Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs

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High-quality quantum mechanical (QM) calculations provide physically based descriptions of molecular systems that are free of empirical parameters. This contrasts with force-field computations based on simple and entirely nonphysical, analytical functions that must be completely parametrized for a given purpose. The costs of high-quality QM computations, however, can be enormous, limiting them to small model systems with ~50+ atoms. Thus, a major challenge of the QM approach is how to extrapolate data computed on model systems to intact biomolecules of biological interest. QM calculations have been used to study the basic molecular forces in nucleic acids. A notable accomplishment of these studies has been to clarify the nature of aromatic base stacking. Another important application of modern QM computations is to furnish reference data for parametrizing molecular modeling force fields. In this chapter, we provide a summary of the nature of QM calculations, their strengths, limitations, and relation to other methods. Then, we review the use of high-level ab initio (first principles) QM methods to calculate geometries and energies of fundamental nucleotide interactions in RNA 3D structures.