Aromaticity of strongly bent benzene rings: persistence of a diatropic ring current and its shielding cone in [5]paracyclophane

Direct evaluation of the induced π current density in [5]paracyclophane (1) shows that, despite the significant non-planarity (α = 23.2°) enforced by the pentamethylene bridge, there is only a modest (ca. 17%) reduction in the π ring current, justifying the use of shielding-cone arguments for the assignment of (1)H NMR chemical shifts of 1 and the claim that the non-planar benzene ring in 1 retains its aromaticity (on the magnetic criterion).     

Effect on ring current of the Kekulé vibration in aromatic and antiaromatic rings

Derivative current-density maps are used to follow the changes in ring-current (and hence, on the magnetic criterion, the changes in aromaticity) with the Kekulé vibrations of the prototypical aromatic, antiaromatic, and nonaromatic systems of benzene, cyclooctatetraene (COT), and borazine. Maps are computed at the ipsocentric CHF/6-31G**//RHF/6-31G** level. The first-derivative map for benzene shows a growing-in of localized bond currents, and the second-derivative map shows a pure, paratropic "antiring-current", leading to the conclusion that vibrational motion along the Kekulé mode will reduce the net aromaticity of benzene, on average. For planar-constrained D(4h) COT, the Kekulé mode (positive for reduction of bond-length alternation) increases paratropicity at both first and second order, indicating an average increase in antiaromaticity with zero-point motion along this mode. On the ring-current criterion, breathing expansions of benzene and D(4h) COT reduce aromaticity and increase antiaromaticity, respectively.     

A simple model for multicomponent etching

We consider the situation where a multicomponent solid is etched using one or more acids. Of fundamental interest is the rate of surface etching but when this involves multicomponent surface reactions, it becomes unclear how the overall rate can be estimated. In this paper, we sketch a simple model designed to determine the effective etching rate by means of an atomic scale model of the etching process.     

Distance measures for dynamic citation networks

Acyclic digraphs arise in many natural and artificial processes. Among the broader set, dynamic citation networks represent an important type of acyclic digraph. For example, the study of such networks includes the spread of ideas through academic citations, the spread of innovation through patent citations, and the development of precedent in common law systems. The specific dynamics that produce such acyclic digraphs not only differentiate them from other classes of graphs, but also provide guidance for the development of meaningful distance measures. In this article, we develop and apply our sink distance measure together with the single-linkage hierarchical clustering algorithm to both a two-dimensional directed preferential attachment model as well as empirical data drawn from the first quarter-century of decisions of the United States Supreme Court. Despite applying the simplest combination of distance measure and clustering algorithm, analysis reveals that more accurate and more interpretable clusterings are produced by this scheme.     

Defining protease specificity with proteomics: a protease with a dibasic amino acid recognition motif is regulated by a two-component signal transduction system in Salmonella.

Microbial proteases play diverse and important roles in bacterial virulence but their detection and characterisation is often hampered by their limited abundance or lack of expression in the absence of suitable environmental signals. We describe here a sensitive proteomic approach to detect proteases that are under the control of a virulence regulator and to characterise their recognition motifs. Using MG++-depleted growth media or a mutant strain of Salmonella in which the PhoP-PhoQ virulence regulatory system is constitutively active, truncated forms of DnaK, elongation factor G, elongation factor Tu and ribosomal protein S1 proteins were detected. Two other global regulatory mutants and cells exposed to acid or to oxidative stress failed to produce the truncated proteins, indicating specific control of the protease activity by the PhoP-PhoQ system. Our results suggest that at least two proteases are induced. To define the proteolytic cleavage sites of one of the proteases, peptides from each of the truncated proteins were identified by tryptic mass fingerprinting/nanoelectrospray mass spectrometry and mapped onto the sequence of the intact protein. Alignment of the regions around the cut site indicates that the protease recognises a dibasic amino acid motif characteristic of the omptin protease family. The induction of such proteases in bacteria depleted of Mg++ ions may contribute to the PhoPQ-mediated resistance of Salmonella to cationic antimicrobial peptides. Additionally, our results suggest it would be prudent to keep the concentration of this ion above micromolar levels during bacterial sample preparation for proteomic analyses.     

Finding Large p-Colored Diameter Two Subgraphs

Given a coloring of the edges of the complete graph K on n vertices in k colors, a p-colored subgraph of K_n is any subgraph whose edges only use colors from some p element set. We show for k̿ and k\2hphk that there is always a p-colored diameter two subgraph of K_n containing at least [((k+p)n)/(2k)]\displaystyle{(k+p)n \over 2k} vertices and that this is best possible up to an additive constant l satisfying 0hl<k\2.