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.

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.

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.

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.

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.

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.

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).

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.

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.

Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products.

The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized.

Enantioselective Synthesis of Allenes by Catalytic Traceless Petasis Reactions.

Allenes are useful functional groups in synthesis as a result of their inherent chemical properties and established reactivity patterns. One property of chemical bonding renders 1,3-substituted allenes chiral, making them attractive targets for asymmetric synthesis. While there are many enantioselective methods to synthesize chiral allenes from chiral starting materials, fewer methods exist to directly synthesize enantioenriched chiral allenes from achiral precursors. We report here an asymmetric boronate addition to sulfonyl hydrazones catalyzed by chiral biphenols to access enantioenriched allenes in a traceless Petasis reaction. The resulting Mannich product from nucleophilic addition eliminates sulfinic acid, yielding a propargylic diazene that performs an alkyne walk to afford the allene. Two enantioselective approaches have been developed; alkynyl boronates add to glycolaldehyde imine to afford allylic hydroxyl allenes, and allyl boronates add to alkynyl imines to form 1,3-alkenyl allenes. In both cases, the products are obtained in high yields and enantioselectivities.

Highly Oxygenated Multifunctional Compounds in α-Pinene Secondary Organic Aerosol.

Highly oxygenated multifunctional organic compounds (HOMs) originating from biogenic emissions constitute a widespread source of organic aerosols in the pristine atmosphere. However, the molecular forms in which HOMs are present in the condensed phase upon gas-particle partitioning remain unclear. In this study, we show that highly oxygenated molecules that contain multiple peroxide functionalities are readily cationized by the attachment of Na+ during electrospray ionization operated in the positive ion mode. With this method, we present the first identification of HOMs characterized as C8-10H12-18O4-9 monomers and C16-20H24-36O8-14 dimers in α-pinene derived secondary organic aerosol (SOA). Simultaneous detection of these molecules in the gas phase provides direct evidence for their gas-to-particle conversion. Molecular properties of particulate HOMs generated from ozonolysis and OH oxidation of unsubstituted (C10H16) and deuterated (C10H13D3) α-pinene are investigated using coupled ion mobility spectrometry with mass spectrometry. The systematic shift in the mass of monomers in the deuterated system is consistent with the decomposition of isomeric vinylhydroperoxides to release vinoxy radical isotopologues, the precursors to a sequence of autoxidation reactions that ultimately yield HOMs in the gas phase. The remarkable difference observed in the dimer abundance under O3- versus OH-dominant environments underlines the competition between intramolecular hydrogen migration of peroxy radicals and their bimolecular termination reactions. Our results provide new and direct molecular-level information for a key component needed for achieving carbon mass closure of α-pinene SOA.

Unanticipated Stickiness of α-Pinene.

The adsorption of α-pinene to solid surfaces is an important primary step during the chemical conversion of this common terpene over mesoporous materials, as well as during the formation of atmospheric aerosols. We provide evidence of tight and loose physisorbed states of α-pinene bound on amorphous SiO2 as determined by their adsorption entropy, enthalpy, and binding free energies characterized by computational modeling and vibrational sum frequency generation (SFG) spectroscopy. We find that adsorption is partially (40-60%) irreversible over days at 294-342 K and 1 ATM total pressure of helium, which is supported by molecular dynamics (MD) simulations. The distribution of α-pinene orientation remains invariant with temperature and partial pressure of α-pinene. Using the Redlich-Peterson adsorption model in conjunction with a van't Hoff analysis of adsorption isotherms recorded for up to 2.6 Torr α-pinene in 1 ATM total pressure of helium, we obtain ΔS°ads, ΔH°ads, and ΔG°ads values of -57 (±7) J mol-1 K-1, -39 (±2) kJ mol-1, and -22 (±5) kJ mol-1, respectively, associated with the reversibly bound population of α-pinene. These values are in good agreement with density functional theory (DFT)-corrected force field calculations based on configurational sampling from MD simulations. Our findings are expected to have direct implications on the conversion of terpenes by silica-based catalysts and for the synthesis of secondary organic aerosol (SOA) in atmospheric chambers and flow tubes.

Asymmetric Traceless Petasis Borono-Mannich Reactions of Enals: Reductive Transposition of Allylic Diazenes.

The traceless Petasis borono-Mannich reaction of enals, sulfonylhydrazines, and allylboronates, catalyzed by chiral biphenols, results in an asymmetric reductive transposition of the in situ generated allylic diazene. Acyclic 1,4-diene products bearing either alkyl- or aryl-substituted benzylic stereocenters are afforded in excellent yields and enantiomeric ratios of up to 99:1. The use of crotylboronates in the reaction results in concomitant formation of two stereocenters in either a 1,4-syn or anti relationship from the corresponding E- or Z-crotylboronate used in the reaction. The use of ß-monosubstituted enals in the asymmetric traceless Petasis borono-Mannich reaction of crotylboronates installs tertiary methyl-bearing stereocenters in good yields and high enantioselectivities.

Vibrational Mode Assignment of α-Pinene by Isotope Editing: One Down, Seventy-One To Go.

This study aims to reliably assign the vibrational sum frequency generation (SFG) spectrum of α-pinene at the vapor/solid interface using a method involving deuteration of various methyl groups. The synthesis of five deuterated isotopologues of α-pinene is presented to determine the impact that removing contributions from methyl group C-H oscillators has on its SFG response. 0.6 cm(-1) resolution SFG spectra of these isotopologues show varying degrees of differences in the C-H stretching region when compared to the SFG response of unlabeled α-pinene. The largest spectral changes were observed for the isotopologue containing a fully deuterated vinyl methyl group. Noticeable losses in signal intensities allow us to reliably assign the 2860 cm(-1) peak to the vinyl methyl symmetric stretch. Furthermore, upon removing the vinyl methyl group entirely by synthesizing apopinene, the steric influence of the unlabeled C9H14 fragment on the SFG response of α-pinene SFG can be readily observed. The work presented here brings us one step closer to understanding the vibrational spectroscopy of α-pinene.

Total Synthesis of the Galbulimima Alkaloids Himandravine and GB17 Using Biomimetic Diels-Alder Reactions of Double Diene Precursors.

The enantioselective total syntheses of himandravine and GB17 were completed through a common biomimetic strategy involving Diels-Alder reactions of unusual double diene containing linear precursors. The double diene precursors, containing or lacking a C12 substituent as required to produce GB17 or himandravine, respectively, were found to undergo Diels-Alder reactions to afford mixtures of regioisomeric cycloadducts that map onto the alternative carbocyclic frameworks of both himandravine and GB17. Computational investigations revealed that these Diels-Alder reactions proceed via transition state structures of similar energy that have a high degree of bispericyclic character and that the low levels of regioselectivity observed in the reactions are a consequence of competing orbital interaction and distortion energies. The combined experimental and computational results provide valuable insights into the biosynthesis of the Galbulimima alkaloids.

Uptake of epoxydiol isomers accounts for half of the particle-phase material produced from isoprene photooxidation via the HO2 pathway.

The oxidation of isoprene is a globally significant source of secondary organic material (SOM) of atmospheric particles. The relative importance of different parallel pathways, however, remains inadequately understood and quantified. SOM production from isoprene photooxidation was studied under hydroperoxyl-dominant conditions for <5% relative humidity and at 20 °C in the presence of highly acidic to completely neutralized sulfate particles. Isoprene photooxidation was separated from SOM production by using two continuously mixed flow reactors connected in series and operated at steady state. Two online mass spectrometers separately sampled the gas and particle phases in the reactor outflow. The loss of specific gas-phase species as contributors to the production of SOM was thereby quantified. The produced SOM mass concentration was directly proportional to the loss of isoprene epoxydiol (IEPOX) isomers from the gas phase. IEPOX isomers lost from the gas phase accounted for (46 ± 11)% of the produced SOM mass concentration. The IEPOX isomers comprised (59 ± 21)% (molecular count) of the loss of monitored gas-phase species. The implication is that for the investigated reaction conditions the SOM production pathways tied to IEPOX isomers accounted for half of the SOM mass concentration.

Beyond local group modes in vibrational sum frequency generation.

We combine deuterium labeling, density functional theory calculations, and experimental vibrational sum frequency generation spectroscopy into a form of "counterfactual-enabled molecular spectroscopy" for producing reliable vibrational mode assignments in situations where local group mode approximations are insufficient for spectral interpretation and vibrational mode assignments. We demonstrate the method using trans-ß-isoprene epoxydiol (trans-ß-IEPOX), a first-generation product of isoprene relevant to atmospheric aerosol formation, and one of its deuterium-labeled isotopologues at the vapor/silica interface. We use our method to determine that the SFG responses that we obtain from trans-ß-IEPOX are almost exclusively due to nonlocal modes involving multiple C-H groups oscillating at the same frequency as one vibrational mode. We verify our assignments using deuterium labeling and use DFT calculations to predict SFG spectra of additional isotopologues that have not yet been synthesized. Finally, we use our new insight to provide a viable alternative to molecular orientation analysis methods that rely on local mode approximations in cases where the local mode approximation is not applicable.