BioPPSy: An Open-Source Platform for QSAR/QSPR Analysis

The reliability of quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) models is often difficult to assess due to the problems of accessing the tools and data used to build the models. We present here BioPPSy, which aims to fill this gap by providing an easy-to-use open-source software platform. We demonstrate the program capabilities by calculating three key properties used in drug discovery, aqueous solubility, Caco-2 cell permeability and blood-brain barrier permeability. A comparison is made with a number of previously reported methods, taken from the literature, for each property. </p

Mapping the Three-Dimensional Nanostructure of the Ionic Liquid–Solid Interface Using Atomic Force Microscopy and Molecular Dynamics Simulations

Ionic liquids (ILs) are a widely investigated class of solvents for scientific and industrial applications due to their desirable and “tunable” properties. The IL–solid interface is a complex entity, and despite intensive investigation, its true nature remains elusive. The understanding of the IL–solid interface has evolved over the last decade from a simple 1D double layer, to a 2D ordered interface, and finally a liquid-specific, complex 3D ordered liquid interface. However, most studies depend solely on one technique, which often only examine one aspect of the interfacial nanostructure. Here, a holistic study of the protic IL–solid interface is presented, which provides a more detailed picture of IL interfacial solvation. The 3D nanostructure of the ethylammonium nitrate (EAN)–mica interface is investigated using a combination of 1D, 2D, and 3D amplitude modulated-atomic force microscopy and molecular dynamics simulations. Importantly, it is found that the EAN–mica interface is more complex than previously reported, possessing surface-adsorbed, near-surface, surface-normal, and lateral heterogeneity, which propagates at relatively large distances from the solid substrate. The work presented in this study meaningfully enhances the understanding of the IL–solid interface

Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution

Nanomaterials have the potential to transform biological and biomedical research, with applications ranging from drug delivery and diagnostics to targeted interference of specific biological processes. Most existing research is aimed at developing nanomaterials for specific tasks such as enhanced biocellular internalization. However, fundamental aspects of the interactions between nanomaterials and biological systems, in particular, membranes, remain poorly understood. In this study, we provide detailed insights into the molecular mechanisms governing the interaction and evolution of one of the most common synthetic nanomaterials in contact with model phospholipid membranes. Using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we elucidate the precise mechanisms by which citrate-capped 5 nm gold nanoparticles (AuNPs) interact with supported lipid bilayers (SLBs) of pure fluid (DOPC) and pure gel-phase (DPPC) phospholipids. On fluid-phase DOPC membranes, the AuNPs adsorb and are progressively internalized as the citrate capping of the NPs is displaced by the surrounding lipids. AuNPs also interact with gel-phase DPPC membranes where they partially embed into the outer leaflet, locally disturbing the lipid organization. In both systems, the AuNPs cause holistic perturbations throughout the bilayers. AFM shows that the lateral diffusion of the particles is several orders of magnitude smaller than that of the lipid molecules, which creates some temporary scarring of the membrane surface. Our results reveal how functionalized AuNPs interact with differing biological membranes with mechanisms that could also have implications for cooperative membrane effects with other molecules

Low-temperature liquid platinum catalyst

Insights into metal–matrix interactions in atomically dispersed catalytic systems are necessary to exploit the true catalytic activity of isolated metal atoms. Distinct from catalytic atoms spatially separated but immobile in a solid matrix, here we demonstrate that a trace amount of platinum naturally dissolved in liquid gallium can drive a range of catalytic reactions with enhanced kinetics at low temperature (318 to 343 K). Molecular simulations provide evidence that the platinum atoms remain in a liquid state in the gallium matrix without atomic segregation and activate the surrounding gallium atoms for catalysis. When used for electrochemical methanol oxidation, the surface platinum atoms in the gallium–platinum system exhibit an activity of ~2.8×107mAmgPt−1, three orders of magnitude higher than existing solid platinum catalysts. Such a liquid catalyst system, with a dynamic interface, sets a foundation for future exploration of high-throughput catalysis. [Figure not available: see fulltext.