The New Design Nanocapsules from Interactions between Atoms and Carbon Nanotubes with End Caps

A massive interest has arisen in nanocapsule, and it is used in different fields. Carbon nanotubes and fullerene are the most commonly used nanomaterials due to their remarkable properties, such as optical, mechanical, electrical, and thermal properties. Especially in biomedical science, nanocapsules are highly recommended to be applied as carriers for drugs. From the Magic bullet theory, it is expected that the nanocapsules can deliver drugs to the target cells, which can reduce the side effects on the nontargeted cells. In this research, we design a new nanocapsule consisting of a finite-length single-wall carbon nanotube with two end caps which are hemispheres of C60 fullerene. By using elementary mechanics and mathematical modelling, we can determine the exact formulae and their numerical solutions of nonbonded interactions between the nanocapsules and the atoms Li, Na, K, Rb, Cs, Ca, Ni, Zn, and Pb which are assumed to be located in the middle of the nanocapsules. Therefore, the optimal lengths of the carbon nanotubes for each case of atoms are determined. This research is a guideline for studying the interaction between the drug and the nanocapsule in the drug delivery system.

Targeting SARS-CoV-2 nonstructural protein 15 endoribonuclease: an in silico perspective

The newly emerged human coronavirus, SARS-CoV-2, had begun to spread last year and sparked worldwide. In this study, molecular docking is utilized to test some previously approved drugs against the SARS-CoV-2 nonstructural protein 15 (Nsp15). We screened 23 drugs, from which three (saquinavir, valrubicin and aprepitant) show a paramount predicted binding affinity (-9.1, -9.6 and -9.2 kcal/mol, respectively) against SARS-CoV-2 Nsp15. Moreover, saquinavir and aprepitant make nonbonded interactions with Leu201 in the active site cavity of Nsp15, while the drug valrubicin interacts with Arg199 and Leu201. This binding pattern may be effective against the targeted protein, leading to Nsp15 blockage and virus abolition. Additionally, the pharmacological properties of the screened drugs are known since they have been approved against different viruses.

Potential of Mean Force between Bare or Grafted Silica/Polystyrene Surfaces from Self-Consistent Field Theory

We investigate single and opposing silica plates, either bare of grafted, in contact with vacuum or melt phases, using self-consistent field theory. Solid–polymer and solid–solid nonbonded interactions are described by means of a Hamaker potential, in conjunction with a ramp potential. The cohesive nonbonded interactions are described by the Sanchez-Lacombe or the Helfand free energy densities. We first build our thermodynamic reference by examining single surfaces, either bare or grafted, under various wetting conditions in terms of the corresponding contact angles, the macroscopic wetting functions (i.e., the work of cohesion, adhesion, spreading and immersion), the interfacial free energies and brush thickness. Subsequently, we derive the potential of mean force (PMF) of two approaching bare plates with melt between them, each time varying the wetting conditions. We then determine the PMF between two grafted silica plates separated by a molten polystyrene film. Allowing the grafting density and the molecular weight of grafted chains to vary between the two plates, we test how asymmetries existing in a real system could affect steric stabilization induced by the grafted chains. Additionally, we derive the PMF between two grafted surfaces in vacuum and determine how the equilibrium distance between the two grafted plates is influenced by their grafting density and the molecular weight of grafted chains. Finally, we provide design rules for the steric stabilization of opposing grafted surfaces (or fine nanoparticles) by taking account of the grafting density, the chain length of the grafted and matrix chains, and the asymmetry among the opposing surfaces.

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nosé-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.