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

J 2012

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

FONVILLE, Judith M, Marcel SWART, Zuzana VOKACOVA, Vladimir SYCHROVSKY, Judit ŠPONEROVÁ et. al.

Základní údaje

Originální název

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

Autoři

FONVILLE, Judith M, Marcel SWART, Zuzana VOKACOVA, Vladimir SYCHROVSKY, Judit ŠPONEROVÁ, Jiří ŠPONER, Cornelis W HILBERS, F Matthias BICKELHAUPT a Sybren S WIJMENGA

Vydání

Chemistry - A European Journal, WEINHEIM, WILEY-VCH, 2012, 0947-6539

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 5.831

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/chem.201103593

UT WoS

000308879000027

Klíčová slova anglicky

density functional calculations; NMR spectroscopy; nucleic acids; structure elucidation

Štítky

ne MU

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 31. 3. 2015 09:22, Olga Křížová

Anotace

V originále

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, ?, 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 ? angles in the anti and syn domains. Furthermore, a quantitative determination of the ? 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 ? 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.

Citovat

FONVILLE, Judith M, Marcel SWART, Zuzana VOKACOVA, Vladimir SYCHROVSKY, Judit ŠPONEROVÁ, Jiří ŠPONER, Cornelis W HILBERS, F Matthias BICKELHAUPT a Sybren S WIJMENGA. Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2012, roč. 18, č. 39, s. 12372-12387. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201103593.

@article{1076074,
   author = {Fonville, Judith M and Swart, Marcel and Vokacova, Zuzana and Sychrovsky, Vladimir and Šponerová, Judit and Šponer, Jiří and Hilbers, Cornelis W and Bickelhaupt, F Matthias and Wijmenga, Sybren S},
   article_location = {WEINHEIM},
   article_number = {39},
   doi = {http://dx.doi.org/10.1002/chem.201103593},
   keywords = {density functional calculations; NMR spectroscopy; nucleic acids; structure elucidation},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment},
   volume = {18},
   year = {2012}
}

TY  - JOUR
ID  - 1076074
AU  - Fonville, Judith M - Swart, Marcel - Vokacova, Zuzana - Sychrovsky, Vladimir - Šponerová, Judit - Šponer, Jiří - Hilbers, Cornelis W - Bickelhaupt, F Matthias - Wijmenga, Sybren S
PY  - 2012
TI  - Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
JF  - Chemistry - A European Journal
VL  - 18
IS  - 39
SP  - 12372-12387
EP  - 12372-12387
PB  - WILEY-VCH
SN  - 09476539
KW  - density functional calculations
KW  - NMR spectroscopy
KW  - nucleic acids
KW  - structure elucidation
N2  - 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, ?, 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 ? angles in the anti and syn domains. Furthermore, a quantitative determination of the ? 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 ? 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.
ER  -

FONVILLE, Judith M, Marcel SWART, Zuzana VOKACOVA, Vladimir SYCHROVSKY, Judit ŠPONEROVÁ, Jiří ŠPONER, Cornelis W HILBERS, F Matthias BICKELHAUPT a Sybren S WIJMENGA. Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. \textit{Chemistry - A European Journal}. WEINHEIM: WILEY-VCH, 2012, roč.~18, č.~39, s.~12372-12387. ISSN~0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201103593.

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