Computational NMR Methods in the Stereochemical Analysis of Organic Compounds: Are Proton or Carbon NMR Chemical Shift Data More Discriminating?

Computational Structural Revision of Elaeophorbate and Other Triterpenoids with the Help of NAPROC-13. A New Strategy for Structural Revision of Natural Products

A considerable number of natural products have been published in recent years with misassigned structure, even though they had been correctly elucidated in the past. The availability of databases containing revised structures can prevent the amplification of errors in structural elucidation. NAPROC-13, a dereplication tool based on the ¹³C chemical shift, has been used to search for substances that, possessing the same chemical shifts, have been described with different structures. The correct structure of these different structural proposals is verified by computational chemistry. This paper reports the structural revision of nine triterpenoids following this methodology.

Do Double-Hybrid Exchange-Correlation Functionals Provide Accurate Chemical Shifts? A Benchmark Assessment for Proton NMR

A benchmark density functional theory (DFT) study of ¹H NMR chemical shifts for data sets comprising 200 chemical shifts, including complex natural products, has been carried out to assess the performance of DFT methods. Two new benchmark data sets, NMRH33 and NMRH148, have been established. The meta-GGA revTPSS performs remarkably well against the NMRH33 benchmark set (mean absolute deviation (MAD), 0.10 ppm; maximum deviation (max), 0.26 ppm) with the smallest MAD of all evaluated functionals. The best-performing double-hybrid density functional (DHDF), revDSD-BLYP (MAD, 0.16 ppm; max, 0.35 ppm), performs similarly to hybrid-GGA methods (e.g., mPW1PW91/6-311G(d) (MAD, 0.15 ppm; max, 0.36 ppm)), but at a considerably higher computational cost. The results indicate that currently available double-hybrid DFT methods offer no benefit over GGA (including hybrid and meta) functionals in the calculation of ¹H NMR chemical shifts.

A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide

Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.

Characterization of stereoisomeric 5-(2-nitro-1-phenylethyl)furan-2(5H)-ones by computation of 1 H and 13 C NMR chemical shifts and electronic circular dichroism spectra

In the present work, we describe the preparation of two diastereomers from the enantioselective Michael addition of furan-2(5H)-one to (E)-(2-nitrovinyl)benzene catalyzed by a dinuclear Zn-complex. The relative configurations of the diastereomeric products were assigned by comparing nuclear magnetic resonance (NMR) experimental chemical shift data with those computed by density functional theory (DFT) methods. Corrected mean absolute error (CMAE) and CP3 analyses were used to compare the data sets. The absolute configuration of each diastereomer was initially assigned by analysis of electronic circular dichroism (ECD) data, which was consistent with that of the known X-ray crystallographic structure of the product of a related reaction, namely, (R)-5-((R)-1-(4-chlorophenyl)-2-nitroethyl)furan-2(5H)-one.

Isomerism and dynamic behavior of bridging phosphaalkynes bound to a dicopper complex

A dicopper complex featuring a symmetrically bridging nitrile ligand and supported by a binucleating naphthyridine-based ligand, [Cu₂(μ-η ¹ :η ¹ -MeCN)DPFN](NTf₂)₂, was treated with phosphaalkynes (RC[triple bond, length as m-dash]P, isoelectronic analogues of nitriles) to yield dicopper complexes that exhibit phosphaalkynes in rare μ-η ²:η ² binding coordination modes. X-ray crystallography revealed that these unusual "tilted" structures exist in two isomeric forms (R "up" vs. R "sideways"), depending on the steric profile of the phosphaalkyne's alkyl group (R = Me, Ad, or ^t Bu). Only one isomer is observed in both solution and the solid state for R = Me (sideways) and ^t Bu (up). With intermediate steric bulk (R = Ad), the energy difference between the two geometries is small enough that both are observed in solution, and NMR spectroscopy and computations indicate that the solid-state structure corresponds to the minor isomer observed in solution. Meanwhile, treatment of [Cu₂(μ-η ¹:η ¹-MeCN)DPFN](NTf₂)₂ with 2-butyne affords [Cu₂(μ-η ²:η ²-(MeC[triple bond, length as m-dash]CMe))DPFN](NTf₂)₂: its similar ligand geometry demonstrates that the tilted μ-η ²:η ² binding mode is not limited to phosphaalkynes but reflects a more general trend, which can be rationalized via an NBO analysis showing maximization of π-backbonding.

Structure Determination of a Chloroenyne from Laurencia majuscula Using Computational Methods and Total Synthesis

Despite numerous advances in spectroscopic methods through the latter part of the 20th century, the unequivocal structure determination of natural products can remain challenging, and inevitably, incorrect structures appear in the literature. Computational methods that allow the accurate prediction of NMR chemical shifts have emerged as a powerful addition to the toolbox of methods available for the structure determination of small organic molecules. Herein, we report the structure determination of a small, stereochemically rich natural product from Laurencia majuscula using the powerful combination of computational methods and total synthesis, along with the structure confirmation of notoryne, using the same approach. Additionally, we synthesized three further diastereomers of the L. majuscula enyne and have demonstrated that computations are able to distinguish each of the four synthetic diastereomers from the 32 possible diastereomers of the natural product. Key to the success of this work is to analyze the computational data to provide the greatest distinction between each diastereomer, by identifying chemical shifts that are most sensitive to changes in relative stereochemistry. The success of the computational methods in the structure determination of stereochemically rich, flexible organic molecules will allow all involved in structure determination to use these methods with confidence.

A NMR method for relative stereochemical assignments of the tricyclic core of cephalosporolides, penisporolides and related synthetic analogues

A new NMR method is developed to discriminate the four possible diastereomeric SAFLs, leading to revisions of 11 synthetic compounds.

Beyond DP4: an Improved Probability for the Stereochemical Assignment of Isomeric Compounds using Quantum Chemical Calculations of NMR Shifts

The DP4 probability is one of the most sophisticated and popular approaches for the stereochemical assignment of organic molecules using GIAO NMR chemical shift calculations when only one set of experimental data is available. In order to improve the performance of the method, we have developed a modified probability (DP4+), whose main differences from the original DP4 are the inclusion of unscaled data and the use of higher levels of theory for the NMR calculation procedure. With these modifications, a significant improvement in the overall performance was achieved, providing accurate and confident results in establishing the stereochemistry of 48 challenging isomeric compounds.