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Addressing the stereochemistry of complex organic molecules by density functional theory-NMR: vannusal B in retrospective.

ABSTRACT: We have employed density functional theory (DFT) protocols to calculate the NMR properties of the vannusals, a class of natural products whose structures have been the subject of recent investigations. The originally assigned structure of vannusal B was revised after a long synthetic journey which generated a series of closely related diastereomers. In this work we show how DFT calculations based on density functionals and basis sets designed for the prediction of NMR spectra (M06/pcS-2 level of theory) can be used to reproduce the observed parameters, thereby offering to the synthetic chemist a useful tool to discard or accept putative structures of unknown organic molecules.

SUBMITTER: Saielli G

PROVIDER: S-EPMC3100668 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Addressing the stereochemistry of complex organic molecules by density functional theory-NMR: vannusal B in retrospective.

Saielli Giacomo G Nicolaou K C KC Ortiz Adrian A Zhang Hongjun H Bagno Alessandro A

Journal of the American Chemical Society 20110325 15

We have employed density functional theory (DFT) protocols to calculate the NMR properties of the vannusals, a class of natural products whose structures have been the subject of recent investigations. The originally assigned structure of vannusal B was revised after a long synthetic journey which generated a series of closely related diastereomers. In this work we show how DFT calculations based on density functionals and basis sets designed for the prediction of NMR spectra (M06/pcS-2 level of ...[more]

PMID: 21438587

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Project description:We tested a battery of density functional theory (DFT) methods ranging from generalized gradient approximation (GGA) via meta-GGA to hybrid meta-GGA schemes as well as Møller-Plesset perturbation theory of the second order and a single and double excitation coupled-cluster (CCSD) theory for their ability to reproduce accurate gas-phase structures of di- and triatomic molecules derived from microwave spectroscopy. We obtained the most accurate molecular structures using the hybrid and hybrid meta-GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion interactions play an insignificant role. The structures that the CCSD method predicts are of similar quality although at considerably larger computational cost. The structures that GGA and meta-GGA schemes predict are less accurate with the largest absolute errors detected with BLYP and M11-L, suggesting that these methods should not be used if accurate three-dimensional molecular structures are required. Because of numerical problems related to the integration of the exchange-correlation part of the functional and large scattering of errors, most of the Minnesota models tested, particularly MN12-L, M11, M06-L, SOGGA11, and VSXC, are also not recommended for geometry optimization. When maintaining a low computational budget is essential, the nonseparable gradient functional N12 might work within an acceptable range of error. As expected, the DFT-D3 dispersion correction had a negligible effect on the internuclear distances when combined with the functionals tested on nonweakly bonded di- and triatomic inorganic molecules. By contrast, the dispersion correction for the APF-D functional has been found to shorten the bonds significantly, up to 0.064 Å (AgI), in Ag halides, BaO, BaS, BaF, BaCl, Cu halides, and Li and Na halides and hydrides. These results do not agree well with very accurate structures derived from microwave spectroscopy; we therefore believe that the dispersion correction in the APF-D method should be reconsidered. Finally, we found that inaccurate structures can easily lead to errors of few kcal/mol in single-point energies.

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Addressing the stereochemistry of complex organic molecules by density functional theory-NMR: vannusal B in retrospective.

Publications

Addressing the stereochemistry of complex organic molecules by density functional theory-NMR: vannusal B in retrospective.

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