It is applicable with frequently used water models such as TIP3P, TIP4P, TIP4P-Ew, and OPC. For ease of use, a LEaP-based workflow was created, which allows attaching (multiple) dye/linker combinations to a protein prior to further system preparation steps. Following the parameter development described by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] and the adaptation steps described here, AMBER-DYES in AMBER can be extended by additional linkers and fluorescent molecules.We report experimental results from electron diffraction of CS2 nanoclusters embedded in superfluid helium droplets. From detailed measurements of the sizes of doped droplets, we can model the doping statistics under different experimental conditions, thereby obtaining the range of cluster sizes of CS2. Using a least squares fitting procedure, we can then determine the structures and contributions of dimers, trimers, and tetramers embedded in small droplets. While dimers prefer a stable gas phase structure, trimers and tetramers seem to forgo the highly symmetric gas phase structures and prefer compact cuts from the crystalline structure of CS2. In larger droplets containing more than 12 CS2 monomers, the diffraction profile is consistent with a three-dimensional nanostructure of bulk CS2. This work demonstrates the feasibility of electron diffraction for in situ monitoring of nanocluster formation in superfluid helium droplets.Clusters of atoms in dense gold vapor are studied via atomistic simulation with the classical molecular dynamics method. For this purpose, we develop a new embedded atom model potential applicable to the lightest gold clusters and to the bulk gold. Simulation provides the equilibrium vapor phases at several subcritical temperatures, in which the clusters comprising up to 26 atoms are detected and analyzed. The cluster size distributions are found to match both the two-parameter model and the classical nucleation theory with the Tolman correction. For the gold liquid-vapor interface, the ratio of the Tolman length to the radius of a molecular cell in the liquid amounts to ∼0.16, almost exactly the value at which both models are identical. It is demonstrated that the lightest clusters have the chain-like structure, which is close to the freely jointed chain. Thus, the smallest clusters can be treated as the quasi-fractals with the fractal dimensionality close to two. Our analysis indicates that the cluster structural transition from the solid-like to chain-like geometry occurs in a wide temperature range around 2500 K.In plasmonic metals, surface plasmon resonance decays and generates hot electrons and hot holes through non-radiative Landau damping. These hot carriers are highly energetic, which can be modulated by the plasmonic material, size, shape, and surrounding dielectric medium. A plasmonic metal nanostructure, which can absorb incident light in an extended spectral range and transfer the absorbed light energy to adjacent molecules or semiconductors, functions as a "plasmonic photosensitizer." This article deals with the generation, emission, transfer, and energetics of plasmonic hot carriers. It also describes the mechanisms of hot electron transfer from the plasmonic metal to the surface adsorbates or to the adjacent semiconductors. In addition, this article highlights the applications of plasmonic hot electrons in photodetectors, photocatalysts, photoelectrochemical cells, photovoltaics, biosensors, and chemical sensors. It discusses the applications and the design principles of plasmonic materials and devices.An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical molecular dynamics simulations. The rates of these molecular interactions are understood through the wetting rates of water nano-droplets on a bare copper (111) surface. Implementing the Langevin thermostat, the influence of simulation time step, the number of atoms in the system, the frequency at which charge equilibration is performed, and the temperature relaxation rate are all examined. The results indicate that time steps of 0.4 fs are possible when using longer relaxation times for the system temperature, which is almost double the typical time step used for reactive potentials. The use of the charge equilibration allows for a fewer atomic layers to be used in the Cu slab. In addition, charge equilibrium schemes do not need to be performed every time step to ensure accurate charge transfer. Interestingly, the rate of wetting for the nanodroplets is dominantly dependent on the temperature relaxation time, which is predicted to significantly change the viscosity of the water droplets. This work provides a pathway for optimizing simulations using the COMB3 reactive interatomic potential.In this article, we propose a generalized model for nonequilibrium vibrational energy distribution functions. The model can be used, in place of equilibrium (Boltzmann) distribution functions, when deriving reaction rate constants for high-temperature nonequilibrium flows. The distribution model is derived based on the recent ab initio calculations, carried out using potential energy surfaces developed using accurate computational quantum chemistry techniques for the purpose of studying air chemistry at high temperatures. Immediately behind a strong shock wave, the vibrational energy distribution is non-Boltzmann. Specifically, as the gas internal energy rapidly excites to a high temperature, overpopulation of the high-energy tail (relative to a corresponding Boltzmann distribution) is observed in ab initio simulations. As the gas excites further and begins to dissociate, a depletion of the high-energy tail is observed, during a time-invariant quasi-steady state. Since the probability of dissociation is exponentially related to the vibrational energy of the dissociating molecule, the overall dissociation rate is sensitive to the populations of these high vibrational energy states. The non-Boltzmann effects captured by the new model either enhance or reduce the dissociation rate relative to that obtained assuming a Boltzmann distribution.  https://www.selleckchem.com/products/rk-701.html  This article proposes a simple model that is demonstrated to reproduce these non-Boltzmann effects quantitatively when compared to ab initio simulations.