Czech scientists are the first in the world to look inside the atom

Foto: Viktor Čáp

Czech scientists have devised a method that makes them the first in the world to observe the asymmetric distribution of electrons on single atoms of halogen elements. They have confirmed a phenomenon called “sigma-hole” that was theoretically predicted more than thirty years ago but could not be observed. The discovery was published in the prestigious scientific journal Science.

X-ray structures indirectly indicated a sigma-hole with halogen bonding, but scientists lacked visible evidence until now. It is a breakthrough discovery that may make it easier to understand reactions between atoms and molecules and, in the long term, can lead to new drugs, for example. 

This unique experiment was the result of a collaboration between scientists from the Czech Institute of Research and Advanced Technologies at Palacký University, the Institute of Physics of the Academy of Sciences, the Institute of Organic Chemistry and Biochemistry of the Academy of Sciences, and the IT4Inovations Supercomputing Center at the Technical University of Ostrava.

The confirmation of the existence of sigma-holes can be compared to the observation of black holes, whose existence was predicted by Einstein’s theory of relativity in 1915 but was only seen two years ago, “Associate Professor Pavel Jelinek of the Institute of Physics of the Academy of Sciences said. From this point of view, the sigma-hole observation represents a similar milestone at the atomic level, “he added.

“What theory predicted thirty years ago, we have now seen. And when we put the calculated and measured data side by side, it’s the same, ” told Professor Pavel Hobza from the Institute of Organic Chemistry and Biochemistry of the Academy of Sciences with enthusiasm in his voice. “The theory here has overtaken the experiment, but only the experiment is the final proof.”

Every atom consists of a nucleus and a shell, and it is in the shell that electrons play a crucial role in forming the sigma-hole. When halogens (bromine, chlorine, or iodine) combine by covalent bonding with carbon atoms, some negatively charged electrons are transferred to the carbon. In contrast, a positively charged hole (called a sigma-hole) is formed in the halogen atoms, with the rest of the shell filled with electrons that are thus unevenly distributed.

The scientists decided to investigate this phenomenon using a Kelvin probe for force microscopy, but first, they had to find a way to increase its sensitivity. They found that the ideal way to achieve this was to add a xenon atom to the probe’s tip, which allowed them to see what was happening inside the halogen atom.

“I couldn’t believe that we pushed the limit of microscopes’ resolution to the subatomic level,” confided Bruno de la Torre Cerdeño of the Institute of Physics. “I felt pride and also the satisfaction that it opened up the possibility for other researchers to go further and use our findings to discover new phenomena at the atomic and subatomic level,” he commented.

It turns out that halogen bonds and noncovalent interactions play a dominant role in biology and materials science. This makes our current work published in Science even more critical, “Hobza underlined.