Method Proposed to Measure Atom Sizes and Intermolecular Interactions

When supercomputers are used to design novel drugs and electronic devices work on a nanoscale, it becomes highly significant for researchers to interpret the behavior of adjacent molecules toward one another. For this reason, the researchers have to understand the atoms’ sizes with a maximum level of accuracy.

The Front Cover illustrates the effect of geometry-based filtration of intermolecular contacts on their distance distribution. The line-of-sight principle efficiently eliminates the background of randomly distributed contacts and lets one see the trees behind the forest. Image Credit: ChemPhysChem.

While contemporary quantum chemistry techniques can prove useful here, the solutions provided by them can either take months of work to create, or may not be sufficiently precise.

ITMO University researchers and their collaborators from the Russian Academy of Science suggested a novel technique of statistical analysis of sizes and intermolecular interactions of atoms. The researchers’ study appeared on the front page of the ChemPhysChem journal.

From the chemistry viewpoint, all humans live in a realm of perpetual intermolecular interactions. The process of digesting food, brewing tea, or the stiffness of a new kind of plastic collectively relies on the manner of interaction of particular molecules.

The issue is that contemporary quantum chemistry techniques are not sufficient to accurately and fully illustrate the properties of intermolecular interactions.

But in the current scenario, researchers have to be aware of the energy of intermolecular interactions. They require accurate information on how molecules of a novel drug communicate with the cells of an organism or on the molecular structure of the latest semiconductor. Even the slightest variations in the manner of intermolecular interaction can render an invention either completely unfeasible or extremely effective.

Chemists have identified a new method to find out the level at which intermolecular interactions have an impact on the characteristics of a chemical system. The team began to apply the principle of the effective size of atoms, which is most commonly referred to as van der Waals radii. This principle suggests that if atoms approach one another than a particular distance, then their interaction would be important; or else, it can be overlooked.

But owing to the specifics of the technique used for ascertaining van der Waals radii, their values are often undersized by 10% to 15%. Consequently, errors occur in the analysis of chemical systems, and several interactions are overlooked as unimportant.

Now, in association with experts from Nesmeyanov Institute of Organoelement Compounds, a research team from ITMO University has suggested a new technique of statistical analysis that helps establish the size of atoms relatively better.

How do you usually calculate the efficient size of atoms? Well, we have data on all possible interactions between two atoms. If we draw up a graph of the distribution of interatomic distances, we’ll be able to get an average distance that corresponds to the analyzed interaction. Still, this is not always possible, so instead of the most probable distance from the graph we get a different, approximate value.

Ivan Chernyshov, Study Co-Author, Russian Academy of Science

Chernyshov continued, “We succeeded in getting round this problem by coming up with a way to sift the accidental contacts from direct interactions where there are no other screening atoms on the “line of sight” between the centers of the two atoms.”

Although this technique makes it easy to solve a highly complex task from the area of quantum chemistry, it helps achieve data that is adequately accurate and necessary to evaluate the sizes of molecules and atoms and the manner of molecules’ interactions, which are extremely significant considering present-day applications.

Today, scientists actively research interactions between drugs and proteins in organisms. You have a good molecule that has already shown its efficiency, but need to improve it by amplifying the bond with the active center. In order to do that, you take data on the efficient size of these atoms and see which interactions in the structure of the bound protein are important and which can be neglected.

Ivan Chernyshov, Study Co-Author, Russian Academy of Science

The values that have been used till now were determined empirically and had no specific physical sense. Our method will make it possible to significantly increase the precision of such calculations, especially for systems that have not been studied yet,” Chernyshov concluded.

Source: https://en.itmo.ru/

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