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RNA 3D Structure Analysis and Prediction pp 239–279Cite as

Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 27))

Abstract

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.

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Acknowledgments

The authors thank Anton I. Petrov for assistance in organizing data and preparing tables. This work was supported by grants 203/09/1476, P208/12/1878, and P208/11/1822 from the Grant Agency of the Czech Republic, grants AV0Z50040507 and AV0Z50040702 from the Ministry of Education of the Czech Republic, and “CEITEC - Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) from the European Regional Development Fund and by grants from the National Institutes of Health to NBL (grant numbers 1R01GM085328-01A1 and 2R15GM055898-05).

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Authors and Affiliations

  1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic

    Jiří Šponer & Judit E. Šponer

  2. CEITEC – Central European Institute of Technology, Brno, Czech Republic

    Jiří Šponer & Judit E. Šponer

  3. Chemistry Department, Bowling Green State University, Bowling Green, OH, 43403, USA

    Neocles B. Leontis

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  1. Jiří Šponer
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  2. Judit E. Šponer
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  3. Neocles B. Leontis
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Correspondence to Jiří Šponer .

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  1. Dept. Chemistry, Bowling Green State University, Bowling Green, 43403, Ohio, USA

    Neocles Leontis

  2. Inst. Biologie Moleculaire, et Cellulaire, CNRS, rue Rene Descartes 15, Strasbourg CX, 67084, France

    Eric Westhof

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Šponer, J., Šponer, J.E., Leontis, N.B. (2012). Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs. In: Leontis, N., Westhof, E. (eds) RNA 3D Structure Analysis and Prediction. Nucleic Acids and Molecular Biology, vol 27. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25740-7_12

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