Model calculations for copper clusters on Au(111) surfaces

Using the semi-empirical embedded-atom method, the structure of small copper clusters on Au(111) surfaces has been investigated both by static and dynamic calculations. By varying the size of roughly circular clusters, the edge energy per atom is obtained; it agrees quite well with estimates based on experimental results. Small three-dimensional clusters tend to have the shape of a pyramid, whose sides are oriented in the directions of small surface energy. The presence of a cluster is found to distort the underlying lattice of adsorbed copper atoms. (C) 2002 Published by Elsevier Science B.V.

Simulation study of Pd submonolayer films on Au(hkl) and Pt(hkl) and their relationship to underpotential deposition

The structure and stability of palladium adlayers on Au(hkl) and Pt(hkl) were studied at different coverage degrees by means of Monte Carlo simulations using the interatomic potentials of the embedded atom model. In all cases the Pd films were found to grow epitaxially and pseudomorphically with the crystallographic orientation of the substrate. The differences and similarities of the adlayer with the substrate were analyzed.

Changes in surface stress caused by the adsorption of an epitaxial metal monolayer

The adsorption of a metal monolayer on a foreign substrate generates a change in the surface stress. We calculate this change for a number of substrate/adsorbate systems using the embedded-atom method. The results are compared with those obtained from a continuum model. A cycle, in which the stretching of a substrate/adsorbate system is decomposed into several steps, helps in understanding the numerical results. (C) 2000 Elsevier Science B.V. All rights reserved.

Mesophases in Nearly 2D Room-Temperature Ionic Liquids

Computer simulations of (i) a [C(12)mim][Tf2N] film of nanometric thickness squeezed at kbar pressure by a piecewise parabolic confining potential reveal a mesoscopic in-plane density and composition modulation reminiscent of mesophases seen in 3D samples of the same room-temperature ionic liquid (RTIL). Near 2D confinement, enforced by a high normal load, as well as relatively long aliphatic chains are strictly required for the mesophase formation, as confirmed by computations for two related systems made of (ii) the same [C(12)mim][Tf2N] adsorbed at a neutral solid surface and (iii) a shorter-chain RTIL ([C(4)mim][Tf2N]) trapped in the potential well of part i. No in-plane modulation is seen for ii and iii. In case ii, the optimal arrangement of charge and neutral tails is achieved by layering parallel to the surface, while, in case iii, weaker dispersion and packing interactions are unable to bring aliphatic tails together into mesoscopic islands, against overwhelming entropy and Coulomb forces. The onset of in-plane mesophases could greatly affect the properties of long-chain RTILs used as lubricants.

Melting of a tetrahedral network model of silica

Thermal properties of an idealised tetrahedral network model of silica are investigated by Monte Carlo simulations. The interatomic potential consists of anharmonic stretching and bending terms, plus a short range repulsion. The model includes a bond interchange rule similar to the well known Wooten, Winer and Weaire (WWW) algorithm (see Phys. Rev. Lett., 1985, 54, 1392). Simulations reveal an apparent first order melting transition at T = 2200 K. The computed changes in the local coordination upon melting are consistent with experimental and ab initio data.

Dry Excess Electrons in Room-Temperature Ionic Liquids

In this article, we describe general trends to be expected at short times when an excess electron is generated or injected in different room-temperature ionic liquids (RTILs). Perhaps surprisingly, the excess electron does not localize systematically on the positively charged cations. Rather, the excess charge localization pattern is determined by the cation and anion HOMO/LUMO gaps and, more importantly, by their relative LUMO alignments. As revealed by experiments, the short-time (ps/ns) transient UV spectrum of excess electrons in RTILs is often characterized by two bands, a broad band at low energies (above 1000 nm) and another weaker band at higher energies (around 400 nm). Our calculations show that the dry or presolvated electron spectrum (fs) also has two similar features. The broad band at low energies is due to transitions between electronic states with similar character on ions of the same class but in different locations of the liquid. The lower-intensity band at higher energies is due to transitions in which the electron is promoted to electronic states of different character, in some cases on counterions. Depending on the chemical nature of the RTIL, and especially on the anions, excess electrons can localize on cations or anions. Our findings hint at possible design strategies for controlling electron localization, where electron transfer or transport across species can be facilitated or blocked depending on the alignment of the electronic levels of the individual species.

High confidence prediction of essential genes in burkholderia cenocepacia

Essential genes are absolutely required for the survival of an organism. The identification of essential genes, besides being one of the most fundamental questions in biology, is also of interest for the emerging science of synthetic biology and for the development of novel antimicrobials. New antimicrobial therapies are desperately needed to treat multidrug-resistant pathogens, such as members of the Burkholderia cepacia complex.

Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems

The PglB oligosaccharyltransferase (OTase) of Campylobacter jejuni can be functionally expressed in Escherichia coli, and its relaxed oligosaccharide substrate specificity allows the transfer of different glycans from the lipid carrier undecaprenyl pyrophosphate to an acceptor protein. To investigate the substrate specificity of PglB, we tested the transfer of a set of lipid-linked polysaccharides in E. coli and Salmonella enterica serovar Typhimurium. A hexose linked to the C-6 of the monosaccharide at the reducing end did not inhibit the transfer of the O antigen to the acceptor protein. However, PglB required an acetamido group at the C-2. A model for the mechanism of PglB involving this functional group was proposed. Previous experiments have shown that eukaryotic OTases have the same requirement, suggesting that eukaryotic and prokaryotic OTases catalyze the transfer of oligosaccharides by a conserved mechanism. Moreover, we demonstrated the functional transfer of the C. jejuni glycosylation system into S. enterica. The elucidation of the mechanism of action and the substrate specificity of PglB represents the foundation for engineering glycoproteins that will have an impact on biotechnology.

Two distinct but interchangeable mechanisms for flipping of lipid-linked oligosaccharides

Translocation of lipid-linked oligosaccharide (LLO) intermediates across membranes is an essential but poorly understood process in eukaryotic and bacterial glycosylation pathways. Membrane proteins defined as translocases or flippases are implicated to mediate the translocation reaction. The membrane protein Wzx has been proposed to mediate the translocation across the plasma membrane of lipopolysaccharide (LPS) O antigen subunits, which are assembled on an undecaprenyl pyrophosphate lipid carrier. Similarly, PglK (formerly WlaB) is a Campylobacter jejuni-encoded ABC-type transporter proposed to mediate the translocation of the undecaprenylpyrophosphate-linked heptasaccharide intermediate involved in the recently identified bacterial N-linked protein glycosylation pathway. A combination of genetic and carbohydrate structural analyses defined and characterized flippase activities in the C. jejuni N-linked protein glycosylation and the Escherichia coli LPS O antigen biosynthesis. PglK displayed relaxed substrate specificity with respect to the oligosaccharide structure of the LLO intermediate and complemented a wzx deficiency in E. coli O-antigen biosynthesis. Our experiments provide strong genetic evidence that LLO translocation across membranes can be catalyzed by two distinct proteins that do not share any sequence similarity.