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• Molecular dynamic of phenolic organic pollutants (POPs) adsorption on UiO-66. • The adsorption behavior of POPs molecules occurred on the surface of UiO-66. • UiO-66 has highest adsorption capacity for nitrophenol due to the larger interaction of host–guest. • The interaction energy and π-π stacking are quantificationally calculated. • Van der Waals and π-π stacking dominate adsorption between POPs and UiO-66. Metal organic frameworks (MOFs) as an excellent adsorbent have been widely utilized in wastewater treatment due to high specific surface area, high porosity, adjustable structure and surface functionability. To design MOFs materials based on the application for removal of pollutant, understand the adsorption mechanism between pollutant and MOFs from the microscopic scale is necessary but rare. Herein, UiO-66 is selected as the adsorbent to investigate the adsorption mechanisms with phenolic organic pollutants (POPs) on the microscopic scale via MD simulation. Equilibrium configuration and density distribution for three different POPs (phenol, nitrophenol and bisphenol) prove the adsorption behavior occurred on the surface of UiO-66. Obviously, the difference of adsorption capacity proves UiO-66 tends to adsorb the nitrophenol compared to other two molecules and has the lower adsorption capacity for bisphenol due to larger molecule size, and in a neutral environment, it is more conducive to be adsorbed than in an alkaline environment. Mean square displacement (MSD) and radial distribution functions (RDFs) further support this conclusion, which exhibit the introduction of –NO 2 groups can enhance the interaction of host–guest. The H-bonds, π-π stacking and interaction energy between UiO-66 and POPs was quantificationally calculated, the results show Van der Waals and π-π stacking dominate adsorption between POPs and UiO-66. [ABSTRACT FROM AUTHOR]

Various order parameters have been suggested to characterize the local structure of liquid water in bulk. Characterization the local structure of water molecules in the confined systems by various order parameters is important but still unclear. In this work, a series of popular order parameters are used to analyze the local structure of water molecules in carbon nanotubes (CNTs) by molecular dynamics simulation. Based on the value of order parameters, the different structures of water molecules in CNTs and in bulk were discussed. The orientational tetrahedral order (q) and translational tetrahedral order (S k) are much better than local structure index (LSI) to describe the local structure of water in CNTs. We also demonstrated that the local structure of water molecules in the CNT(40,40) is almost the same with that in bulk. The findings could give us a guideline to investigate the water molecules in confined system. [ABSTRACT FROM AUTHOR]

The development of two-dimensional (2D) materials rise new options on the promising application of biosensors and DNA sequencing. Recently, 2D molybdenum disulfide (MoSe 2) material has been successfully fabricated and shows the unique excellent properties. An in-depth understanding of the interfacial interaction between materials and biomolecules is critical in biomedical field. Therefore, the directional selection of double-stranded DNA (ds-DNA) on the MoSe 2 surface was studied by molecular dynamics (MD) simulation in this work. The simulation results showed that the vertical adsorption of double-strand DNA (ds-DNA) on the MoSe 2 surface is favored through terminal bases. With the analysis of interaction energy, the main driving forces to absorb DNA on MoSe 2 is attributed to van der Waals force. In addition, our results indicate that the length and base sequence of ds-DNA are independent of its selection of vertically adsorbed orientation, and the ds-DNA structure is still stable after adsorption on the surface of MoSe 2. These simulation results greatly enhanced our understanding on the interaction between ds-DNA and MoSe 2 , which may be beneficial for improving the development of fast DNA sequencing technology through MoSe2 nanopore in the future. [ABSTRACT FROM AUTHOR]