Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
dc.contributor.author
dc.date.accessioned
2015-11-06T12:05:41Z
dc.date.available
2015-11-06T12:05:41Z
dc.date.issued
2012-09-24
dc.identifier.issn
0947-6539
dc.identifier.uri
dc.description.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
dc.description.sponsorship
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)
dc.format.mimetype
application/pdf
dc.language.iso
eng
dc.publisher
Wiley-VCH Verlag
dc.relation
info:eu-repo/grantAgreement/MICINN//CTQ2008-06532/ES/REACTIVIDAD Y ENLACE QUIMICO EN BIOMEDICINA Y QUIMICA (BIO)INORGANICA/
info:eu-repo/grantAgreement/MICINN//CTQ2011-25086/ES/MODELIZACION MULTIESCALAR EN (BIO)QUIMICA/
MEC/PN 2005-2008/CTQ2005-08797-C02-01
AGAUR/2005-2008/2005SGR 00238
dc.relation.isformatof
Reproducció digital del document publicat a: http://dx.doi.org/10.1002/chem.201103593
dc.relation.ispartof
© Chemistry - A European Journal, 2012, vol. 18, núm. 39, p. 12372-12387
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Articles publicats (D-Q)
dc.rights
Tots els drets reservats
dc.subject
dc.title
Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
dc.type
info:eu-repo/semantics/article
dc.rights.accessRights
info:eu-repo/semantics/embargoedAccess
dc.embargo.terms
Cap
dc.date.embargoEndDate
info:eu-repo/date/embargoEnd/2026-01-01
dc.type.version
info:eu-repo/semantics/publishedVersion
dc.identifier.doi
dc.identifier.idgrec
016715
dc.contributor.funder
dc.relation.ProjectAcronym
dc.identifier.eissn
1521-3765