Crystallographic and ab Initio Study of Pyridine Stacking Interactions. Local Nature of Hydrogen Bond Effect in Stacking Interactions

Abstract

Stacking interactions between pyridine molecules and the influence of simultaneous hydrogen bonds were studied by analyzing data in the Cambridge Structural Database (CSD) and by ab initio calculations. The results show remarkably stronger stacking interactions of pyridines with hydrogen bonds, because of local parallel alignment interactions of OH bonds with the aromatic ring. Data in the crystal structures from the CSD and ab initio calculations show that normal distances (R) in stacking interactions of pyridines with simultaneous hydrogen bonds are shorter than those in stacking interactions without simultaneous hydrogen bonds. Furthermore, the calculated binding energies for stacking are substantially stronger when the pyridines have hydrogen bonds; the binding energy of the stacking interaction between pyridine–water dimers is −6.86 kcal/mol, while that between pyridines is −4.08 kcal/mol. Surprisingly, in the minimum energy structure of the stacked pyridine–water dimers, the contribution of the local parallel-alignment interactions between water and the other pyridine (−2.98 kcal/mol) is slightly larger than the contribution of the stacking interaction between two pyridine molecules (−2.67 kcal/mol). The local influence of hydrogen bonds on stacking, via parallel alignment interactions, can be very important for all systems with heteroaromatic molecules and groups, especially DNA and RNA.