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Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the 1H and 13C-NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when 13C and 1H chemical shift data are combined. The approximate linear dependence of the C1’ shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects

We thank the following organizations for financial support: the Netherlands organization for Scientific Research (NWO-CW and NWO-NCF), the Spanish Ministerio de Ciencia e Innovacion (MICINN projects CTQ2005-08797-C02-01/BQU, CTQ2008-06532/BQU, and CTQ2011-25086/BQU), the Catalan Ministry of Universities, Research and the Information Society (DURSI projects 2005SGR-00238 and 2009SGR528)

© Chemistry - A European Journal, 2012, vol. 18, núm. 39, p. 12372-12387

Wiley-VCH Verlag

Manager: Ministerio de Educación y Ciencia (Espanya)
Ministerio de Ciencia e Innovación (Espanya)
Generalitat de Catalunya. Agència de Gestió d’Ajuts Universitaris i de Recerca
Author: Fonville, Judith M.
Swart, Marcel
Vokáčová, Zuzana
Sychrovský, Vladimír
Šponer, Judit E.
Šponer, Jiří
Hilbers, Cornelis W.
Bickelhaupt, F. Matthias
Wijmenga, Sybren S.
Date: 2012 September 24
Abstract: NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the 1H and 13C-NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when 13C and 1H chemical shift data are combined. The approximate linear dependence of the C1’ shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects
We thank the following organizations for financial support: the Netherlands organization for Scientific Research (NWO-CW and NWO-NCF), the Spanish Ministerio de Ciencia e Innovacion (MICINN projects CTQ2005-08797-C02-01/BQU, CTQ2008-06532/BQU, and CTQ2011-25086/BQU), the Catalan Ministry of Universities, Research and the Information Society (DURSI projects 2005SGR-00238 and 2009SGR528)
Format: application/pdf
Citation: 016715
ISSN: 0947-6539 (versió paper)
1521-3765 (versió electrònica)
Document access: http://hdl.handle.net/10256/11455
Language: eng
Publisher: Wiley-VCH Verlag
Collection: MEC/PN 2009-2011/CTQ2008-06532/BQU
MICINN/PN 2012-2014/CTQ2011-25086
MEC/PN 2005-2008/CTQ2005-08797-C02-01
AGAUR/2005-2008/2005SGR 00238
Reproducció digital del document publicat a: http://dx.doi.org/10.1002/chem.201103593
Articles publicats (D-Q)
Is part of: © Chemistry - A European Journal, 2012, vol. 18, núm. 39, p. 12372-12387
Rights: Tots els drets reservats
Subject: Funcional de densitat, Teoria del
Density functionals
Espectroscòpia de ressonància magnètica nuclear
Nuclear magnetic resonance spectroscopy
Àcids nucleics
Nucleic acids
Title: Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
Type: info:eu-repo/semantics/article
Repository: DUGiDocs

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