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Penicillin resistance is a commonly present and controversial matter due to the misuse by people for various reasons. However, few studies have examined the bioactivity of 5- and 6- membered rings. In this study, we aimed to synthesize a new compound containing a 5-membered ring following a short and low-cost method and combined it with oxazepine ring via Schiff bases to produce a bicyclic molecule (Lactozepine). In vitro examinations were conducted to assess the bioactivity of the prepared compound, including anti-bacterial, anti-fungal and antioxidant activities, which showed a wide zone of inhibition of lactozepine against Streptococcus pneumoniae but no inhibition was shown against Klebsiella pneumoniae and Staphylococcus aureus except at a high concentration similar to the result of the anti-fungal assessment. Furthermore, lactozepine showed significant antioxidant activity against free radical formation. The molecular modeling and docking assessment showed the ability of lactozepine to bind to bacterial proteins and inhibit their growth with the lowest free energy for the greatest and strongest binding affinity with the PDB crystal structures 1VQQ, 2WAE, 1PYY and 1IYS ranging from −6.5 and −7.9 kcal/mol. Moreover, the molecular dynamics (MD) simulation showed that RMSF for the assessed protein’s amino acids remained consistent and tightly bound to lactozepine in the dynamic state. The novel compound lactozepine, with $\delta$-lactam rings attached to oxazepine showed bioactivity promising for in vivo studies in the future.

The coupling of numerical methods in different scales is of great significance in the investigation of intricate multiscale phenomena. This work develops a dynamic coupling approach based on domain decomposition by combining the mesoscale lattice Boltzmann method (LBM) and microscale molecular dynamics (MD) simulations. In the proposed scheme, a two-way concurrent exchange of information between different scales has been achieved. At the atomistic scale, the fluid dynamics are modeled through the particle-based MD method on the framework of the open large-scale atomic/molecular massively parallel simulator (LAMMPS). While at the coarse scale, the fluid system is simulated utilizing the LBM approach, which relies on the collision and streaming of the particles constrained in discretized lattices, adhering to the conservation laws of mass and momentum. The exchange of velocity distributions between the two scales was handled. The accuracy and efficiency of the proposed coupling scheme were validated through simulations of the classic Poiseuille and Couette flows. The obtained results show that satisfactory agreement against pure MD results has been achieved. Moreover, a notable improved efficiency as high as 92.8% has been observed for the coupling scheme in comparison to MD simulations. Due to the inherent parallelism of LBM and MD, the proposed coupling scheme exhibits great potential for extended application in studying complex multiscale phenomena with dynamic coupling between different scales.

The factors that affect the structures and stability of the adducts of cisamminedichloro(2-methylpyridine)platinum(II) with a duplex DNA were probed into by the mixed quantum chemistry and molecular mechanics (QM/MM), molecular dynamics (MD) and molecular mechanics (MM) methods. It shows that the coordinate bonds between Pt and N7G, the hydrogen bond between the amine and O6G, the weak interactions between drug molecule and DNA and the positive electron charge center position of the drug molecule in the adduct affect the stability and the steric selection of the adduct greatly. And in return the structure of the adduct determine the comparatively strengths of the coordinate bonds in the adduct.

In this paper, we use molecular dynamics (MD) simulations and a modified analytic embedded-atom method to investigate the edge dislocation movement without imposed strain at 0 K. The obtained results indicate that the straight lines of the partial dislocations always preserve their original shapes and are parallel to each other during the simulation process. According to the energy of each atom, the positions of both partial dislocation cores are determined. Then the velocities in the period of the relaxation process are investigated in detail. The MD simulations reveal that the MD relaxation time dependence of the edge dislocation mobility is divided into two parts. First, during the initial period ranging from 0 to 6 ps, the relative velocity of the dislocation movement lineally increases with the incremental relaxation time. Second, in the latter period from 6 ps to the end of the simulated process the velocity decreases exponentially as the MD simulation time evolves.

Molecular dynamics (MD) and modified analytical embedded atom method (MAEAM) are used to study the effect of the cross-sectional shape on the nanowire (NW) premelting. The results indicate that the premelting phenomenon occurs far below the melting point. The temperature dependence of mean square displacement (MSD) shows that the shape effect on the premelting phenomenon is obvious. Based on the detailed analysis of the atomic configuration, the premelting activation energy (PAE), and the shape factor, we have further found that the cross-sectional shape has an important effect on the premelting mechanism of the NW.

There are two conventional boundary treatment methods in molecular dynamics (MD) simulation for particle suspension or fiber in cross flow. One is that the fiber is represented by evenly spaced atoms, the other is that the fiber is treated as one mass point. The calculations with the two boundary treatment methods have been compared, it is found that, with the same properties, both methods could generate slip boundary condition on the fiber surface, however the one mass point method could result in very large slip boundary condition on the fiber surface, and the discrepancy could be as high as 2600%.

The classical MD (Molecular Dynamics) method was used to simulate the tension of three kinds of C₂₄₀ isomers, i.e., C₂₄₀ nanotube, chain-like 4C₆₀ fullerene polymer and peanut-like 4C₆₀ fullerene polymer. Then, the semi-empirical PM3 method was used to calculate their electronic structures under tension. Lastly, according to the calculated results, their differences in tensile mechanical properties, as well as the change of their FMO (Frontier Molecular Orbital) energy during tension, were discussed. It is shown that: (1) the load-support capability of the C₂₄₀ molecules has the order of C₂₄₀ nanotube > peanut-like 4C₆₀ polymer > linear 4C₆₀ polymer, but their deformation-support capability has the contrary order, (2) of the C₂₄₀ isomers, the C₂₄₀ nanotube has the best chemical stability, and the chain-like 4C₂₄₀ molecule has the worst one, and (3) the deformed C₂₄₀ isomers have narrower energy-gap between their LUMO and HOMO, and higher chemical activity.

The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), which were then subjected to molecular docking and ADME prediction. These approaches resulted in the identification of five hits, namely, nebivolol, HDY, D42, 796, and LZE having higher Glide docking scores and promising ADME properties with augmented CNS involvement. Moreover, molecular dynamics simulations were performed to validate the inhibitory activity of the hit compounds, and density functional theory calculations were carried out to scrutinize the chemical reactivity of the hits. Subsequent interaction and scaffold analysis identified prominent interactions of the hits with ALK kinase domain and scaffolds with anti-tumor activity against lung cancer cell lines. We strongly believe that the study provides an outlook for the sighting of novel and potent ALK inhibitors in the near future.

Nowadays, hybridization of different algorithms for the optimization of non-conventional machining processes tries to accomplish better results. The paper consists of experimental evolutionary-particle Swarm Optimization (PSO), Quantum-PSO and Gaussian Quantum Particle Swarm Optimization (G-QPSO)-based ANN modeling and comparative investigation on performances such as material removal rate (MRR), machining depth (MD), roughness of surface and overcut (OC) for machining of silica by ECDM process using mixed electrolyte. The paper also shows the co-efficient of NN models for different machining criteria and G-QPSO and also the comparative study of MD, roughness (SR), overcut (OC) as well as MRR using different algorithms and convergence test for fitness of experimental results also propounded to achieve cross-validation of models and multi-response optimal results for micro-machining of Silica by ECDM using PSO, QPSO and GQPSO. It is found that Gaussian Quantum Particle Swarm Optimization (G-QPSO)-ANN is more efficient for ECDM and achieves optimal results at 55-volt, pulse on time 52.3 s, inter-electrode gap (IEG) 30 mm, duty ratio 0.475 and electrolytic concentration 30 (wt.%).

This article has been retracted because it is an English translation of a Chinese paper that was published earlier, with some additional content in the later part. This is inappropriate and violates the scientific rule of anti-plagiarism. We regret that this was not detected before the article was accepted for publication in the journal.

We compared the protein-ligand binding free energies (∆G) obtained by the explicit water model, the MM-GB/SA (molecular-mechanics generalized Born surface area) model, and the docking scoring function. The free energies by the explicit water model and the MM-GB/SA model were calculated by the previously developed Smooth Reaction Path Generation (SRPG) method. In the SRPG method, a smooth reaction path was generated by linking two coordinates, one a bound state and the other an unbound state. The free energy surface along the path was calculated by a molecular dynamics (MD) simulation, and the binding free energy was estimated from the free energy surface. We applied these methods to the streptavidin-and-biotin system. The ∆G value by the explicit water model was close to the experimental value. The ∆G value by the MM-GB/SA model was overestimated and that by the scoring function was underestimated. The free energy surface by the explicit water model was close to that by the GB/SA model around the bound state (distances of < 6 Å), but the discrepancy appears at distances of > 6 Å. Thus, the difference in long-range Coulomb interaction should cause the error in ∆G. The scoring function cannot take into account the entropy change of the protein. Thus, the error of ∆G could depend on the target protein.