分子模拟实验课程建设的探索与实践

We put forward the idea of building a molecular simulation experiment course. After two-year teaching practice, we write the experiment textbook which not only covers the classic experimental projects, but also includes the frontier hot issues, and open exploration experiment. This article summarizes the teaching requirements, basic content, assessment methods, the initial achievements made so far and the prospects for the future.     

Spatially restricted Double Z-Simplified Box Orbital basis sets: Optimization and comparison with some standard basis sets

As part of previous studies, we introduced a new type of basis function named Simplified Box Orbitals (SBOs) that belong to a class of spatially restricted functions which allow the zero differential overlap (ZDO) approximation to be applied with complete accuracy. The original SBOs and their Gaussian expansions SBO-3G form a minimal basis set, which was compared to the standard Slater-type orbital basis set (STO-3G). In the present paper, we have developed the SBO basis functions at double-zeta (DZ) level, and we have assessed the option of expanding the SBO-DZ as a combination of Gaussian functions. Finally, we have determined the quality of the new basis set by comparing the molecular properties calculated with SBO-nG with those achieved with some standard basis sets.     

基于Matlab GUI的微观化学反应过程可视化设计

Based on the quasi-classical trajectory (QCT) method and Matlab GUI technology, we developed a program code for visualizing the collision process of the elementary chemical reactions of the a + bc type. The general methodology of QCT, abstraction of dynamical properties of molecular collisions and the making of Graphical User Interface are introduced. The running results of an application to the reaction F + HCl→HF + Cl is also presented. The results showed that this program could vividly demonstrate the behavior and final state of the atom-diatom collision process in animated form. Students can interact with internal MATLAB code through graphical user interface, observe the reactive behavior and final results in real-time from multiple angles, which helps students to understand the complex reaction mechanism and deepen their perceptual impression of the chemical process at a microscopic atomic/molecular level.     

Experimental and molecular simulating study on promoting electrolyte-immersed mechanical properties of cellulose/lignin separator for lithium-ion battery

Lithium-ion batteries have been developing intensively and earn an unprecedented reputation, yet advanced performance and safety issue still require considerable investigation. Separator is vital to comprehensive properties of batteries, where the mechanical properties are key to breaking through of new-type separator. Unfortunately, electrolyte submersion has caused damage to strength of cellulose separator. Whereupon, in this work, cellulose separator is optimized by introducing lignin particles to promote electrolyte-immersed mechanical strength. Experiments are conducted concerning surface morphology, contact angle, porosity, electrolyte uptake, mechanical properties and electrochemical performance. Molecular simulation is implemented to explore the mechanism of tensile behavior of cellulose and lignin subjected to electrolyte solvents. Experimental results confirm positive effect of lignin addition in improving mechanical properties and simultaneously maintaining impressive electrochemical performance of the cellulose/lignin composites separators. Besides, lignin addition amount of 2.5% and 5% is recommended to achieve promising overall properties. Molecular simulation has successfully unveiled that weakening of cellulose separator submerged in electrolyte is resulted by the deformed cellulose amorphous region and the promoting effect of adding lignin is contributed from the new hydrogen bonds generated between cellulose and lignin molecules. Hopefully, this work provides novel insight on preparing remarkable separator and mechanism of materials behavior.     

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Redox- and protonation-state driven substrate-protein dynamics in respiratory complex I

Respiratory complex I is a key enzyme in the electron transport chains of mitochondria and bacteria. It transfers two electrons to quinone and couples this redox reaction to proton pumping to electrically charge the membrane it is embedded in. The charge and pH gradient across the membrane drives the synthesis of ATP. The redox reaction and proton pumping in complex I are separated in space and time, which raises the question of how the two reactions are coupled so efficiently. Here, we focus on the unique ～35 Å long tunnel of complex I, which houses the binding site of quinone reduction. We discuss the redox and protonation reactions that occur in this tunnel and how they influence the dynamics of protein and substrate. On the basis of recent structural data and results from molecular simulations, we review how quinone reduction and dynamics may be coupled to proton pumping in complex I.     

Understanding cathode materials in aqueous zinc–organic batteries

Organic electrode materials (OEMs) are being investigated as promising candidates for aqueous zinc-ion batteries (AZIBs) owing to their environmental friendliness, cost-effectiveness, and structural diversity, and tunability. Understanding the correlation between structural regulation of OEMs and their electrochemical property in AZIBs is vital to rational design of OEMs. Herein, we first discuss the fundamentals of the energy storage mechanism of OEMs. Then, strategies to improve the electrochemical performance, including the specific capacity, voltage, rate capability, and cycling stability, are elaborated from the perspective of molecular engineering. Finally, we share our views on the remaining challenges and prospects of OEMs in AZIBs.     

Performance evaluation of functionalized ordered mesoporous silica for VOCs adsorption by molecular dynamics simulation

Volatile organic compounds (VOCs) are growing pollutants now that cause the serious environmental pollution and threaten human health. The functionalized ordered mesoporous silica (FOMS) has attracted considerable attention in adsorbing VOCs. In this paper, the molecular dynamics simulation was used to simulate the adsorption performance of FOMS on VOCs (acetone, ethyl acetate and toluene). After simulating different pore sizes (2 nm, 3 nm and 4 nm) adsorption performances of ordered mesoporous silica (OMS) on VOCs, OMS with a pore size of 4 nm was selected to further study the influence of functional groups (vinyl, methyl, and phenyl). The following law was obtained: the saturated adsorption capacities of vinyl-functionalized OMS (V-FOMS) to acetone, ethyl acetate and toluene were 3.045 mmol.g^?1, 2.568 mmol.g^?1 and 1.976 mmol.g^?1 respectively; the saturated adsorption capacities of methyl-functionalized OMS (M-FOMS) to acetone, ethyl acetate and toluene were 2.798 mmol.g^?1, 2.312 mmol.g^?1 and 1.698 mmol.g^?1 respectively; the saturated adsorption capacities of phenyl-functionalized OMS (P-FOMS) to acetone, ethyl acetate and toluene were 2.124 mmol.g^?1, 1.941 mmol.g^?1 and 1.539 mmol.g^?1 respectively. These results show that the adsorption ability of FOMS for different adsorbates follows the sequence of acetone > ethyl acetate > toluene. Furthermore, the interaction between functional groups (vinyl, methyl and phenyl) in FOMS and VOCs was explored. It is found that the interaction between different functional groups and adsorbates is different (interaction energy effect). This interaction energy effect promotes FOMS to better adsorb VOCs. This work would provide fundamental understanding and guidance for the development of novel adsorption materials for the adsorption of VOCs.     

Functional analysis of repositioned anilide derivatives as anticancer compounds

Off the different types cancers 40% of the population have been observed to be affected by leukemia. Contemporary therapeutics is focusing on generation of new synthetic analogues that can exert maximum positive physiological effect with minimum dosage and negligible deleterious side effects. New generation pharmacists are focusing on such promising effects of Imatinib (a potential anti-cancer drug molecule), Dasatinib, Pelitinib and Nilotinib. The present research study focuses on novel synthesized anilides derivative against BCR-ABL kinase as potential anti-leukemic agent. Validation of the compounds by molecular docking with specific BCR-ABL kinase confirmed their activity. Toxicity prediction of these compounds helped to identify sustainability as therapeutic molecules. The IC₅₀ values were calculated (211 ug, 175 ug, 272ug for compounds A, B, C resp.) and the mode of cell death was gauged by DNA laddering assay. The cells were observed to be induced for programmed cell death. By validating and in-vivo testing of three synthesized compounds, the compound B was observed to be more stable thermodynamically with a potentially vital active site and appears to be a promising anti-leukemic factor. The present research thus lays a preliminary platform in world of pharmaceutics, where these new analogues appear to be efficient, target specific and less toxic molecules.     

Treatment activity of a mixed-ligand coordination polymer on gastric carcinoma

Reaction of 4,4′,4″-nitrilotribenzoic acid (H₃L), a C₃-symmetric ligand, with the divalent Co(II) salt Co(NO₃)₂·6H₂O in the present of the N-donor ligand 1,2-di(4-pyridyl)ethylene (DPE) affords a new mixed-ligand coordination polymer with the chemical formula of [Co₃(TNB)(DPE)₂]·2H₂O·DMF (1). In this study, CCK-8 assay was used to determine the effect of novel compound on proliferation of gastric cancer cells. The VEGF signaling pathway in gastric cancer cells was determined through employing real-time PCR after treatment of the above complex. Further, molecular docking simulation confirmed that the biological activity was coming from the carboxyl groups through the hydrogen bonding interactions with the receptor protein, the pyridine group only bonded with the Co ion for the formation of the Co complex.