Stacking and Spreading Interaction in N-Heteroaromatic Systems

Abstract

π-π interactions in heteroaromatic systems are ubiquitous in biological systems. In the present study, stabilization energies of stacked and hydrogen-bonded dimers of N-heteroaromatic systems (pyridine, pyrazine, sym-triazine, and sym-tetrazine) have been computed using a benchmark quality coupled cluster through the perturbative triples (CCSD(T)) method at the estimated complete basis set (CBS) limit. In the case of stacking, monomer units are found to be stacked in parallel planes with displaced geometries. The stabilization energies for the most stable stacked geometry of pyridine, pyrazine, sym-triazine, and sym-tetrazine dimers are found to be -3.39, -4.14, -4.02, and -3.90 kcal/mol, respectively at the est. CCSD(T)/CBS level of theory, which is clearly larger than the stabilization energy for the most stable geometry of the benzene dimer. In the case of spreading, hydrogen bonded dimers and trimers are stabilized by weak C-H···N interactions. The stabilization energies for the stacked and the spread out complexes are found to be comparable. The stabilization energy for the trimers is computed using the MP2, MP3, and B3LYP-D methods. The present study is aimed at unraveling the basis of preferred conformations of N-heteroaromatic dimers. These model systems explain partly the stability of double helical DNA and RNA structures that are formed by stacking and hydrogen bonding between nucleic acid bases.

Reaction of anhydrous zinc chloride with 2,3-thiophenedicarbaldehyde bis(semicarbazone) (2,3BSTCH2) and bis(thiosemicarbazone) (2,3BTSTCH2): Crystal structure of {[C6H5N2S]+[ZnCl3(C6H4N2S)]−} complex

“…4b). In addition, π-π interactions between the aromatic cycles in two different planes occur as already observed in similar structures (Alshahateet et al, 2004;Mishra et al, 2010).…”

An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

“…In this perspective, it may be interesting to verify if similar improvement with respect to the standard OPLS description could be gained by the present protocol, without the adoption of adjunctive model functions. Finally, very recent high level QM calculations on pyridine trimers[51, 53] have revealed that three‐body effects contribute negligibly, enforcing the reliability of our protocol, which is based on the parameterization of QM computed two‐body interactions.…”

“…[49] Despite benzene has often been used as model system to study aromatic π − π complexes, nitrogen hetero‐atoms are present in nucleic acid bases, influencing the stacking energies between bases, and hence the structure of DNA. More in general, many biologically important molecules as amino acids often contain aromatic heterocycles, and their interactions have been shown[50–53] to differ consistently from those found in the benzene dimer. Secondarily, pyridine has been recently[54] tested as a benchmark for the implementation of a new FF, the OPLS‐CS, whose results were shown to improve the standard OPLS[55] description.…”

Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase

“…[6][7][8][9][10][11] On the other hand, there are extensive theoretical studies on the π -stacking interaction in the aromatic dimers. [12][13][14][15][16][17][18][19][20][21][22][23][24] The πstacked configuration is also not observed in the experiment in the case of the benzene dimer, which is undoubtedly the most thoroughly studied aromatic dimer in the literature. 25,26 Interestingly, the T-shaped structure of the benzene dimer observed in the experiment is more stable than the π -stacked a) Author to whom correspondence should be addressed.…”