Minimizing the risk of deducing wrong natural product structures from NMR data

Structure Revision of Formyl Phloroglucinol Meroterpenoids: A Unified Approach Using NMR Fingerprinting and DFT NMR and ECD Analyses

NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (1a) and eucalypcamal K (2a). NMR fingerprinting PCA analyses identified 1a as an oxepine-diformyl phloroglucinol and 2a as an oxepine 3-acyl-1-formyl phloroglucinol, contrary to their initial assignments as pyrano-diformyl and pyrano 3-acyl-1-formyl phloroglucinols, respectively. Extensive reinterpretation of their reported one- and two-dimensional NMR data, coupled with GIAO DFT-calculated 1H and 13C NMR chemical shift and DP4+ analyses, supported the unequivocal reassignment of eucalyprobusal C to 1b and eucalypcamal K to 2b. The absolute configurations of the revised oxepine-containing phloroglucinol meroterpenoids were confirmed via the reinterpretation of their reported ROESY and NOESY NMR data, along with comparative TDDFT-calculated and experimental ECD spectra.

Assessment of the Long-Range NMR C,H Coupling of a Series of Carbazolequinone Derivatives

Synthesis, the complete 1H- and 13C-NMR assignments, and the long-range C,H coupling constants (nJC,H) of some hydrogen-deficient carbazolequinones, assessed by a J-HMBC experiment, are reported. In these molecules, the protons, used as entry points for assignments, are separated by several bonds with non-protonated atom carbons. Therefore, the use of long-range NMR experiments for the assignment of the spectra is mandatory; we used HSQC and HMBC. On the other hand, the measured heteronuclear (C,H) coupling constants 2J to 5J) allow us to choose the value of the long-range delay used in the HMBC experiment less arbitrarily in order to visualize a desired correlation in the spectrum. The chemical shifts and the coupling constant values can be used as input for assignments in related chemical structures.

The Ethics of Publishing Biomedical and Natural Products Research

Given that the essence of Science is a search for the truth, one might expect that those identifying as scientists would be conscientious and observant of the demands this places on them. However, that expectation is not fulfilled universally as, not too surprisingly, egregious examples of unethical behavior appear and are driven by money, personal ambition, performance pressure, and other incentives. The reproducibility-, fact-, and truth-oriented modus operandi of Science has come to face a variety of challenges. Organized into 11 cases, this article outlines examples of compromised integrity from borderline to blatant unethical behavior that disgrace our profession unnecessarily. Considering technological developments in neural networks/artificial intelligence, a host of factors are identified as impacting Good Ethical Practices. The goal is manifold: to raise awareness and offer perspectives for refocusing on Science and true scientific evidence; to trigger discussion and developments that strengthen ethical behavior; to foster the recognition of the beauty, simplicity, and rewarding nature of scientific integrity; and to highlight the originality of intelligence.

Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls

Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.

Structure Revision of Anti-Inflammatory Indole Alkaloids with a 1,2-Benzisoxazole Ring

(R)- and (S)-2-(benzo[d]isoxazol-3-yl)-2-ethylindolin-3-one [(±)-1] were previously isolated from NIRAM, a natural blue dye from Polygonum tinctorium, and their structures were initially proposed to possess a 1,2-benzisoxazole ring. In this study, the structures of (±)-1 were revised to have an indole-anthranilic acid fused tetracyclic ring rather than the 1,2-benzisoxazole ring by reanalysis of one-dimensional (1D) and two-dimensional (2D) NMR followed by density functional theory (DFT) chemical shift calculation, DP4+ technique, and ECD simulation.

NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures

Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy.

Structure Revision of Balsamisides A-D and Establishment of an Empirical Rule for Distinguishing Four Classes of Biflavonoids

Balsamisides A-D (1-4) are anti-inflammatory and neurotrophic biflavonoidal glycosides originally proposed to possess an epoxide functionality at the C-2/C-3 position. However, there are inconsistencies in their 13C NMR chemical shift values with those of previously reported analogs, indicating that reanalysis of NMR data for structures of 1-4 is necessary. Computational methods aided by the DP4+ probability technique and ECD calculations enabled structural reassignment of 1-4 to have a 2,3-dihydro-3-hydroxyfuran (3-DHF) instead of an epoxide. Additionally, two new biflavonoidal glycosides, balsamisides E and F (14 and 18), possessing a 2,3-dihydro-2-hydroxyfuran (2-DHF) and a 1,4-dioxane ring, respectively, were characterized by conventional NMR and MS data analysis as well as DP4+ and ECD methods. Systematic 13C NMR analysis was performed on the four aforementioned classes of biflavonoids with a 2- or 3-DHF, epoxide, or 1,4-dioxane. As a result, diagnostic 13C NMR chemical shift values of C-2/C-3 for rapid determination of these four biflavonoid classes were formulated, and based on this first empirical rule for (bi)flavonoids eight previously reported ones were structurally revised.

Puzzling Out the Structure of Novofumigatamide: Total Synthesis of Constitutional Isomers. Part II

The total synthesis of several constitutional isomers showing a different connectivity of the macrolactam ring with the hexahydropyrrolo[2,3-b]indole core, as well as those arising from the positional exchange of the valine and the anthranilate units of the structure originally proposed for (−)-novofumigatamide, has been carried out. The constitutional isomers with 12-membered ring macrolactam connected with the pyrroloindoline framework through the indole nitrogen, and the acetyl group at the pyrrole nitrogen, of endo relative configuration, were prepared through the condensation between the tryptophan and valine edges derived from l- or d-tryptophan and l-valine amino acids. The corresponding exo products are highly unstable structures difficult to isolate and characterize. A second group of isomeric structures synthesized considered the positional exchange between the valine and the anthranilate residues within the macrolactam ring in the originally proposed macrocyclic structure. Comparison of the spectroscopic data allowed us to discard these alternative structures for the natural product.

Electron Diffraction of 3D Molecular Crystals

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2N-1 Diastereomers

Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.

Bayesian Inference Applied to NMR-Based Configurational Assignments by Floating Chirality Distance Geometry Calculations

Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the quality and probability of structural elucidations using Bayesian inference in combination with floating chirality distance geometry simulations. Here, we will discuss the configurational analysis of three complex natural products including isopinocampheol (1), plakilactone H (2), and iodocallophycoic acid A (3) using NMR restraints of various types and in different combinations (residual dipolar couplings (RDCs) and NOE-derived distances). Our results quantitatively demonstrate how reliably molecular geometries can be inferred from experimental NMR data, unequivocally unveiling remaining assignment ambiguities. The methodology presented here can dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data in chemistry.

Total Synthesis and Structural Assignment of (-)-Fusaequisin A

(-)-Fusaequisin A is an irregularly assembled polyketide isolated from the ascomycete Fusarium equiseti. Fusaequisin A shares a carbon backbone with curvicollide C from the ascomycete Podospora curvicolla but its absolute configuration remained hitherto unsettled. Herein, we document the total synthesis of (-)-fusaequisin A and its 4-O-desmethyl derivative following a central-to-lateral building block strategy. Catalytic asymmetric Claisen rearrangement, Julia-Kocienski olefination and olefin cross-metathesis served as key C/C-connecting transformations. The constitution and absolute configuration of (-)-fusaequisin A was deduced and the original structural assignment was adjusted.

ACD/Structure Elucidator: 20 Years in the History of Development

The first methods associated with the Computer-Assisted Structure Elucidation (CASE) of small molecules were published over fifty years ago when spectroscopy and computer science were both in their infancy. The incredible leaps in both areas of technology could not have been envisaged at that time, but both have enabled CASE expert systems to achieve performance levels that in their present state can outperform many scientists in terms of speed to solution. The computer-assisted analysis of enormous matrices of data exemplified 1D and 2D high-resolution NMR spectroscopy datasets can easily solve what just a few years ago would have been deemed to be complex structures. While not a panacea, the application of such tools can provide support to even the most skilled spectroscopist. By this point the structures of a great number of molecular skeletons, including hundreds of complex natural products, have been elucidated using such programs. At this juncture, the expert system ACD/Structure Elucidator is likely the most advanced CASE system available and, being a commercial software product, is installed and used in many organizations. This article will provide an overview of the research and development required to pursue the lofty goals set almost two decades ago to facilitate highly automated approaches to solving complex structures from analytical spectroscopy data, using NMR as the primary data-type.

Combining HPLC-DAD-QTOF-MS and HPLC-SPE-NMR to Monitor In Vitro Vitetrifolin D Phase I and II Metabolism

By combining HPLC-DAD-QTOF-MS and HPLC-SPE-NMR, the in vitro metabolism of vitetrifolin D, a pharmacologically active key molecule from Vitex agnus-castus in liver cell fractions, was investigated. Twenty-seven phase I and phase II metabolites were tentatively identified from the culture broth by HPLC-DAD-QTOF-MS. The subsequent HPLC-SPE-NMR analysis allowed for the unequivocal structural characterization of nine phase I metabolites. Since the preparative isolation of the metabolites was avoided, the substance input was much lower than in conventional strategies. The study did prove that the use of hyphenated instrumental analysis methodologies allows for the successful performance of in vitro metabolism studies, even if the availability of substances is very limited.

Structural Revision of Hyperibrin B and Hyperscabrones H and I by Biosynthetic Considerations, NMR Analysis, and Chemical Synthesis

Previously, Gao et al. reported the isolation and structural determination of three natural products, hyperibrin B (HB), hyperscabrone H (HH), and hyperscabrone I (HI), from Hypericum scabrum. HB and HH had different NMR spectroscopic data, but they were assigned identical structures. Furthermore, these compounds should be derived from bicyclic polyprenylated acylphloroglucinols (BPAPs) via degradation, but the assigned structural features of the prenyl and prenylmethyl groups being cis and meta-substituted on the cyclohexanone core were not consistent with their biosynthetic origin. In this note, we revise the structures of HB, HH, and HI via NMR and MS spectroscopic analyses and biosynthetic considerations. We also complete a total synthesis of the revised structure of HB as well as its analogue, hyperibrin A, to further confirm the revision. The revised structures of HB, HH, and HI have not been reported.

The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol

A systematic investigation of the experimental ¹³C-NMR spectra published in Molecules during the period of 1996 to 2015 with respect to their quality using CSEARCH-technology is described. It is shown that the systematic application of the CSEARCH-Robot-Referee during the peer-reviewing process prohibits at least the most trivial assignment errors and wrong structure proposals. In many cases, the correction of the assignments/chemical shift values is possible by manual inspection of the published tables; in certain cases, reprocessing of the original experimental data might help to clarify the situation, showing the urgent need for a public domain repository. A comparison of the significant key numbers derived for Molecules against those of other important journals in the field of natural product chemistry shows a quite similar level of quality for all publishers responsible for the six journals under investigation. From the results of this study, general rules for data handling, data storage, and manuscript preparation can be derived, helping to increase the quality of published NMR-data and making these data available as validated reference material.

Inverse halogen dependence in anion 13C NMR

Halogens cause pronounced and systematic effects on the 13C NMR chemical shift (δ13C) of an adjacent carbon nucleus, usually leading to a decrease in the values across the halogen series. Although this normal halogen dependence (NHD) is known in organic and inorganic compounds containing the carbon atom in its neutral and cationic forms, information about carbanions is scarce. To understand how δ13C changes in molecules with different charges, the shielding mechanisms of CHX3, CX3+, and CX3- (X = Cl, Br, or I) systems are investigated via density functional theory calculations and further analyzed by decomposition into contributions of natural localized molecular orbitals. An inverse halogen dependence (IHD) is determined for the anion series as a result of the negative spin-orbit contribution instead of scalar paramagnetic effects. The presence of a carbon nonbonding orbital in anions allows magnetic couplings that generate a deshielding effect on the nucleus and contradicts the classical association between δ13C and atomic charge.

Application of INADEQUATE NMR techniques for directly tracing out the carbon skeleton of a natural product

INTRODUCTION

Nuclear magnetic resonance (NMR) measurement of ¹ J_CC coupling by two-dimensional (2D) INADEQUATE (incredible natural abundance double quantum transfer experiment), which is a special case of double-quantum (DQ) spectroscopy that offers unambiguous determination of ¹³ C-¹³ C spin-spin connectivities through the DQ transitions of the spin system, is especially suited to solving structures rich in quaternary carbons and poor in hydrogen content (Crews rule).

OBJECTIVE

To review published literature on the application of NMR methods to determine structure in the liquid-state, which specifically considers the interaction of a pair of carbon-13 (¹³ C) nuclei adjacent to one another, to allow direct tracing out of contiguous carbon connectivity using 2D INADEQUATE.

METHODOLOGY

A comprehensive literature search was implemented with various databases: Web of Knowledge, PubMed and SciFinder, and other relevant published materials including published monographs. The keywords used, in various combinations, with INADEQUATE being present in all combinations, in the search were 2D NMR, ¹ J_CC coupling, natural product, structure elucidation, ¹³ C-¹³ C connectivity, cryoprobe and CASE (computer-assisted structure elucidation)/PANACEA (protons and nitrogen and carbon et alia).

RESULTS

The 2D INADEQUATE continues to solve "intractable" problems in natural product chemistry, and using milligram quantities with cryoprobe techniques combined with CASE/PANACEA experiments can increase machine time efficiency. The ¹³ C-¹³ C-based structural elucidation by dissolution single-scan dynamic nuclear polarisation NMR can overcome disadvantages of ¹³ C insensitivity at natural abundance. Selected examples have demonstrated the trajectory of INADEQUATE spectroscopy from structural determination to clarification of metabolomics analysis and use of DFT (density functional theory) and coupling constants to clarify the connectivity, hybridisation and stereochemistry within natural products.

CONCLUSIONS

Somewhat neglected over the years because of perceived lack of sensitivity, the 2D INADEQUATE NMR technique has re-emerged as a useful tool for solving natural products structures, which are rich in quaternary carbons and poor in hydrogen content.

"One-Shot" Measurement of Residual Chemical Shift Anisotropy Using Poly-γ-benzyl-l-glutamate as an Alignment Medium

A method for the measurement of residual chemical shift anisotropy in one experiment using a biphasic isotropic/anisotropic lyotropic liquid crystalline medium based on poly-γ-benzyl-l-glutamate as the alignment medium is presented. This approach is demonstrated on the model compound strychnine and neotricone, a depsidone natural product with a questionable structural assignment based on comparison with the closely related excelsione and in-depth density functional theory calculations.