Czech scientists become first to observe an inhomogeneous electron charge distribution on an atom


Until now, observing subatomic structures was beyond the resolution capabilities of direct imaging methods, and this seemed unlikely to change. Czech scientists, however, have presented a method with which they became the first in the world to observe an inhomogeneous electron charge distribution around a halogen atom, thus confirming the existence of a phenomenon that had been theoretically predicted but never directly observed.

Comparable to the first observation of a black hole, the breakthrough will facilitate understanding of interactions between individual atoms or molecules as well as of chemical reactions, and it opens a path to refinement of the material and structural properties of various physical, biological, and chemical systems. The breakthrough was published in Science.

In an extensive interdisciplinary collaboration, scientists from the Czech Advanced Technology and Research Institute (CATRIN) of Palacky University Olomouc,
the Institute of Physics of the Czech Academy of Sciences (FZU), the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague), and the IT4Inovations Supercomputing Center at VSB – Technical University of Ostrava have succeeded in dramatically increasing the resolution capabilities of scanning microscopy, which several years ago enabled humankind to image individual atoms, and have thus moved beyond the atomic level to subatomic phenomena.

The scientists have, for the very first time, directly observed an asymmetric electron density distribution on single atoms of halogen elements, the so-called sigma-hole. In doing so, they have definitively confirmed its existence, theoretically predicted some 30 years ago, and have overcome one of science’s longstanding challenges.

Confirming the existence of the theoretically predicted sigma-holes is not unlike observing black holes, which had never been seen until only two years ago despite being predicted in 1915 by the general theory of relativity. Viewed in that sense, its not much of an exaggeration to say that the imaging of the sigma-hole represents a similar milestone at the atomic level, explains Pavel Jelínek of FZU and CATRIN, a leading expert on the theoretical and experimental study of the physical and chemical properties of molecular structures on the surface of solid substances.

Until now, the existence of the phenomenon known as a sigma-hole had been indirectly demonstrated by X-ray crystal structures with a halogen bond, which revealed the surprising reality that chemically bonded halogen atoms of one molecule and nitrogen or oxygen atoms of a second molecule, which should repel one another, are in proximity and thus attract one another. This observation was in blatant contradiction with the premise that these atoms carry a homogenous negative charge and repel each other through electrostatic force.

This led the scientists to examine the subatomic structure of halogen using Kelvin probe force microscopy. They began by developing a theory describing the mechanism of the atomic resolution of the Kelvin probe, which allowed them to optimize the experimental conditions for imaging sigma-holes. The subsequent combination of experimental measurements and advanced quantum chemical methods resulted in a remarkable breakthrough – the first experimental visualization of an inhomogeneous electron density charge distribution, i.e. a sigma-hole – and the definitive confirmation of the concept of halogen bonds.


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