Miniaturized, spatially addressable microchips of peptides and peptidomimetics are powerful tools for high-throughput biomedical and pharmaceutical research and the advancement of proteomics. Here we report an efficient and flexible method for the parallel synthesis of peptides on individually addressable microchips, using digital photolithography and photogenerated acid in the deprotection step. We demonstrate that we are able to synthesize thousands of peptides in a 1 cm(2) area on a microchip using 20 natural amino acids as well as synthetic amino acid analogs, with high stepwise yields and short reaction-cycle times. Epitope screening experiments using a p53 antibody (PAb240) produced clearly defined binding patterns. The peptidomimetic sequences on the microchip show specific antibody binding and provide insights into the molecular details responsible for specificity of epitope binding. Our approach requires just a conventional synthesizer and a computer-controllable optical module, thereby allowing potential development of peptide microchips for various pharmaceutical and proteomic applications in routine research laboratories.

Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little experimental data exist about molecular scale behavior of heavy ions and their complexes at interfaces, especially under technologically significant conditions. It has recently been shown that PtCl6 2complexes adsorb at positively charged interfaces in a two-step process that cannot fit into well-known empirical trends, such as Hofmeister series. Here, a combined vibrational sum frequency generation and molecular dynamics study reveals that a unique interfacial water structure is connected to this peculiar adsorption behavior. A novel sub-ensemble analysis of MD simulation results show that after adsorption, PtCl6 2complexes partially retain their first and second hydration spheres, and it is possible to identify three different types of water molecules around them based on their orientational structures and hydrogen bonding strengths. These results have important implications for relating interfacial water structure and hydration enthalpy to the general understanding of specific ion effects. This in turn influences interpretation of heavy metal ion distribution across and reactivity within, liquid interfaces.

The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.

Using a unique combination of slab-layering analyses and identification of truly interfacial molecules, this work examines water/vapor and water/n-hexane interfaces, specifically the structural and dynamic perturbations of the interfacial water molecules at different locations within the surface capillary waves. From both the structural and dynamic properties analyzed, it is found that these interfacial water molecules dominate the perturbations within the interfacial region, which can extend deep into the water phase relative to the Gibbs dividing surface. Of more importance is the demonstration of structural and dynamic heterogeneity of the interfacial water molecules at the capillary wave front, as indicated by the dipole orientation and the structural and dynamic behavior of hydrogen bonds and their networks.

The properties of confined water are relevant to many chemical, geological, and biological phenomena, where they underpin essential changes to molecular scale reactivity–perturbing both the energetic and configurational landscape. Though much prior literature has focused on hydrophilic confinement, the hydrophobic confinement of water is less well understood. Here, we use molecular dynamics simulations to investigate the structures and dynamics of water in hydrophobic all-silica zeolites that have sequentially smaller pore dimensions. Of special interest is the role that pure geometric restriction imparts, relative to the rugged potential energy landscape for water interacting with the atomistic pore surface. These two effects were studied via the hydrogen bond dynamics, specifically the rates and mechanisms of hydrogen bond breakage and formation. Measuring the dynamic features as a function of scaling the water:zeolite interaction energy revealed that geometric restriction is responsible for 67%–86% of the total perturbations to water upon confinement in MFI (depending on the property) while the water:surface interactions are responsible for 14%–33%. The relative magnitude of the interaction of water with the pore surface was confirmed by second order Møller–Plesset perturbation theory. Thus, in a highly confined environment, the weak water-surface interaction should not be neglectedeven in hydrophobic adsorbents to which zeolites and other materials like carbon nanotubes belong.