Revisiting van der Waals Radii
From Comprehensive Structural Analysis to Knowledge-Based Classification of Interatomic Contacts
Ivan Yu Chernyshov (ITMO University)
Ivan V. Ananyev (National Research University Higher School of Economics (HSE University))
E.A. Pidko (ITMO University, TU Delft - ChemE/Inorganic Systems Engineering, TU Delft - ChemE/Algemeen)
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Abstract
Weak noncovalent interactions are responsible for structure and properties of almost all supramolecular systems, such as nucleic acids, enzymes, and pharmaceutical crystals. However, the analysis of their significance and structural role is not straightforward and commonly requires model studies. Herein, we describe an efficient and universal approach for the analysis of noncovalent interactions and determination of van der Waals radii using the line-of-sight (LoS) concept. The LoS allows to unambiguously identify and classify the “direct” interatomic contacts in complex molecular systems. This approach not only provides an improved theoretical base to molecular “sizes” but also enables the quantitative analysis of specificity, anisotropy, and steric effects of intermolecular interactions.
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