Communication pubs.acs.org/crystal
Crystallographic and ab Initio Study of Pyridine Stacking Interactions. Local Nature of Hydrogen Bond Effect in Stacking Interactions Dragan B. Ninković, Goran V. Janjić,† and Snežana D. Zarić*,‡ Innovation center, Department of Chemistry, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia † ICTM, University of Belgrade, Njegoševa 12, 11 000 Belgrade, Serbia ‡ Department of Chemistry, University of Belgrade, Studentski trg 16, 11 000 Belgrade, Serbia S Supporting Information *
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.
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O−H bonds lies parallel to the C6 aromatic ring.9 Analysis of the crystal structures from the CSD and high level ab initio calculations reveals that the parallel alignment interactions can be significantly strong (ΔECCSD(T)(limit) = −2.45 kcal/mol) at large horizontal displacements, out of the aromatic ring and out of the C−H bond region. To the best of our knowledge, the study of interaction between noncoordinated pyridine molecules in crystal structures from the CSD has not been performed. Here we present the results obtained by analyzing the geometries of stacking interactions between two pyridine molecules in crystal structures from the CSD and by ab initio calculations, including the CCSD(T) level, of the model systems. The influence of hydrogen bonds formed with the pyridine nitrogen atom was also studied. The results show surprisingly stronger stacking interactions of pyridines with hydrogen bond, because of local parallel alignment OH interactions with the other pyridine ring (Figure 1). The study is based on the crystal structures archived in the CSD (November 2010 release, version 5.32).13 The crystal
tacking interactions of aromatic rings are important in various systems,1 while stacking interactions of heteroaromatic rings are especially important in biological systems.2 Recently, stacking interactions of heteroaromatic and substituted rings have been intensively studied with the interesting observation that substituent effects can be described as arising from local, direct interactions of the substituent with the proximal vertex of the other ring.1a Compared to studies on the benzene dimer, there is quite a small number of theoretical studies on pyridine dimers, in spite of their importance.3−6 A head to tail-displaced geometry was predicted to be the most stable, and the stacking energy of the two pyridines was −3.39 kcal/mol (est. CCSD(T)limit).4b A geometrical analysis of stacking interactions with aromatic nitrogen-containing ligands based on data from the Cambridge Structural Database (CSD) showed that nitrogen-containing aromatic rings usually form slipped stacking interactions.7,8 Stacking interactions are generally studied between aromatic organic molecules or fragments; however, it was shown that other planar molecules and fragments can also be involved in stacking interactions.9−12 We have recently recognized the parallel alignment interactions of water and aromatic rings that resemble the stacking interactions. In parallel alignment interactions, either the whole water molecule or one of its © 2012 American Chemical Society
Received: October 20, 2011 Revised: January 15, 2012 Published: January 18, 2012 1060
dx.doi.org/10.1021/cg201389y | Cryst. Growth Des. 2012, 12, 1060−1063
Crystal Growth & Design
Communication
structures, 44 stacking interactions are of pyridines with hydrogen bonds, while, in 22 interactions, pyridines are without hydrogen bonds. Stacking interactions of pyridines with hydrogen bonds show pick at lower R values (3.4−3.5 Ǻ ) compared to the stacking interactions without H-bonds (3.6− 3.7 Ǻ ) (Figure 3).
Figure 1. Stacking interaction of pyridine molecules (a) and stacking interaction of pyridine−water dimers (b).
structures involving free pyridines were screened for intermolecular contacts. The CSD search program ConQuest 1.1314 was used to retrieve structures satisfying the following criteria: (a) the crystallographic R factor
