Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis₂ complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis₂ is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.     

Dynamic stability of externally pressurized elastic rings subjected to high rates of loading

Of interest here is the influence of loading rate on the stability of structures where inertia is taken into account, with particular attention to the comparison between static and dynamic buckling. This work shows the importance of studying stability via perturbations of the initial conditions, since a finite velocity governs the propagation of disturbances. The method of modal analysis that determines the fastest growing wavelength, currently used in the literature to analyze dynamic stability problems, is meaningful only for cases where the velocity of the perfect structure is significantly lower than the associated wave propagation speeds.     

电场下离子型聚合物复合囊泡结构变化的分子动力学模拟

利用粗粒化分子动力学模拟研究了电场作用下离子型聚合物复合囊泡形变与破裂的过程.定量分析了囊泡破裂过程中的结构变化,包括囊泡的形变程度、破裂速度、组分分布以及破裂后的结构.研究表明,电场强度较弱时,囊泡表面所吸附的聚电解质首先脱落,囊泡由球形结构转变为椭球结构.随着电场强度增大,离聚物的离子侧基发生重新排布,囊泡表面电荷的有序结构被破坏,导致囊泡的结构无法维持而破裂,囊泡塌缩,分裂形成离聚物团簇,并进一步破裂为小尺寸的离聚物聚集体,均匀分散于溶液中.本文利用分子动力学模拟明确了电场中离子型高分子复合囊泡破裂过程的分子机理,为药物释放技术的优化及发展提供了理论支持.     

Metadynamics simulations of R–NHC reductive elimination in intermediate palladium complexes of cross-coupling and Mizoroki–Heck reactions

Exploring the free energy surface of the R–NHC coupling reaction in the key intermediates of the Mizoroki–Heck and cross-coupling catalytic cycles has been conducted by the methods of biased and unbiased molecular dynamics. Molecular dynamics simulations were carried out both in vacuum and in a polar solvent, with the following main observations on the influence of the media: (1) the solvent prevents the dissociation of the solvate ligand, so the R–NHC coupling proceeds in a four-coordination complex (rather than in a three-coordination one, as in the case of a gas-phase reaction); (2) in the condensed phase, the potential barrier of the reaction is significantly higher compared to the same process in vacuum (17.7 vs. 21.8 kcal mol^-1); (3) polar solvent stabilizes the R–NHC coupling product. The reaction in a polar medium is exergonic (ΔG = −3.9 kcal mol^-1), in contrast to the in vacuum modeling, where the process is endergonic (ΔG = 0.4 kcal mol^-1).     

基于结构虚拟筛选发现蛋白质精氨酸甲基转移酶5抑制剂

蛋白质精氨酸甲基转移酶5(PRMT5)是蛋白质甲基转移酶家族(PRMTs)的重要一员,其主要生理功能是催化精氨酸单对称二甲基化。PRMT5的上调发生在不同类型的肿瘤中,并与不良预后密切相关,已被视为肿瘤治疗中的潜在靶点。近年来,已有多种PRMT5抑制剂进入临床试验,但目前尚未有药物获批上市。本研究基于Glide对接的虚拟筛选和生物活性实验,发现化合物8018-1271对PRMT5酶的抑制活性IC₅₀值为13.56±0.86μmol/L,并通过分子动力学揭示其与PRMT5蛋白结构域的相互作用模式。本研究所得化合物8018-1271可作为进一步改造的先导化合物,为新型PRMT5抑制剂的发现提供参考。     

Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods

An analysis of the crystal structure of thermolysin revealed four possible precursor clusters (hexamers) of its crystal. Using the method of molecular dynamics and plots of root mean square fluctuation, root mean square deviation and radius of gyration, the most stable hexamer, which is a precursor cluster,was determined. The importance of the established structure of the thermolysin precursor cluster for determining the mechanism of crystal formation is shown.     

初始微观结构缺陷和断裂的温度依赖及相关性

纳米线(NW)结构内的微观结构缺陷对NW的机械性能存在一定的影响。NW断裂位置的预测关系着纳米器件应用的寿命,进而引起了人们的广泛关注。在本工作中,基于统计分析,分别研究了单晶铜纳米线(Cu NW)拉伸过程中出现的断裂位置以及在应力屈服点处产生的初始微观结构缺陷(初始缺陷)的位置对温度的依赖性,进一步探究了两者之间的联系。利用分子动力学(MD)模拟了单晶Cu NW在20~300 K的温度范围内的拉伸状态,共包含6个体系,各温度体系包含300个独立的样本。基于机器学习,采用density-based spatial clustering of applications with noise (DBSCAN)算法,将hexagonal close-packed (hcp)原子划分为各个初始缺陷以进一步确定其位置。统计结果显示,当温度低于50 K时,初始缺陷的位置集中在NW的两端。随着模拟温度的上升,MD模拟结果展现了单晶Cu NW的拉伸过程中的杨氏模量、平均屈服应力、平均势能等机械性能对温度的依赖性。温度的升高进一步促使了更多初始缺陷的产生,并使得初始缺陷的位置由统计分布的两端向中间平均化。与初始缺陷相比,各温度下的断裂位置集中在两端。统计结果表明,模拟的温度范围对NW的断裂位置无明显影响,但对初始缺陷的产生具有明显影响。当温度低于100 K时,初始缺陷的位置分布与断裂位置分布呈现了一致性。由于两者具有不同的温度依赖,其差异随着温度的上升逐渐显现。对不同温度下的微观结构形变行为观察发现,断裂失效明显受到NW两端的表面效应和阻挡效应的影响。最终的断裂位置受塑性形变中后期的影响,与应力屈服区产生的初始缺陷无直接联系。     

Study on gas adsorption and desorption characteristics on water injection coal

To study the desorption mechanism of methane in coal by H₂O injection and establish the Wiser molecular structure model of bituminous coal, the Grand Canonical Monte Carlo method was used to study the desorption behavior of CH₄ in coal with different amounts of H₂O injection at molecular scale. The results showed that at 293 K, the maximum adsorption capacity of H₂O was about 16 mmol/g, and that of CH₄ was about 8 mmol/g, which was about twice that of CH₄. This indicates that H₂O has a stronger adsorption capacity than CH₄. For methane-bearing coal, when the amount of water injected is 100, the average relative concentration of CH₄ is 0.5446, and the average relative concentration of CH₄ decreases by 33.77% compared to the water content of 20. Under the same time conditions, the root mean square displacement and diffusion coefficient of CH₄ decrease with the increase of H₂O injection quantity. With the increase of H₂O injection, the motion velocity of CH₄ in vacuum layer decreased. When water was injected, methane was trapped in the coal by water. The more H₂O injected, the more methane trapped in the coal, and the less methane desorption. This research lays a theoretical foundation for further research involving coal-water interaction.     

Multidynamic Crystalline Molecular Rotors Comprising an N-Heterocyclic Carbene Binuclear Au(I) Complex Bearing Multiple Rotators

We report multidynamic molecular rotations in crystals using a concave-shape N-heterocyclic carbene (NHC) binuclear Au(I) complex rotor bearing pyrazine and tetrahydrofuran (THF) molecules as multicomponent rotators. Single-crystal X-ray diffraction (XRD) measurements revealed that two THF molecules are located near the central pyrazine encapsulated by two bulky NHC ligands. From ²H solid-state NMR analysis, it was observed that the pyrazine rotated in a 2-fold site exchange with a 180° rotational angle and a 31 kJ mol⁻¹ energy barrier, while the THF molecules showed a 23°-38° libration with a lower energy barrier (14 kJ mol⁻¹). Interestingly, the pyrazine rotation was accelerated when the THF molecules rotated in fast site exchange with a large angle of libration, suggesting that the rotators exhibit multidynamics in a correlated manner.