Transport properties of acetone aqueous solutions: molecular dynamics simulation and NMR studies

Two quantities η_rel and are applied to study the nonideal acetone–water association mixture. An all-atom acetone model and a TIP5P water model have been adopted for molecular dynamics simulation. We study the transport properties of the system comparing the 's of strong hydrogen bond and weak contact based on transport properties, MD simulations together with NMR experimental data and find good agreement of concentration dependence, which exhibits the cooperation effect.     

Molecular dynamics simulations on the structures and properties of ε-CL-20-based PBXs ——Primary theoretical studies on HEDM formulation design

Five polymer bonded explosives (PBXs) with the base explosive ε-CL-20 (hexanitrohexaazaisowurtzi- tane), the most important high energy density compound (HEDC), and five polymer binders (Estane 5703, GAP, HTPB, PEG, and F2314) were constructed. Molecular dynamics (MD) method was employed to investigate their binding energies (Ebind), compatibility, safety, mechanical properties, and energetic properties. The information and rules were reported for choosing better binders and guiding formula- tion design of high energy density material (HEDM). According to the calculated binding energies, the ordering of compatibility and stability of the five PBXs was predicted as ε-CL-20/PEG > ε-CL-20/ Estane5703 ≈ε-CL-20/GAP > ε-CL-20/HTPB > ε-CL-20/F2314. By pair correlation function g(r) analyses, hydrogen bonds and vdw are found to be the main interactions between the two components. The elasticity and isotropy of PBXs based ε-CL-20 can be obviously improved more than pure ε-CL-20 crystal. It is not by changing the molecular structures of ε-CL-20 for each binder to affect the sensitivity. The safety and energetic properties of these PBXs are mainly influenced by the thermal capability (C°p) and density (ρ) of binders, respectively.     

The properties and structures of the mono- and the di- vacancy in Cu crystal

The structures and energies of formation and migration of the mono- and di-vacancy in Cu crystal have been described and calculated with modified analytical embedded atom method (MAEAM). The lattice relaxation is considered with molecular dynamics (MD) method at T=0 K. The results show the FN di-vacancy is the most stable and likely occurs in practice from the energy minimization. Compared with the mono-vacancy, the formation energy of the FN di-vacancy is higher than that of a mono-vacancy, but lower than that of two isolated mono-vacancy. The preferred migration mechanism of the FN di-vacancy is multi-jump of either vacancy (rotating the di-vacancy). The calculated migration energy of the FN di-vacancy is lower than that of a mono-vacancy, so the FN di-vacancy is easier to migrate. All of the calculated results are in good agreement with the experimental values.     

Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

功能性超薄有序分子沉积膜的制备及其结构研究

1991年G.Decher等首次探讨了阴阳离子与聚电解质交替沉积制备有机超薄膜的方法。我们在完善成膜技术和发展成膜基质的基础上,详细研究了其成膜过程与膜的结构,并定义这种新的自组装超薄有序膜为分子沉积膜——MD膜。MD膜是利用阴阳离子的静电吸附反应特性,通过相反离子体系的交替分子沉积制备的层状有序自组装多层超薄膜。需要指出的是,分子沉积既是有机超薄膜的制备技术,本身又是一种自组装超薄有序膜。MD膜制备工艺简单,热稳定性和长期稳定性好,不受基体形状与面积限制。     

Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.     

Tight‐binding molecular dynamics simulation of Si?H bond dissociation in silicon clusters

New model of Si? H bond dissociation is proposed and tested in the cluster Si₁₀H₁₆ by the simulation approach that combines classic molecular dynamics method and the self‐consistent tight‐binding electronic and total energy calculation one. It is shown that the monohydride Si? H bond is unstable with respect to silicon dangling bond and bend‐bridge Si? H? Si bond formation when this cluster traps the single positive charge and that hydrogen migrates through a path involving rather rotation around the Si? Si bond than the center of this bond (the bond‐centered position). These results can be useful for understanding hydrogen‐related phenomena at surfaces, interfaces, and internal voids of various hydrogenated silicon systems: electronic devices, silicon solar cells, and nanocrystalline and porous silicon. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 351–359, 2003     

Effect of concentration on surfactant micelle shapes —A molecular dynamics study

Many aspects of the behavior of surfactants have not been well understood due to the coupling of many different mechanisms. Computer simulation is, therefore, attractive in the sense that it can explore the effect of different mechanisms separately. In this paper, the shapes, structures and sizes of sodium dodecylbenzenesulfonate (SDBS) micelles under different concentrations in an oil/water mixture were studied via molecular dynamics (MD) simulations using a simplified atomistic model which basically maintains the hydrophile and lipophile properties of the surfactant molecules. Above the critical micellar concentration (cmc), surfactant molecules aggregate spontaneously to form a wide variety of assemblies, from spherical to rodlike, wormlike and bilayer micelles. Changes in their ratios of the principle moments of inertia (g₁/g₃, g₂/g₃) indicated the transition of micelle shapes at different concentrations. The aggregation number of micelle is found to have a power-law dependence on surfactant concentration.     

Hydration of copper(II) amino acids complexes

Hydration of the copper(II) bis‐complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis–trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained. Analysis of the MD trajectories reveals the competition for a copper(II) axial position between water molecules or water molecules and the functional chain groups of the ligands and confirms the suggestion on the pentacoordination of copper(II) in such complexes. MD simulations show that only one axial position of Cu(II) is basically occupied at each time step while in average the coordination number more than 5 is observed. © 2017 Wiley Periodicals, Inc.     

Computation of the hindrance factor for the diffusion for nanoconfined ions: molecular dynamics simulations versus continuum-based models

We report the self-diffusion coefficients and hindrance factor for the diffusion of ions into cylindrical hydrophilic silica nanopores (hydrated silica) determined from molecular dynamics (MD) simulations. We make a comparison with the hindered diffusion coefficients used in continuum-based models of nanofiltration (NF). Hindrance factors for diffusion estimated from the macroscopic hydrodynamic theory were found to be in fair quantitative agreement with MD simulations for a protonated pore, but they strongly overestimate diffusion inside a deprotonated pore.