Unraveling molecular transformations on surfaces: a critical comparison of oxidation reactions on coinage metals

The coinage metals, copper, silver, and gold, have unique characteristics for selective oxidation catalysis, particularly for partial oxidation of alcohols and olefins. A basic understanding of surface chemistry at the molecular level can help facilitate the improvement of current catalytic processes and the designing of new catalytic systems. In this critical review, the current state of knowledge of these reactions is reviewed. First, both the experimental and theoretical methods necessary for understanding surface reactivity are discussed with a specific set of examples directly related to these reactions. Next the state of understanding of the surface chemistry of the oxidation reactions of alcohols and olefins on these three coinage metals is reviewed and the reaction pathways are compared. Clear relationships between the low pressure surface science studies and more practical catalytic conditions are illustrated. Finally, recent theoretical advances in this area are discussed as well as possible future directions in this field (132 references).     

Potassium ion mediated collagen microfibril assembly on mica

Potassium ion can critically effect the interaction between collagen microfibrils and mica leading to different ordered structures that vary dramatically with changing ion concentration. AFM images of the structures formed at different ion concentrations appear to be intermediate stages in the progression from disordered to ordered film. At 200 mM potassium ion concentration, a nanometer-thick array of aligned and bundled microfibrils covering large areas can be created easily and reproducibly on mica.     

An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.     

Structure of incommensurate gold sulfide monolayer on Au(111)

We develop an atomic-scale model for an ordered incommensurate gold sulfide (AuS) adlayer which has previously been demonstrated to exist on the Au(111) surface, following sulfur deposition and annealing to 450 K. Our model reproduces experimental scanning tunneling microscopy images. Using state-of-the-art Wannier-function-based techniques, we analyze the nature of bonding in this structure and provide an interpretation of the unusual stoichiometry of the gold sulfide layer. The proposed structure and its chemistry have implications for related S-Au interfaces, as in those involved in self-assembled monolayers of thiols on Au substrates.     

Creation of mammalian single- and double-stranded DNA surfaces: a real-time QCM-D study

The quartz crystal microbalance with dissipation monitoring (QCM-D) is an excellent method for studying the creation of DNA-based surfaces and films. Previous studies have used QCM-D to focus on the construction of DNA surfaces composed of short synthetic DNA oligomers or plasmid DNA. Here, we have used QCM-D to monitor the creation of genomic single- and double-stranded calf thymus DNA surfaces on a polycation adsorbed to a SiO2 support. We have successfully monitored the hybridization between the ssDNA surfaces and their complementary strands in solution and have also shown that DNA multilayer formation can be observed using denatured calf thymus DNA. We have furthermore established that the ssDNA and dsDNA surfaces show different binding characteristics to ethidium bromide, a common dsDNA intercalator, demonstrating the potential use of such surfaces to identify possible DNA ligands.