Chemists at the University of Warwick come up with new technique to map the exact location of atoms in molecules

Renowned physicist Richard Feynman once said that the easiest way to analyse any complex chemical compound would be to look at it and see where the atoms are. While this may sound amusing, Chemists from the Warwick Chemistry Department, have been making use of an instrument called Scanning Tunnelling Microscope (STM) to do just this.

STM can normally only reveal the overall shape and position of molecules in a material but does not have the precision required to determine their exact atomic structure

In STM, effectively a tip is brought close to the sample surface, a bias voltage is applied and the tunnelling of electrons through the vacuum between the tip and the surface is measured. The resulting tunnelling current is a function of many factors that enable us to determine what lies on the surface beneath the tip. This sounds simple however there are limitations to this technique. STM can normally only reveal the overall shape and position of molecules in a material but does not have the precision required to determine their exact atomic structure.

 Now researchers in the Warwick Chemistry department have come up with a way around this. Through the new ‘super STM’ technique, developed by Professor Giovanni Constantini and Assistant Professor Gabrielle Sosso, individual locations of atoms can be mapped and the nature of intermolecular interactions between them can be discerned. Through this technique, not only can researchers distinguish between hydrogen and halogen bonding but also spot any impurities in the sample. This would have far reaching effects, especially in the world of pharmaceuticals.

Both hydrogen and halogen bonding are types of intermolecular interactions, where these interactions are what keep molecules together. It is hydrogen bonding, for example, which gives water its cohesive properties so that rain is water drops rather than water molecules. Science is brilliant when it provides answers to questions that I did not even think of. Anyway, back to STM!

this new technique provided evidence of halogen bonding governing the assemblies of molecules and determined the locations of carbon and halogen (group 7 in the periodic table) atoms.

 All this is amazing but then you ask: how the researchers did this? How did they manage to get such a close look at the atoms? The STM needle was tipped with carbon monoxide and frozen to 7 Kelvin (or minus 266 degrees centigrade). The researchers compared standard STM outcomes with this ultrahigh resolution STM. The surface they used was a brominated polycyclic aromatic molecule laid on a gold surface. Through this study, they were able to demonstrate that standard STM measurements could not conclusively establish the nature of intermolecular interactions at play here. However this new technique provided evidence of halogen bonding governing the assemblies of molecules and determined the locations of carbon and halogen (group 7 in the periodic table) atoms.

This study was a coupling between solid state chemistry and computational chemistry. Besides the experiments conducted on the STM, calculations were employed which also successfully yielded the outcome obtained from the STM analysis. Density Functional Theory (DFT) calculations predicted a stronger interaction energy for halogen bonding than hydrogen bonding in this system. Besides, via electron density topology analysis, they identified characteristic features of halogen bonding in the system, as recognised by the International Union of Pure and Applied Chemistry (IUPAC). The DFT calculations, in agreement with the ultrahigh resolution STM result, predicted that the above mentioned sample was held together preferentially by halogen bonding interactions rather than hydrogen bonding interactions. This served as a final nail in the coffin, and a testament to the clarity that is brought about by the coupling of experimental and computational chemistry.

this technique would also allow researchers to identify any impurities in their samples which could lead to the development of new pharmaceuticals that are purer than ever

Professor Constantini shares how the researchers believe that “a significant fraction of difficult or controversial molecular structures that have been discussed in the literature over the last decades could be quickly and clearly solved by using this approach”.

As mentioned earlier, this technique would also allow researchers to identify any impurities in their samples which could lead to the development of new pharmaceuticals that are purer than ever. Dr Sosso remarks that with the ability to identify halogen bonds with this certainty comes the opportunity to be able to employ them as an essential tool to engineer the next generation of molecular systems of drug delivery, something that traditionally has been the pride of primarily hydrogen bonding. He further added that “it is essential that, as we did in this work, we bring together experiments and simulations – in order to deliver a comprehensive picture of this still largely unexplored molecular interaction.