Modeling the binding of protoporphyrin IX,verteporfin, and chlorin e6 to SARS-CoV-2 proteins

Chemistry of Heterocyclic Compounds - In this work, we analyze the latest data on the molecular docking of a range of SARS-CoV-2 proteins to protoporphyrin IX, verteporfin, and chlorin e6, as well...     

Efficient Population Transfer in a Λ-Type Quantum System Coupled to a Gold Nanoparticle Using STIRAP Shortcuts

A theoretical investigation on the population transfer in a Λ-type quantum system near a spherical gold nanoparticle under application of two stimulated Raman adiabatic passage (STIRAP) shortcuts and efficiency comparison with conventional STIRAP. It combines the density matrix approach for system dynamics, with classical electromagnetic calculations used to obtain the modified electric field amplitudes of the applied pulses and the Purcell factor of the quantum system due to the presence of the nanoparticle. The efficiency of population transfer is investigated by varying the distance between the quantum system and the nanoparticle, the free-space decay rate of quantum states, the mutual polarization, and the Rabi frequencies of each STIRAP shortcut pulses. In all cases, at least one of the applied shortcuts is more efficient than conventional STIRAP, while in most cases both perform better. When the pump and Stokes fields of the shortcuts have radial and tangential polarizations with respect to the nanoparticle surface, respectively, high transfer efficiency is obtained for small distances of the quantum system to the nanoparticle, moderate free space decay rates and large Rabi frequencies of the fields, while when the pulse polarizations are interchanged, the transfer becomes highly efficient only at large distances.     

Micro-Raman Characterization of Structural Features of High-k Stack Layer of SOI Nanowire Chip,Designed to Detect Circular RNA Associated with the Development of Glioma

The application of micro-Raman spectroscopy was used for characterization of structural features of the high-k stack (h-k) layer of “silicon-on-insulator” (SOI) nanowire (NW) chip (h-k-SOI-NW chip), including Al₂O₃ and HfO₂ in various combinations after heat treatment from 425 to 1000 °C. After that, the NW structures h-k-SOI-NW chip was created using gas plasma etching optical lithography. The stability of the signals from the monocrine phase of HfO₂ was shown. Significant differences were found in the elastic stresses of the silicon layers for very thick (>200 nm) Al₂O₃ layers. In the UV spectra of SOI layers of a silicon substrate with HfO₂, shoulders in the Raman spectrum were observed at 480–490 cm⁻¹ of single-phonon scattering. The h-k-SOI-NW chip created in this way has been used for the detection of DNA-oligonucleotide sequences (oDNA), that became a synthetic analog of circular RNA–circ-SHKBP1 associated with the development of glioma at a concentration of 1.1 × 10⁻¹⁶ M. The possibility of using such h-k-SOI NW chips for the detection of circ-SHKBP1 in blood plasma of patients diagnosed with neoplasm of uncertain nature of the brain and central nervous system was shown.     

Metabolic Evaluation of Urine from Patients Diagnosed with High Grade (HG) Bladder Cancer by SPME-LC-MS Method

Bladder cancer (BC) is a common malignancy of the urinary system and a leading cause of death worldwide. In this work, untargeted metabolomic profiling of biological fluids is presented as a non-invasive tool for bladder cancer biomarker discovery as a first step towards developing superior methods for detection, treatment, and prevention well as to further our current understanding of this disease. In this study, urine samples from 24 healthy volunteers and 24 BC patients were subjected to metabolomic profiling using high throughput solid-phase microextraction (SPME) in thin-film format and reversed-phase high-performance liquid chromatography coupled with a Q Exactive Focus Orbitrap mass spectrometer. The chemometric analysis enabled the selection of metabolites contributing to the observed separation of BC patients from the control group. Relevant differences were demonstrated for phenylalanine metabolism compounds, i.e., benzoic acid, hippuric acid, and 4-hydroxycinnamic acid. Furthermore, compounds involved in the metabolism of histidine, beta-alanine, and glycerophospholipids were also identified. Thin-film SPME can be efficiently used as an alternative approach to other traditional urine sample preparation methods, demonstrating the SPME technique as a simple and efficient tool for urinary metabolomics research. Moreover, this study’s results may support a better understanding of bladder cancer development and progression mechanisms.     

Remarkable Structural and Electronic Features of the Complex Formed by Trimeric Copper Pyrazolate with Pentaphosphaferrocene

According to spectroscopic (NMR, IR, UV/Vis) study, the interaction of pentaphosphaferrocene [Cp*Fe(η⁵‐P₅)] with trimeric copper pyrazolate [(Cu{3,5‐(CF₃)₂Pz})₃] yields a new compound that is astonishingly stable in solution. Single‐crystal X‐ray analysis reveals unprecedented structural changes in the interacting molecules and the unique type of coordination [Cp*Fe(μ₃‐η⁵:η²,η²‐P₅){Cu(3,5‐(CF₃)₂Pz)}₃]. As a result of the 90° macrocycle folding, the copper atoms are able to behave both as a Lewis acid and as a Lewis base in the interaction with the cyclo‐P₅ ligand.     

A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase

Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host–pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl‐3‐phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP‐Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum‐mechanics/molecular‐mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front–side substrate‐assisted S_Ni‐type reaction.     

Electroless Deposition of III–V Semiconductor Nanostructures from Ionic Liquids at Room Temperature

Group III–V semiconductor nanostructures are important materials in optoelectronic devices and are being researched in energy‐related fields. A simple approach for the synthesis of these semiconductors with well‐defined nanostructures is desired. Electroless deposition (galvanic displacement) is a fast and versatile technique for deposition of one material on another and depends on the redox potentials of the two materials. Herein we show that GaSb can be directly synthesized at room temperature by galvanic displacement of SbCl₃/ionic liquid on electrodeposited Ga, on Ga nanowires, and also on commercial Ga. In situ AFM revealed the galvanic displacement process of Sb on Ga and showed that the displacement process continues even after the formation of GaSb. The bandgap of the deposited GaSb was 0.9±0.1 eV compared to its usual bandgap of 0.7 eV. By changing the cation in the ionic liquid, the redox process could be varied leading to GaSb with different optical properties.     

Influence of Synthesis pH and Oxidative Strength of the Catalyzing Acid on the Morphology and Chemical Structure of Hydrothermal Carbon

A specific control of the morphology and chemical structure of hydrothermal carbon (HTC) is of crucial importance for its application, both in catalyst supports or electrochemical devices. Here we show how the morphology, that is, particles size and homogeneity, and the distribution of functional groups can be controlled by the control of the synthesis pH of the hydrothermal carbonization. A complementary analysis of liquid byproducts by HPLC provides useful information on the nature of the polymeric species produced during the poly‐condensation in the hydrothermal process and reveals the potential implementation of the process into the biorefinery concept. The acidic byproducts levulinic acid and formic acid determine the hydrothermal carbonization autocatalytically by additional supply of protons to the reaction medium. Thus, for a starting pH>3, only minor structural differences can be detected for HTC. The use of oxidizing acids favors higher yields of HTC and improves carbonization towards higher condensed carbon domains. Scaling up the process in a stirred 2 L batch reactor favors carbonization leading to higher condensed carbonaceous products. The relative trends of pH variation are maintained.     

Optical bistability in a nonlinear optical coupler with a negative index channel

We discuss a novel kind of nonlinear coupler with one channel filled with a negative index metamaterial. The opposite directionality of the phase velocity and the energy flow in the negative index metamaterial channel facilitates an effective feedback mechanism that leads to optical bistability and gap soliton formation.