Heavy Atom Quantum Mechanical Tunneling in Total Synthesis.

Contributions from quantum mechanical tunneling to the rates of several radical coupling reactions between carbon sp2 centers used as key steps in natural product total syntheses were computed using density functional theory. Contributions ranging from ∼15-52% from tunneling were predicted at room temperature, thereby indicating that tunneling plays an important role in the rates of these reactions and should perhaps be considered when designing complex synthetic schemes.

Correction: Ring-opening yields and auto-oxidation rates of the resulting peroxy radicals from OH-oxidation of α-pinene and ß-pinene.

[This corrects the article DOI: 10.1039/D2EA00133K.].

Organic synthesis in the study of terpene-derived oxidation products in the atmosphere.

Covering: 1997 up to 2022Volatile biogenic terpenes involved in the formation of secondary organic aerosol (SOA) particles participate in rich atmospheric chemistry that impacts numerous aspects of the earth's complex climate system. Despite the importance of these species, understanding their fate in the atmosphere and determining their atmospherically-relevant properties has been limited by the availability of authentic standards and probe molecules. Advances in synthetic organic chemistry directly aimed at answering these questions have, however, led to exciting discoveries at the interface of chemistry and atmospheric science. Herein we provide a review of the literature regarding the synthesis of commercially unavailable authentic standards used to analyze the composition, properties, and mechanisms of SOA particles in the atmosphere.

Large Gas-Phase Source of Esters and Other Accretion Products in the Atmosphere.

Dimeric accretion products have been observed both in atmospheric aerosol particles and in the gas phase. With their low volatilities, they are key contributors to the formation of new aerosol particles, acting as seeds for more volatile organic vapors to partition onto. Many particle-phase accretion products have been identified as esters. Various gas- and particle-phase formation pathways have been suggested for them, yet evidence remains inconclusive. In contrast, peroxide accretion products have been shown to form via gas-phase peroxy radical (RO2) cross reactions. Here, we show that these reactions can also be a major source of esters and other types of accretion products. We studied α-pinene ozonolysis using state-of-the-art chemical ionization mass spectrometry together with different isotopic labeling approaches and quantum chemical calculations, finding strong evidence for fast radical isomerization before accretion. Specifically, this isomerization seems to happen within the intermediate complex of two alkoxy (RO) radicals, which generally determines the branching of all RO2-RO2 reactions. Accretion products are formed when the radicals in the complex recombine. We found that RO with suitable structures can undergo extremely rapid C-C ß scissions before recombination, often resulting in ester products. We also found evidence of this previously overlooked RO2-RO2 reaction pathway forming alkyl accretion products and speculate that some earlier peroxide identifications may in fact be hemiacetals or ethers. Our findings help answer several outstanding questions on the sources of accretion products in organic aerosol and bridge our knowledge of the gas phase formation and particle phase detection of accretion products. As esters are inherently more stable than peroxides, this also impacts their further reactivity in the aerosol.

Unanticipated Hydrophobicity Increases of Squalene and Human Skin Oil Films Upon Ozone Exposure.

The C-H and O-H oscillators on the surfaces of thin films of human-derived skin oil and squalene are probed under ambient conditions (300 K, 1 atm total pressure, 40% RH) using second-order vibrational spectroscopy and contact angle goniometry before and after exposure to ppb amounts of ozone. Skin oil and squalene are found to produce different vibrational sum frequency generation spectra in the C-H stretching region, while exposure to ozone results in surface spectra for both materials that is consistent with a loss of C-H oscillators. The measured contact angles show that the hydrophobicity of the films increases following exposure to ozone, consistent with the reduction in C═C···H2O ("πH") bonding interactions that is expected from C═C double bond loss due to ozonolysis and indicating that the polar functional groups formed point toward the films' interiors. Implications for heterogeneous indoor chemistry are discussed.

Recent strategies and tactics for the enantioselective total syntheses of cyclolignan natural products.

Covering: 2000 to 2021Lignan natural products are found in many different plant species and possess numerous useful biological properties, such as anti-inflammatory, antiviral, antioxidant, antibacterial, and antitumor activities. Their utility in both traditional and conventional medicine, coupled with their structural diversity has made them popular synthetic targets over many decades. This review specifically addresses the cyclolignan subclass of the family, which possess both a C8-C8' and a C2-C7' linkage between two different phenylpropene units. We present a comprehensive overview of the diverse strategies employed by chemists to achieve enantioselective total syntheses of cyclolignans covering: 2000 to 2021.

Molecular Chirality and Cloud Activation Potentials of Dimeric α-Pinene Oxidation Products.

The surface activity of ten atmospherically relevant α-pinene-derived dimers having varying terminal functional groups and backbone stereochemistry is reported. We find ∼10% differences in surface activity between diastereomers of the same dimer, demonstrating that surface activity depends upon backbone stereochemistry. Octanol-water (KOW) and octanol-ammonium sulfate partitioning coefficient (KOAS) measurements of our standards align well with the surface activity measurements, with the more surface-active dimers exhibiting increased hydrophobicity. Our findings establish a link between molecular chirality and cloud activation potential of secondary organic aerosol particles. Given the diurnal variations in enantiomeric excess of biogenic emissions, possible contributions of such a link to biosphere:atmosphere feedbacks as well as aerosol particle viscosity and phase separation are discussed.

Electrochemical and Photocatalytic Oxidative Coupling of Ketones via Silyl Bis-enol Ethers.

Diastereoselective oxidative coupling of ketones through a silyl bis-enol ether intermediate by anodic and photocatalytic oxidation is reported. These methods provide several 1,4-diketones in good yields without the need for stoichiometric metal oxidants. The strategic use of a silicon tether enables the coupling of both aromatic and aliphatic ketones as well as the synthesis of quaternary centers. Cyclic voltammetry is used to gain insight into the oxidation events of the reaction.

Streptomyces buecherae sp. nov., an actinomycete isolated from multiple bat species.

A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of white-nose syndrome, and described using multi-locus sequencing analysis. Swabs from both the cave myotis bat (Myotis velifer) and the Brazilian free-tailed bat (Tadarida brasiliensis) in southern New Mexico bore isolates AC536, AC541T and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541T with neighbors Streptomyces rubidus (NRRL B-24619T), Streptomyces guanduensis (NRRL B-24617T), and Streptomyces yeochonensis (NRRL B-24245T). A complete genome of the type strain was assembled to determine its taxonomy and secondary metabolite potential. ANI comparisons between all closely related types strains are shown to be well below the 95-96% species delineation. DNA-DNA relatedness between AC541T and its nearest neighbors ranged between 23.7 and 24.1% confirming novelty. Approximately 1.49 Mb or 17.76% of the whole genome is devoted to natural product biosynthesis. The DNA G + C content of the genomic DNA of the type strain is 73.13 mol %. Micromorphology depicts ovoid spores with smooth surfaces in flexuous chains. Strains presented an ivory to yellow hue on most ISP media except inorganic salts-starch agar (ISP4) and can grow on D-glucose, mannitol, and D-fructose, but exhibited little to no growth on L-arabinose, sucrose, D-xylose, inositol, L-rhamnose, D-raffinose, and cellulose. This clade possesses the capability to grow from 10 to 45 °C and 12.5% (w/v) NaCl. There was strain growth variation in pH, but all isolates thrive at alkaline levels. Based on our polyphasic study of AC541T, the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541T (= JCM 34263T, = ATCC TSD201T).

Genome Mining and Metabolomics Uncover a Rare d-Capreomycidine Containing Natural Product and Its Biosynthetic Gene Cluster.

We report the metabolomics-driven genome mining of a new cyclic-guanidino incorporating non-ribosomal peptide synthetase (NRPS) gene cluster and full structure elucidation of its associated hexapeptide product, faulknamycin. Structural studies unveiled that this natural product contained the previously unknown (R,S)-stereoisomer of capreomycidine, d-capreomycidine. Furthermore, heterologous expression of the identified gene cluster successfully reproduces faulknamycin production without an observed homologue of VioD, the pyridoxal phosphate (PLP)-dependent enzyme found in all previous l-capreomycidine biosynthesis. An alternative NRPS-dependent pathway for d-capreomycidine biosynthesis is proposed.

Access to α-Pyrazole and α-Triazole Derivatives of Ketones from Oxidative Heteroarylation of Silyl Enolethers.

The synthesis of α-pyrazole and α-triazole derivatives of ketones by the ceric ammonium nitrate-mediated oxidative coupling of enolsilanes with heteroarenes is reported. The reaction proceeds under mild reaction conditions to provide a diversity of products, including sterically hindered fully substituted derivatives.

Synergistic Uptake by Acidic Sulfate Particles of Gaseous Mixtures of Glyoxal and Pinanediol.

The uptake of gaseous organic species by atmospheric particles can be affected by the reactive interactions among multiple co-condensing species, yet the underlying mechanisms remain poorly understand. Here, the uptake of unary and binary mixtures of glyoxal and pinanediol by neutral and acidic sulfate particles is investigated. These species are important products from the oxidation of volatile organic compounds (VOCs) under atmospheric conditions. The uptake to acidic aerosol particles greatly increased for a binary mixture of glyoxal and pinanediol compared to the unary counterparts. The strength of the synergism depended on the particle acidity and water content (i.e., relative humidity). The greater uptake was up to 2.5× to 8× at 10% relative humidity (RH) for glyoxal and pinanediol, respectively. At 50% RH, it was 2× and 1.2× for the two species. Possible mechanisms of acid-catalyzed cross reactions between the species are proposed to explain the synergistic uptake. The proposed mechanisms are applicable to a broader extent across atmospheric species having carbonyl and hydroxyl functionalities. The results thus suggest that synergistic uptake reactions can be expected to significantly influence the gas-particle partitioning of VOC oxidation products under atmospheric conditions and thus greatly affect their atmospheric transport and lifetime.

Ion Mobility Mass Spectrometry as an Efficient Tool for Identification of Streptorubin B in Streptomyces coelicolor M145.

Ion mobility spectrometry was utilized to corroborate the identity of streptorubin B (2) as the natural product produced by Streptomyces coelicolor. Natural product 2 was initially assigned as butylcycloheptylprodigiosin (3), and only relatively recently was this assignment clarified. We present additional evidence of this assignment by comparing collisional cross sections (Ω) of synthetic standards of 2, 3, and metacycloprodigiosin (4) to the cyclic prodiginine produced by S. coelicolor. Calculated theoretical Ω values demonstrate that cyclic prodiginines could be identified without standards. This work highlights ion mobility as an efficient tool for the dereplication of natural products.

A computational framework to explore large-scale biosynthetic diversity.

Genome mining has become a key technology to exploit natural product diversity. Although initially performed on a single-genome basis, the process is now being scaled up to mine entire genera, strain collections and microbiomes. However, no bioinformatic framework is currently available for effectively analyzing datasets of this size and complexity. In the present study, a streamlined computational workflow is provided, consisting of two new software tools: the 'biosynthetic gene similarity clustering and prospecting engine' (BiG-SCAPE), which facilitates fast and interactive sequence similarity network analysis of biosynthetic gene clusters and gene cluster families; and the 'core analysis of syntenic orthologues to prioritize natural product gene clusters' (CORASON), which elucidates phylogenetic relationships within and across these families. BiG-SCAPE is validated by correlating its output to metabolomic data across 363 actinobacterial strains and the discovery potential of CORASON is demonstrated by comprehensively mapping biosynthetic diversity across a range of detoxin/rimosamide-related gene cluster families, culminating in the characterization of seven detoxin analogues.

Synthesis and surface spectroscopy of α-pinene isotopologues and their corresponding secondary organic material.

Atmospheric aerosol-cloud interactions remain among the least understood processes within the climate system, leaving large uncertainties in the prediction of future climates. In particular, the nature of the surfaces of aerosol particles formed from biogenic terpenes, such as α-pinene, is poorly understood despite the importance of surface phenomena in their formation, growth, radiative properties, and ultimate fate. Herein we report the coupling of a site-specific deuterium labeling strategy with vibrational sum frequency generation (SFG) spectroscopy to probe the surface C-H oscillators in α-pinene-derived secondary organic aerosol material (SOM) generated in an atmospheric flow tube reactor. Three α-pinene isotopologues with methylene bridge, bridgehead methine, allylic, and vinyl deuteration were synthesized and their vapor phase SFG spectra were compared to that of unlabeled α-pinene. Subsequent analysis of the SFG spectra of their corresponding SOM revealed that deuteration of the bridge methylene C-H oscillators present on the cyclobutane ring in α-pinene leads to a considerable signal intensity decrease (ca. 30-40%), meriting speculation that the cyclobutane moiety remains largely intact within the surface bound species present in the SOM formed upon α-pinene oxidation. These insights provide further clues as to the complexity of aerosol particle surfaces, and establish a framework for future investigations of the heterogeneous interactions between precursor terpenes and particle surfaces that lead to aerosol particle growth under dynamically changing conditions in the atmosphere.

Natural products from thioester reductase containing biosynthetic pathways.

Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.

Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics.

Natural products (NPs) are a rich source of medicines, but traditional discovery methods are often unsuccessful due to high rates of rediscovery. Genetic approaches for NP discovery are promising, but progress has been slow due to the difficulty of identifying unique biosynthetic gene clusters (BGCs) and poor gene expression. We previously developed the metabologenomics method, which combines genomic and metabolomic data to discover new NPs and their BGCs. Here, we utilize metabologenomics in combination with molecular networking to discover a novel class of NPs, the tyrobetaines: nonribosomal peptides with an unusual trimethylammonium tyrosine residue. The BGC for this unusual class of compounds was identified using metabologenomics and computational structure prediction data. Heterologous expression confirmed the BGC and suggests an unusual mechanism for trimethylammonium formation. Overall, the discovery of the tyrobetaines shows the great potential of metabologenomics combined with molecular networking and computational structure prediction for identifying interesting biosynthetic reactions and novel NPs.

Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization.

The total synthesis of tambromycin (1), a recently isolated tetrapeptide, is reported. This unusual natural product possesses a highly modified tryptophan-derived indole fragment fused to an α-methylserine-derived oxazoline ring, and a unique noncanonical amino acid residue named tambroline (11). A convergent synthesis of tambromycin was achieved by a 13-step route that leveraged recent developments in the field of C-H functionalization to prepare the complex indole fragment, as well as an efficient synthesis of tambroline that featured a diastereoselective amination of homoproline.

A Strategy for the Convergent and Stereoselective Assembly of Polycyclic Molecules.

The stereoselective oxidative coupling of cyclic ketones via silyl bis-enol ethers followed by ring-closing metathesis is shown to be a general and powerful reaction sequence for the preparation of diverse polycyclic scaffolds from simple precursors. The modular strategy successfully constructs substructures prevalent in numerous bioactive natural product families, varying in substitution and carbocyclic composition. Several of the prepared compounds were shown to possess potent cytotoxic activity against a panel of tumor cell lines. The utility of this strategy was further demonstrated by a concise and highly convergent 17-step formal synthesis of the complex antimalarial marine diterpene, (+)-7,20-diisocyanoadociane.