The structure and properties of water films in contact with metal surfaces are crucial to understand the chemical and electrochemical processes involved in energy-related technologies. The nature of thin water films on Pd, Pt, and Ru has been investigated by first-principles molecular dynamics to assess how the chemistry at the water–metal surface is responsible for the diversity in the behavior of the water layers closer to the metal. The characteristics of liquid water: the radial distribution functions, coordination, and fragment speciation appear only for unconfined water layers of a minimum of 1.4 nm thick. In addition, the water layer is denser in the region closest to the metal for Pd and Pt, where seven- and five-membered ring motifs appear. These patterns are identical to those identified by scanning tunneling microscopy for isolated water bilayers. On Ru densification at the interface is not observed, water dissociates, and protons and hydroxyl groups are locked at the surface. Therefore, the acid–base properties in the area close to the metal are not perturbed, in agreement with experiments, and the bulk water resembles an electric double layer. Confinement affects water making it closer to ice for both structural and dynamic properties, thus being responsible for the higher viscosity experimentally found at the nanoscale. All these contributions modify the solvation of reactants and products at the water–metal interface and will affect the catalytic and electrocatalytic properties of the surface.

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc = N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows β-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates β-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and small-angle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel β-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions.Postprint (published version

Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca

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Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca(2+) have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating PO3(4) from the solution.