Water dimer diffusion on Pd{111} assisted by an H-bond donor-acceptor tunneling exchange

Based on the results of density functional theory calculations, a novel mechanism for the diffusion of water dimers on metal surfaces is proposed, which relies on the ability of H bonds to rearrange through quantum tunneling. The mechanism involves quasifree rotation of the dimer and exchange of H-bond donor and acceptor molecules. At appropriate temperatures, water dimers diffuse more rapidly than water monomers, thus providing a physical explanation for the experimentally measured high diffusivity of water dimers on Pd{111} [Mitsui et al., Science 297, 1850 (2002)]

General model for water monomer adsorption on close-packed transition and noble metal surfaces

Ab initio density functional theory has been used to investigate the adsorption of H2O on several close-packed transition and noble metal surfaces. A remarkably common binding mechanism has been identified. On every surface H2O binds preferentially at an atop adsorption site with the molecular dipole plane nearly parallel to the surface. This binding mode favors interaction of the H2O 1b(1) delocalized molecular orbital with surface wave functions

Evolution of protein domain architectures

This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution