Mechanism of the forbidden [3s,5s]-sigmatropic shift: orbital symmetry influences stepwise mechanisms involving diradical intermediates

The mechanisms of [3s,5s]-sigmatropic shifts of octa-1,3,7-triene and 7-methylenenona-1,3,8-triene have been elaborated using B3LYP and BPW91 density functional theory and CASPT2 methods. These orbital symmetry forbidden rearrangements are stepwise, involving diradical intermediates. A comparison with several [3,3]-sigmatropic shifts of substituted hexadienes and of [5,5]-sigmatropic shifts that are allowed, but nevertheless follow stepwise paths, shows that the activation barrier for the disallowed [3,5] shift is significantly larger than that for the stepwise reactions that are orbital symmetry allowed. Cyclic diradicals that have an aromatic circuit of electrons including the two radical centers and conjugated pi or sigma bonds are stabilized as compared to cyclic diradicals with an antiaromatic circuit of electrons. This applies to the transition states leading to and from the diradicals and influences the activation energies of stepwise sigmatropic shifts. The magnitudes of these effects are small but will have a significant influence on the rates of competing processes. This series of calculations has been used to assess the relative capabilities of the two functionals. We find that BPW91 underestimates the endothermicity of diradical formation and the barrier to diradical formation whereas B3LYP overestimates these quantities.     

Enumeration of total yeasts and molds in foods by the SimPlate Yeast and Mold-Color Indicator method and conventional culture methods: collaborative study

The relative effectiveness of the SimPlate Yeast and Mold-Color Indicator method (Y&M-CI) was compared to the U.S. Food and Drug Administration's (FDA) Bacteriological Analytical Manual (BAM) method and the proposed International Organization for Standardization (ISO) method, ISO/CD 21527, for enumerating yeasts and molds in foods. Test portions were prepared and incubated according to the conditions stated in both the BAM and ISO methods. Six food types were analyzed: frozen corn dogs, nut meats, frozen fruits, cake mix, cereal, and fresh cheese. Nut meats, frozen fruits, and fresh cheese were naturally contaminated. All other foods were artificially contaminated with either a yeast or mold. Seventeen laboratories throughout North America and Europe participated in the study. Three method comparisons were conducted. In general, there was <0.3 mean log count difference in recovery between the SimPlate method and the 2 corresponding reference methods. Moreover, mean log counts between the 2 reference methods were also very similar. The repeatability (Sr) and reproducibility (SR) standard deviations were comparable between the 3 method comparisons. These results indicate that the BAM method and the SimPlate method are equivalent for enumerating yeast and mold populations in foods. Similarly, the SimPlate method is comparable to the proposed ISO method when test portions are prepared and incubated as defined in the proposed ISO method.     

Redox,transmetalation, and stacking properties of tetrathiafulvalene-2,3,6,7-tetrathiolate bridged tin,nickel, and palladium compounds

Here we report that capping the molecule TTFtt (TTFtt = tetrathiafulvalene-2,3,6,7-tetrathiolate) with dialkyl tin groups enables the isolation of a stable series of redox congeners and facile transmetalation to Ni and Pd. TTFtt has been proposed as an attractive building block for molecular materials for two decades as it combines the redox chemistry of TTF and dithiolene units. TTFttH₄, however, is inherently unstable and the incorporation of TTFtt units into complexes or materials typically proceeds through the in situ generation of the tetraanion TTFtt⁴⁻. Capping of TTFtt⁴⁻ with Bu₂Sn²⁺ units dramatically improves the stability of the TTFtt moiety and furthermore enables the isolation of a redox series where the TTF core carries the formal charges of 0, +1, and +2. All of these redox congeners show efficient and clean transmetalation to Ni and Pd resulting in an analogous series of bimetallic complexes capped by 1,2-bis(diphenylphosphino)ethane (dppe) ligands. Furthermore, by using the same transmetalation method, we synthesized analogous palladium complexes capped by 1,1′-bis(diphenylphosphino)ferrocene (dppf) which had been previously reported. All of these species have been thoroughly characterized through a systematic survey of chemical and electronic properties by techniques including cyclic voltammetry (CV), ultraviolet-visible-near infrared spectroscopy (UV-vis-NIR), electron paramagnetic resonance spectroscopy (EPR), nuclear magnetic resonance spectroscopy (NMR) and X-ray diffraction (XRD). These detailed synthetic and spectroscopic studies highlight important differences between the transmetalation strategy presented here and previously reported synthetic methods for the installation of TTFtt. In addition, the utility of this stabilization strategy can be illustrated by the observation of unusual TTF radical–radical packing in the solid state and dimerization in the solution state. Theoretical calculations based on variational 2-electron reduced density matrix methods have been used to investigate these unusual interactions and illustrate fundamentally different levels of covalency and overlap depending on the orientations of the TTF cores. Taken together, this work demonstrates that tin-capped TTFtt units are ideal reagents for the installation of redox-tunable TTFtt ligands enabling the generation of entirely new geometric and electronic structures.

Capping TTFtt enables facile transmetalation in three different oxidation states.     

Vibronic effects accelerate the intersystem crossing processes of the through-space charge transfer states in the triptycene bridged acridine–triazine donor–acceptor molecule TpAT-tFFO

Quantum chemical studies employing combined density functional and multireference configuration interaction methods suggest five excited electronic states to be involved in the prompt and delayed fluorescence emission of TpAT-tFFO. Three of them, a pair of singlet and triplet charge transfer (CT) states (S₁ and T₁) and a locally excited (LE) triplet state (T₃), can be associated with the (Me → N) conformer, the other two CT-type states (S₂ and T₂) form the lowest excited singlet and triplet states of the (Me → Ph) conformer. The two conformers, which differ in essence by the shearing angle of the face-to-face aligned donor and acceptor moieties, are easily interconverted in the electronic ground state whereas the reorganization energy is substantial in the excited singlet state, thus explaining the two experimentally observed time constants of prompt fluorescence emission. Forward and reverse intersystem crossing between the singlet and triplet CT states is mediated by vibronic spin–orbit interactions involving the LE T₃ state. Low-frequency vibrational modes altering the distance and alignment of the donor and acceptor π-systems tune the S₁ and T₃ states (likewise S₂ and T₃) into and out of resonance. The enhancement of intersystem crossing due to the interplay of vibronic and spin–orbit coupling is considered a general feature of organic through-space charge-transfer thermally activated delayed fluorescence emitters.

DFT/MRCI quantum chemical studies suggest five excited electronic states to be involved in the prompt and delayed fluorescence emission of TpAT-tFFO.     

The Extracts of Polygonum cuspidatum Root and Rhizome Block the Entry of SARS-CoV-2 Wild-Type and Omicron Pseudotyped Viruses via Inhibition of the S-Protein and 3CL Protease

COVID-19, resulting from infection by the SARS-CoV-2 virus, caused a contagious pandemic. Even with the current vaccines, there is still an urgent need to develop effective pharmacological treatments against this deadly disease. Here, we show that the water and ethanol extracts of the root and rhizome of Polygonum cuspidatum (Polygoni Cuspidati Rhizoma et Radix), a common Chinese herbal medicine, blocked the entry of wild-type and the omicron variant of the SARS-CoV-2 pseudotyped virus into fibroblasts or zebrafish larvae, with IC₅₀ values ranging from 0.015 to 0.04 mg/mL. The extracts were shown to inhibit various aspects of the pseudovirus entry, including the interaction between the spike protein (S-protein) and the angiotensin-converting enzyme II (ACE2) receptor, and the 3CL protease activity. Out of the chemical compounds tested in this report, gallic acid, a phytochemical in P. cuspidatum, was shown to have a significant anti-viral effect. Therefore, this might be responsible, at least in part, for the anti-viral efficacy of the herbal extract. Together, our data suggest that the extracts of P. cuspidatum inhibit the entry of wild-type and the omicron variant of SARS-CoV-2, and so they could be considered as potent treatments against COVID-19.     

A structure determination protocol based on combined analysis of 3D-ED data,powder XRD data,solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine

We report the crystal structure of a new polymorph of l-tyrosine (denoted the β polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic ¹³C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state ¹³C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the β polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and β polymorphs.

A new polymorph of l-tyrosine is reported, with the crystal structure determined by combined analysis of 3D-ED data and powder XRD data, augmented by information from periodic DFT-D calculations and solid-state ¹³C NMR data.     

Simple models for the diurnal cycle and convectively coupled waves

This paper presents a study of the diurnal cycle of tropical precipitation and its interaction with convectively coupled waves in the context of simple models with crude vertical resolution. One and two baroclinic mode models are tested in both the context of a one-column model and the context of a full spatial dependency that permits waves to propagate and interact with the diurnal cycle. It is found that a one baroclinic mode model is capable of reproducing a realistic diurnal cycle of tropical precipitation both over land and over the ocean provided an adequate switch function is used to mimic the congestus preconditioning mechanism that operates in the multicloud model of Khouider and Majda. However, a full two baroclinic mode multicloud model is needed to capture the interaction of convectively coupled tropical waves with the diurnal cycle. In a more conventional mass flux parameterization framework, both one and two baroclinic mode models fail to capture the diurnal cycle of tropical precipitation.     

Plate-based diversity subset screening: an efficient paradigm for high throughput screening of a large screening file

The screening files of many large companies, including Pfizer, have grown considerably due to internal chemistry efforts, company mergers and acquisitions, external contracted synthesis, or compound purchase schemes. In order to screen the targets of interest in a cost-effective fashion, we devised an easy-to-assemble, plate-based diversity subset (PBDS) that represents almost the entire computed chemical space of the screening file whilst comprising only a fraction of the plates in the collection. In order to create this file, we developed new design principles for the quality assessment of screening plates: the Rule of 40 (Ro40) and a plate selection process that insured excellent coverage of both library chemistry and legacy chemistry space. This paper describes the rationale, design, construction, and performance of the PBDS, that has evolved into the standard paradigm for singleton (one compound per well) high-throughput screening in Pfizer since its introduction in 2006.     

Determination of Cadmium in Plant Tissues by Electrothermal Atomisation Atomic Absorption Spectrometry with Matrix/Analyte Modification and Smith-Hieftje Background Correction

Abstract

Pressure decomposition in a microwave oven provides a rapid means of sample preparation for plant tissue analyses. The use of delayed atomisation cuvettes, Smith-Hieftje background correction and matrix/analyte modification enables accurate determinations of cadmium concentrations in plant materials to be made. However, care should be taken to restrict the concentrations of modifier used, as too high a concentration may lead to problems with both tube life and over-correction by the Smith-Hieftje background correction system.     

Total synthesis of amorfrutin A via a palladium-catalyzed migratory prenylation–aromatization sequence

The total synthesis of amorfrutin A, a prenyl bibenzyl natural product has been achieved in five steps from 2,2,6-trimethyl-4H-1,3-dioxin-4-one. The key step of the synthesis is an efficient palladium(0)-catalyzed decarboxylative prenylation migration and aromatization sequence.