Fingerprinting Organofluorine Molecules via Position-Specific Isotope Analysis
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Engineering↗
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Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors
SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K dimer ) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K dimer . Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro WT -ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.
60 APPLIED LIFE SCIENCES↗
Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions
Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.
Infrared spectroscopy↗
Temperature Dependences of Peak Positions in Pair Distribution Function of Metallic Liquids
Abstract not provided
Zhang, Wenbiao↗
The Unexpected Role of Cations in the Self-Assembly of Positively Charged Amphiphiles at Liquid/Liquid Interfaces
Conventional wisdom suggests that cations play a minimal role in the assembly of cationic amphiphiles. Here, we show that at liquid/liquid (L/L) interfaces, specific cation effects can modulate the assemblies of hydrophobic tails in an oil phase despite being attached to cationic headgroups in the aqueous phase. In this work, we used oligo-dimethylsiloxane (ODMS) methyl imidazolium amphiphiles to identify these specific interactions at hexadecane/aqueous interfaces. Small cations, such as Li + , bind to the O atoms in the ODMS tail and pin it to the interface, thereby imposing a kinked conformation-as evidenced by vibrational sum frequency generation spectroscopy and molecular dynamics simulations. While larger Cs + ions more readily partition to the interface, they do not form analogous complexes. Our data not only point to ways for controlling amphiphile structure at L/L interfaces but also suggest a means for the separation of Li + , or related applications, in soft-matter electronics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Atomistic Positioning of Defects in Helium Ion Treated Single-Layer MoS 2
Structuring materials with atomic precision is the ultimate goal of nanotechnology and is becoming increasingly relevant as an enabling technology for quantum electronics/spintronics and quantum photonics. Here, we create atomic defects in monolayer MoS 2 by helium ion (He-ion) beam lithography with a spatial fidelity approaching the single-atom limit in all three dimensions. Using low-temperature scanning tunneling microscopy (STM), we confirm the formation of individual point defects in MoS 2 upon He-ion bombardment and show that defects are generated within 9 nm of the incident helium ions. Atom-specific sputtering yields are determined by analyzing the type and occurrence of defects observed in high-resolution STM images and compared with Monte Carlo simulations. Both theory and experiment indicate that the He-ion bombardment predominantly generates sulfur vacancies.
Two-dimensional materials↗
Initial Stage of Nanoscale Imaging in Positive Tone Extreme UV Photoresists: The Influence of the Polymer Sequence
Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.
Absorption↗