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Atmospheric oxidation of monoterpenes (C10H16) contributes to ambient particle number and mass concentrations due, in part, to the resulting peroxy radicals undergoing auto-oxidation to low-volatility highly oxygenated molecules (HOMs).

This review highlights examples of synthetic organic chemistry used in the context of studying terpene-derived oxidation products in the atmosphere, with a focus on species produced from biogenic isoprene, pinene and caryophyllene.

Highly oxygenated organic molecules (HOMs) from α-pinene ozonolysis have been shown to be significant contributors to secondary organic aerosol (SOA), yet our mechanistic understanding of how the peroxy-radical-driven autoxidation leads to their formation in this system is still limited. The involved isomerisation reactions such as H-atom abstractions followed by O2 additions can take place on sub-second timescales in short-lived intermediates, making the process challenging to study. Similarly, while the end-products and sometimes radical intermediates can be observed using mass spectrometry, their structures remain elusive. Therefore, we propose a method utilising selective deuterations for unveiling the mechanisms of autoxidation, where the HOM products can be used to infer which C atoms have taken part in the isomerisation reactions. This relies on the fact that if a C−D bond is broken due to an abstraction by a peroxy group forming a −OOD hydroperoxide, the D atom will become labile and able to be exchanged with a hydrogen atom in water vapour (H2O), effectively leading to loss of the D atom from the molecule. In this study, we test the applicability of this method using three differently deuterated versions of α-pinene with the newly developed chemical ionisation Orbitrap (CI-Orbitrap) mass spectrometer to inspect the oxidation products. The high mass-resolving power of the Orbitrap is critical, as it allows the unambiguous separation of molecules with a D atom (mD=2.0141) from those with two H atoms (mH2=2.0157). We found that the method worked well, and we could deduce that two of the three tested compounds had lost D atoms during oxidation, suggesting that those deuterated positions were actively involved in the autoxidation process. Surprisingly, the deuterations were not observed to decrease HOM molar yields, as would have been expected due to kinetic isotope effects. This may be an indication that the relevant H (or D) abstractions were fast enough that no competing pathways were of relevance despite slower abstraction rates of the D atom. We show that selective deuteration can be a very useful method for studying autoxidation on a molecular level and likely is not limited to the system of α-pinene ozonolysis tested here.

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···H

The surface activity of ten atmospherically relevant α-pinene-derived dimers having varying terminal functional groups and backbone stereochemistry is reported. We find ~10 percent 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.

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.

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.

Monoalkyl diazene species are versatile intermediates that have enabled many useful synthetic transformations in complex chemical environments. Herein we report the reductive transposition of 1,2-allenols for the direct synthesis of dienes through an alkene walk process.

We examine synthesized standards of structurally related β-caryophyllene ozonolysis products at the air/water and air/ammonium sulfate (aq) interfaces using polarization-resolved standard- and high...

The synthesis and surface-specific spectroscopic analysis of α-pinene isotopologues and their corresponding secondary organic material is reported., 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.

By integrating organic synthesis, secondary organic aerosol synthesis and collection, density functional theory (DFT) calculations, and vibrational sum frequency generation (SFG) spectroscopy, we identify close spectral matches between the surface vibrational spectra of β-caryophyllene-derived secondary organic material (SOM) and those of β-caryophyllene aldehyde and β-caryophyllonic acid at various interfaces. Combined with the record high surface tension depression described previously for these same oxidation products, we discuss possibilities for an intrinsically chemical origin for cloud activation by terpene-derived surfactants. Although the present study does not unequivocally identify the synthesized and analyzed oxidation products on the β-caryophyllene-derived SOM surfaces, these two compounds appear to be the most surface active out of the series and have also been foci of previous β-caryophyllene field and laboratory studies. An orientation analysis by phase-resolved SFG spectroscopy reveals a...

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (−)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening., Canvass, a crowd-sourced library of natural products, was evaluated through HTS in a spectrum of disease-relevant assays to survey the broad biological potential of natural products in drug discovery.

International audience; Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.

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.

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, AC541(T) and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541(T) with neighbors Streptomyces rubidus (NRRL B-24619(T)), Streptomyces guanduensis (NRRL B-24617(T)), and Streptomyces yeochonensis (NRRL B-24245(T)). 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 AC541(T) 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 AC541(T), the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541(T) (= JCM 34263(T), = ATCC TSD201(T)).

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.

Liquid–liquid phase separation (LLPS) in organic aerosol particles can impact several properties of atmospheric particulate matter, such as cloud condensation nuclei (CCN) properties, optical properties, and gas-to-particle partitioning. Yet, our understanding of LLPS in organic aerosols is far from complete. Here, we report on LLPS of one-component and two-component organic particles consisting of α-pinene- and β-caryophyllene-derived ozonolysis products and commercially-available organic compounds of relevance to atmospheric organic particles. In the experiments involving single-component organic particles, LLPS was observed in 8 out of 11 particle types studied. LLPS almost always occurred when the oxygen-to-carbon elemental ratio (O : C) was ≤ 0.44, but did not occur when O : C was > 0.44. The phase separation occurred by spinodal decomposition, and when LLPS occurred, two liquid phases co-existed up to ~ 100 % relative humidity (RH). In the experiments involving two-component organic particles, LLPS was observed in 23 out of 25 particles types studied. LLPS almost always occurred when the average was O : C ≤ 0.67, but never occurred when the average O : C was > 0.67. The phase separation occurred by spinodal decomposition or growth of a second phase at the surface of the particles. When LLPS occurred, two liquid phases co-existed up to ~ 100 %. These results provide further evidence that LLPS is likely a frequent occurrence in organic aerosol particles in the troposphere, even in the absence of inorganic salts.

Summary We used unlabeled and deuterium-labeled precursors to generate and characterize secondary organic aerosol (SOA), a class of atmospheric constituents that rank among the least understood in the climate system, while circumventing the typical problems caused by spectral similarity of SOA mass fragments in aerosol mass spectrometry. We used highly sensitive single-particle mass spectrometers to measure mixing via semi-volatile gas-phase exchange between SOA from biogenic precursors (terpenes) and an anthropogenic precursor (toluene). These are common laboratory mimics for ambient SOA. The experiments showed that particles derived from isoprene and α-pinene ozonolysis undergo fast exchange via evaporation and condensation of semi-volatile constituents without any signs of diffusion limitations, even when the relative humidity (RH) is

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.

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...

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.

The development of a triflimide-catalyzed annulation of benzylic alcohols with allylsilanes for the synthesis of indane or tetralin structures is reported. In this fragment coupling reaction, complexity is built rapidly from readily available starting materials to yield diverse sets of products with up to three contiguous stereocenters. Indanes or tetralins can be generated from common precursors depending on the structure of the allylsilane reagent used. The concise synthesis of several lignan natural products highlights the utility of this newly devised methodology.

Data associated to the work "A computational framework to explore large-scale biosynthetic diversity"

Genome sequencing has revealed that a far greater number of natural product biosynthetic pathways exist than there are known natural products. To access these molecules directly and deterministically, a new generation of heterologous expression methods is needed. Cell-free protein synthesis has not previously been used to study nonribosomal peptide biosynthesis, and provides a tunable platform with advantages over conventional methods for protein expression. Here, we demonstrate the use of cell-free protein synthesis to biosynthesize a cyclic dipeptide with correct absolute stereochemistry. From a single-pot reaction, we measured the expression of two nonribosomal peptide synthetases larger than 100 kDa, and detected high-level production of a diketopiperazine. Using quantitative LC-MS and synthetically prepared standard, we observed production of this metabolite at levels higher than previously reported from cell-based recombinant expression, approximately 12 mg/L. Overall, this work represents a first step to apply cell-free protein synthesis to discover and characterize new natural products.

A rotationally fluid state of α-pinene at fused silica/vapor interfaces is revealed by computational and experimental vibrational sum frequency generation (SFG) studies. We report the first assignment of the vibrational modes in the notoriously congested C–H stretching region of α-pinene and identify its bridge methylene group on the four-membered ring (“βCH2”) as the origin of its dominant spectral feature. We find that the spectra are perfused with Fermi resonances that need to be accounted for explicitly in the computation of vibrational spectra of strained hydrocarbons such as α-pinene. The preferred orientations of α-pinene are consistent with optimization of van der Waals contacts with the silica surface that results in a bimodal distribution of highly fluxional orientations in which the βCH2 group points “towards” or “away from” the surface. Classical molecular dynamics simulations further provide rotational diffusion constants of 49 ± 1 ps and 2580 ± 60 ps, which are attributed to two broad types ...

For more than half a century the pharmaceutical industry has sifted through natural products produced by microbes, uncovering new scaffolds and fashioning them into a broad range of vital drugs. We sought a strategy to reinvigorate the discovery of natural products with distinctive structures using bacterial genome sequencing combined with metabolomics. By correlating genetic content from 178 actinomycete genomes with mass spectrometry-enabled analyses of their exported metabolomes, we paired new secondary metabolites with their biosynthetic gene clusters. We report the use of this new approach to isolate and characterize tambromycin, a new chlorinated natural product, composed of several nonstandard amino acid monomeric units, including a unique pyrrolidine-containing amino acid we name tambroline. Tambromycin shows antiproliferative activity against cancerous human B- and T-cell lines. The discovery of tambromycin via large-scale correlation of gene clusters with metabolites (a.k.a. metabologenomics) illuminates a path for structure-based discovery of natural products at a sharply increased rate., By correlating metabolite profiles for hundreds of soil bacteria with their interpreted genomes, the gene cluster encoding a new peptide natural product was identified—which included genes that produce a new amino acid (tambroline).

We assess the capabilities of eight popular density functional theory (DFT) functionals, in combination with several basis sets, as applied to calculations of vibrational sum frequency generation (SFG) spectra of the atmospherically relevant isoprene oxidation product trans-β-isoprene epoxydiol (IEPOX) and one of its deuterated isotopologues at the fused silica/vapor interface. We use sum of squared differences (SSD) and total absolute error (TAE) calculations to estimate the performance of each functional/basis set combination in producing SFG spectra that match experimentally obtained spectra from trans-β-IEPOX and one of its isotopologues. Our joined SSD/TAE analysis shows that while the twist angle of the methyl C3v symmetry axis of trans-β-IEPOX relative to the surface is sensitive to the choice of DFT functional, the calculated tilt angle relative to the surface normal is largely independent of the functional and basis set. Moreover, we report that hybrid functionals such as B3LYP, ωB97X-D, PBE0, and B97-1 in combination with a modest basis set, such as 6-311G(d,p), provides good agreement with experimental data and much better performance than pure functionals such as PBE and BP86. However, improving the quality of the basis set only improves agreement with experimental data for calculations based on pure functionals. A conformational analysis, based on comparisons of calculated and experimental SFG spectra, suggests that trans-β-IEPOX points all of its oxygen atoms toward the silica/vapor interface.

Development of the self-assembled monolayer/MALDI mass spectrometry (SAMDI) platform to enable a high-throughput optimization of a traceless Petasis reaction is described. More than 1800 unique reactions were conducted simultaneously on an array of self-assembled monolayers of alkanethiolates on gold to arrive at optimized conditions, which were then successfully transferred to the solution phase. The utility of this reaction was validated by the efficient synthesis of a variety of di- and trisubstituted allenes.

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. Two bioinformatic tools, BiG-SCAPE and CORASON, enable sequence similarity network and phylogenetic analysis of gene clusters and their families across hundreds of strains and in large datasets, leading to the discovery of new natural products.

By integrating organic synthesis, secondary organic aerosol synthesis and collection, DFT calculations, and vibrational sum frequency generation spectroscopy, we identify close spectral matches between the surface vibrational spectra of β-caryophyllene-derived secondary organic material and those of β-caryophyllene aldehyde and β-caryophyllonic acid at various interfaces. Combined with the record high surface tension depression described previously for these same oxidation products, we discuss possibilities for an intrinsically chemical origin for cloud activation by terpene-derived surfactants. Although the present study does not unequivocally identify the synthesized and analyzed oxidation products on the β-caryophyllenederived SOM surfaces, these two compounds appear to be the most surface active out of the series, and have also been foci of previous β-caryophyllene field and laboratory studies.An orientation analysis by phase-resolved SFG spectroscopy reveals a “pincer-like” configuration of the β-caryophyllene oxidation products, albeit on a model quartz surface, that somewhat resembles the orientation of inverse double-tailed surfactants at the surfaces biological systems. The structural information suggests that the less polar moiety of a surface-localized oxidation product, such as those studied here, may be the first site-of-contact for a gas-phase molecule approaching an SOA particle containing surface-active β-caryophyllene oxidation products.

Genome mining has become a key technology to explore and exploit natural product diversity through the identification and analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on a single-genome basis; currently, the process is being scaled up to large-scale mining of pan-genomes of entire genera, complete strain collections and metagenomic datasets from which thousands of bacterial genomes can be extracted at once. However, no bioinformatic framework is currently available for the effective analysis of datasets of this size and complexity. Here, we provide a streamlined computational workflow, tightly integrated with antiSMASH and MIBiG, that consists of two new software tools, BiG-SCAPE and CORASON. BiG-SCAPE facilitates rapid calculation and interactive visual exploration of BGC sequence similarity networks, grouping gene clusters at multiple hierarchical levels, and includes a ‘glocal’ alignment mode that accurately groups both complete and fragmented BGCs. CORASON employs a phylogenomic approach to elucidate the detailed evolutionary relationships between gene clusters by computing high-resolution multi-locus phylogenies of all BGCs within and across gene cluster families (GCFs), and allows researchers to comprehensively identify all genomic contexts in which particular biosynthetic gene cassettes are found. We validate BiG-SCAPE by correlating its GCF output to metabolomic data across 403 actinobacterial strains. Furthermore, we demonstrate the discovery potential of the platform by using CORASON to comprehensively map the phylogenetic diversity of the large detoxin/rimosamide gene cluster clan, prioritizing three new detoxin families for subsequent characterization of six new analogs using isotopic labeling and analysis of tandem mass spectrometric data.

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.

Data associated to the work "A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data"

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.

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.

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 β-monosubstituted enals in the asymmetric traceless Petasis borono-Mannich reaction of crotylboronates installs tertiary methyl-bearing stereocenters in good yields and high enantioselectivities.

The ring-opening metathesis polymerization (ROMP) of apopinene is reported. We find that apopinene reacts with Ru-based metathesis catalysts to provide an all trans-polymer with a polydispersity index (PDI) as low as 1.6 and molecular weights in the 1100 to 15 600 g·mol–1 range (9–127 monomer units). Because apopinene is readily prepared in one-step from myrtenal or two-steps from α-pinene, both of which are commercially available and naturally abundant, these studies indicate that apopinene might find future use as a new biorenewable precursor for the sustainable production of ROMP-based materials.

The microbial world offers a rich source of bioactive compounds for those able to sift through it. Technologies capable of quantitatively detecting natural products while simultaneously identifying known compounds would expedite the search for new pharmaceutical leads. Prior efforts have targeted histone deacetylases in fungi to globally activate the production of new secondary metabolites, yet no study has directly assessed its effects with minimal bias at the metabolomic level. Using untargeted metabolomics, we monitored changes in >1000 small molecules secreted from the model fungus, Aspergillus nidulans, following genetic or chemical reductions in histone deacetylase activity (HDACi). Through quantitative, differential analyses, we found that nearly equal numbers of compounds were up- and down-regulated by >100 fold. We detected products from both known and unknown biosynthetic pathways and discovered that A. nidulans is capable of producing fellutamides, proteasome inhibitors whose expression was induced by ∼100 fold or greater upon HDACi. This work adds momentum to an "omics"-driven resurgence in natural products research, where direct detection replaces bioactivity as the primary screen for new pharmacophores.

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-β-isoprene epoxydiol (trans-β-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-β-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.

The surfaces of secondary organic aerosol particles are notoriously difficult to access experimentally, even though they are the key location where exchange between the aerosol particle phase and its gas phase occurs. Here, we overcome this difficulty by applying standard and sub- 1 cm(-1) resolution vibrational sum frequency generation (SFG) spectroscopy to detect C-H oscillators at the surfaces of secondary organic material (SOM) prepared from the ozonolysis of α-pinene at Harvard University and at the University of California, Irvine, that were subsequently collected on Teflon filters as well as CaF2 windows using electrostatic deposition. We find both samples yield comparable SFG spectra featuring an intense peak at 2940 cm(-1) that are independent of spectral resolution and location or method of preparation. We hypothesize that the SFG spectra are due to surface-active C-H oscillators associated with the four-membered ring motif of α-pinene, which produces an unresolvable spectral continuum of approximately 50 cm(-1) width reminiscent of the similar, albeit much broader, O-H stretching continuum observed in the SFG spectra of aqueous surfaces. Upon subjecting the SOM samples to cycles in relative humidity (RH) between

The formation of atmospheric cloud droplets due to secondary organic aerosol (SOA) particles is important for quantifying the Earth’s radiative balance under future, possibly warmer, climates, yet is only poorly understood. While cloud activation may be parametrized using the surface tension depression that coincides with surfactant partitioning to the gas–droplet interface, the extent to which cloud activation is influenced by both the chemical structure and reactivity of the individual molecules comprising this surfactant pool is largely unknown. We report herein considerable differences in the surface tension depression of aqueous pendant droplets that contain synthetically prepared ozonolysis products derived from α-pinene and β-caryophyllene, the most abundant of the monoterpenes and sesquiterpenes, respectively, that are emitted over the planet’s vast forest ecosystems. Oxidation products derived from β-caryophyllene were found to exhibit significantly higher surface activity than those prepared from α-pinene, with the critical supersaturation required for cloud droplet activation reduced by 50% for β-caryophyllene aldehyde at 1 mM. These considerable reductions in the critical supersaturation were found to coincide with free energies of adsorption that exceed ∼25 kJ/mol, or just one hydrogen bond equivalent, depending on the ammonium sulfate and oxidation product concentration in the solution. Additional experiments showed that aldehyde-containing oxidation products exist in equilibrium with hydrated forms in aqueous solution, which may modulate their bulk solubility and surface activity. Equilibration time scales on the order of 10–5 to 10–4 s calculated for micrometer-sized aerosol particles indicate instantaneous surface tension depression in the activation processes leading to cloud formation in the atmosphere. Our findings highlight the underlying importance of molecular structure and reactivity when considering cloud condensation activity in the presence of SOA particles., Surface tension depression caused by atmospheric ozonolysis products derived from α-pinene and β-caryophyllene highlight the importance of molecular structure and reactivity when considering cloud activation potential of secondary organic aerosol.

Secondary organic aerosol (SOA) particles, formed from gas-phase biogenic volatile organic compounds (BVOCs), contribute large uncertainties to the radiative forcing that is associated with aerosols in the climate system. Reactive uptake of surface-active organic oxidation products of BVOCs at the gas–aerosol interface can potentially decrease the overall aerosol surface tension and therefore influence their propensity to act as cloud condensation nuclei (CCN). Here, we synthesize and measure some climate-relevant physical properties of SOA particle constituents consisting of the isoprene oxidation products α-, δ-, and cis- and trans-β-IEPOX (isoprene epoxide), as well as syn- and anti-2-methyltetraol. Following viscosity measurements, we use octanol–water partition coefficients to quantify the relative hydrophobicity of the oxidation products while dynamic surface tension measurements indicate that aqueous solutions of α- and trans-β-IEPOX exhibit significant surface tension depression. We hypothesize that the surface activity of these compounds may enhance aerosol CCN activity, and that trans-β-IEPOX may be highly relevant for surface chemistry of aerosol particles relative to other IEPOX isomers.