An international research team, which included scientists from the Faculty of Science at Palacký University and the Institute of Physics of the Czech Academy of Sciences, has succeeded in unraveling the complex mechanism by which a chemical bond is formed during a collision between molecules. The experts found that the reaction only takes place if the molecules are oriented towards each other within a very narrow range of angles – within the so-called cone of reaction. This joint research has thus provided an answer to one of the fundamental questions of chemistry: under what conditions do chemical bonds form between molecules. The results of the study Spatially resolving the cone of reaction for a single molecule were published in the prestigious scientific journal Science.
Many chemical reactions begin with the collision of two particles. However, for a new chemical bond to form, it is not enough for the molecules simply to come into contact. Their collision must occur with sufficient energy, in the correct relative orientation and at the right location. Under normal conditions, such as in solutions or gases, molecules collide chaotically, and the precise parameters of these collisions cannot therefore be controlled.
Molecules under control
Scientists were able to control the collisions of individual molecules on a copper surface and monitored the process using a scanning tunnelling microscope. They used the instrument not only to visualise individual molecules, but also to deliberately accelerate the reactants towards one another. They subsequently analysed each collision with atomic-level resolution. This enabled them to determine unequivocally whether a new chemical bond had formed between the molecules.
“What is hidden in the statistics of billions of collisions in conventional chemistry, we have managed to break down into individual cases and map directly.” Adam Matěj
A key finding of the study is that the outcome of a collision is determined by the extremely precise orientation of the molecules. A new bond was formed only when the target molecule was oriented within a few degrees of the direction of movement of the other molecule. When rotated by more than fifteen degrees, the molecules simply bounced off each other without any reaction.
The precise orientation of the molecules is crucial
“For the first time, we were able to observe, using a single molecule, exactly how precisely it must be oriented for the reaction to take place at all. What is hidden in the statistics of billions of collisions in conventional chemistry, we have managed to break down into individual cases and map directly,” said Adam Matěj from the Department of Physical Chemistry at the Faculty of Science.
The theoretical part of the study, in which researchers from Palacký University and the Institute of Physics of the Czech Academy of Sciences were involved, played a significant role. Using quantum-mechanical calculations, they explained why the ‘reaction cone’ is so narrow. It turned out that the reactive carbon atom is surrounded by hydrogen atoms, which block the access of the reacting molecule from almost all directions.
The arrangement of atoms restricts access to the reaction
The calculations also shed light on a surprising experimental result. The chemical reaction took place even when the molecule moved along an adjacent row of copper atoms, where, according to the original assumptions, no bond should have formed.
“The strength of this work lies in the fact that the experiment and theory have been brought together into a single picture. The microscope showed what happens during the collision, and the calculations explained why.” Pavel Jelínek
“The explanation lies in the slight displacement of a single copper atom on the surface. The target’s bond to the surface pulls it out of its position and brings it close enough to the neighbouring row that it can literally take over the projectile and direct it to the correct spot. This shows that the surface is not merely a passive substrate, but actively participates in the reaction itself and can even facilitate pathways that would otherwise be unfavourable,” noted Adam Matěj.
The surface also determines the course of the reaction
The results are significant for the development of so-called surface reactions, in which new materials and nanostructures are purposefully assembled from individual molecules. A better understanding of the influence of the spatial arrangement of molecules will enable the design of molecular building blocks so that they bond more reliably and efficiently. This represents an important step towards the development of technologies based on the controlled construction of structures atom by atom.
“The strength of this work lies in the fact that experiment and theory have been brought together into a single picture. The microscope showed what happens during the collision, and the calculations explained why. Without a theoretical model, we would have found it difficult to discover that the movement of a single surface atom is behind the unexpected course of the reaction,” added Pavel Jelínek from the Institute of Physics of the Czech Academy of Sciences.
The study Spatially resolving the cone of reaction for a single molecule was produced in collaboration between researchers from the University of Graz, the Institute of Physics of the Czech Academy of Sciences, Palacký University in Olomouc, Charles University and Humboldt University in Berlin.