Ions and solvation at biointerfaces

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid

We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

Electrode potential dependent desolvation and resolvation of germanium(100) in contact with aqueous perchlorate electrolytes

The electrode potential dependence of the hydration layer on an n-Ge(100) surface was studied by a combination of in situ and operando electrochemical attenuated total reflection infrared (ATR-IR) spectroscopy and real space density functional theory (DFT) calculations. Constant-potential DFT calculations were coupled to a modified generalised Poisson-Boltzmann ion distribution model and applied within an ab initio molecular dynamics (AIMD) scheme. As a result, potential-dependent vibrational spectra of surface species and surface water were obtained, both experimentally and by simulations. The experimental spectra show increasing absorbance from the Ge-H stretching modes at negative potentials, which is associated with an increased negative difference absorbance of water-related OH modes. When the termination transition of germanium from OH to H termination occurs, the surface switches from hydrophilic to hydrophobic. This transition is fully reversible. During the switching, the interface water molecules are displaced from the surface forming a "hydrophobic gap". The gap thickness was experimentally estimated by a continuum electrodynamic model to be ≈2 Å. The calculations showed a shift in the centre of mass of the interface water by ≈0.9 Å due to the surface transformation. The resulting IR spectra of the interfacial water in contact with the hydrophobic Ge-H show an increased absorbance of free OH groups, and a decreased absorbance of strongly hydrogen bound water. Consequently, the surface transformation to a Ge-H terminated surface leads to a surface which is weakening the H-bond network of the interfacial water in contact.