In-silico Study of the Developed Hydroxychloroquine-based ACE2 Inhibitor Molecules Against COVID-19: Molecular Modeling and Docking

In the present study, we will verify the action of hydroxychloroquine-based derivatives on ACE2 which is considered to be the main portal of entry of the SARS-CoV-2 virus and constitutes an exciting target given its relative genetic stability compared to viral proteins. Thus, 81 molecules derived from hydroxychloroquine by substitutions at 4 different positions were generated in-silico and then studied for their affinity for ACE2 by molecular docking. Only 4 molecules were retained because of their affinity and bioavailability demonstrated by molecular dynamics and molecular docking calculations using COSMOtherm and Materials Studio software.

Experiment and simulation of single inhibitor SH110 for void-free TSV copper filling

Three-dimensional integration with through-silicon vias (TSVs) is a promising microelectronic interconnection technology. Three-component additives are commonly used for void-free TSV filling. However, optimising the additive concentrations is an expensive process. To avoid this, a single-component additive was developed: 3-(2-(4,5-dihydrothiazol-2-yl) disulfanyl) propane-1-sulfonic acid/sulfonate (SH110). Sodium 3,3′-dithiodipropane sulfonate (SPS) and SH110 were used as additives for TSV electroplating copper filling. SH110 resulted in void-free filling, whereas large keyhole voids were found for SPS. To understand how the additives affect the filling mechanism, linear sweep voltammetry of the plating solutions was carried out. The interactions between the Cu surface and additives were simulated by molecular dynamics (MD) analysis using Materials Studio software, and quantum chemistry calculations were conducted using GAUSSIAN 09W. SH110 adsorbs to the Cu surface by both 4,5-dihydrothiazole (DHT) and 3-mercaptopropane sulfonate (MPS) moieties, while SPS is adsorbed only by MPS moieties. MD simulations indicated that the adsorption of the coplanar MPS moiety is the main factor governing acceleration. Quantum chemistry calculations showed that DHT provides an inhibitory effect for TSV filling, while MPS acts as an accelerator for SH110. SH110 is an excellent additive exhibiting both the acceleration and the suppression necessary for achieving void-free TSV filling.

New Insights on Sodium Oleate Adsorption on Quartz for Iron Direct Flotation under Weak-Acidic Condition

To study the sodium oleate (NaOL) adsorption on quartz and its effect on flotation under weak-acidic conditions, the adsorption characteristics of NaOL on the surface of quartz were determined at pH = 6.5 by Fourier transform infrared spectroscopy (FTIR). The solution chemical calculation results show that NaOL exists as oleic acid (HOL) under weakly acidic conditions. The existence form and charge distribution of quartz and HOL were analyzed by Molecular Dynamics Simulation (MDS) using Materials Studio (MS) software, and the results showed that HOL is prone to the (101) and (100) surfaces of quartz under weak-acidic conditions by hydrogen bonding. The flotation verification test with NaOL as a collector was also performed under weak-acidic conditions. The flotation test led to a partial flotation of quartz into the froth products, reducing the grade of hematite direct flotation concentrate, which is consistent with industrial production.

Effect of Temperature on Formaldehyde Diffusion in Cellulose Amorphous Region: A Simulation Study

A formaldehyde-cellulose amorphous region model at the micro-level was established using the molecular dynamics software Materials Studio to simulate the change of cellulose and formaldehyde molecules in an external temperature field. The diffusion coefficients of formaldehyde molecules increased as the temperature increased. Moreover, the total number of hydrogen bonds decreased, and the interaction energy in the formaldehyde-cellulose model was reduced, which confirmed this conclusion and indicated that temperature increase could enhance the diffusion of formaldehyde in cellulose. The mechanical parameters of cellulose were analyzed in terms of Young’s modulus, shear modulus, bulk modulus, Poisson’s ratio, and the ratio of bulk modulus to shear modulus (K/G), which were affected by the temperature. The elastic modulus (E, G, and K) of cellulose decreased as the temperature increased, while the Poisson’s ratio V and K/G values increased. The results of the research explain how elevated temperature can promote the release of formaldehyde in furniture from a microscopic perspective, which supports each other with the results of previous experimental data and practical applications in production.

Molecular simulation on mechanism of thiophene hydrodesulfurization on surface of Ni2P

Hydrodesulfurization reaction, as the last step of hydrothermal cracking reaction, is of great significance for the reduction of viscosity and desulfurization of heavy oil. Based on Density Functional Theory and using Dmol3 module of Materials Studio, this research simulated the adsorption and hydrodesulfurization of thiophene on Ni2P (001) surface, and discussed the hydrodesulfurization reaction mechanism of thiophene on Ni2P (001) surface. It was found that the direct hydrodesulfurization of thiophene had more advantages than the indirect hydrodesulfurization of thiophene. Finally, the optimal reaction path was determined: C4H4S+H2→C4H6.

The Ring Formation Mechanism in Cyclization of Berberine

Berberine hydrochloride is a natural alkaloid with significant antitumor activities against many types of cancer cells, can be synthesized by cyclic reaction with hydrochloride condensate and glyoxal as raw materials and copper chloride as catalyst. In this study, the transition and energy change for the each reaction step was calculated by the density functional theory program Dmol3 in Materials Studio 2017. and the results testified that there are two ring formation in the cycliztion process, and according to the result we proposed the mechanism of this cyclization reaction. We also use infrared and ultraviolet spectroscopy to monitor the reaction process in real time and prove the ring formation process. The reaction mechanism was firstly proposed at the basic results of above.