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.

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.

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.

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.

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.

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.

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.

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.

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.

The effects of an ionic liquid on unimolecular substitution processes: the importance of the extent of transition state solvation.

The reaction of bromodiphenylmethane and 3-chloropyridine, which proceeds concurrently through both unimolecular and bimolecular mechanisms, was examined in mixtures of acetonitrile and an ionic liquid. As predicted, the bimolecular rate constant (k2) gradually increased as the amount of ionic liquid in the reaction mixture increased, as a result of a minor enthalpic cost offset by a more significant entropic benefit. Addition of an ionic liquid had a substantial effect on the unimolecular rate constant (k1) of the reaction, with at least a 5-fold rate enhancement relative to acetonitrile, which was found to be due to a significant decrease in the enthalpy of activation, partially offset by the associated decrease in the entropy of activation. This is in contrast to the effects seen previously for aliphatic carbocation formation, where the entropic cost dominated reaction outcome. This change is attributed to a lessened ionic liquid-transition state interaction, as the incipient charges in the transition state were delocalized across the neighbouring π systems. By varying the mole fraction of ionic liquid in the reaction mixture the ratio between k1 and k2 could be altered, highlighting the potential to use ionic liquids to control which pathway a reaction proceeds through.

Ionic liquid effects on a multistep process. Increased product formation due to enhancement of all steps.

The reaction of a series of substituted benzaldehydes with hexylamine was examined in acetonitrile and an ionic liquid. In acetonitrile, as the electron withdrawing nature of the substituent increases, the overall addition-elimination process becomes faster as does the build-up of the aminol intermediate. Under equivalent conditions in an ionic liquid, less intermediate build up is observed, and the effect on the rate on varying the substituent is different to that in acetonitrile. Extensive kinetic analysis shows that the ionic liquid solvent increases the rate constant of all steps of the reaction, resulting in faster product formation relative to acetonitrile; these effects increase with the proportion of ionic liquid in the reaction mixture. Differences in the equilibrium position of the addition step in the ionic liquid were found to account for both the decrease in intermediate build up relative to acetonitrile, as well as the differing trend in the overall rate of product formation as the substituent was changed. The microscopic origins of these ionic liquid effects were probed through temperature dependent analyses, highlighting the subtle balance of interactions between the ionic liquid and species along the reaction coordinate, particularly the importance of charge development in the transition state.

Developing principles for predicting ionic liquid effects on reaction outcome. The importance of the anion in controlling microscopic interactions.

A series of ionic liquids containing anions of differing coordination strength were investigated as solvents for the condensation reaction of an alkyl amine and an aromatic aldehyde. As predicted, the rate constant of the process was found to increase with the proportion of the ionic liquid in the reaction mixture. Temperature-dependent kinetic analyses demonstrated that by varying the ability of the anion to interact with the cation the magnitude of both the enthalpy and entropy of activation could be controlled in a predictable manner, with the activation parameters being linearly dependent on the ionic liquid basicity. Interestingly, the unexpected trend in the rate constants observed when altering the anion of the ionic liquid highlighted the presence of more subtle secondary microscopic interactions involving the anion, further emphasizing the fragility of the enthalpy - entropy balance.

Developing principles for predicting ionic liquid effects on reaction outcome. A demonstration using a simple condensation reaction.

The effects of a series of ionic liquids, with systematic variations in the cation, on the condensation of an alkyl amine with an aromatic aldehyde were investigated, and the outcomes compared with those predicted based on related reactions. The addition of ionic liquids increased the observed rate constant; the mole fraction dependence of this increase was qualitatively consistent with predictions. Temperature-dependent kinetic analyses were used to demonstrate that the microscopic origins of the effects were as forecast, though the relative weighting of enthalpic and entropic contributions was dependent on the salt used.

Norovirus genotypes present in oysters and in effluent from a wastewater treatment plant during the seasonal peak of infections in Ireland in 2010.

We determined norovirus (NoV) concentrations in effluent from a wastewater treatment plant and in oysters during the peak period of laboratory-confirmed cases of NoV infection in Ireland in 2010 (January to March). Weekly samples of influent, secondary treated effluent, and oysters were analyzed using real-time quantitative reverse transcription-PCR for NoV genogroup I (GI) and genogroup II (GII). The mean concentration of NoV GII (5.87 × 10(4) genome copies 100 ml(-1)) in influent wastewater was significantly higher than the mean concentration of NoV GI (1.40 × 10(4) genome copies 100 ml(-1)). The highest concentration of NoV GII (2.20 × 10(5) genome copies 100 ml(-1)) was detected in influent wastewater during week 6. Over the study period, a total of 931 laboratory-confirmed cases of NoV GII infection were recorded, with the peak (n = 171) occurring in week 7. In comparison, 16 cases of NoV GI-associated illness were reported during the study period. In addition, the NoV capsid N/S domain was molecularly characterized for selected samples. Multiple genotypes of NoV GI (GI.1, GI.4, GI.5, GI.6, and GI.7) and GII (GII.3, GII.4, GII.6, GII.7, GII.12, GII.13, and GII.17), as well as 4 putative recombinant strains, were detected in the environmental samples. The NoV GII.4 variant 2010 was detected in wastewater and oyster samples and was the dominant strain detected in NoV outbreaks at that time. This study demonstrates the diversity of NoV genotypes present in wastewater during a period of high rates of NoV infection in the community and highlights the potential for the environmental spread of multiple NoV genotypes.

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.

Concentration of norovirus during wastewater treatment and its impact on oyster contamination.

The concentrations of Escherichia coli, F-specific RNA bacteriophage (FRNA bacteriophage), and norovirus genogroup I (NoV GI) and norovirus genogroup II (NoV GII) in wastewater were monitored weekly over a 1-year period at a wastewater treatment plant (WWTP) providing secondary wastewater treatment. A total of 49 samples of influent wastewater and wastewater that had been treated by primary and secondary wastewater treatment processes (primary and secondary treated wastewater) were analyzed. Using a real-time reverse transcription-quantitative PCR (RT-qPCR), the mean NoV GI and NoV GII concentrations detected in effluent wastewater were 2.53 and 2.63 log(10) virus genome copies 100 ml(-1), respectively. The mean NoV concentrations in wastewater during the winter period (January to March) (n = 12) were 0.82 (NoV GI) and 1.41 (NoV GII) log units greater than the mean concentrations for the rest of the year (n = 37). The mean reductions of NoV GI and GII during treatment were 0.80 and 0.92 log units, respectively, with no significant difference detected in the extent of NoV reductions due to season. No seasonal trend was detected in the concentrations of E. coli or FRNA bacteriophage in wastewater influent and showed mean reductions of 1.49 and 2.13 log units, respectively. Mean concentrations of 3.56 and 3.72 log(10) virus genome copies 100 ml(-1) for NoV GI and GII, respectively, were detected in oysters sampled adjacent to the WWTP discharge. A strong seasonal trend was observed, and the concentrations of NoV GI and GII detected in oysters were correlated with concentrations detected in the wastewater effluent. No seasonal difference was detected in concentrations of E. coli or FRNA bacteriophage detected in oysters.

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.

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.