Total Synthesis and Structure Assignment of (+)-Hexacyclinol

Exploring Diversity through Dimerization in Natural Products by a Rational Tandem Mass-Based Molecular Network Strategy

The step- and atom-efficient dimerization strategy is frequently used in nature to build structural complexity and diversity. We propose the rationale and structural features of the versatile monomers that are responsible for "diversity through dimerization". Using 5-FAM-maleimide combined with a UHPLC-MS/MS-FBMN workflow, we successfully identified a diverse set of dimeric natural products from fungus Panus rudis F01315, in which all four complex 4'5-ring scaffolds are derived from one monomeric epoxyquinol and endowed with functional diversity.

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

There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.

Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights

In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.

Theoretical prediction of 13C NMR spectrum of mixed triglycerides by mean of GIAO calculations to improve vegetable oils analysis

This pioneering study based on GIAO-DFT methods is aimed to the best prediction of ¹³C Nuclear Magnetic Resonances (NMR) arising from triglycerides (and also glycerols), known to be the main component of vegetable oils. Provided that fatty esters bound to the glycerol moiety are not affected by the other esterification chains, and slightly affected by their own esterification position (2- internal, or 1/3- external), eight natural molecules are first optimized despite the challenging presence of many non-hydrogen atoms and the large conformational freedom. This preliminary study sheds light on the total chemical shift prediction concerning five fatty esters (Oleic, Palmitic, Linoleic, Stearic and Linolenic) either present in internal or external positions (ten fragments in total); these results display a very good matching to the experimental profile recorded for several vegetable oils chosen as natural mixtures of glycerides. In order to further improve the theoretical to experimental matching, ten simplified triglycerides with the mentioned fatty esters in the two different esterification positions, and flanked by acetyl esters, were studied and optimized. Beyond the best matching reached so far, we notice that the theoretical rationalisation of the overcrowding in the 28.7-29 ppm spectral region in unable to decode the necessary resolution, nonetheless the same theoretical prediction can still drive the appropriate assignments (as for the fifth and sixth carbon attribution of every chain) even against actual misleading reports.

Total Synthesis of (+)-Pestalofone A and (+)-Iso-A82775C

We describe the total synthesis of epoxyquinoid natural products (+)-pestalofone A and (+)-iso-A82775C. The synthesis of (+)-16-oxo-iso-A82775C, the putative biosynthetic precursor of pestalofone C, is also presented. The allene moiety present in (+)-iso-A82775C and (+)-16-oxo-iso-A82775C was constructed from the ketodiene-yne group via a biosynthetically relevant sequence involving a conjugate reduction and a base-catalyzed tautomerization. Attempted Diels-Alder reaction-based dimerizations of (+)-16-oxo-iso-A82775C and (+)-iso-A82775C toward pestalofones B and C are also described.

Questions in natural products synthesis research that can (and cannot) be answered using computational chemistry

Questions of relevance to those working in the field of natural products synthesis that can be answered, at least in part, using computational chemistry approaches are described. Illustrative examples are provided, as are descriptions of limitations.

Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals

The various factors influencing the accuracy of ¹³C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.

Social Media, Peer Review, and Responsible Conduct of Research (RCR) in Chemistry: Trends, Pitfalls, and Promises

Over the last two decades, various themes inherent in the responsible conduct of research (RCR) in chemistry have been brought to light through prominent cases of research misconduct. This article will describe a few of these cases especially through the lens of social media such as blogs and Twitter. A case will be made that these wholly novel modalities of online discussion are now complementing, and in some cases even circumventing some of the limitations of traditional peer review in chemistry. We present in detail our evaluation of three recent cases of RCR along with several other social media illustrations. These cases have been selected to be representative and showcase several of the most prominent issues at the intersection of traditional and social-media based peer review. In each case, basic details are presented along with a brief discussion of the underlying issues-readers interested in deeper analysis of each subject are referred to a collection of relevant articles and websites. This perspective focuses on the most important RCR issues that have arisen in the past decade, a time which we believe coincides with the serious participation of the scientific community in general, and the chemistry community in particular, in social media-based, citizen-enabled peer-review. A discussion of important trends in RCR in the age of social media, outstanding developments in this area, and questions of enduring interest for the near future concludes the article.

Asymmetric transformations of achiral 2,5-cyclohexadienones

Cyclohexadienones are versatile platforms for performing asymmetric synthesis as evidenced by the numerous natural product syntheses that exploit their diverse reactivity profile. However, there are few general methods available for the direct asymmetric synthesis of chiral cyclohexadienones. To circumvent this problem, several researchers have developed catalytic asymmetric methods that employ readily available achiral 2,5-cyclohexadienones as substrates. Many of these reactions are desymmetrizations in which one of the enantiotopic alkenes of an achiral dienone is transformed. Others involve selective reaction at one alkene of an unsymmetrically substituted, achiral dienone. This review will cover advances in this area over the last 20 years and the application of these strategies in complex molecule synthesis.

A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts

This protocol is intended to provide chemists who discover or make new organic compounds with a valuable tool for validating the structural assignments of those new chemical entities. Experimental ¹H and/or ¹³C NMR spectral data and its proper interpretation for the compound of interest is required as a starting point. The approach involves the following steps: (i) using molecular mechanics calculations (with, e.g., MacroModel) to generate a library of conformers; (ii) using density functional theory (DFT) calculations (with, e.g., Gaussian 09) to determine optimal geometry, free energies and chemical shifts for each conformer; (iii) determining Boltzmann-weighted proton and carbon chemical shifts; and (iv) comparing the computed chemical shifts for two or more candidate structures with experimental data to determine the best fit. For a typical structure assignment of a small organic molecule (e.g., fewer than ∼10 non-H atoms or up to ∼180 a.m.u. and ∼20 conformers), this protocol can be completed in ∼2 h of active effort over a 2-d period; for more complex molecules (e.g., fewer than ∼30 non-H atoms or up to ∼500 a.m.u. and ∼50 conformers), the protocol requires ∼3-6 h of active effort over a 2-week period. To demonstrate the method, we have chosen the analysis of the cis- versus the trans-diastereoisomers of 3-methylcyclohexanol (1-cis versus 1-trans). The protocol is written in a manner that makes the computation of chemical shifts tractable for chemists who may otherwise have only rudimentary computational experience.

Structural revision of cephalosporolide J and bassianolone

The NMR spectra for three "natural" products: cephalosporolide C (Ces-C), cephalosporolide J (Ces-J), and bassianolone were found to be identical, and we proposed that Ces-C was the correct structure for the reported spectra. The first total synthesis of the proposed structure for Ces-J was achieved to support our structural revision for Ces-J. Chemical transformations of bassianolone and computational prediction of (13)C NMR spectra allowed us to conclude that Ces-C was the correct structure for bassianolone. Our synthetic and computational studies suggested that these "different" natural products Ces-C, Ces-J, and bassianolone have the same structure: Ces-C.

Walking in the woods with quantum chemistry--applications of quantum chemical calculations in natural products research

This Highlight describes applications of quantum chemical calculations to problems in natural products chemistry, including the elucidation of natural product structures (distinguishing between constitutional isomers, distinguishing between diastereomers, and assigning absolute configuration) and determination of reasonable mechanisms for their formation.

Using NMR to identify and characterize natural products

Over the past 28 years there have been several thousand publications describing the use of 2D NMR to identify and characterize natural products. During this time period, the amount of sample needed for this purpose has decreased from the 20-50 mg range to under 1 mg. This has been due to both improvements in NMR hardware and methodology. This review will focus on mainly methodology improvements, particularly in pulse sequences, acquisition and processing methods which are particularly relevant to natural product research, with lesser discussion of hardware improvements.

Unambiguous structure elucidation of heterocyclic products from condensation-cyclisation reactions of enaminones by 2D INADEQUATE and 15N NMR

The reaction of enaminones with 3-amino-2-cyanopent-2-enedinitrile can lead to an array of 12 possible products, depending on the reaction pathway and tautomerization. The use of 2D INADEQUATE and (15)N NMR for the unambiguous structure elucidation of the reaction products is discussed in this manuscript.

Prediction of the structure of nobilisitine a using computed NMR chemical shifts

1H and 13C NMR computed chemical shifts are determined for eight diastereomers of the originally proposed structure of nobilisitine A, which has recently been shown to be incorrect. On the basis of comparison of the computed chemical shifts with those reported experimentally, we predict that the true structure of nobilisitine A is likely the diastereomer shown here or its enantiomer.

Asymmetric synthesis of tertiary thiols and thioethers

Enantiomerically pure tertiary thiols provide a major synthetic challenge, and despite the importance of chiral sulfur-containing compounds in biological and medicinal chemistry, surprisingly few effective methods are suitable for the asymmetric synthesis of tertiary thiols. This review details the most practical of the methods available.

Efficient, scalable asymmetric synthesis of an epoxy quinol via Noyori desymmetrization of a meso diketone

Epoxy quinol 1a was prepared on a multi-gram scale by Noyori transfer hydrogenative desymmetrization of the readily available meso epoxy diketone 4. Although the intrinsic enantioselectivity for the desymmetrization was modest (82:18 er at 4% conversion), a highly enantiopure product (99.6:0.4 er) could be obtained in one operation in 44% yield via kinetic resolution of the minor enantiomer with long reaction times (48 h), or in 73% yield by combination with an enzymatic resolution of a 93:7 er mixture.

Chemical probing reveals insights into the signaling mechanism of inflammasome activation

Caspase-1-mediated IL-1β production is generally controlled by two pathways. Toll-like receptors (TLRs) recognize pathogen-derived products and induce NF-κB-dependent pro-IL-1β transcription; NOD-like receptors (NLRs) assemble caspase-1-activating inflammasome complexes that sense bacterial products/danger signals. Through a targeted chemical screen, we identify bromoxone, a marine natural product, as a specific and potent inhibitor of the caspase-1 pathway. Bromoxone is effective over diverse inflammatory stimuli including TLR ligands plus ATP/nigericin, cytosolic DNA, flagellin and Bacillus anthracis lethal toxin. Bromoxone also efficiently suppresses caspase-1 activation triggered by several types of bacterial infection. Bromoxone acts upstream or at the level of the inflammasome in a transcription-independent manner. Bromoxone also inhibits pro-IL-1β expression by targeting components upstream of IKK in the TLR-NF-κB pathway. The unique dual activities of bromoxone are shared by the known TAK1 inhibitor that specifically blocks Nalp3 inflammasome activation. Hinted from the mechanistic and pharmacological properties of bromoxone, we further discover that several known NF-κB inhibitors that act upstream of IKK, but not those targeting IKK or IKK downstream, are potent blockers of different NLRs-mediated caspase-1 activation. Our study uncovers a possible non-transcriptional molecular link between the NLR (Nalp3)-mediated inflammasome pathway and TLR-NF-κB signaling, and suggests a potential strategy to develop new anti-inflammatory drugs.

(+)-hexacyclinol

A SAMPLE OF THE TITLE COMPOUND [SYSTEMATIC NAME: (1aS,2aS,3S,5aS,6aS,7R,7aS,7bS,8R,8aS,10R)-7-hydr-oxy-3-(1-meth-oxy-1-methyl-ethyl)-10-(2-methyl-1-propen-yl)-1a,5a,6a,7,7a,7b,8,8a-octa-hydro-2H-8,2a-(epoxy-methano)phenanthro[2,3-b:6,7-b']bis-oxirene-2,5(3H)-dione], C(23)H(28)O(7), was generated by enanti-oselective synthesis. There are three mol-ecules of the compound in the crystallographic asymmetric unit. Hydrogen bonding between alcohol H atoms and keto groups of adjacent mol-ecules appears to stabilize the structure. The compound is enanti-omerically pure but the absolute configuration could not be determined directly in this study. Accordingly, the illustrated configuration was assigned on the basis of the nature of the chiral nonracemic precursor used in the synthesis.

A unified strategy for enantioselective total synthesis of cladiellin and briarellin diterpenes: total synthesis of briarellins E and F and the putative structure of alcyonin and revision of its structure assignment

Enantioselective total syntheses of briarellin E (12) and briarellin F (13), as well as the structure originally proposed for the cladiellin diterpene alcyonin (10), have been realized. Comparison of the spectral data for synthetic 10, natural alcyonin, cladiellisin (33), and cladiellaperoxide (34), as well as chemical transformations of 10 and natural alcyonin, suggest that the structure of this coral metabolite is allylic peroxide 11. The unified approach detailed herein can be used to access both C4-deoxygenated and C4-oxygenated cladiellins and briarellins. The central step in these syntheses is acid-promoted condensation of (Z)-alpha,beta-unsaturated aldehydes 17 with cyclohexadienyl diols 18 to form intermediates 16 incorporating the hexahydroisobenzofuran core and five stereocenters of these marine diterpenes (Scheme 1 ).

A systematic approach for the generation and verification of structural hypotheses

During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum-mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction, which is best performed either by an incremental or neural net algorithm. The time-consuming QM calculations can then be applied, if necessary, to one or more of the 'best' structures to confirm the suggested solution.