Sybren Wijmenga

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Organization: Radboud Universiteit Nijmegen , Belgium
Department: 1 Present address: Department of Zoology
Title: (PhD)
Co-reporter:Dr. Judith M. Fonville;Dr. Marcel Swart;Dr. Zuzana Voká&x10d;ová;Dr. Vladimír Sychrovský;Dr. Judit E. &x160;poner;Dr. Ji&x159;í &x160;poner;Dr. Cornelis W. Hilbers;Dr. F. Matthias Bickelhaupt;Dr. Sybren S. Wijmenga
Chemistry - A European Journal 2012 Volume 18( Issue 39) pp:12372-12387
Publication Date(Web):
DOI:10.1002/chem.201103593

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.

Co-reporter:Niels K.J. Hermkens, Martin C. Feiters, Floris P.J.T. Rutjes, Sybren S. Wijmenga, Marco Tessari
Journal of Magnetic Resonance (March 2017) Volume 276() pp:
Publication Date(Web):1 March 2017
DOI:10.1016/j.jmr.2017.01.011
•EXSY experiment combined with 1H para-H2 hyperpolarization at high field.•This experiment provides the substrate dissociation rates in asymmetric SABRE complexes.•100-fold reduction in measuring time is obtained compared to standard methods.SABRE (Signal Amplification By Reversible Exchange) is a nuclear spin hyperpolarization technique based on the reversible concurrent binding of small molecules and para-hydrogen (p-H2) to an iridium metal complex in solution. At low magnetic field, spontaneous conversion of p-H2 spin order to enhanced longitudinal magnetization of the nuclear spins of the other ligands occurs. Subsequent complex dissociation results in hyperpolarized substrate molecules in solution. The lifetime of this complex plays a crucial role in attained SABRE NMR signal enhancements. Depending on the ligands, vastly different dissociation rates have been previously measured using EXSY or selective inversion experiments. However, both these approaches are generally time-consuming due to the long recycle delays (up to 2 min) necessary to reach thermal equilibrium for the nuclear spins of interest. In the cases of dilute solutions, signal averaging aggravates the problem, further extending the experimental time. Here, a new approach is proposed based on coherent hyperpolarization transfer to substrate protons in asymmetric complexes at high magnetic field. We have previously shown that such asymmetric complexes are important for application of SABRE to dilute substrates. Our results demonstrate that a series of high sensitivity EXSY spectra can be collected in a short experimental time thanks to the NMR signal enhancement and much shorter recycle delay.Download high-res image (124KB)Download full-size image
D-ribose 5-(dihydrogen phosphate)
phosphoribosylpyrophosphate synthetase*from esche
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D-Ribitol,1-C-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-, 5-(tetrahydrogentriphosphate), (1S)- (9CI)
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