A dehydrogen is an ‘under-wrapped’ hydrogen bond in a protein that is purported to be a hot spot for binding due to the favorable replacement of water with hydrocarbon upon binding of another protein. A model at the level of dielectric constants is used to test the validity of the claim that moving a hydrogen bond from high dielectric (i.e. a dehydron) to low dielectric (i.e. after binding of another protein) is actually a thermodynamically favorable process. In simulation, several proteins have been shown to undergo a dewetting transition when fixed components are separated a small distance. A new atomic-level hydrophobicity scale is combined with topographical information to characterize protein interfaces. The relationship between hydrophobicity and topography for protein surfaces known to be involved in binding is examined. This framework is then applied to identify surface characteristics likely to have an affect on the occurrence of a dewetting transition. Cadmium selenide (CdSe) nanoparticles form nanospheres or nanorods when grown in solutions of varying concentrations of the surfactants hexylphosphonic acid (HPA) and trioctylphosphine oxide (TOPO). Relative binding free energies are calculated for HPA and TOPO to the solvent-accessible faces of CdSe crystals. Binding free energies calculated with a Molecular Mechanics-Generalized Born model are used to identify a set of low free energy structures for which the solvation free energy is refined with the solution to the Poisson equation. These relative binding free energies provide information about the relative growth rates of these crystal faces in the presence of surfactants. Relative growth rates are then used to help understand why nanoparticles form certain shapes in the presence of specific surfactants. / text

The optical and chemical properties of the materials used in catalytic and sensing applications directly determine the characteristics of the resultant catalyst or sensor. It is well known that a catalyst needs to have high activity, selectivity, and stability to be viable in an industrial setting. The hydrogenation activity of palladium catalysts is known to be excellent, but the industrial applications are limited by the cost of obtaining catalyst in amounts large enough to make their use economical. As a result, alloying palladium with a cheaper, more widely available metal while maintaining the high catalytic activity seen in monometallic catalysts is, therefore, an attractive option. Similarly, the optical properties of nanoscale materials used for sensing must be attuned to their application. By adjusting the shape and composition of nanoparticles used in such applications, very fine changes can be made to the frequency of light that they absorb most efficiently. The design, synthesis, and characterization of (i) size controlled monometallic palladium nanoparticles for catalytic applications, (ii) nickel-palladium bimetallic nanoparticles and (iii) silver-palladium nanoparticles with applications in drug detection and biosensing through surface plasmon resonance, respectively, will be discussed. The composition, size, and shape of the nanoparticles formed were controlled through the use of wet chemistry techniques. After synthesis, the nanoparticles were analyzed using physical and chemical characterization techniques such as X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), and Scanning Transmission Electron Microscopy- Energy-Dispersive Spectrometry (STEM-EDX). The Pd and Ni-Pd nanoparticles were then supported on silica for catalytic testing using mass spectrometry. The optical properties of the Ag-Pd nanoparticles in suspension were further investigated using ultraviolet-visible spectrometry (UV-Vis). Monometallic palladium particles have been synthesized and characterized to establish the effects of nanoparticle size on catalytic activity in methanol decomposition. The physicochemical properties of the synthesized palladium-nickel nanoparticles will be discussed, as a function of the synthesis parameters. The optical characteristics of the Ag and Pd nanoparticles will be determined, with a view toward tuning the response of the nanoparticles for incorporation in sensors. Analysis of the monometallic palladium particles revealed a dependence of syngas production on nanoparticle size. The peak and steady state TOFs increased roughly linearly with the average nanoparticle diameter. The amount of coke deposited on the particle surfaces was found to be independent on the size of the nanoparticles. Shape control of the nickel-palladium nanoparticles with a high selectivity for (100) and (110) facets (≤ 80%) has been demonstrated. The resulting alloy nanoparticles were found to have homogeneous composition throughout their volume and maintain FCC crystal structure. Substitution of Ni atoms in the Pd lattice at a 1:3 molar ratio was found to induce lattice strains of ~1%. The Ag nanocubes synthesized exhibited behavior very similar to literature values, when taken on their own, exhibiting a pair of distinct absorbance peaks at 350 nm and 455 nm. In physical mixtures with the Pd nanoparticles synthesized, their behavior showed that the peak position of the Ag nanocubes' absorbance in UV-Vis could be tuned based on the relative proportions of the Ag and Pd nanoparticles present in the suspension analysed. The Ag polyhedra synthesized for comparison showed a broad doublet peak throughout the majority of the visible range before testing as a component in a physical mixture with the Pd nanoparticles. The addition of Pd nanoparticles to form a physical mixture resulted in some damping of the doublet peak observed as well as a corresponding shift in the baseline absorbance proportional to the amount of Pd added to the mixture.