Through DFT calculations, a systematic description of O2 adsorption and dissociation processes over Rh(100) and Rh(111) surfaces has been provided. The dominance of parallel orientation in molecularly adsorbed states and during the impinging processes has been identified, along with the explicit adsorption configurations and preferred impinging trajectories on both surfaces. The dissociation of O2 is found to occur either by precursor-mediated adsorption or by direct dissociation. O2 in its initial precursor state dissociates facilely on Rh(100), but this is a little harder on Rh(111) by going through a two-step process. The latter can be described as a preliminary rotation and subsequent dissociation, with the final locations of two O atoms disturbed easily by coadsorbed O atoms surrounding the dissociating O2 molecule due to the existence of a relatively flat potential energy surface stage along the way. The present work may provide the basis for kinetic modeling to investigate the catalytic properties on a realistic scale.

•Ligand displacement assay based on DNAzyme-catalyzed CL detection was developed for screening anticancer drug via stabilizing promoter DNA.•Alkaloid/G4 DNA interaction of end-stacking mode between alkaloid and Pu22 DNA demonstrated the feasibility of the proposed mechanism.•Microfluidic-based CL approach showed the advantage of automatic, high throughput with just trace amount of sample and reagent consumption.Some natural heterocyclic alkaloids containing planar group show potential to complex with specific promoter region of protooncogene for stabilizing the G-quadruplex (G4) structure which nowadays promises to be a target in anticancer drug design. However, in view of the polymorphic characteristics and structural complexity of heterocyclic alkaloids, it is desirable to develop high-throughput and low-consumption approach for anticancer drug screening. In this paper, an intensive study on alkaloid ligand/G4 DNA interaction has been conducted, demonstrating that the end-stacking interaction is the favorable binding mode between the oncogene-related Pu22 G4 DNA and the heterocyclic alkaloid ligand. Based on structural feasibility and energy minimization, a ligand displacement assay for screening alkaloid ligand in stabilizing the oncogene target G4 has been developed, which also helps to facilitate the assessment of drug specificity. Coupled with microfluidic-based DNAzyme-catalytic chemiluminescence detection, the approach showed the advantages of high sensitivity, high throughput with low sample and reagent consumptions.

Graphene is an ideal membrane for selective separation because of its unique properties and single-layer structure. Considerable efforts have been made to alter the permeability of graphene. In this study, we investigate the pathways for an oxygen atom to pass through graphene sheets. We also identify the effect of the ripple's curvature in graphene sheets on the energy barrier of permeation through density functional theory calculations. Results show that oxygen atoms can easily pass through the concave side of graphene ripples with a large curvature. The analysis of transition states reveals that the space where an oxygen atom passes through keeps an almost identical structure with similar bond lengths regardless of the curvature. We find that the Cu(111) substrate may draw out the C–C bond lengths of graphene at the Cu(111) surface because of the strong interaction between the graphene edge and copper atoms. Consequently, the energy barrier of the permeation of oxygen atoms through graphene is reduced. These results suggest that the rippling of graphene significantly affects its permeation.

Understanding the influence of aspect ratio on water immersion into silica nanoholes is of significant importance to the etching process of semiconductor fabrication and other water immersion-related physical and biological processes. In this work, the processes of water immersion into silica nanoholes with different height/width aspect ratios (ϕ = 0.87, 1.92, 2.97, 4.01, 5.06) and different numbers of water molecules (N = 9986, 19972, 29958, 39944) were studied by molecular dynamics simulations. A comprehensive analysis has been conducted about the detailed process of water immersion and the influence of aspect ratios on water immersion rates. Five distinguishable stages were identified for the immersion process with all studied models. The results reveal that water can easily immerse into the silica nanoholes with larger ϕ and smaller N. The calculation also suggests that aspect ratios have a greater effect on water immersion rates for larger N numbers. The mechanism of the water immersion process is discussed in this work. We also propose a mathematical model to correlate the complete water immersion process for different aspect ratios.

Activation of the Ti4 cluster on defective graphene for water adsorption and dissociation was investigated via density functional theory. Both the vacancy and the Ti cluster can promote the water dissociation reaction. The vacancy can efficiently enhance the adsorption of Ti atoms to stabilize the cluster. However, compared to the role of the vacancy, the cluster plays a more important role in activating water dissociation. A single water molecule and a second one can almost freely dissociate with (or without) a low barrier on the Ti4 cluster, the barriers are substantially lower than that on a single Ti atom. The Ti4 cluster decorated graphene is a promising candidate for activation of the dissociation of water molecules.

Protein-based nanoparticles represent a promising approach to carry polypeptide and protein drugs. Using both theory and experimentation, an interferon α-1b (IFN) delivery system carried by bovine serum albumin (BSA) nanoparticles was designed. Theoretical results indicate the most probable binding site and interaction mechanism for IFN on BSA. IFN has a higher binding affinity with BSA compared with small chemical drugs. The drug loading is about 8 mg/g, significantly higher than those reported in other literature. The release profiles differ between the nanoparticles prepared by the incorporation method and the adsorption method. The adsorption of IFN on BSA nanoparticles is monolayer adsorption. The fact that IFN was carried successfully by BSA nanoparticles establishes a solid basis for expanding the drug loading field of BSA nanoparticles to proteins and polypeptides.

Using calculations from first principles and harmonic transition state theory, we investigated the permeability of a single graphene sheet to protons and hydrogen atoms. Our results show that while protons can readily pass through a graphene sheet with a low tunneling barrier, for hydrogen atoms the barriers are substantially higher. At the same time, the presence of defects in the membrane can significantly reduce the penetration barrier in a region that extends beyond the defect site itself.

Biomolecular-carbon nanotube (CNT) complexes are of great importance in biological and biomedical devices, and recently spontaneous encapsulation of biomolecules into CNTs has attracted great interest. In this work, we explored the diameter selectivity of the protein encapsulation in CNTs via molecular dynamics simulations, and the free energy changes of the systems were calculated for mechanism exploration. It is proved that there is an optimal tube size which provides the most effective encapsulation for a given protein molecule, and the encapsulations in the overlarge and overcrowded tubes are hindered by different factors based on the analysis of system energy contribution. In addition, the significance of the solvents for the system is also of concern.

Activation of the Ti4 cluster on defective graphene for water adsorption and dissociation was investigated via density functional theory. Both the vacancy and the Ti cluster can promote the water dissociation reaction. The vacancy can efficiently enhance the adsorption of Ti atoms to stabilize the cluster. However, compared to the role of the vacancy, the cluster plays a more important role in activating water dissociation. A single water molecule and a second one can almost freely dissociate with (or without) a low barrier on the Ti4 cluster, the barriers are substantially lower than that on a single Ti atom. The Ti4 cluster decorated graphene is a promising candidate for activation of the dissociation of water molecules.

Using calculations from first principles and harmonic transition state theory, we investigated the permeability of a single graphene sheet to protons and hydrogen atoms. Our results show that while protons can readily pass through a graphene sheet with a low tunneling barrier, for hydrogen atoms the barriers are substantially higher. At the same time, the presence of defects in the membrane can significantly reduce the penetration barrier in a region that extends beyond the defect site itself.