Divergent Reactivity of 1,2,3-Benzotriazin-4(3H)-ones: Photocatalytic Synthesis of 3-Substituted Isoindolinones Achieved through a Nitrogen-Mediated Hydrogen Atom Shift.

A regioselective visible-light-mediated denitrogenative alkene insertion of 1,2,3-benzotriazin-4(3H)-ones was developed to access 3-substituted isoindolinones, an important structural motif present in many biologically active molecules and natural products. Notably, divergent reactivity was achieved by switching from reported nickel catalysis (where C3-substituted 3,4-dihydroisoquinolin-1(2H)-ones form) to photocatalysis, where photocatalytic denitrogenation and a subsequent nitrogen-mediated hydrogen atom shift lead to exclusive 3-substituted isoindolinone formation. The developed photocatalytic reaction is compatible with activated terminal alkenes and cyclic α,ß-unsaturated esters and ketones, with wide functional group tolerance for N-substitution of the 1,2,3-benzotriazin-4(3H)-ones. The utility of this procedure is highlighted by a gram-scale synthesis and postsynthetic amidation. To understand the origin of this unique product selectivity, experimental and computational mechanistic studies were performed.

A Photoreactor-Interfaced Mass Spectrometer: An Online Platform to Monitor Photochemical Reactions.

An experimental platform is reported that allows for the online characterization of photochemical reactions by coupling a continuous flow photoreactor, equipped with LED light irradiation and a dual-tipped ESI source, directly to a mass spectrometer with electrospray ionization. The capabilities of this platform are demonstrated with two classes of photoreactions: (1) the photopolymerization of methyl methacrylate and (2) photocatalyzed alkyne insertion into a 1,2,3-benzotriazinone. The online technique provides rapid information to inform the underlying photochemical mechanism and evaluate the overall photochemistry.

Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland.

Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.

Amplicon-Based High-Throughput Sequencing Method for Genotypic Characterization of Norovirus in Oysters.

Norovirus is a highly diverse RNA virus often implicated in foodborne outbreaks, particularly those associated with shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbor various pathogens, including human-pathogenic viruses. The application of Sanger or amplicon-based high-throughput sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges: (i) distinguishing multiple genotypes/variants in a single sample and (ii) low concentrations of norovirus RNA. Here, we assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerases and reverse transcriptases (RTs) were compared, and performance was evaluated based on (i) the number of reads passing quality filters per sample, (ii) the number of correct genotypes identified, and (iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterize norovirus populations in naturally contaminated oysters. IMPORTANCE While foodborne outbreaks account for approximately 14% of norovirus cases (L. Verhoef, J. Hewitt, L. Barclay, S. Ahmed, R. Lake, A. J. Hall, B. Lopman, A. Kroneman, H. Vennema, J. Vinjé, and M. Koopmans, Emerg Infect Dis 21:592-599, 2015), we do not have standardized high-throughput sequencing methods for genotypic characterization in foodstuffs. Here, we present an optimized amplicon high-throughput sequencing method for the genotypic characterization of norovirus in oysters. This method can accurately detect and characterize norovirus at concentrations found in oysters grown in production areas impacted by human wastewater discharges. It will permit the investigation of norovirus genetic diversity in complex matrices and contribute to ongoing surveillance of norovirus in the environment.

An Investigation into the In Vitro Metabolic Stability of Aryl Sulfonyl Fluorides for their Application in Medicinal Chemistry and Radiochemistry.

Molecules that feature a sulfonyl fluoride (SO2F) moiety have been gaining increasing interest due to their unique reactivity and potential applications in synthetic chemistry, medicinal chemistry, and other biological uses. A particular interest is towards 18F-radiochemistry where sulfonyl fluorides can be used as a method to radiolabel biomolecules or can be used as radiofluoride relay reagents that facilitate radiolabeling of other molecules. The low metabolic stability of sulfonyl fluoride S-F bonds, however, presents an issue and limits the applicability of sulfonyl fluorides. The aim of this work was to increase understanding of what features contribute to the metabolic instability of the S-F bond in model aryl sulfonyl fluorides and identify approaches to increasing sulfonyl fluoride stability for 18F-radiochemistry and other medicinal, synthetic chemistry and biological applications. To undertake this, 14 model aryl sulfonyl fluorides compounds with varying functional groups and substitution patterns were investigated, and their stabilities were examined in various media, including phosphate-buffered saline and rat serum as a model for biological conditions. The results indicate that both electronic and steric factors affect the stability of the S-F bond, with the 2,4,6-trisubstituted model aryl sulfonyl fluorides examined displaying the highest in vitro metabolic stability.

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus.

In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. IMPORTANCE In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

Impact of COVID-19 Nonpharmaceutical Interventions on the Extent of Norovirus Contamination in Oyster Production Areas in Ireland during Winter 2020 to 2021.

ABSTRACT: A significant decrease in norovirus prevalence and concentration was observed in oyster production areas in Ireland during winter 2020 to 2021. Oyster production areas impacted by human wastewater discharges that had been undergoing norovirus surveillance since 2018 were investigated. Samples collected in the winter seasons of 2018 to 2019 and 2019 to 2020, prior to when the COVID-19 pandemic interventions were applied, showed a prevalence of 94.3 and 96.6%, respectively, and geometric mean concentrations of 533 and 323 genome copies per g, respectively. These values decreased significantly during the winter of 2020 to 2021 (prevalence of 63.2% and geometric concentration of below the limit of quantification), coinciding with the control measures to mitigate the transmission of severe acute respiratory syndrome coronavirus 2 of the genus Betacoronavirus. Divergence between norovirus GI and GII prevalence and concentrations was observed over the 3-year monitoring period. Norovirus GII was the dominant genogroup detected in winter 2020 to 2021, with over half of samples positive, although concentrations detected were significantly lower than prepandemic winters, with a geometric mean concentration of below the limit of quantification.

Synthesis of Long-Chain Alkanoyl Benzenes by an Aluminum(III) Chloride-Catalyzed Destannylative Acylation Reaction.

This paper describes the facile synthesis of haloaryl compounds with long-chain alkanoyl substituents by the destannylative acylation of haloaryls bearing tri-n-butyltin (Bu3Sn) substituents. The method allows the synthesis of many important synthons for novel functional materials in a highly efficient manner. The halo-tri-n-butyltin benzenes are obtained by the lithium-halogen exchange of commercially available bis-haloarenes and the subsequent reaction with Bu3SnCl. Under typical Friedel-Crafts conditions, i.e., the presence of an acid chloride and AlCl3, the haloaryls are acylated through destannylation. The reactions proceed fast (<5 min) at low temperatures and thus are compatible with aromatic halogen substituents. Furthermore, the method is applicable to para-, meta-, and ortho-substitution and larger systems, as demonstrated for biphenyls. The generated tin byproducts were efficiently removed by trapping with silica/KF filtration, and most long-chain haloaryls were obtained chromatography-free. Molecular structures of several products were determined by X-ray single-crystal diffraction, and the crystal packing was investigated by mapping Hirshfeld surfaces onto individual molecules. A feasible reaction mechanism for the destannylative acylation reaction is proposed and supported through density functional theory (DFT) calculations. DFT results in combination with NMR-scale control experiments unambiguously demonstrate the importance of the tin substituent as a leaving group, which enables the acylation.

Evaluation of Norovirus Reduction in Environmentally Contaminated Pacific Oysters During Laboratory Controlled and Commercial Depuration.

Norovirus contamination of oysters is the lead cause of non-bacterial gastroenteritis and a significant food safety concern for the oyster industry. Here, norovirus reduction from Pacific oysters (Crassostrea gigas), contaminated in the marine environment, was studied in laboratory depuration trials and in two commercial settings. Norovirus concentrations were measured in oyster digestive tissue before, during and post-depuration using the ISO 15216-1 quantitative real-time RT-PCR method. Results of the laboratory-based studies demonstrate that statistically significant reductions of up to 74% of the initial norovirus GII concentration was achieved after 3 days at 17-21 °C and after 4 days at 11-15 °C, compared to 44% reduction at 7-9 °C. In many trials norovirus GII concentrations were reduced to levels below 100 genome copies per gram (gcg-1; limit of quantitation; LOQ). Virus reduction was also assessed in commercial depuration systems, routinely used by two Irish oyster producers. Up to 68% reduction was recorded for norovirus GI and up to 90% for norovirus GII reducing the geometric mean virus concentration close to or below the LOQ. In both commercial settings there was a significant difference between the levels of reduction of norovirus GI compared to GII (p < 0.05). Additionally, the ability to reduce the norovirus concentration in oysters to < LOQ differed when contaminated with concentrations below and above 1000 gcg-1. These results indicate that depuration, carried out at elevated (> 11 °C) water temperatures for at least 3 days, can reduce the concentration of norovirus in oysters and therefore consumer exposure providing a practical risk management tool for the shellfish industry.

High Throughput Sequencing for the Detection and Characterization of RNA Viruses.

This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

Base-Free Cross-Couplings of Aryl Diazonium Salts in Methanol: PdII -Alkoxy as Reactivity-Controlling Intermediate.

Pd-catalyzed cross-coupling reactions of aryl diazonium salts are generally assumed to proceed via cationic PdII intermediates which in turn would be highly reactive in the subsequent transmetalation step. Contrary to this belief, we herein report our observation and rationalization of opposing reactivities of ArN2+ in Suzuki (=effective) and Stille (=ineffective) cross-couplings in MeOH. Our systematic experimental and computational studies on the roles of transmetalating agent, solvent, base and the likely involvement of in situ formed diazoether derivatives challenge the currently accepted mechanism. Our data suggest that the observed solvent dichotomy is primarily due to PdII -methoxy intermediates being formed, which are unreactive with arylstannanes, but highly reactive with arylboronic acids, complementing the Suzuki "Pd-oxy" mechanism with the direct demonstration of transmetalation of a PdII -alkoxy complex. Lewis acids were found to circumvent this reactivity divergence, promoting efficient couplings regardless of the employed conditions or coupling partners.

Development of tethered dual catalysts: synergy between photo- and transition metal catalysts for enhanced catalysis.

While dual photocatalysis-transition metal catalysis strategies are extensively reported, the majority of systems feature two separate catalysts, limiting the potential for synergistic interactions between the catalytic centres. In this work we synthesised a series of tethered dual catalysts allowing us to investigate this underexplored area of dual catalysis. In particular, Ir(i) or Ir(iii) complexes were tethered to a BODIPY photocatalyst through different tethering modes. Extensive characterisation, including transient absorption spectroscopy, cyclic voltammetry and X-ray absorption spectroscopy, suggest that there are synergistic interactions between the catalysts. The tethered dual catalysts were more effective at promoting photocatalytic oxidation and Ir-catalysed dihydroalkoxylation, relative to the un-tethered species, highlighting that increases in both photocatalysis and Ir catalysis can be achieved. The potential of these catalysts was further demonstrated through novel sequential reactivity, and through switchable reactivity that is controlled by external stimuli (heat or light).

Estimating the distribution of norovirus in individual oysters.

Norovirus in oysters is a significant food safety risk. A recent ISO detection method allows for reliable and repeatable estimates of norovirus concentrations in pooled samples, but there is insufficient data to estimate a distribution of copies per animal from this. The spread of norovirus accumulated across individual oysters is useful for risk assessment models. Six sets of thirty individual Crassostrea gigas oysters were tested for norovirus concentration levels by reverse-transcription quantitative PCR (RT-qPCR): three from a commercial harvest site, and three post-depuration. Five sets had norovirus GII means above the limit of quantification (LOQ), and one below the LOQ, but above the limit of detection. No norovirus GI was detected in pooled tests, and individual oysters were not tested for norovirus GI. Depuration was shown to reduce the mean concentration of GII copies, but not to affect the shape of the distribution around the mean. Deconvoluting the uncertainty of the method, the coefficient of variation was stationary (0.45 ±â€¯0.2). The best fit distribution was either a lognormal distribution or a gamma. Multiplying these distributions by the weight of oyster digestive tissues gave an estimate for the count mean. This was used as the parameter λ in three compound Poisson distributions: Poisson-lognormal, Poisson-gamma, and Poisson-K. No model was found to fit better than the others, with advantages for each. All three could be used in future risk assessments. Preliminary validation of sampling uncertainty using repeated testing data from a previous study suggests that these results have predictive power.

Ion-Reagent Interactions Contributing to Ionic Liquid Solvent Effects on a Condensation Reaction.

Molecular dynamics simulations of solutions of hexan-1-amine or 4-methoxybenzaldehyde in acetonitrile, an ionic liquid/acetonitrile mixture (χIL =0.2), and a number of different (neat) ionic liquids were performed, to further understand the solvent effects on the condensation reaction of these species. This work indicates that, in the presence of an ionic liquid, the amine group of hexan-1-amine is exclusively solvated by the components of the ionic liquid, and not by acetonitrile, and that the anion interacts with the aldehyde group of 4-methoxybenzaldehyde. These interactions showed little dependence on the proportion of the ionic liquid present. When varying the cation of the ionic liquid there were changes in the cation-amine interaction, and 1-butyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide ([Bm2 im][N(CF3 SO2 )2 ]) was found to order more than expected about the amine. This ordering is likely the origin of the large rate constant values determined in [Bm2 im][N(CF3 SO2 )2 ] for this condensation reaction and explains an anomaly seen previously. When changing the anion, changes were seen in the interactions between both the cation and anion with hexan-1-amine, and the anion with 4-methoxybenzaldehyde. The differing magnitude of these interactions likely causes subtle changes in the activation parameters for this condensation reaction, and provides an explanation for the anomalous rate constant values previously determined when varying the anion.

Modular Functionalization of Arenes in a Triply Selective Sequence: Rapid C(sp2 ) and C(sp3 ) Coupling of C-Br, C-OTf, and C-Cl Bonds Enabled by a Single Palladium(I) Dimer.

Full control over multiple competing coupling sites would enable straightforward access to densely functionalized compound libraries. Historically, the site selection in Pd0 -catalyzed functionalizations of poly(pseudo)halogenated arenes has been unpredictable, being dependent on the employed catalyst, the reaction conditions, and the substrate itself. Building on our previous report of C-Br-selective functionalization in the presence of C-OTf and C-Cl bonds, we herein complete the sequence and demonstrate the first general arylations and alkylations of C-OTf bonds (in <10 min), followed by functionalization of the C-Cl site (in <25 min), at room temperature using the same air- and moisture-stable PdI dimer. This allowed the realization of the first general and triply selective sequential C-C coupling (in 2D and 3D space) of C-Br followed by C-OTf and then C-Cl bonds.

The Impact of Winter Relocation and Depuration on Norovirus Concentrations in Pacific Oysters Harvested from a Commercial Production Site.

Oysters contaminated with norovirus present a significant public health risk when consumed raw. In this study, norovirus genome copy concentrations were determined in Pacific oysters (Magallana gigas) harvested from a sewage-impacted production site and then subjected to site-specific management procedures. These procedures consisted of relocation of oysters to an alternative production area during the norovirus high-risk winter periods (November to March) followed by an extended depuration (self-purification) under controlled temperature conditions. Significant differences in norovirus RNA concentrations were demonstrated at each point in the management process. Thirty-one percent of oyster samples from the main harvest area (Site 1) contained norovirus concentrations > 500 genome copies/g and 29% contained norovirus concentrations < 100 genome copies/g. By contrast, no oyster sample from the alternative harvest area (Site 2) or following depuration contained norovirus concentrations > 500 genome copies/g. In addition, 60 and 88% of oysters samples contained norovirus concentrations < 100 genome copies/g in oysters sampled from Site 2 and following depuration, respectively. These data demonstrate that site-specific management processes, supported by norovirus monitoring, can be an effective strategy to reduce, but not eliminate, consumer exposure to norovirus genome copies.

Palladium-Catalyzed Decarbonylative Trifluoromethylation of Acid Fluorides.

While acid fluorides can readily be made from widely available or biomass-feedstock-derived carboxylic acids, their use as functional groups in metal-catalyzed cross-coupling reactions is rare. This report presents the first demonstration of Pd-catalyzed decarbonylative functionalization of acid fluorides to yield trifluoromethyl arenes (ArCF3 ). The strategy relies on a Pd/Xantphos catalytic system and the supply of fluoride for transmetalation through intramolecular redistribution to the the Pd center. This strategy eliminated the need for exogenous and detrimental fluoride additives and allows Xantphos to be used in catalytic trifluoromethylations for the first time. Our experimental and computational mechanistic data support a sequence in which transmetalation by R3 SiCF3 occurs prior to decarbonylation.

Investigating Solvent Effects of an Ionic Liquid on Pericyclic Reactions through Kinetic Analyses of Simple Rearrangements.

Simple Cope and Claisen rearrangements were investigated in an ionic liquid and a range of molecular solvents through a series of kinetic studies. Analysis of the solvent effects on the Cope rearrangement of 3-phenyl-1,5-hexadiene indicated that a solvophobic effect was responsible for the observed rate enhancement in the ionic liquid, and that this was due to preferential solvation of the transition state. A similar solvophobic effect contributes to the ionic liquid solvent effect on the Claisen rearrangement of allyl vinyl ether, although the ability of the ionic liquid to stabilise the incipient charges in the transition state also likely contributes to the rate increase observed in the ionic liquid solvent. The activation parameter data suggest that in this case the ionic liquid was interacting with species along the reaction coordinate through general coulombic interactions (more acetonitrile-like) rather than through hydrogen-bonding interactions (less ethanol-like).

Understanding the Effect of Solvent Structure on Organic Reaction Outcomes When Using Ionic Liquid/Acetonitrile Mixtures.

The rate constant for the reaction between hexan-1-amine and 4-methoxybenzaldehyde was determined in ionic liquids containing an imidazolium cation. The effect on the rate constant of increasing the length of the alkyl substituent on the cation was examined in a number of ionic liquid/acetonitrile mixtures. In general it was found that there was no significant effect of changing the alkyl substituent on the rate constant of this process, suggesting that any nanodomains in these mixtures do not have a significant effect on the outcome of this process. A series of small-angle X-ray scattering and wide-angle X-ray scattering experiments were performed on mixtures of the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Bmim][N(CF3SO2)2]) and acetonitrile; this work indicated that the main structural changes in the mixtures occur by about a 0.2 mole fraction of ionic liquid in the mixture (χIL). This region at which the main changes in the solvent structuring occurs corresponds to the region at which the main changes in the rate constant and activation parameters occur for SN2 and condensation reactions examined previously; this is the first time that such a correlation has been observed. To examine the ordering of the solvent about the nucleophile hexan-1-amine, WAXS experiments were performed on a number of [Bmim][N(CF3SO2)2]/acetonitrile/hexan-1-amine mixtures, where it was found that some of the patterns featured asymmetric peaks as well as additional peaks not observed in the [Bmim][N(CF3SO2)2]/acetonitrile mixtures; this suggests that the addition of hexan-1-amine to the mixture affects the bulk structure of the liquid. The SAXS/WAXS patterns of mixtures of 1-butyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide ([Bm2im][N(CF3SO2)2]) and acetonitrile were also determined, with the results suggesting that [Bm2im][N(CF3SO2)2] is more ordered than [Bmim][N(CF3SO2)2] due to an enhancement in the short-range interactions.

NMR Diffusion Measurements as a Simple Method to Examine Solvent-Solvent and Solvent-Solute Interactions in Mixtures of the Ionic Liquid [Bmim][N(SO2 CF3 )2 ] and Acetonitrile.

The self-diffusion coefficients of each component in mixtures of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Bmim][N(SO2 CF3 )2 ]) and acetonitrile were determined. The results suggest that the hydrodynamic boundary conditions change from "stick" to "slip" as the solvent composition transitions from "ionic liquid dissolved in acetonitrile" (χIL <0.4) to "acetonitrile dissolved in ionic liquid" (χIL >0.4). At higher χIL , the acetonitrile species are affected by "cage" and "jump" events, as the acetonitrile molecules reside nearer to the charged centre on the ions than in the "non-polar" regions. The self-diffusion coefficients of hexan-1-amine, dipropylamine, 1-hexanol and dipropylether in mixtures of [Bmim][N(SO2 CF3 )2 ] and acetonitrile were determined. In general, the nitrogen-containing solutes were found to diffuse slower than the oxygen-containing solutes; this indicates that there are greater ionic liquid-N interactions than ionic liquid-O interactions. This work demonstrates that the self-diffusion coefficients of species can provide valuable information about solvent-solvent and solvent-solute interactions in mixtures containing an ionic liquid.