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

Experimental and Computational NMR Studies of Large Alkaloids Exemplified With Vindoline Trimer: Advantages and Limitations

The complete 1H and 13C NMR assignments of a trimeric vindoline together with its individual components, dimeric vindolicine and monomeric vindoline, are performed based on a thorough analysis of the ROESY, COSY, HSQC, and HMBC spectra in combination with the state-of-the-art quantum-chemical calculations. A spatial structure of vindoline trimer is determined by means of computational conformational analysis in combination with the probability distribution map of its basic conformers. On the example of monoterpene indole alkaloid, the trimer vindoline, the present study reveals the power of modern computational NMR to perform identification and stereochemical studies of large natural compounds with some limitations, which may arise in the quantum chemical computing workflow.

Concise Synthesis of Cyctetryptomycin A and B Enabled by Zr-Catalyzed Dimerization

A concise synthetic strategy utilizing a Zr catalyst for the construction of cyctetryptomycin A and B is reported. Cyctetryptomycin A and B are recently isolated, complex tetrameric natural products for which total synthesis has not been previously reported. This study presents a practical approach for the construction of two consecutive quaternary carbon centers with a Zr catalyst. Furthermore, the first total synthesis of cyctetryptomycin A and B was achieved by this Zr-catalyzed radical coupling. The radical dimerization reaction mediated by the Zr catalyst required 1,2-bis(diphenylphosphino)ethane (dppe) as an indispensable additive. Through both experimental and theoretical investigations into the mechanism of this Zr-catalyzed reaction, the specific role of dppe was elucidated. In addition, the synthetic approach was extended to enable the practical synthesis of other dimeric natural products, including tetratryptomycin A, dibrevianamide F, and ditryptophenaline. Finally, the synthetic mechanism of cyctetryptomycin A and B, through the oxidative macrocyclization of tetratryptomycin A by CttpC, was newly elucidated by both experimental and docking simulations.

Complexity-Building Exhaustive Dearomatization of Benzenoid Aromatics within an ESIPT-Initiated Three-Step Photochemical Cascade

Dearomative cycloadditions offer rapid access to complex 3D molecular architectures, commonly via a sp2-to-sp3 rehybridization of two atoms of an aromatic ring. Here we report that the 6e π-system of a benzenoid aromatic pendant could be exhaustively depleted within a single photochemical cascade. An implementation of this approach involves the initial dearomative [4+2] cycloaddition of the Excited State Intramolecular Proton Transfer (ESIPT)-generated azaxylylene, followed by two consecutive [2+2] cycloadditions of auxiliary π moieties strategically positioned in the photoprecursor. Such photochemical cascade fully dearomatizes the benzenoid aromatic ring, saturating all six sp2 atoms to yield a complex sp3-rich scaffold with high control of its 3D molecular shape, rendering it a robust platform for rapid systematic mapping of underexplored chemical space. Significant growth of molecular complexity-starting with a modular synthesis of photoprecursors from readily available building blocks-is quantified by Böttcher score calculations.

Structural diversity and chemical logic underlying the assembly of monoterpene indole alkaloids oligomers

Covering: up to 2024This review aims to draw a parallel between all known oligomers of monoterpene indole alkaloids (MIAs) by illustrating the chemical logic underlying their assembly. For this purpose, oligomeric MIAs were first comprehensively listed and organized according to the names of the backbones of their constitutive monomers and the binding sites. From this extensive list, an oligomer network was generated and unprecedented MIA statistics were mined and shared herein. Subsequently, oligomeric MIAs were categorized according to the number of connections instigated between their monomeric components (single, double, triple, and mixed tethering), then subdivided according to the uniqueness or combination of oligomerization assembly reactions. This effort outlined oligomerization trends in a scaffold-specific manner, and established binding reactivity patterns facilitating the comprehension of the associated biosynthetic processes. At last, this review illustrates a unique initiative in crafting a comprehensive repository of machine-readable metadata for MIA oligomers that could be leveraged for chemoinformatic purposes.

Synthesis and Structure Revision of Securingine E

Chemical synthesis plays a crucial role in confirming and revising the structures of natural products. Through meticulous synthetic efforts, NMR spectroscopic and single-crystal X-ray diffraction analyses, DFT calculations, and mass spectrometric investigations, we revised the structure of securingine E. The revised structure of securingine E was unambiguously confirmed by its chemical synthesis.

Bent naphthodithiophenes: synthesis and characterization of isomeric fluorophores

Thiophene-containing heteroarenes are one of the most well-known classes of π-conjugated building blocks for photoactive molecules. Isomeric naphthodithiophenes (NDTs) are at the forefront of this research area due to their straightforward synthesis and derivatization. Notably, NDT geometries that are bent - such as naphtho[2,1-b:3,4-b']dithiophene (α-NDT) and naphtho[1,2-b:4,3-b']dithiophene (β-NDT) - are seldom employed as photoactive small molecules. This report investigates how remote substituents impact the photophysical properties of isomeric α- and β-NDTs. The orientation of the thiophene units plays a critical role in the emission: in the α(OHex)R2 series conjugation from the end-caps to the NDT core is apparent, while in the β(Oi-Pent)R2 series minimal change is observed unless strong electron acceptors, such as β(Oi-Pent)(PhCF3)2, are employed. This push-pull acceptor-donor-acceptor (A-D-A) fluorophore exhibits positive fluorosolvatochromism that correlates with increasing solvent polarity parameter, E T(30). In total, these results highlight how remote substituents are able to modulate the emission of isomeric bent NDTs.

Kallopterolides A-I, a New Subclass of seco-Diterpenes Isolated from the Southwestern Caribbean Sea Plume Antillogorgia kallos

Kallopterolides A-I (1-9), a family of nine diterpenoids possessing either a cleaved pseudopterane or a severed cembrane skeleton, along with several known compounds were isolated from the Caribbean Sea plume Antillogorgia kallos. The structures and relative configurations of 1-9 were characterized by analysis of HR-MS, IR, UV, and NMR spectroscopic data in addition to computational methods and side-by-side comparisons with published NMR data of related congeners. An investigation was conducted as to the potential of the kallopterolides as plausible in vitro anti-inflammatory, antiprotozoal, and antituberculosis agents.

A Very Deep Graph Convolutional Network for 13C NMR Chemical Shift Calculations with Density Functional Theory Level Performance for Structure Assignment

Nuclear magnetic resonance (NMR) chemical shift calculations are powerful tools for structure elucidation and have been extensively employed in both natural product and synthetic chemistry. However, density functional theory (DFT) NMR chemical shift calculations are usually time-consuming, while fast data-driven methods often lack reliability, making it challenging to apply them to computationally intensive tasks with a high requirement on quality. Herein, we have constructed a 54-layer-deep graph convolutional network for 13C NMR chemical shift calculations, which achieved high accuracy with low time-cost and performed competitively with DFT NMR chemical shift calculations on structure assignment benchmarks. Our model utilizes a semiempirical method, GFN2-xTB, and is compatible with a broad variety of organic systems, including those composed of hundreds of atoms or elements ranging from H to Rn. We used this model to resolve the controversial J/K ring junction problem of maitotoxin, which is the largest whole molecule assigned by NMR calculations to date. This model has been developed into user-friendly software, providing a useful tool for routine rapid structure validation and assignation as well as a new approach to elucidate the large structures that were previously unsuitable for NMR calculations.

Oxidative Control of Photoinduced Cascade Electrocyclizations in Aromatic Azido Imines to Access Complex Fused Imidazoles or Pyrazoles

Photoinduced cascade of two 6π-electron six- and five-center electrocyclizations in aromatic azido imines is oxidatively controlled to yield complex fused benzimidazoles or indazoles. Formation of benzimidazoles occurs via an unprecedented carbon-to-nitrogen o-iminoaryl 1,2-shift.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

Systematic Photoassisted Access to Designer Polyheterocycles via Modular Blocks and Scaffolding

Diverse polyheterocycles are accessed via scaffolded photoassisted synthesis involving decarboxylative aromatization of the primary photoproducts from intramolecular cycloadditions of azaxylylenes and tethered heteroaromatic unsaturated pendants.

Machine learning-assisted structure annotation of natural products based on MS and NMR data

Covering: up to March 2023Machine learning (ML) has emerged as a popular tool for analyzing the structures of natural products (NPs). This review presents a summary of the recent advancements in ML-assisted mass spectrometry (MS) and nuclear magnetic resonance (NMR) data analysis to establish the chemical structures of NPs. First, ML-based MS/MS analyses that rely on library matching are discussed, which involves the utilization of ML algorithms to calculate similarity, predict the MS/MS fragments, and form molecular fingerprint. Then, ML assisted MS/MS structural annotation without library matching is reviewed. Furthermore, the cases of ML algorithms in assisting structural studies of NPs based on NMR are discussed from four perspectives: NMR prediction, functional group identification, structural categorization and quantum chemical calculation. Finally, the review concludes with a discussion of the challenges and the trends associated with the structural establishment of NPs based on ML algorithms.

Penicitone: Structural Reassignment of a Proposed Natural Product Acid Chloride

The proposed structure for the natural product penicitone, which contained a chemically improbable acid chloride functional group, was reassigned to a more probable structure using a combination of chemical knowledge, computer-assisted structure elucidation, and DFT methods.

Complexity-Building ESIPT-Assisted Synthesis of Fused Polyheterocyclic Sulfonamides

Excited State Intramolecular Proton Transfer (ESIPT), originally discovered and explored in depth in a number of extensive photophysical studies, is more recently rediscovered as a powerful synthetic tool, offering rapid access to complex polyheterocycles. In our prior work we have employed ESIPT in aromatic o-keto amines and amides, leading to diverse primary photoproducts-complex quinolinols or azacanes possessing a fused lactam moiety-which could additionally be modified in short, high-yielding postphotochemical reactions to further grow complexity of the heterocyclic core scaffold and/or to decorate it with additional functional groups. Given that sulfonamides are generally known as privileged substructures, in this study we pursued two goals: (i) To explore whether sulfonamides could behave as proton donors in the context of ESIPT-initiated photoinduced reactions; (ii) To assess the scope of subsequent complexity-building photochemical and postphotochemical steps, which give access to polyheterocyclic molecular cores with fused cyclic sulfonamide moieties. In this work we show that this is indeed the case. Simple sulfonamide-containing photoprecursors produced the sought-after heterocyclic products in experimentally simple photochemical reactions accompanied by significant step-normalized complexity increases as corroborated by the Böttcher complexity scores.

Structure elucidation of an aspidofractinine-type monoterpene indole alkaloid from Melodinus reticulatus

The structure and complete NMR assignments of aspidoreticulofractine, an aspidofractinine N-oxide, are reported. Its structure was elucidated based on a combination of spectroscopic techniques including 1D and 2D NMR, high-resolution mass spectrometry, and electronic circular dichroism.

Bromination of endo-7-norbornene derivatives revisited: failure of a computational NMR method in elucidating the configuration of an organic structure

Previously we reported on the bromination of endo-7-bromonorbornene at different temperatures yielding mixtures of addition products. The structural elucidations of the formed compounds were achieved by NMR spectroscopy. Particularly, the γ-gauche effect and long-range couplings were instrumental in assigning the stereochemistry of the adducts. However, in a recent paper, Novitskiy and Kutateladze claimed that based on an applied machine learning-augmented DFT method for computational NMR that the structure of the product, (1R,2R,3S,4S,7s)-2,3,7-tribromobicyclo[2.2.1]heptane was wrong. With the aid of their computational method, they revised a number of published structures, including ours, and assigned our product the structure (1R,2S,3R,4S,7r)-2,3,7-tribromobicyclo[2.2.1]heptane. To fit their revised structure, they proposed an alternative mechanism featuring a skeletal rearrangement without the intermediacy of a carbocation. Herein, we are not only confirming the structure originally assigned by us through crucial NMR experiments, we also present the ultimate structural proof by means of X-ray crystallography. Moreover, we disprove the mechanism proposed by the aforementioned authors based on sound mechanistic reasoning and point to an oversight by the authors that led them to an erroneous mechanistic pathway.

Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT

NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 ¹H and 4230 ¹³C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for ¹H and 92% for ¹³C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (¹H) and from 0.38 to 1.07 ppm (¹³C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.

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.

seco-Pregnane Glycosides from Australian Caustic Vine (Cynanchum viminale subsp. australe)

Cynanchum viminale subsp. australe, more commonly known as caustic vine, is a leafless succulent that grows in the northern arid zone of Australia. Toxicity toward livestock has been reported for this species, along with use in traditional medicine and its potential anticancer activity. Disclosed herein are novel seco-pregnane aglycones cynavimigenin A (5) and cynaviminoside A (6), together with new pregnane glycosides cynaviminoside B (7) and cynavimigenin B (8). Cynavimigenin B (8) contains an unprecedented 7-oxobicyclo[2.2.1]heptane moiety in the seco-pregnane series, likely arising from a pinacol-type rearrangement. Interestingly, these isolates displayed only limited cytotoxicity in cancer and normal human cell lines, in addition to low activity against acetylcholinesterase and Sarcoptes scabiei bioassays, suggesting that 5-8 are not associated with the reported toxicity of this plant species.

Complexity-Building Photoinduced Cascade Involving Csp2-Csp3 Coupling of Aromatic Amides via [2 + 2] Reactivity of ESIPT-Generated o-Azaxylylenes

A new mode for complexity-building photochemical cascades which offers experimentally simple transition metal-free intramolecular C_sp²-C_sp³ cross coupling of aromatic amides is attained via an unprecedented [2 + 2] reactivity of ESIPT-generated azaxylylenes. Coupled with short and straightforward postphotochemical modifications of the primary photoproducts, these cascades allow for a significant step-normalized growth of molecular complexity while accessing diverse and complex polyheterocyclic molecular architectures.

Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria

Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.

Synthesis of High-Order and High-Oxidation State Securinega Alkaloids

Securinega alkaloids, composed of more than 100 members characterized by the compact tetracyclic scaffold, have fascinated the synthetic community with their structural diversity and notable bioactivities. On the basis of the structural phenotype, oligomerizations and oxidations are major biosynthetic diversification modes of the basic Securinega framework. Despite the rich history of synthesis of basic monomeric Securinega alkaloids, the synthesis of oligomeric Securinega alkaloids, as well as oxidized derivatives, has remained relatively unexplored because of their extra structural complexity. In the first half of this Account, our synthetic studies toward high-order Securinega alkaloids are described. We aimed to establish a reliable synthetic method to form C14-C15' and C12-C15' bonds, which are prevalent connection modes between monomers. During our total synthesis of flueggenine C (9), we have invented an accelerated Rauhut-Currier reaction capable of forming the C14-C15' bond stereoselectively. Installation of the nucleophilic functionality to the Michael acceptor, which ushers the C-C bond forming conjugate addition to follow the intramolecular pathway, was the key to success. The C12-C15' linkage, which was inaccessible via an accelerated Rauhut-Currier reaction, was established by devising a complementary cross-coupling/conjugate reduction-based dimerization strategy that enabled the total synthesis of flueggenines D (11) and I (14). In this approach, the C12-C15' linkage was established via a Stille cross-coupling, and the stereochemistry of the C15' position was controlled during the following conjugate reduction step. In the later half of this Account, our achievements in the field of high-oxidation state Securinega alkaloids synthesis are depicted. We have developed oxidative transformations at the N1 and C2-C4 positions, where the biosynthetic oxidation event occurs most frequently. The discovery of a VO(acac)₂-mediated regioselective Polonovski reaction allowed us to access the key 2,3-dehydroallosecurinine (112). Divergent synthesis of secu'amamine A (62) and fluvirosaones A (60) and B (61) was accomplished by exploiting the versatile reactivities of the C2/C3 enamine moiety in 112. We have also employed a fragment-coupling strategy between menisdaurilide and piperidine units, which allowed the installation of various oxygen-containing functionality on the piperidine ring. Combined with the late-stage, light-mediated epimerization and well-orchestrated oxidative modifications, collective total synthesis of seven C4-oxygenated securinine-type natural products was achieved. Lastly, the synthesis of flueggeacosine B (70) via two synthetic routes from allosecurinine (103) was illustrated. The first-generation synthesis (seven overall steps) employing Pd-catalyzed cross-coupling between stannane and thioester to form the key C3-C15' bond enabled the structural revision of the natural product. In the second-generation synthesis, we have invented visible-light-mediated, Cu-catalyzed cross-dehydrogenative coupling (CDC) between an aldehyde and electron-deficient olefin, which streamlined the synthetic pathway into four overall steps. Organisms frequently utilize dimerization (oligomerization) and oxidations during the biosynthesis as a means to expand the chemical space of their secondary metabolites. Therefore, methods and strategies for dimerizations and oxidations that we have developed using the Securinega alkaloids as a platform would be broadly applicable to other alkaloids. It is our sincere hope that lessons we have learned during our synthetic journey would benefit other chemists working on organic synthesis.

Collective total synthesis of C4-oxygenated securinine-type alkaloids via stereocontrolled diversifications on the piperidine core

Securinega alkaloids have fascinated the synthetic chemical community for over six decades. Historically, major research foci in securinega alkaloid synthesis have been on the efficient construction of the fused tetracyclic framework that bears a butenolide moiety and tertiary amine-based heterocycles. These "basic" securinega alkaloids have evolved to undergo biosynthetic oxidative diversifications, especially on the piperidine core. However, a general synthetic solution to access these high-oxidation state securinega alkaloids is lacking. In this study, we have completed the total synthesis of various C4-oxygenated securinine-type alkaloids including securingines A, C, D, securitinine, secu'amamine D, phyllanthine, and 4-epi-phyllanthine. Our synthetic strategy features stereocontrolled oxidation, rearrangement, and epimerization at N1 and C2-C4 positions of the piperidine core within (neo)securinane scaffolds. Our discoveries provide a fundamental synthetic solution to all known securinine-type natural products with various oxidative and stereochemical variations around the central piperidine ring.

Brief overview of recently reported misassigned natural products and their in silico revisions enabled by DU8ML, a machine learning-augmented DFT computational NMR method

Mostly covering 2018 to 2022This Highlight article describes a personal selection of recent misassigned structures of natural products and their revision with the aid of DU8ML, a machine learning-augmented DFT computational method for fast and accurate calculations of solution NMR chemical shifts and spin-spin coupling constants.

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.