Theoretical insights into the nature of intermolecular interactions in cytosine dimer

Abstract

In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers.

Can Stacking Interactions Exist Beyond the Commonly Accepted Limits?

“…The HSM idea was confirmed, e.g., by application of NBO method to the π···π stacked systems, , which shows that, in orbital terms, the stacking interactions are formed primarily by the bonding π orbitals of one ring donating electron density primarily to the antibonding π orbitals of the second ring, and secondarily to the one-center Rydberg antibonding orbitals of the π-bonded atoms of the second ring, and vice versa . It must be noted that generalized knowledge of the π···π interaction origins and quantitative predictions of geometries and energies are not available yet; however, recently a lot of theoretical calculations have been made in this field, associated with both real and model systems. ,− The model systems, that are extensively analyzed, are those containing small aromatic molecules like pyridine and benzene, arranged in selected arbitrary geometries. ,− They are good examples of systems in which π···π interactions are present and they are easy to explore with quantum chemistry methods. Although a lot of theoretical and experimental studies have been made in this field, there is no general description of geometrical factors which enable us to resolve the stacking interactions.…”

“…22 It must be noted, that generalised knowledge of the π•••π interactions origins, quantitative predictions of geometries and energies are not available yet, however, recently a lot of theoretical calculations have been made in this field, associated with both real and model systems. 21,23,24,25,26,27 The model systems, that are extensively analysed, are those ones containing small aromatic molecules like pyridine and benzene, arranged in selected arbitrary geometries. 23,28,29,30,31,32 They are good examples of systems in which π•••π interactions are present and they are easy to explore with the quantum chemistry methods.…”

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

“…Properties of cytosine nucleobases have been frequently addressed in QC. These studies investigated stacked complexes with cytosine both in the ground ,− and excited states. − The most recent efforts computing highly accurate interaction energies for multiple conformations of cytosine dimers including conformations from diverse parts of the PES are from 2015, where, however, only a marginal increase in the level of theory was used compared to an earlier study from 2004. Both studies utilized partially the same structures.…”