IsoStar Program Suite for Studies of Noncovalent Interactions in Crystals of Chemical Compounds

Abstract

Both Cambridge Crystallographic Data Centre (CCDC) and Protein Data Bank (PDB) provide unique opportunities for finding information about the structures of chemical and biochemical compounds in the solid state. The IsoStar—a knowledge-based library of intermolecular interactions—is a very powerful tool for automatic analysis of a large amount of data from these databases. The IsoStar program suite could help chemists in understanding of probability of occurrence (frequencies) and spatial characteristics (directionalities) of noncovalent contacts (including hydrogen, halogen, and chalcogen bonds, as well as interactions involving π-systems) between pairs of chemical functional groups; this web application may also be useful for crystal engineers, crystallographers, medicinal chemists, and researchers in fields of computational chemistry and molecular modeling.

Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0

“…These resources include CIPDB, RING, ExptNCI, PLIP, MolADI, ProteinTools, and others. [22][23][24][25][26][27][28][29][30][31][32][33][34] In Table S13, you can find a comprehensive list of The distribution of cation-aromatic motifs based on distance parameters showed a general increase in motif count with distance, leading to Gaussian distributions. This suggests that most cation-aromatic interactions are either weak or moderately strong.…”

“…There are several resources available for obtaining information on noncovalent interactions, including cation‐π interactions in proteins and other molecular systems. These resources include CIPDB, RING, ExptNCI, PLIP, MolADI, ProteinTools, and others 22‐34 . In Table S13, you can find a comprehensive list of databases, web servers, and software programs specifically designed for identifying and analyzing these interactions.…”

“…Exploring various aspects of cation-π interactions, such as dependence on curvature and electronic factors, 9 energy decomposition analysis, 10 solvation effects, 11 complexation with metal ions, 12 contrasting preferences between nitrogen-and phosphorous-substituted rings, 13 and structural and energetic preferences of cation binding. 14 Furthermore, explicit solvent effects on cation-π interactions, 15 size dependence of cyclic and acyclic π-systems, 16 contrasting structural and energetic characteristics of bare and coordinatively saturated metal ions, 17 and analysis of aromatic π-networks in proteins 18 have been investigated [19][20][21][22][23][24][25][26][27] that have collectively contributed to an enhanced understanding of cation-π interactions in diverse biological and chemical contexts.…”