we have resolved the reaction mechanism of a complex chemical reaction that is catalyzed by a silver surface, and we have determine the microscopic driving forces (selective dissipation and entropy) that govern the global reaction kinetics. And we have produced a few beautiful images at the same time.

Calculation of selective dissipation
Theoretical calculation of microscopic energy dissipation for a specific reaction step. The brightness of the atoms shows where the release chemical energy is dissipated.

Why is it important?

The investigated chemical transformation (coupling and cyclization of so-called “enediyne” molecules) is a promising route for the on-surface synthesis of two-dimensional carbon based materials, such as graphene nanoribbons. While we did not yet demonstrate a viable pathway towards such structures at high yield (even though polymeric chains have been synthesized using this approach), further design of the molecular precursors is based on the understanding gained in this study. Of course, real life catalysts often exhibit a variety of defects and impurities, which were not considered in this investigation, but the microscopic understanding demonstrated here is nevertheless important for more complex systems as well.

In summary, this study is a proof of principle that stabilization and identification of intermediates of complex organic reactions is possible at the single-molecule level using atomic force microscopy. Furthermore, the microscopic insights about the driving forces of surface-supported reactions (selective dissipation and entropy) are important for many different fields, such as catalysis, nanotechnology, and biochemistry.

To read more about this work, check out our publication in Nature Chemistry: “Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy” (doi: 10.1038/nchem.2506)

* Images adapted by permission from Macmillan Publishers Ltd: Nature Chemistry, advance online publication, 2 May 2016 (doi:10.1038/nchem.2506).