Natural Products Containing the Oxetane and Related Moieties Present Additional Challenges for Structure Elucidation: A DU8+ Computational Case Study

Overcoming the ring tension: computational approaches to stereochemical assignments and geometrical insights in small heterocycles

In this study, we evaluate the performance of the DP4+ and MM-DP4+ methods on molecules featuring small heterocyclic rings. A dataset of 71 molecules containing three- and four-membered heterocycles, known for their stereochemical assignment challenges, was analyzed. We compared molecular geometries optimized at different computational levels, including MMFF and B3LYP/6-31G*, to assess deviations in key geometric parameters relative to the heterocycle structures. Furthermore, the geometric properties of these molecules were investigated using various force fields to evaluate their differences. Our aim was to assess the reliability of B3LYP/6-31G* in comparison with more accurate methods and to elucidate how different force fields influence in geometric precision.

Biocatalytic enantioselective formation and ring-opening of oxetanes

Although biocatalysis offers complementary or alternative approaches to traditional synthetic methods, the limited range of available enzymatic reactions currently poses challenges in synthesizing a diverse array of desired compounds. Consequently, there is a significant demand for developing novel biocatalytic processes to enable reactions that were previously unattainable. Herein, we report the discovery and subsequent protein engineering of a unique halohydrin dehalogenase to develop a biocatalytic platform for enantioselective formation and ring-opening of oxetanes. This biocatalytic platform, exhibiting high efficiency, excellent enantioselectivity, and broad scopes, facilitates the preparative-scale synthesis of chiral oxetanes and a variety of chiral γ-substituted alcohols. Additionally, both the enantioselective oxetane formation and ring-opening processes are proven scalable for large-scale transformations at high substrate concentrations, and can be integrated efficiently in a one-pot, one-catalyst cascade system. This work expands the enzymatic toolbox for non-natural reactions and will promote further exploration of the catalytic repertoire of halohydrin dehalogenases in synthetic and pharmaceutical chemistry.

Phosphine-catalyzed enantioselective and diastereodivergent [3+2] cyclization for the construction of oxetane dispirooxindole skeletons

We have developed a phosphine catalyzed asymmetric [3+2] cyclization of 3-oxetanone derived MBH carbonates with activated methyleneoxindole, to construct oxetane dispirooxindole skeletons. Diastereodivergent synthesis was realized via the control of the phosphine catalyst. The (-)-DIOP provides the syn diastereoisomers, while the spiro phosphine (R)-SITCP achieves the anti-epimers.

Visible-Light-Mediated [2+2] Photocycloadditions of Alkynes

Visible-light-mediated [2+2] photocycloaddition reaction can be considered an ideal solution due to its green and sustainable properties, and is one of the most efficient methods to synthesize four-membered ring motifs. Although research on the [2+2] photocycloaddition of alkynes is challenging because of the diminished reactivity of alkynes, and the more significant ring strain of the products, remarkable achievements have been made in this field. In this article, we highlight the recent advances in visible-light-mediated [2+2] photocycloaddition reactions of alkynes, with focus on the reaction mechanism and the late-stage synthetic applications. Advances in obtaining cyclobutenes, azetines, and oxetene active intermediates continue to be breakthroughs in this fascinating field of research.

1,4-Pd Migration-Enabled Synthesis of Fused 4-Membered Rings

1,4-Palladium migration has been widely used for the functionalization of remote C-H bonds. However, this mechanism has been limited to aryl halide precursors. This work reports an unprecedented Pd0-catalyzed cyclobutanation protocol producing valuable fused cyclobutanes starting from cycloalkenyl (pseudo)halides. This reaction takes place via alkenyl-to-alkyl 1,4-Pd migration, followed by intramolecular Heck coupling. The method performs best with cyclohexenyl precursors, giving access to a variety of substituted bicyclo[4,2,0]octenes. Reactants containing an N-methyl or methoxy group give rise to fused azetidines or oxetanes, respectively, via the same mechanism. Kinetic and deuterium-labeling studies point to a rate-limiting C(sp3)-H activation step.

DBU-Catalyzed Diastereo/Regioselective Access to Highly Substituted Spiro-oxetane Oxindoles via Ring Annulation of Isatins and Allenoates

A facile and efficient method for the diastereo/regioselective synthesis of highly functionalized spiro-oxetane oxindoles has been described. The 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)-catalyzed reaction proceeds via spiro-annulation of isatins and allenoates. The reaction is compatible with a wide range of isatins containing electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) with various allenoates affording the corresponding products in acceptable yields. It is noteworthy that this is the first protocol for constructing structurally diverse motifs of highly functionalized spiro-oxetane oxindoles of pharmaceutical relevance.

Propargyl Alcohols as Bifunctional Reagents for Divergent Annulations of Biphenylamines via Dual C-H Functionalization/Dual Oxidative Cyclization

The C-H functionalization strategy provides access to valuable molecules that previously required convoluted synthetic attempts. Dual C-H unsymmetrical functionalization, with a single bifunctional reagent, is an effective tactic. Propargyl alcohols (PAs), despite containing a reactive C≡C bond, have not been explored as building blocks via oxidative cleavage. Annulations via C-H activation are a versatile and synthetically attractive strategy. We disclose PA as a new bifunctional reagent for unsymmetrical dual C-H functionalization of biphenylamine for regioselectively annulated outcomes. On tuning the conditions, the annulation bifurcated towards an unusual dual oxidative cyclization. This method accommodates a wide range of PAs and showcases late-stage diversification of some natural products.

Two Radical SAM Enzymes Are Necessary and Sufficient for the In Vitro Production of the Oxetane Nucleoside Antiviral Agent Albucidin

Oxetanocin A and albucidin are two oxetane natural products. While the biosynthesis of oxetanocin A has been described, less is known about albucidin. In this work, the albucidin biosynthetic gene cluster is identified in Streptomyces. Heterologous expression in a nonproducing strain demonstrates that the genes alsA and alsB are necessary and sufficient for albucidin biosynthesis confirming a previous study (Myronovskyi et al. Microorganisms 2020, 8, 237). A two-step construction of albucidin 4'-phosphate from 2'-deoxyadenosine monophosphate (2'-dAMP) is shown to be catalyzed in vitro by the cobalamin dependent radical S-adenosyl-l-methionine (SAM) enzyme AlsB, which catalyzes a ring contraction, and the radical SAM enzyme AlsA, which catalyzes elimination of a one-carbon fragment. Isotope labelling studies show that AlsB catalysis begins with stereospecific H-atom transfer of the C2'-pro-R hydrogen from 2'-dAMP to 5'-deoxyadenosine, and that the eliminated one-carbon fragment originates from C3' of 2'-dAMP.

Peculiar Reaction Products and Mechanisms Revisited with Machine Learning-Augmented Computational NMR

DU8ML, a fast and accurate machine learning-augmented density functional theory (DFT) method for computing nuclear magnetic resonance (NMR) spectra, proved effective for high-throughput revision of misassigned natural products. In this paper, we disclose another important aspect of its application: correction of unusual reaction mechanisms originally proposed because of incorrect product structures.

Iboga-type alkaloids with Indolizidino[8,7-b]Indole scaffold and bisindole alkaloids from Tabernaemontana bufalina Lour

Phytochemical investigation on the aerial parts of Tabernaemontana bufalina Lour. (Apocynaceae) led to the identification of four undescribed monoterpenoid indole alkaloids named taberbufamines A-D, an undescribed natural product, and fourteen known indole alkaloids. The structures of the undescribed alkaloids were established by spectroscopic and computational methods, and their absolute configurations were further determined by quantum chemical TDDFT calculations and the experimental ECD spectra. Taberbufamines A and B possessed an uncommon skeleton incorporating an indolizidino [8,7-b]indole motif with a 2-hydroxymethyl-butyl group attached at the pyrrolidine ring. Biosynthetically, Taberbufamines A and B might be derived from iboga-type alkaloid through rearrangement. Vobatensine C showed significant bioactivity against A-549, Bel-7402, and HCT-116 cells with IC₅₀ values of 2.61, 1.19, and 1.74 μM, respectively. Ervahanine A showed antimicrobial activity against Bacillus subtilis, Mycobacterium smegmatis, and Helicobacter pylori with MIC values of 4, 8, and 16 μg/mL, respectively. 19(S)-hydroxyibogamine was shown as butyrylcholinesterase inhibitor (IC₅₀ of 20.06 μM) and α-glycosidase inhibitor (IC₅₀ of 17.18 μM), while tabernamine, ervahanine B, and ervadivaricatine B only showed α-glycosidase inhibitory activities with IC₅₀ values in the range of 0.95-4.61 μM.

DU8ML: Machine Learning-Augmented Density Functional Theory Nuclear Magnetic Resonance Computations for High-Throughput In Silico Solution Structure Validation and Revision of Complex Alkaloids

Machine learning (ML) profoundly improves the accuracy of the fast DU8+ hybrid density functional theory/parametric computations of nuclear magnetic resonance spectra, allowing for high throughput in silico validation and revision of complex alkaloids and other natural products. Of nearly 170 alkaloids surveyed, 35 structures are revised with the next-generation ML-augmented DU8 method, termed DU8ML.

Hexahydroazulene-2(1H)-one Sesquiterpenoids with Bridged Cyclobutane, Oxetane, and Tetrahydrofuran Rings from the Stems of Daphne papyracea with α-Glycosidase Inhibitory Activity

Chemical investigation of an alcoholic extract from the stem of Daphne papyracea ("Xuehuagou") led to the isolation of the tetracyclic sesquiterpenoid daphnepapytone A (1), containing a unique caged skeleton with a cyclobutane ring having three tetrasubstituted chirality centers. Also isolated were new guaiane sesquiterpenoids, namely, daphnepapytones B-H (2-8), and one 1,5-diphenylpentanone 2-hydroxy-5-oxo-daphneone (9), together with 26 known compounds. The cyclic metabolites share a 5-isoprenyl-hexahydroazulene-2(1H)-one skeleton with different substitution patterns and a bridged cyclobutane, oxetane, or tetrahydrofuran ring. The planar structures and relative configuration of the new compounds were elucidated on the basis of spectroscopic analysis aided by DFT ¹³C NMR calculations. The absolute configurations of 1-7 were determined by X-ray single-crystal diffraction or TDDFT-ECD calculations. Daphnepapytones A and C (1 and 3), 2-hydroxy-5-oxodaphneone (9), daphnenone (10), daphneone (11), and 3-methyldaphneolone (12) showed α-glycosidase inhibitory activity, with IC₅₀ values of 159.0, 102.3, 139.3, 43.3, 145.0, and 126.1 μM, respectively.

DU8+ Computations Reveal a Common Challenge in the Structure Assignment of Natural Products Containing a Carboxylic Anhydride Moiety

DU8+ computations of NMR spectra revealed a relatively common error in the structure assignment of carboxylic anhydride-containing natural products. Computationally driven revisions of ten of these structures are reported in this Note. The majority of the misassigned structures featured a hydroxy group that is proximal to the proposed anhydride moiety and capable of lactone formation.

Nickel(II)-Based Building Blocks with Schiff Base Derivatives: Experimental Insights and DFT Calculations

We have recently reported a series of neutral square planar tridentate Schiff base (L) complexes of the general formula [(L)M(py)], showing relatively high first-order hyperpolarizabilities and NLO redox switching behavior. In the present study, new members of this family of compounds have been prepared with the objective to investigate their potential as building blocks in the on-demand construction of D-π-A push–pull systems. Namely, ternary nickel(II) building blocks of general formula [(L^A/D)Ni(4-pyX)] (4–7), where L^A/D stands for an electron accepting or donating dianionic O,N,O-tridentate Schiff base ligand resulting from the monocondensation of 2-aminophenol or its 4-substituted nitro derivative and β-diketones R-C(=O)CH₂C(=O)CH₃ (R = methyl, anisyl, ferrocenyl), and 4-pyX is 4-iodopyridine or 4-ethynylpyridine, were synthesized and isolated in 60–78% yields. Unexpectedly, the Sonogashira cross-coupling reaction between the 4-iodopyridine derivative 6 and 4-ethynylpyridine led to the formation of the bis(4-pyridyl) acetylene bridged centrosymmetric dimer [{(L^D)Ni}₂(µ²-py-C≡C-py)] (8). Complexes 4–8 were characterized by elemental analysis, FT-IR and NMR spectroscopy, single crystal X-ray diffraction and computational methods. In each compound, the four-coordinate Ni(II) metal ion adopts a square planar geometry with two nitrogen and two oxygen atoms as donors occupying trans positions. In 8, the Ni…Ni separation is of 13.62(14) Å. Experimental results were proved and explained theoretically exploiting Density Functional Theory calculations.

Taxonomy Driven Discovery of Polyketides from Aspergillus californicus

Five new polyketides were isolated from the rare filamentous fungus Aspergillus californicus IBT 16748 including calidiol A (1); three phthalide derivatives califuranones A₁, A₂, and B (2-4); and a pair of enantiomers (-)-calitetralintriol A (-5) and (+)-calitetralintriol A (+5) together with four known metabolites (6-9). The structures of the new products were established by extensive spectroscopic analyses including HRMS and 1D and 2D NMR. The absolute configurations of two diastereomers 2 and 3 and the enantiomers (-5) and (+5) were assigned by comparing their experimental and calculated ECD data, whereas the absolute configuration of 4 was proposed by analogy. Compound 1 showed moderate activity against methicillin-resistant Staphylococcus aureus.

A DFT/machine-learning hybrid method for the prediction of 3 JHCCH couplings

A machine learning model for the prediction of vicinal proton-proton couplings has been developed based on a hybrid representation that includes geometrical and electronic parameters derived from natural bond orbital (NBO) analysis of low-level BLYP/STO-3G computations. The model can predict ³ J_HH couplings with accuracy comparable or better than the well-known Altona equation, and it can provide sensible ³ J_HH predictions in systems not well handled by the Altona equation such as epoxide or cyclopropane rings.

Systematic Analysis of the Role of Substituents in Oxiranes, Oxetanes, and Oxathietanes Chemical Shifts

The important role substituents play on proton chemical shifts in heterocyclic compounds was investigated in detail. For this purpose, a considerable number of model oxiranes, oxetanes, and oxathietanes with different substituents were studied in a systematic way. In addition, the oxygen and sulfur heteroatom influence on the chemical shift values was analyzed. The density functional theory (DFT) approximation was employed together with the M06 and the B3LYP functionals and the aug-pcS-1 and the 6-311++G** basis sets. We carried out a careful analysis of the shift values and the changes in the corresponding molecular electrostatic potential surfaces due to substitution. We observed that chemical shift values for the protons closest to the substituents are larger for the chloro and fluoro derivatives than those for the cyano and ethynyl ones. The presence of oxygen as well as sulfur in the ring causes an increase of the chemical shift values, most pronounced for the atom closest to the substituent. A large decrease of the proton shifts was observed when going from methylenecyclopropane to methyleneoxirane that can be attributed to π-electron resonance. Protons diagonal to the substituents behaved in a different way depending on their cis or trans disposition with respect to them. The conclusions of the present study will be useful in theoretical and experimental work on NMR spectra of heterocyclic compounds.

Abiotic scaffolds in medicinal chemistry: not a waste of chemical space

It is well established that medicinal chemists should depart from the flat, sp²-dominated nature of traditional drugs and incorporate complexities of bioactive natural products, such as sp³-richness, 3D topology and chirality. There is a gray area, however, in the relevance of newly developed chemical scaffolds that exhibit these complexities but do not correlate to anything observed in nature. This can leave synthetic methodologists searching for structural similarities between their newly developed products and known natural products in search of justification. This article offers a perspective on how these types of complex 'abiotic' scaffolds can be appreciated purely on the basis of their structural novelty, and identifies the unique advantages arising when a complex chemical entity unrecognized by nature is introduced to biological systems.

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.

Quantum mechanical NMR full spin analysis in pharmaceutical identity testing and quality control

Issues related to pharmaceutical quality are arising at an alarming rate. Pharmaceutical quality concerns both the Active Pharmaceutical Ingredients (APIs) and the Finished Drug Product/ Formulation. Recently, there has been a significant increase in the number of reports of harmful impurities in marketed drug formulations. Impurities range from solvents, reactants, adulterants, and catalysts to synthetic byproducts. Quality concerns in commercial preparations may also arise due to shelf life stability. Furthermore, a number of falsified and substandard drug cases have been reported. Most of the techniques which are currently in place can, at best, detect the impurities, but cannot identify them unless they are already known and can be compared to a standard. On the other hand, ¹H NMR spectroscopy detects all the hydrogen containing species, typically provides information to elucidate structures partially or even completely, and through its absolute quantitative capabilities even can detect the presence hydrogen-free species indirectly. The structural properties that produce ¹H NMR signals as characteristic representations of a given molecule are the chemical shifts (δ in ppm) and coupling constants (J in Hz). Along with the line widths (ω_1/2 in Hz), these parameters are bound to both the molecule and the NMR experimental conditions by quantum mechanical (QM) principles. This means that the ¹H NMR spectra of APIs can be precisely calculated and compared to the experimental data. This review explains how ¹H NMR spectroscopy coupled with Full Spin Analysis can contribute towards the quality control of pharmaceuticals by improving structural dereplication and achieving simultaneous quantification of both APIs and their contaminants.

The Discreet Structural Diversity of Briarellins: DU8+ Guided Multiple Structure Revisions Yielded Two Unknown Structural Types

Briarellins, a subset of C2-C11 cyclized cembranoids, were proposed to contain a C3-C14 ether or lactone bridge, similar to asbestinins. However, the total synthesis of the proposed structure of briarellin J revealed a misassignment. We revisited briarellins, computationally, with the help of a recently developed hybrid DFT/parametric method, DU8+, and revised the structures of briarellin C14-C3 ε-lactones to new structural types containing either a C14-C11 or C14-C12 lactone bridge. The original structures of briarellin and asbestinin ethers were confirmed.

Misassigned Polyoxygenated Sterols and Reassignments of Their Structures

This review will summarize the authors’ studies on the reassignments of structures of 9 natural polyoxygenated sterols (24 S)-24-ethylcholest-8-ene-3β,5α,6β,7α-tetrol (1), (24 S)-24-ethylcholest-8(14)-ene-3β,5α,6β,7α-tetrol (2), (22 E)-24-methylcholesta-8(14),22-diene-3β,5α,6β,7α-tetrol (3), 5β,6β-epoxy-(22 E)-ergosta-8,22-diene-3β,7β-diol (4), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14α-pentol (5), 3β,5α,6β,8β,14α-pentahydroxy-(22 E)-ergost-22-en-7-one (6), 5β,6β-epoxy-24-methylenecholesta-8,24(28)-diene-3β,7α,11α-triol (7), 6β-acetoxy-(22 E)-10α-ergosta-7,22-diene-3β,5α-diol (8), and 8α,9α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,14α-triol (9). The structures of 1 to 9 have been reassigned as (24 S)-5α,6α-epoxy-24-ethylcholest-8-ene-3β,7α-diol (16), (24 S)-5α,6α-epoxy-24-ethylcholest-8(14)-ene-3β,7α-diol (17), 5α,6α-epoxy-(22 E)-ergosta-8(14),22-diene-3β,7α-diol (13), 5α,6α-epoxy-(22 E)-ergosta-8,22-diene-3β,7α-diol (12), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14β-pentol (25), 5α,6α;8α,14α-diepoxy-3β-hydroxy-(22 E)-ergost-22-en-7-one (18), 5α,6α-epoxyergosta-8,24(28)-diene-3β,7α,11α-triol (21), 6β-acetoxy-(22 E)-ergosta-7,22-diene-3β,5α-diol (26), and 8α,14α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,9α-triol (28), respectively, from the results of careful reexamination of the published1H and13C NMR spectral data.

Reisolation and Configurational Reinvestigation of Cottoquinazolines E-G from an Arthropod-Derived Strain of the Fungus Neosartorya fischeri

The reported fumiquinazoline-related alkaloids cottoquinazolines E-G (1-3) were reisolated from solid cultures of the fungus Neosartorya fischeri, which was isolated from the medicinal arthropod Cryptotympana atrata. The unresolved issues regarding the absolute configurations (for cottoquinazolines E and F) prompted a reinvestigation of the configurations for all three compounds, as enabled by extensive spectroscopic methods, comparisons of experimental electronic circular dichroism data, and X-ray crystallography. In addition, cottoquinazoline F (2) showed significant antibacterial activity against ESBL-producing Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus faecalis with MIC values of 8, 32, 32, and 16 μg/mL, respectively.

Escaping from Flatland: [2 + 2] Photocycloaddition; Conformationally Constrained sp3-rich Scaffolds for Lead Generation

Pressure on researchers to deliver new medicines to the patient continues to grow. Attrition rates in the research and development process present a significant challenge to the viability of the current model of drug discovery. Analysis shows that increasing the three-dimensionality of potential drug candidates decreases the risk of attrition, and it is for this reason many workers have taken a new look at the power of photochemistry, in particular photocycloadditions, as a means to generate novel sp³-rich scaffolds for use in drug discovery programs. The viability of carrying out photochemical reactions on scale is also being addressed by the introduction of new technical developments.