Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors

SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CL^pro or M^pro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CL^pro active site. These compounds will facilitate further 3CL^pro inhibitor design.     

Charge‐Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy

Adenosine radicals tagged with a fixed‐charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born–Oppenheimer molecular dynamics, ab initio, and excited‐state calculations led to unambiguous assignment of adenosine radicals as N‐7 hydrogen atom adducts. The charge‐tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.     

Chemical composition of PM_(2.5) during winter in Tianjin,China

PM2.5 samples for 24 h were collected during winter in Tianjin,China. The ambient mass concentration and chemical composition of the PM2.5 were determined. Ionic species were analyzed by ion chromatog-raphy,while carbonaceous species were determined with the IMPROVE thermal optical reectance(TOR) method,and inorganic elements were measured by inductively coupled plasma-atomic emission spec-trometer. The daily PM2.5 mass concentrations ranged from 48.2 to 319.2 g/m3 with an arithmetic average of 144.6 g/m3. ...     

Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains

We investigate the microscopic mechanisms responsible for microdomain alignment in block copolymer solutions exposed to an electric field. Using time-resolved synchrotron small-angle x-ray scattering, we reveal two distinct processes, i.e., grain boundary migration and rotation of entire grains, as the two dominant microscopic mechanisms. The former dominates in weakly segregating systems, while the latter is predominant in strongly segregated systems. The kinetics of the processes are followed as a function of polymer concentration and temperature and are correlated to the solution viscosity.     

Reduction of the effective rotational Hamiltonian for pyramidal XY3 molecules with a large-amplitude inversion motion

The previously described reduction of the effective rotational Hamiltonian for semirigid molecules of C_3v or D₃ point group symmetry [M. R. Aliev and V. T. Aleksanyan, Opt. Spectrosc.24, 201–206 (1968)] has been extended to nonrigid molecules with a significant inversion splitting of the energy levels (e.g., NH₃, H₃O⁺, CH₃^?, or SiH₃ molecules). Although for semirigid molecules like PH₃ or AsH₃, the parameters α and η′₃ which appear in the terms α[J₊³ + J_?³, J_z]₊ and η′₃(J₊⁶ + J_?⁶) are almost completely correlated, the effects of the inversion splitting and the accidental resonance which can occur between the interacting rotational levels in nonrigid molecules make it possible to determine α and η′₃ separately. The results of fitting the experimental data for ¹⁴NH₃ and ¹⁵NH₃ [?. Urban, Romola D'Cunha, K. Narahari Rao, and D. Papou?ek, Canad. J. Phys.62, 1775–1791 (1984); Romola D'Cunha, ?. Urban, K. Narahari Rao, L. Henry, and A. Valentin, J. Mol. Spectrosc.111, 352–360 (1985)] are in agreement with this conclusion. The possibility of the determination of the sign of η₃ from a simultaneous analysis of the allowed and Δk = ±3 forbidden transitions in semirigid XY₃ molecules has been discussed.     

Electron paramagnetic resonance of Fe3+ in KNbO3 at 300 K

In the orthorhombic phase of KnbO₃ an EPR spectrum of Fe³⁺ substitutional for Nb⁵⁺ has been observed with the main axis parallel to the pseudocubic one of the orthorhombic phase. The cubic parameter a is very close to the one in BaTiO₃. A second spectrum probably due to local charge compensation is also reported.     

Synthetische anthracyclinone XVI synthese hydroxylierter anthrachinone durch regioselektive Diels-Alder-reaktion

Naturally occurring quinones such as 7-methyljuglone, chrysophanol, emodin, helminthosporin, phomarin and physcion were prepared via Diels-Alder reaction and PCC-oxidation of the allylic alkohols obtained from the adducts.     

Direct evidence for a very low atom displacement threshold energy around the 〈110〉 directions in copper

The dependence of the displacement cross section of Cu on electron energy and crystal orientation has very accurately been determined by high-voltage electron microscopy. The minimum displacement threshold energy of (9.5 ± 0.5) eV occurs at an angle of 10° from 〈110〉 directions.