No 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.

The geometry of hydrogen bonds in the crystal structures from the Cambridge Structural Database and calculated data show that water coordination to a metal ion has a remarkable influence on hydrogen bonds. The calculated energies of hydrogen bonds of coordinated water are much stronger, even if the aqua complex is neutral.

A study of crystal structures from the Cambridge Structural Database (CSD) and DFT calculations reveals that parallel pyridine-pyridine and benzene-pyridine interactions at large horizontal displacements (offsets) can be important, similar to parallel benzene-benzene interactions. In the crystal structures from the CSD preferred parallel pyridine-pyridine interactions were observed at a large horizontal displacement (4.0-6.0 Å) and not at an offset of 1.5 Å with the lowest calculated energy. The calculated interaction energies for pyridine-pyridine and benzene-pyridine dimers at a large offset (4.5 Å) are about 2.2 and 2.1 kcal mol(-1), respectively. Substantial attraction at large offset values is a consequence of the balance between repulsion and dispersion. That is, dispersion at large offsets is reduced, however, repulsion is also reduced at large offsets, resulting in attractive interactions.

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations. Calculated at the very accurate CCSD(T)/CBS level of theory, the cyclohexane-benzene interaction energy is -3.27 kcal mol, which is significantly stronger than the interaction in the benzene dimer (-2.84 kcal mol) indicating the importance of aliphatic-aromatic interactions.