Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules

Abstract

Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

“…This last conclusion was supported by later studies, which found that H-bonded pyridine rings have a clear preference for offsets of 1.25–1.75 Å. When the rings are not H-bonded, the offset is very variable and the separation between the ring planes increases. , …”

“…When the rings are not H-bonded, the offset is very variable and the separation between the ring planes increases. 218,219 Geronimo et al found that positively charged nitrogen heterocycles (pyridinium and imidazolium) form offset, antiparallel stacking interactions much more often than edgeto-face contacts. The close proximity of the anionic counterions is very important in stabilizing the stacking arrangement.…”

Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals

“…Stacking interactions are central to many areas of chemistry, including the binding of ligands to proteins and nucleic acids, − and harnessing such interactions lies at the heart of drug design. , In this context, understanding π-stacking interactions involving heterocycles is of paramount importance because heterocyclic fragments abound in drugs and bioactive natural products. − Model π-stacking interactions involving heterocycles have been studied both experimentally − and theoretically, , with the primary aim of unraveling the many factors that control their strength and preferred orientation. For instance, there have been numerous computational studies − of non-covalent interactions involving pyridine as a model N-heterocycle, building on the seminal work on the benzene–pyridine and pyridine–pyridine dimers by Hohenstein and Sherrill .…”

Two Polymorphic Forms of a Six-Coordinate Mononuclear Cobalt(II) Complex with Easy-Plane Anisotropy: Structural Features, Theoretical Calculations, and Field-Induced Slow Relaxation of the Magnetization

“…Among different benzene core monocarboxylic acids, 3,5-dinitrobenzoic acid (3,5-Hdnb) represents a particularly interesting multifunctional ligand due to the presence of one carboxylic group capable of binding to metal ions in both anionic and neutral acid forms, two nitro groups for both complexation and noncovalent interactions and an aromatic ring favoring π-stacking interactions. In addition, an ancillary ligand like pyridine (py) is useful to prevent undesired aggregation of metal centers binding through its nitrogen atom as well as to provide supramolecular contacts. − …”